IMCBio International PhD Program - IMCBio PhD Call 2026

The acto-myosin cytoskeleton shapes cells and tissues. They direct the formation of embryos such as C. elegans, Drosophila, mouse as well as the structures of single cells and tissues in vitro. Their physics has been described with the active gel descriptions. However, their regulations by the small Rho GTPases were missing so far although they are known to be essential.
The Riveline team is involved in an international network with scientists from the field aiming at understanding the self-organisation rules of these regulated active gels, i.e. acto-myosin cytoskeleton under the regulation of the small Rho GTPases. We compare cells in vitro, cells in vivo, and theory in an integrated manner. We use microfabrication, cell biology, quantitative imaging and theory to characterize their generic rules of self-organisations.
The PhD will consist in designing new directions to study these regulated active gels with controlled conditions. Acto-myosin cytoskeleton structures and their regulations by Rho GTPases will be monitored by live microscopy, quantitative biology and cryo-EM tomography. Stress generation will be evaluated in each situation from molecular to mesoscopic scales. The topic could be oriented to different directions depending on the background and tastes of the applicant.
Collaborations have started along these directions and they will continue with Florian Faessler (IGBMC) for cryo-EM and Karsten Kruse (Geneva University) for theoretical physics.

Keywords: cytoskeleton, acto-myosin, polarity, biological physics, cryo-EM

Relevant publications:

- Linjie Lu, Tristan Guyomar, Quentin Vagne, Rémi Berthoz, Alejandro Torres-Sánchez, Michèle Lieb, Cecilie Martin-Lemaitre, Kobus van Unen, Alf Honigmann, Olivier Pertz, Daniel Riveline*, Guillaume Salbreux*, Polarity-driven three-dimensional spontaneous rotation of a cell doublet, Nature Physics 20, 1194–1203 (2024).
- Karsten Kruse*, Rémi Berthoz, Luca Barberi, Anne-Cécile Reymann, Daniel Riveline*, Acto-myosin clusters as active units shaping living matter, Current Biology 34, 1045-1058 (2024).
- V. Wollrab, R. Thiagarajan, A. Wald, K. Kruse, D. Riveline, Still and rotating myosin clusters determine cytokinetic ring constriction. Nat. Commun. 7, 11860 (2016).
 

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Actin, a self-assembling biopolymer, plays a crucial role via the formation of dynamic networks that determine cellular shape and mechanical properties. De novo mutations in cytoskeletal actin (ACTB and ACTG1 genes) lead to a wide range of rare diseases, termed non-muscle actinopathies (NMA). Neurological impairment is the most frequent feature across the whole NMA spectrum. The mechanisms linking precisely actin disfunction to these neurological symptoms, the extent of their severity as well as their progression remain so far unknown. Together with collaborators, the Reymann team aims to understand the molecular to functional consequences of these cytoplasmic actin variants using the model organism C. elegans.

Nine human substitutions, chosen to span a large range of severity in patients, were successfully recapitulated in C. elegans actin-coding gene using CRISPR/Cas9 editing. The main objective of the proposed PhD project is to identify the cellular and molecular mechanisms at play associated with the observed neurodevelopment disorders. We will specifically probe neurogenesis, neuronal migration and neuronal maturation including axonal growth capacities. One of the advantages, is that C. elegans invariance in lineage, cell fate acquisition and body plan is enabling to detect subtle developmental defects due to our ability to identify single neurons. We will notably rely on the very advantageous NeuroPAL transgene, including 41 neuronal fate markers in the form of fluorescent reporters, that enables to unambiguously identify each individual neuron.

Keywords: actin, C. elegans, neurodevelopmental disorders, rare disease

Relevant publications:

- Classification of human actin pathological variants using C. elegans CRISPR-generated models. Hecquet T., Arbogast N., Suhner D., Goetz A., Amann G., Yürekli S., Marangoni F., S. Quintin, N. Greve J., Di Donato N., Reymann AC, iScience, Ocober 2025, https://doi.org/10.1016/j.isci.2025.113652

- In vivo detection of ALFA-tagged proteins in C. elegans with a transgenic fluorescent nanobody. Quintin S, Saad MI, Amann G, Reymann AC. MicroPubl Biol. 2025 Apr 18;2025:10.17912/micropub.biology.001542. doi: 10.17912/micropub.biology.001542.

- The kinesin Kif21b regulates radial migration of cortical projection neurons through a non-canonical function on actin cytoskeleton. Rivera RA, Asselin L, Tilly P, Benoit R, Batisse C, Richert L, Batisse J, Morlet B, Levet F, Schwaller N, Mély Y, Ruff M, Reymann AC, Godin J, Cell Reports, July 2023. doi: 10.1016/j.celrep.2023.112744

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

This project explores how the brain regulates energy balance and metabolism through molecular mechanisms linking neuronal calcium signaling to feeding behavior. Energy homeostasis depends on hypothalamic circuits that integrate hormonal and nutritional cues to control appetite and energy expenditure. Dysregulation of these systems contributes to obesity and type 2 diabetes.

Our previous work identified CaMK1D, a gene associated with type 2 diabetes, as a key regulator in AgRP neurons, modulating responses to fasting and hormones such as ghrelin. This reveals a signaling pathway connecting neuronal activity to metabolic regulation.

The project combines molecular, imaging, and physiological approaches to study how calcium-dependent mechanisms shape hypothalamic control of metabolism. In vivo studies in diet-induced obesity models will assess how manipulating this pathway affects feeding behavior and energy expenditure.

Conducted at IGBMC, a world-leading institute in neuroscience and metabolic research, this project offers an exceptional environment for training in cutting-edge techniques, interdisciplinary collaboration, and high-impact research. By linking cellular signaling to whole-body energy homeostasis, it aims to uncover novel therapeutic targets for obesity and metabolic disorders, providing an exciting opportunity to contribute to translational neuroscience research.

Keywords: Energy Homeostasis, Hypothalamus, Calcium Signaling, AgRP Neurons, Obesity

Relevant publications:

- CaMK1D signalling in AgRP neurons promotes ghrelin-mediated food intake. Vivot K et al. Nat Metab. 2023

- Lysosomal degradation of newly formed insulin granules contributes to β cell failure in diabetes. Pasquier A et al. Nat Commun. 2019

- Distinct changes in endosomal composition promote NLRP3 inflammasome activation. Zhang Z, et al. Nat Immunol. 2023

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

The immense contractile force generated by skeletal muscle is transmitted and dissipated at the muscle–tendon junction (MTJ), a highly specialized interface between muscle and tendon. This site is particularly vulnerable to injury during exercise, and its architecture undergoes significant remodeling with sustained physical activity and ageing. Understanding how the unique cellular structure and function of the MTJ are established and regulated is therefore of fundamental importance.

Our previous single-nucleus RNA sequencing (snRNA-Seq) studies revealed that myonuclei positioned at the MTJ adopt a distinct transcriptomic identity compared to other myonuclei within the same muscle fiber. Interestingly, these transcriptomes remained largely unchanged despite structural remodeling and functional improvement after exercise, pointing to a critical role for post-transcriptional regulation.

To address this, our team has developed innovative genetic and molecular tools to selectively profile the translatome and manipulate gene expression at the MTJ. This PhD project aims to: (i) map translational changes in the MTJ during exercise and ageing, (ii) elucidate how specific transcripts are selected for local translation, and (iii) identify tendon-derived signals that regulate this process. This work will uncover new mechanisms of subcellular specialization and muscle adaptation.

Keywords: skeletal muscle, protein translation, muscle-tendon junction, ageing, exercise

Relevant publications:

- Kim, M*., Franke, V*., Brandt, B., Lowenstein, E.D., Schowel, V., Spuler S., Akaline, A., and Birchmeier, C. (2020) Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells. Nature Communications. 11, 6375. *, co-first authors.

- Cristofer Calvo*, Coalesco Smith*, Taejeong Song, Sakthivel Sadayappan, Douglas P. Millay# and Minchul Kim#. Loss of Ufsp1 does not cause major changes at the neuromuscular junction. Plos One. *, co-first authors. #, co-correspondence.

- Kim, M*., Wende, H.,*, Walcher, J., Cheret, C., Kempa, S., Lewin, G., and Birchmeier, C. (2018) Maf links Neuregulin1 signaling to cholesterol synthesis in myelinating Schwann cells. Genes & Development. 2018. May 1;32(9-10):645-657. (Cover paper). *, co-first authors.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

During immune responses, B cells diversify their immunoglobulin (Ig) genes through somatic hypermutation (SHM) and class switch recombination (CSR), processes that refine antibody affinity and alter isotype without changing antigen specificity. SHM introduces mutations into Ig variable regions, generating clonal variants selected for improved antigen binding. CSR recombines the Ig heavy chain variable region with distinct constant regions, switching the expressed antibody from IgM to IgG, IgE, or IgA.

Both reactions are initiated by Activation-Induced Cytidine Deaminase (AID), which deaminates cytosines in DNA. The resulting uracils are recognized mainly by Uracil-DNA glycosylase (Ung), leading to mutations during SHM or double-strand breaks during CSR.

Despite extensive studies, how AID-induced lesions are funneled to an error-prone DNA repair pathway remains unclear. Through a genome-wide CRISPR/Cas9 screen, we identified Fam72a as a key regulator of this balance. Fam72a controls UNG2, the nuclear isoform of Ung, by limiting its protein levels (Rogier et al. Nature. 2021 ; rdcu.be/cBYhU)

Building on these findings, we will perform a focused CRISPR screen targeting genes encoding Fam72a- and UNG2-interacting proteins (identified by co-immunoprecipitation and mass spectrometry) using an UNG2–EGFP knock-in B cell line. Promising hits will be individually disrupted to explore their mechanistic roles. Finally, we aim to generate conditional knockout mouse models to dissect candidate gene functions in vivo.

This comprehensive approach seeks to unravel the intricate connections between Fam72a, Ung2, and their interacting partners, shedding light on the molecular processes underlying error-prone DNA repair in the context of AID-induced DNA damage during antibody diversification.

Keywords: Antibody diversification, Somatic Hypermutation, Class Switch recombination, programmed DNA Damage/Repair, CRISPR/Cas9 screening, Genome Editing, AID, Fam72a, Uracil DNA glycosylase

Relevant publications:

Rogier, M. et al. Fam72a enforces error-prone DNA repair during antibody diversification. Nature 600, 329, doi:10.1038/s41586- 021-04093-y (2021).

Yilmaz, D. et al. Activation of homologous recombination in G1 preserves centromeric integrity. Nature, doi:10.1038/s41586-021- 04200-z (2021).

Thomas-Claudepierre, A.S., et al. Mediator facilitates transcriptional activation and dynamic long-range contacts at the IgH locus during class switch recombination. J Exp Med 213, 303-312 (2016).

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

De novo mutations in the RARb gene, which codes for the retinoic acid receptor beta (RARb), cause rare neurodevelopmental disease (MCOPS12) with severe motor and cognitive deficits (Caron et al. 2024). RARb is a transcription factor which is activated upon binding to retinoic acid (RA), an active form of vitamin A. We have recently generated a series of mouse models carrying MCOPS12-causing RARb mutations. These mice recapitulate the key features of the disease including progressive neurological symptoms (dystonia-like motor abnormalities) and cognitive deficits (memory deficits). Analyses of neural cell populations indicate abnormal development and/or functions of oligodendrocytes, a neural cell type responsible for myelin production and trophic support of neuronal networks. We hypothesis that abnormal functions of RARb lead to oligodendrocyte dysfunction, which drives both, neurodevelopmental symptoms and postnatal MCOPS12 progression. We propose to address this hypothesis by investigating the contribution of RARb to oligodendrocyte cell lineage development using dedicated reporter mice, and determine functional role of RARb in oligodendrocytes by studying effects of RARb loss-of-function and mouse models of MCOPS12 during embryonic and post-natal brain development. The ChIPseq, single nuclei RNAseq, spatial transcriptomics and proteomics, will be used to identify underlaying molecular mechanisms whereas pharmacological and gene-editing manipulations of primary oligodendrocyte cultures will be employed to challenge specific molecular and cell-biology questions. This study should allow revealing the molecular basis of oligodendrocyte heterogeneity in the brain and their contribution to overall brain development and functions. As an ambition of the project is to identify new therapeutic strategies and targets, we will test whether enhancing the RARb signaling pharmacologically may improve oligodendrocyte functions and stop MCOPS12 progression.

Keywords: rare diseases, neurodegeneration, regenerative medicine, oligodendrocytes, retinoid receptors, protein interactions, mouse models of disease

Relevant publications:

- Zinter N, Ye T, Semaan H, Fraulob V, Plassard D, Krezel W. Compromised retinoic acid receptor beta expression accelerates the onset of motor, cellular and molecular abnormalities in a mouse model of Huntington's disease. Neurobiol Dis. 2025 Aug;212:106943. doi: 10.1016/j.nbd.2025.106943.

- Caron V, Chassaing N, …, Michaud JL. Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta. Genet Med. 2023 Aug;25(8):100856. doi: 10.1016/j.gim.2023.100856.

- Ciancia M, Rataj-Baniowska M, Zinter N, Baldassarro VA, Fraulob V, Charles AL, Alvarez R, Muramatsu SI, de Lera AR, Geny B, Dollé P, Niewiadomska-Cimicka A, Krężel W. Retinoic acid receptor beta protects striatopallidal medium spiny neurons from mitochondrial dysfunction and neurodegeneration. Prog Neurobiol. 2022 May;212:102246

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Cellular senescence and the Senescence-Associated Secretory Phenotype (SASP) play dual roles in tumorigenesis. Cellular senescence, a state of stable cell-cycle arrest, can act as a tumor-suppressive mechanism by halting the proliferation of damaged or transformed cells. However, senescent cells also secrete a complex mixture of pro-inflammatory cytokines, growth factors, and proteases (SASP), which can paradoxically promote tumor growth, immune evasion, and metastasis by modifying the tumor microenvironment. Understanding the interplay between senescence, SASP, and cancer progression offers opportunities to design novel therapies that either enhance the tumor-suppressive effects or mitigate the pro-tumorigenic consequences of senescence, leading to more effective cancer treatments. Recent and ongoing work in our lab has identified that senescent cells can instruct developmental fate and reprogramming, which we believe could have significant impact on cancer cell fate and their behavior in tumors. The PhD project will explore how senescent cells can promote developmental reprogramming and influence tumor progression. This will involve performing single cell sequencing (RNA, ATAC) to identify which genes are activated by senescent cells in different cancer models following therapy, and to explore how they confer diverse fates on the tumor. These genes will then be functionally inhibited in culture, and in vivo in tumors, to further interrogate the mechanisms by which therapy-induced senescence promotes tumor progression and recurrence. Techniques will include sequencing approaches, cell culture, molecular biology approaches and working with mouse models of cancer.

Keywords: Senescence, cancer, therapy, reprogramming, plasticity, aging, mouse models

Relevant publications:

- Sampaio Gonçalves, D., Dulac, L., Ritschka, R., Rhinn, M., Klein, A., Wyatt, C.D., Irimia, M., Keyes, W.M. Senescent cells exhibit features of developmental signaling centres. BioRxiv https://doi.org/10.1101/2025.10.30.685565

- Durik, M., Sampaio Gonçalves, D., Spiegelhalter, C., Messaddeq, N., Keyes, W.M. Senescent cells deposit intracellular contents through adhesion-dependent fragmentation (2023) BioRxiv doi: https://doi.org/10.1101/2023.01.11.523642 

- Ritschka, B., Storer, M., Mas, A., Heinzmann, F., Ortells, M.C., Morton, J.P., Sansom, O.J., Zender, L. and Keyes, W.M. (2017) The senescence-associated secretory phenotype induces cellular plasticity and tissue regeneration Genes & Development, 31(2):172-183 

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Several observations in diverse species suggest that large polynucleated cells can exhibit functionally distinct nuclei. This is intriguing as all these nuclei bathe in a common cytoplasm and show a generic tissue identity. Yet some can also express a subset of (domain-) specific genes – and maintain it over time! The goal of this project is to understand how functional nuclear compartmentalization is implemented within such cells, and protected against diffusion to the whole cell.

For this, we will use a transparent in vivo model with an extensive genetic tool box: the large syncytium, called Hyp7, in C. elegans.  Hyp7 is formed during embryogenesis by the fusion of 23 cells, and lines the ventral and dorsal sides of the worm along an antero-posterior axis. This tissue is characterized by the homogeneous expression of markers in all the nuclei, that can be visualized using fluorescent reporters in live animals. Now, our lab has confirmed that some, but not all, Hyp7 nuclei express specific factors. Thus, in this single polynucleated cell, like in myofibers, discrete nuclei can exhibit a specialised expression profile. The project will use this model to address the following important questions:

A- Which nuclei exactly within hyp7 express unique markers, and are they always the same ?

B- How do regionalised messengers remain localized in a specific region of this giant cell? In particular, are there structures within Hyp7 that limit the diffusion along the antero-posterior axis of molecules (messenger RNA and proteins)? Indeed, such structures, formed by membrane invaginations have been observed in the syncytium formed by the worm germ line.

C- When cells fuse to Hyp7 during development, how fast are they transcriptionally reprogrammed to exhibit a Hyp7 identity and does this involve the reprogramming factors necessary for natural transdifferentiation in the worm?

D- What happens when additional cell nuclei are forced to fuse to Hyp7: in these additional nuclei, is the expression of their own markers lost after fusion?

E- What is the function of these nuclei with a specific identity?

Several experimental approaches will be implemented: single nuclei RNAseq to evaluate the number of differentially expressed genes in a syncytium, forced cell fusions, genetic approaches (incl. CRISPR/cas9), transgenesis, high-end microscopy on live animals and in situ hybridization on single RNA molecules (smFISH). This work aims to elucidate the mechanisms allowing differential expression and compartmentalisation of information within a large polynuclear cell, and their role. This will have important implications for the understanding of human muscle physiology, where nuclei below the neuro-muscular junction for instance have been shown to exhibit a specific identity, and their associated pathologies.

Keywords: Syncytium, nuclear domains, regionalized expression, functional compartimentalisation, snRNAseq, C. elegans

Relevant publications:

- Daniele T., Cury J., Morin M.C., Ahier A., Isaia D. & Jarriault S. (2025) Essential and dual effects of Notch activity on a natural transdifferentiation event. Nat. Communications 16, 75, and BioRxiv, doi: https://doi.org/10.1101/2024.09.11.612396

- Riva C., Gally C., Hajduskova M., Suman S.K., Ahier A. & Jarriault S. (2021) A natural transdifferentiation event involving mitosis is empowered by integrating signaling inputs with conserved plasticity factors. Cell Rep. 40(12):111365. doi: 10.1016/j.celrep.2022.111365

- Sequential histone-modifying activities determine the robustness of transdifferentiation. Zuryn S., Ahier A., Portoso M., Redhouse White E., Margueron R., Morin M.C. & Jarriault S. Science 345(6198):826-829.  (2014).  Cited « Recommended » by Faculty 1000.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Mammalian embryogenesis is a tightly regulated process in which gastrulation establishes the three primary germ layers (ectoderm, mesoderm, and endoderm), which give rise to all adult tissues and organs. Although gastrulation is essential and evolutionarily conserved, it exhibits notable diversity across closely related mammalian species, raising the question of which molecular mechanisms drive species-specific differences in early development. This PhD project will investigate how DNA sequences derived from transposable elements (TEs), which account for nearly 50% of mammalian genomes, contribute to the evolution of gene regulatory networks. We will test whether TEs establish species-specific regulatory elements that control cell fate decisions during gastrulation. Using human embryonic stem cells and in vitro models of early development (gastruloids), we will generate regulatory maps of gastrulation using single-cell approaches. Based on these data, the PhD student will (1) identify TE subfamilies associated with germ-layer-specific gene expression, (2) perturb selected subfamilies using CRISPR-based methods, (3) characterize effects on tissue patterning using advanced microscopy to monitor germ layer emergence, and (4) assess transcriptomic (RNA-seq) and epigenomic (CUT&Tag) responses following perturbation. This work will clarify how fast-evolving genomic elements influence human embryonic development and may provide insights into species-specific developmental disorders, with broader relevance for understanding human reproductive biology.

Keywords: Human development, cell fate, transposable elements, gene regulation, stem cells, gastruloids, genome editing (CRISPR), single-cell analysis, epigenetics, evolution

Relevant publications:

- Rosspopoff O#, Martins F#, Trono D. New ingredients for old recipes. Nature Genetics. 2023 Dec;55(12):2023–4.

- Milovanović D, Duc J, Matsushima W, Hamelin R, Planet E, Offner S, Rosspopoff O*† , Trono D*† . Tissue-specific restriction of TE-derived regulatory elements safeguards cell-type identity. bioRxiv; 2025 [cited 2025 May 16]. p. 2025.05.13.653700. Available from: https://www.biorxiv.org/content/10.1101/2025.05.13.653700v1. (Accepted in Cell reports).

- Rosspopoff O*, Milovanović D, Offner S, Raclot C, Lau K, Duhoo Y, Duc J, Planet E, Damery C, Begnis M, Pojer F, Trono D*. Transposable element co-option drives transcription factor neofunctionalization. bioRxiv; 2025 [cited 2025 Mar 23]. p. 2025.03.01.640934. Available from: https://www.biorxiv.org/content/10.1101/2025.03.01.640934v1. (in review).

This project is self-funded by the team proposing the project.

Cell fate specification, which underpins human development and disease pathogenesis, is orchestrated by a combination of highly interlinked molecular features, including the epigenome and the three-dimensional (3D) chromatin organisation. However, how these features causally influence one another and their propagation through the cell cycle remains poorly understood. Evidence from our group shows that the DNA replication timing programme, defined as the temporal order in which the genome is duplicated during S phase, is necessary for epigenome establishment in the following cell cycle. Yet, its direct contribution to cell fate transitions and organismal development remains unclear. This project will differentiate human gastruloids from wild type and DNA replication timing perturbed human embryonic stem cells, and will densely sample this dynamic process at sub-cell cycle temporal resolution for low input/ single cell epigenome and replication profiling. Neural network modelling on the resulting data will delineate the temporally resolved regulatory cascade linking DNA replication, the epigenome and 3D chromatin organisation governing cell fate transitions. This project will result in two far-reaching deliverables: 1) identification of novel S phase DNA replication-coupled regulatory networks of epigenome remodelling during human early development and 2) one of the first causal epigenomic models for human early development and, more broadly, a generalizable computational framework to study dynamic regulation in diverse biological systems.

Keywords: Computational biology, epigenomics, cell cycle, human gastruloid

Relevant publications:

- Klein, K.N.*, Zhao, P.A.*, Lyu, X*., Sasaki, T., Bartlett, D.A., Singh, A.M., Tasan, I., Zhang, M., Watts, L.P., Hiraga, S.-i., Natsume, T., et al. (2021). Replication timing maintains the global epigenetic state in human cells. Science 372, 371-378. (*Contributed Equally)

- Zhao, P.A.†, Li, R., Adewunmi, T., Garber, J., Gustafson, C., Kim, J., Malone, J., Savage, A., Skene, P., & Li, X. J. (2025). SPARROW reveals microenvironment-zone-specific cell states in healthy and diseased tissues. Cell Systems, 16(3), 101235. https://doi.org/10.1016/j.cels.2025.101235 (†Lead Corresponding Author)

- Emerson, D.J.*, Zhao, P.A.*, Cook, A.L.*, Barnett, R.J., Klein, K.N., Saulebekova, D., Ge, C., Zhou, L., Simandi, Z., Minsk, M.K., et al. (2022). Cohesin-mediated loop anchors confine the locations of human replication origins. Nature 606(7915): 812-819. (*Contributed Equally)

This project is self-funded by the team proposing the project.

Cancer cells differ from normal cells displaying high level of proliferative capacity. That creates cancer cell vulnerabilities, which can be targeted therapeutically. One of the cellular machineries which are “hijacked” by cancer cells are the nuclear pore complexes (NPCs). NPCs constitute the sole communication gates between the nucleus and the cytoplasm and ensure cellular function and survival. Nucleoporins (Nups) are the building protein units of the NPCs and represent an “achilles heel” of cancer cells. Cancer cells increase their NPC number to adapt to proliferative demand and depletion of Nups required for NPC assembly can selectively kill cancer cells and reduce tumor growth, providing a strong proof of principle for targeting Nups in cancer disease. However, the molecular mechanisms on how rapid spatial assembly of the NPCs can be achieved in cancer cells and how exactly misregulation of Nups homeostasis can cause cancer disease remain largely unknown. Our published findings identified a novel mechanism on how spatial assembly and increased biogenesis of NPCs can be achieved in cancer cells. We plan to characterize the role of newly identified factors in Nups homeostasis in relevant cellular cancer models. Inhibition of these factors should selectively reduce viability of cancer cells. This research may create unprecedented therapeutic perspectives for cancer patients.

Keywords: cancer, nuclear pore complexes, nucleoporins, nucleocytoplasmic transport, cancer-specific vulnerabilities

Relevant publications:

- Krupina K., Kleiss C., Metzger T., Fournane S., Schmucker S., Hofmann K., Fischer B., Paul N., Porter I.M., Raffelsberger W., Poch O., Swedlow J.R., Brino L. and Sumara I. (2016) Ubiquitin receptor protein UBASH3B drives Aurora B recruitment to mitotic microtubules. Developmental Cell. Jan 11, 36 (1): 63–78.

- Agote-Aran A., Schmucker S., Jerabkova K., Boyer I.J., Berto A., Pacini L., Ronchi P., Kleiss C., Guerard L., Schwab Y., Moine H., Mandel J-L., Jacquemont S., Bagni C. and Sumara I. (2020) Spatial control of nucleoporin condensation by fragile X-related proteins. EMBO Journal. Oct 15; 39 (20): e104467

- Liao Y., Andronov L., Liu X., Lin J., Guerber L., Lu L., Agote-Aran A., Pangou E., Ran L., Kleiss C., Qu M., Schmucker S., Cirillo L., Zhang Z., Riveline D., Gotta M., Klaholz B.P. and Sumara I. (2024) UBAP2L ensures homeostasis of nuclear pore complexes at the intact nuclear envelope. Journal of Cell Biology. Jul 1;223(7):e202310006.

Transcription factors are key molecular determinants of cellular identity during development and in human diseases. They interpret our genome via recognition of specific DNA sequences, resulting in target genes being switched ‘on’ or ‘off’. Our recent research revealed a new type of gene regulation based on sensing of A/T nucleotide content (Pantier et al, 2021). In particular, the transcription factor SALL4 binds to short AT-rich motifs on the genome, and its function is essential for stem cell identity in vitro and embryonic development in vivo.

In this PhD project, you will exploit state-of-the-art genomics techniques in genetically engineered embryonic stem cells to dissect the molecular function of SALL4: regulation of transcription via long range enhancer-promoter looping (1), regulation of 3D genome structure via modulation of lamina-associated domains (2). These investigations will help us better understand how transcription factors interact across different genomic scales in order to control cell identity.

Keywords: embryonic stem cells, transcription, genome architecture, transcription factors, SALL4, CRISPR/Cas9 engineering, next-generation sequencing

Relevant publications:

- K. Chhatbar, S. Giuliani, T. Quante, B. Alexander-Howden, J. Selfridge, J. Guy, T. Auchynnikava, C. Spanos, T. Mathieson, G. Sanguinetti, A. Bird, R. Pantier, Pervasive binding of the stem cell transcription factor SALL4 shapes the chromatin landscape, bioRxiv (2025) https://doi.org/10.1101/2025.11.14.688441

- R. Pantier, K. Chhatbar, T. Quante, K. Skourti-Stathaki, J. Cholewa-Waclaw, G. Alston, B. Alexander-Howden, H.Y. Lee, A.G. Cook, C.G. Spruijt, M. Vermeulen, J. Selfridge, A. Bird, SALL4 controls cell fate in response to DNA base composition, Molecular Cell (2021) https://doi.org/10.1016/j.molcel.2020.11.046

- J.A. Watson*, R. Pantier*, U. Jayachandran, K. Chhatbar, B. Alexander-Howden, V. Kruusvee, M. Prendecki, A. Bird, A.G. Cook, Structure of SALL4 zinc finger domain reveals link between AT-rich DNA binding and Okihiro syndrome, Life Science Alliance (2023) *co-fist authorship. https://doi.org/10.26508/lsa.202201588

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

This project aims to identify the epigenetic mechanisms that control the diversification of macrophages using the model of Drosophila melanogaster. Macrophages are innate immune cells known for phagocytosing debris and pathogens, acting as first responders during embryonic development, and continuing to serve important roles in various tissues into adulthood. Their responses in diseases, such as neurodegenerative disorders and cancers, can either help or worsen symptoms, depending on their behaviour, which is influenced by their environmental conditioning and previous immune challenges. Studies have shown that macrophages can retain a "memory" of immune challenges, affecting their future responses.

Previous work by the laboratory has characterized macrophages at different developmental stages, showing their diversification, which includes chromatin remodelling. The project will examine how the epigenetic landscape of macrophages changes from the embryonic to larval stages using single-cell ATACseq data and will characterize the molecular mechanisms behind the development of macrophage subpopulations, focusing on the impact of a key transcription factor, Gcm, and its interactions with non-coding RNA (ncRNA) on the chromatin remodelling.

The findings of this study will provide deeper insights into the molecular mechanisms regulating macrophage diversification, will lead to future researches on macrophage behaviour in pathological conditions like infections and cancer as well as on the role of ncRNA in the mammalian macrophages.

Keywords: Drosophila, macrophage, non coding RNA, high throughput sequencing

Relevant publications:

- Sakr, R., P. B. Cattenoz, A. Pavlidaki, L. Ciapponi, M. Marzullo et al., 2022 Novel cell- and stage-specific transcriptional signatures defining Drosophila neurons, glia and hemocytes. bioRxiv: 2022.2006.2030.498263.

- Pavlidaki, A., R. Panic, S. Monticelli, C. Riet, Y. Yuasa et al., 2022 An anti-inflammatory transcriptional cascade conserved from flies to humans. Cell Rep 41: 111506.

- Cattenoz, P. B., A. Popkova, T. D. Southall, G. Aiello, A. H. Brand et al., 2016 Functional Conservation of the Glide/Gcm Regulatory Network Controlling Glia, Hemocyte, and Tendon Cell Differentiation in Drosophila. Genetics 202: 191-219.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Eukaryotic DNA is compacted by assembly into chromatin. Processes like gene transcription and DNA damage response (DDR) require localized changes in chromatin compaction. The mammalian SWI/SNF complex (mSWI/SNF), a multisubunit ATP‐dependent chromatin remodeling complex that slides or evicts nucleosomes from the chromatin fibre is in part responsible for regulating DNA accessibility in these contexts. The importance of mSWI/SNF in human health is underscored by the fact that its deregulation, by point mutations or misexpression, is associated to numerous diseases including cancer. Consequently, it is of paramount importance to fully understand at the molecular level how mSWI/SNF functions, but this goal has not been attained yet. mSWI/SNF comprises recently identified ‘auxiliary’ subunits, the molecular function and atomic structure of which remain largely unknown. Mounting evidence shows that those genes deregulation (mutations or alterations in expression levels) have an important impact on cancer, but the molecular basis explaining their relationship to cancer remains unknown. By using a combination of cryo-EM, biochemistry, live cell imaging and genomic, we aim to gain a better understanding of the function of the auxiliary subunits within the SWI/SNF complex. The project is expected to establish phenotype-genotype-therapy correlations, identify novel drug targets and provide structural insights into mutants SWI/SNF complexes. Ultimately this project will bridge fundamental chromatin biology with translational oncology, paving the way for precision medicine strategies.

Keywords:

Relevant publications: chromatin remodeling, disease, molecular mechanism

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Abnormal gene expression patterns are a hallmark of cancer, with the loss or gain in gene activity often driven by mutations in regulatory sequences, including single nucleotide polymorphisms (SNPs), or altered epigenetic landscapes such as DNA methylation.

Transcription factors (TFs) are key regulatory proteins that bind specific DNA sequence motifs to control the expression of their target genes. The presence of SNPs or the gain or loss of DNA methylation at motifs can alter TF binding. On the other hand, changes in DNA methylation levels at regulatory regions is a hallmark of cancer, however, again, it has been difficult to define the underlying mechanism and direct impact of these changes on gene activity.

Here we will explore computationally how SNPs and altered DNA methylation levels in motifs for ubiquitously expressed TFs that drive the activity of cancer cell dependent genes influence gene expression. We will specifically focus on binding sites of TFs such as BANP and NRF1 that are sensitive to DNA methylation. This will lay the foundation for a functional study to determine if BANP and NRF1 indeed drive the expression of the linked genes and open the door to a new therapeutic strategy where genetic and epigenetic editing could be used to reset detrimental gene expression changes.

Keywords: Computational Biology; Gene regulation; Cancer; Transcription factors; DNA methylation

Relevant publications:

Balaramane D*, Spill YG*, Weber M#, Bardet AF#. MethyLasso: a segmentation approach to analyze DNA methylation patterns and identify differentially methylated regions from whole-genome datasets. Nucleic Acid Research (2024) gkae880

Detilleux D*, Spill YG*, Balaramane D, Weber M#, Bardet AF#. Pan-cancer predictions of transcription factors mediating aberrant DNA methylation. Epigenetics & Chromatin (2022) 15:10

Domcke S*, Bardet AF*, Ginno P, Hartl D, Burger L, Schübeler D. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature (2015) 528(7583):575-9

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

The histone variant H3.3 is a key component of chromatin architecture, enriched at active regulatory regions and within gene bodies. Mutations affecting critical H3.3 residues, most notably G34R and K27M, define major subgroups of pediatric high-grade gliomas (pHGGs) and profoundly disrupt the epigenome by altering histone modifications, chromatin organization, and transcriptional control. However, the mechanisms through which these mutants reshape epigenetic landscapes remain poorly understood.

Using embryonic stem cells (ESCs) expressing H3.3 WT, G34R, or K27M, our group established a model to dissect these alterations. We showed that mutant H3.3 accumulates strongly on chromatin, promotes H3K9me3/TRIM28 recruitment, and induces widespread reactivation of young endogenous retroviruses (ERVs). MeDIP-seq further revealed a global loss of 5mC and 5hmC, indicating major disruption of DNA modification pathways, although the genomic and sequence specificity of these changes remain unclear.

This PhD project will address these gaps using Nanopore long-read sequencing to generate base-resolution maps of 5mC and 5hmC in H3.3 WT and mutant ESCs. This approach will reveal the genomic locations and cytosine contexts affected by demethylation and clarify whether specific ERV families display altered modification states. Nanopore Long reads will also enable the detection of structural variants and potential ERV mobilization. Integrated bioinformatic analyses combining nanopore methylation profiles with RNA-seq, ChIP-seq/CUT&Tag, ATAC-seq, and MNase-seq will reconstruct how H3.3 mutations drive methylome erosion, chromatin remodeling, and ERV dysregulation.

This computationally oriented thesis will clarify the mechanistic links between mutant H3.3, DNA demethylation, and retrotransposon activation, with important implications for understanding epigenetic deregulation and its contribution to tumorigenesis in pHGGs.

Keywords: Nanopore sequencing, DNA methylation, High-grade pediatric gliomas, Histone variant H3.3, chromatin, epigenetic, endogenous retroviruses

Relevant publications:

- Ibrahim A, Papin C, Mohideen-Abdul Kareem, Le Gras S, Stoll I, Bronner C, Dimitrov S,  Klaholz B, Hamiche A. MeCP2 is a microsatellite binding protein that protects CA repeats from nucleosome invasion. Science. 2021. Jun 25;372(6549):eabd558.

- Papin C, Le Gras S, Ibrahim A, Salem H, Karimi MM, Stoll I, Ugrinova I, Schröder M, Fontaine-Pelletier E, Omran Z, Bronner C, Dimitrov S, Hamiche A. CpG Islands Shape the Epigenome Landscape. J Mol Biol. 2021 Mar 19;433(6):166659.

- Papin C, Ibrahim A, Le Gras S, Velt A, Stoll I, Jost B, Menoni H, Bronner C, Dimitrov S, Hamiche A. Combinatorial DNA methylation codes at repetitive elements. Genome Research. 2017. Jun;27(6):934-946.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Niemann-Pick disease Type C (NPC) is a rare genetic disorder caused by mutations in NPC1 or NPC2 genes, which encode lysosomal cholesterol transporters. These mutations lead to the toxic buildup of cholesterol in lysosomes. NPC patients suffer from neurodegeneration and liver disease, and most die within the first decade of life. Reducing lysosomal cholesterol burden is therefore a major therapeutic need, but the mechanisms capable of clearing this accumulation remain elusive. Identifying pathways promoting cholesterol clearance will be key to developing effective therapies for NPC.

We performed a CRISPR knockout screen to identify genes that could be targeted to reduce lysosomal cholesterol accumulation in NPC cells. Surprisingly, we found that the knockout of several genes involved in the production and transport of specific classes of phospholipids strongly reduces lysosomal cholesterol in NPC cells.

The goal of this PhD project is to determine the mechanism by which the abolished synthesis of these specific phospholipid classes clears lysosomal cholesterol accumulation in NPC cells. To address this, we will use a combination of super-resolution live imaging, neuronal cell models, and proteomic techniques. This will be essential for determining whether the identified pathway could represent a new therapeutic target in the context of NPC.

Keywords: Lysosomes, Cholesterol, Niemann-Pick Type C, Cell Biology, Live-imaging, Proteomic

Relevant publications:

- Wilhelm LP, Wendling C, Védie B, Kobayashi T, Chenard MP, Tomasetto C, et al. STARD3 mediates endoplasmic reticulum-to-endosome cholesterol transport at membrane contact sites. EMBO J. 2017 May 15;36(10):1412–33.

- Di Mattia T, Martinet A, Ikhlef S, McEwen AG, Nominé Y, Wendling C, et al. FFAT motif phosphorylation controls formation and lipid transfer function of inter-organelle contacts. EMBO J. 2020 Dec 1;39(23):e104369.

- Boutry M, DiGiovanni LF, Demers N, Fountain A, Mamand S, Botelho RJ, et al. Arf1-PI4KIIIβ positive vesicles regulate PI(3)P signaling to facilitate lysosomal tubule fission. J Cell Biol. 2023 Sep 4;222(9):e202205128.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Translocation Renal Cell Carcinoma (tRCC) represents a rare but highly aggressive subtype of kidney cancer that predominantly affects children, adolescents, and young adults. These tumors are driven by chromosomal translocations involving TFE3 or related MiT family transcription factors. Despite their severity, there are currently no approved treatments for metastatic tRCC, making it crucial to uncover their molecular mechanisms and identify new therapeutic vulnerabilities. Our multidisciplinary team has developed innovative murine models expressing human TFE3 fusion oncogenes such as NONO-TFE3 and ASPSCR1-TFE3 specifically in kidney tissue. These models provide a unique opportunity to functionally dissect tumor initiation, progression, and microenvironmental interactions in vivo. This PhD project will combine molecular biology, functional genomics, bioinformatics, and translational oncology to explore the convergence of oncogenic mechanisms between mouse and human tRCC. The project includes four interconnected objectives:

1. Functional Characterization of Murine Models
   Investigate tumor development kinetics, early and late oncogenic events, and microenvironmental remodeling using advanced imaging and molecular profiling.
2. Cross-Species Comparative Analysis
   Compare oncogenic programs and tumor microenvironments in murine and human tRCC, identifying shared and divergent pathways that drive malignancy.
3. Pathway Convergence and Functional Validation
   Integrate data from murine models, human tumor samples, and cell lines to uncover conserved signaling and metabolic dependencies amenable to therapeutic targeting.
4. Identification of Novel Therapeutic Targets
   Use functional genomics, in vitro perturbation studies, and drug-response assays to validate promising targets and lay the groundwork for personalized therapies.

This project sits at the intersection of functional biology, computational analysis, and translational medicine. It leverages cutting-edge technologies, including Single-cell RNA sequencing and spatial transcriptomics to map tumor heterogeneity and ecosystem interactions, Multi-omics integration to reveal convergent molecular circuits between species and CRISPR-based functional screens to validate key drivers and druggable targets. By elucidating the shared molecular underpinnings of MiT family tRCC across species, this project aims to establish a functional framework for precision oncology in rare kidney cancers, providing a scientific foundation for next-generation therapeutic strategies and improving outcomes for young patients with these challenging malignancies.

Keywords: renal cell carcinomas, mice models, spatial transcriptomics, single-cell RNAseq, MiT family transcription factors

Relevant publications:

- Helleux A, Davidson G, Lallement A, Hourani FA, Haller A, Michel I, Fadloun A, Thibault-Carpentier C, Su X, Lindner V, Tricard T, Lang H, Tannir NM, Davidson I, Malouf GG. TFE3 fusions drive oxidative metabolism and ferroptosis resistance in translocation renal cell carcinoma. EMBO Mol Med. 2025 May;17(5):1041-1070. doi: 10.1038/s44321-025-00221-7. Epub 2025 Mar 27. PMID: 40148585; PMCID: PMC12081665.

- Davidson G, Helleux A, Vano YA, Lindner V, Fattori A, Cerciat M, Elaidi RT, Verkarre V, Sun C, Chevreau C, Bennamoun M, Lang H, Tricard T, Fridman WH, Sautes-Fridman C, Su X, Plassard D, Keime C, Thibault-Carpentier C, Barthelemy P, Oudard S, Davidson I, Malouf GG. Roles of mesenchymal-like tumour cells and myofibroblastic cancer-associated fibroblasts in progression and therapeutic response of clear-cell renal cell carcinoma. Cancer Research, 2023 Sep 1;83(17):2952-2969. 

- Vokshi BH*, Davidson G*, Tawanaie Pour Sedehi N, Helleux A, Rippinger M, Haller A, Gantzer J, Thouvenin J, Baltzinger P, Bouarich R, Manriquez V, Zaidi S, Rao P, Msaouel P, Su X, Lang H, Tricard T, Lindner V, Surdez D, Kurtz JE, Bourdeaut F, Tannir NM, Davidson I and Malouf GG. SMARCB1 regulates a TFCP2L1-MYC transcriptional switch promoting renal medullary carcinoma transformation and ferroptosis resistance. Nat Commun. 2023 May 26;14(1):3034.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

The cohesin complex is a major player in the 3D organization of eukaryotic genomes and is involved in sister chromatid cohesion, chromosome segregation, DNA replication and repair, and the regulation of gene transcription. Mutations in cohesin are found in numerous cancers and cause neurodevelopmental diseases called cohesinopathies, such as the Cornelia de Lange Syndrome (CdLS).
Cohesin’s functions are entirely dependent on its ATPase activity. How this activity contributes to cohesin's functions remains poorly understood. We have identified specific mechanisms underlying the cohesin ATPase cycle as well as specific regions and residues within the cohesin ATPase domain that are essential for this activity (Vitoria Gomes et al., 2024; doi:10.1016/j.celrep.2024.114656).
The proposed thesis project will study in detail the impact of the characterized regions and residues on cohesin's ATPase activity. Mutants of these regions and residues, but also mutants from CdLS patients, will be tested for their ability to bind ATP, form the ATPase domain, and hydrolyze ATP. These studies will be complemented by structural analyses by cryo-EM to understand the conformational impacts of these regions and residues on cohesin. This project will further be complemented by studies of these mutants by our collaborators through genome-wide analyses in iPSCs and using the zebrafish.

Keywords: Cohesin, ATPase, SMC complexes, Sister chromatid cohesion, Chromatin loops

Relevant publications:

- Vitoria Gomes et al. (2024) The cohesin ATPase cycle is mediated by specific
conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase
domains. Cell Rep., 43, 114656. doi: 10.1016/j.celrep.2024.114656.
- Marek et al. (2021) Species-selective targeting of pathogens revealed by the atypical structure and active site of Trypanosoma cruzi histone deacetylase DAC2. Cell Rep., 37, 110129. doi: 10.1016/j.celrep.2021.110129.
- Ramos-Morales et al. (2021) The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucl. Acids Res., 49, 6529-6548. doi: 10.1093/nar/gkab436.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Eukaryotic ribosomes are complex molecular machines whose assembly is tightly controlled to ensure faithful protein biosynthesis. Ribosome assembly is initiated in the nucleolus by the transcription and processing of ribosomal RNAs, which together with ribosomal proteins form pre-60S ribosomal particles. The pre-60S particles mature by transiently interacting with various assembly factors during cytosolic export. The nearly 5000 residues long maturation factor Rea1 is vital for the export of the pre-60S particles. Rea1 belongs to the AAA+ protein family and harnesses the energy of ATP hydrolysis to remove assembly factors from pre-60S particles. ATP hydrolysis in the Rea1 hexameric AAA+ ring drives the remodeling of the ≈1700aa linker extension of the AAA+ ring, which in turn creates the mechanical force for assembly factor removal. Rea1 mechanism is poorly, despite its key importance for ribosome maturation. We have recently characterized ATP dependent linker remodeling by low-resolution negative stain electron microscopy. In this project, we aim for high-resolution cryoEM investigations on ATP dependent Rea1 linker remodeling. The PhD student will be trained in the recombinant expression and purification of Rea1 mutants as well as in state-of-the-art cryoEM. These structural investigations will be complemented by in-vitro as well in-vivo activity assays carried out in collaboration with external partners. He/she will also learn to work in a highly international environment and to develop project management skills. Furthermore, presentation skills will be acquired due to regular progress meetings and the attendance of international conferences.

Keywords: Rea1, molecular machines, ribosome maturation, AAA+ proteins, cryo-electron microscopy, structural biology

Relevant publications:

- Remodelling of Rea1 linker domain drives the removal of assembly factors from pre-ribosomal particles. Busselez J, Koenig G, Dominique C, Klos T ,Velayudhan D, Sosnowski P, Marechal N, Crucifix C,  ,Gizardin-Fredon H ,Cianferani S, Benjamin A, Henry Y, Anthony H, Schmidt H. Nat Commun 2024

- The CryoEM structure of the Saccharomyces cerevisiae ribosome maturation factor Rea1. Sosnowski P, Urnavicius L, Boland A, Fagiewicz R, Busselez J, Papai G, Schmidt H. Elife 2018.

- Structure of human cytoplasmic dynein-2 primed for its power stroke. Schmidt H, Zalyte R, Urnavicius L, Carter AP. Nature 2015.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Type 2 DNA topoisomerases (Topo2) control DNA topology during replication, transcription and chromosome segregation. Essential for cell proliferation, these enzymes serve as targets for various classes of antineoplastic agents used in current cancer therapies. Resistance or non-response to cancer treatments highlights the need for personalized therapeutic strategies and a deeper understanding of their mechanisms of action.

We obtained high resolution cryoEM reconstruction of the human Topo2a isoform, in complex with DNA and anti-cancer molecules (Vanden Broeck et al, Nat. Comm 2021). Recent results from our team on the homologous bacterial enzyme showed that forming nucleoprotein complexes requires the use of more physiologically-relevant DNA substrates to capture functional conformational states (Vayssieres et al, Science 2024; Vanden Broeck et al, Nat. Comm 2019). The Topo2 are part of large complexes associated with chromatin factors and regulated by post-translational modifications (Bedez et al, Sci. Rep. 2018; Lotz et al., Can. Drug. Resist. 2020, Mazzoleni et al., J Mol Biol 2025 ahead of print). This thesis proposal aims at providing functional and structural knowledge on the enzymatic mechanisms and on cellular complexes of Topo2 in the context of chromatin. Our team has established international collaborations on complementary technologies, and cellular models to investigate the molecular architecture of Topo2 cellular complexes, as well as the interplay between drug resistance and the post-translational modifications of the Topo2.

Keywords: DNA topoisomerase, chromatin, Structural biology, cancer

Relevant publications:

- Vayssières M, Marechal N., Yun L., Lopez Duran  B., Murugasamy NK, Fogg  JM, Zechiedrich L., Nadal M., Lamour V. (2024). Structural basis of DNA crossover capture by Escherichia coli DNA gyrase. Science,384(6692):227-232. doi: 10.1126/science.adl5899.

- Vanden Broeck A, Lotz C, Drillien R, Bedez C, Lamour V (2021). Structural basis for the allosteric regulation of Human Topoisomerase 2α. Nat. Commun. 12, 2962. https://doi.org/10.1038/s41467-021-23136-6.

- Vanden Broeck A, Lotz C, Ortiz J, Lamour V. (2019) Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex. Nat. Commun., 10, 4935. https://doi.org/10.1038/s41467-019-12914-y.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

The ribosome is a molecular machinery that goes through different phases including initiation, elongation and termination of messenger RNA translation. Protein synthesis is catalysed by the ribosome and is regulated by protein factors that bind transiently to the ribosome during the different phases. Over the past few years, our research group succeeded in purifying the human ribosome to high homogeneity and determined its three-dimensional structure to ~3 Å resolution using cryo-EM (Khatter et al., Nature 2015; Natchiar et al., Nature 2017). The structure provided unprecedented insights into the detailed architecture of the human ribosome down to the atomic level with the visualization of side-chain positions and conformations of ribosomal RNAs and proteins and even chemical modifications of the rRNA (Nature 2017 & Nat Struct Mol Biol 2024). This opens unique possibilities in studying the molecular mechanism of protein synthesis in humans by analysing functional complexes of the human ribosome with mRNA, tRNAs and ribosomal factors bound. The aim of this PhD project is the structural analysis of factor-bound human ribosome complexes, explore the role rRNA expansion segments (protruding of the ribosome at its surface) and of polyribosome assemblies. The study will comprise the biochemical preparation of the ribosome, the reconstitution and biophysical characterization of the human ribosome complexes and the determination of the atomic structure from purified complexes by single particle cryo-EM or directly in the cell using the on-site latest-generation cryo focused ion beam (FIB) to prepare cell lamellae and reconstruct the complexes in 3D by cryo electron tomography using cutting-edge technologies (on-site high-resolution cryo electron microscopy, single particle image processing and 3D reconstruction, tomography & sub-tomogram averaging, atomic model refinement etc. as established and described in the publications of our group  (Khatter et al. Nature 2015, Natchiar et al. Nature 2017, Klaholz Acta Cryst. 2019, Fréchin et al. J Struct Biol. 2023, Barchet et al. J Struct Biol. 2023, Holvec et al., NSMB, 2024). This project will allow a better understanding of the function of the human ribosome, which is an important medical target including for cancer, thus having implications for the development of antibiotics and inhibitors (Myasnikov et al., 2016; Natchiar et al., 2017; Gilles et al., 2020). The project will benefit from the technological platforms in Integrated Structural Biology available as part of the FRISBI and Instruct-ERIC infrastructures hosted at the Centre for Integrative Biology at the IGBMC required for this project.

Keywords: human ribosome, structure-function, structural biology, high-resolution cryo electron microscopy

Relevant publications:

- S. Holvec, C. Barchet, A. Lechner, L. Fréchin, S. N. T. De Silva, I. Hazemann, P. Wolff, O. von Loeffelholz & B. P. Klaholz. The structure of the human 80S ribosome at 1.9 Å resolution reveals the molecular role of chemical modifications and ions in RNA. Nat Struct Mol Biol., 2024, 31, 1251-1264. https://doi.org/10.1101/2023.11.23.568509  & https://doi.org/10.1038/s41594-024-01274-x  & https://www.nature.com/articles/s41594-024-01275-w  

- C. Barchet, L. Fréchin, S. Holvec, I. Hazemann, O. von Loeffelholz & B. P. Klaholz. Focused classifications and refinements in high-resolution single particle cryo-EM analysis. J Struct Biol., 2023, 215, 4, 108015. https://doi.org/10.1016/j.jsb.2023.108015

- S. K. Natchiar, A. G. Myasnikov, H. Kratzat, I. Hazemann & B. P. Klaholz. Visualization of chemical modifications in the human 80S ribosome structure. Nature, 2017, 551, 472-477. http://dx.doi.org/10.1038/nature24482

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

To develop or adapt to the conditions they encounter, organisms must produce the proteins that they need in adequate quantities. The synthesis of these cellular factors is carried out by ribosomes, which use the instructions encoded in messenger RNAs (mRNAs) to guide the synthesis of each of the different proteins. Protein production is finely regulated by controlling the synthesis of messenger RNAs, their availability to ribosomes, or the elimination of obsolete messenger RNAs.

The project aims to highlight a direct, previously unanticipated, molecular connection between the ribosome and the mRNA decay machinery. The team’s recent results demonstrate functional and molecular interactions between these two processes. In particular, the host team has recently obtained experimental evidence for a direct interaction between the yeast ribosomal protein Asc1 and a factor implicated in translational control and mRNA decay. Based on this information, we propose that Asc1 forms an interaction platform that coordinates translation with mRNA decay. The project objectives are thus (1) to identify the Asc1 interactome, (2) to characterize selected interactions biochemically and structurally (the latter through a collaboration), and (3) to elucidate how Asc1 and these interactions contribute to the functional coupling between ribosomes and mRNA decay. Phylogenetic information and structural modelling suggest further that this process is conserved in human. This possibility will also be addressed experimentally. The project will involve in vivo analyses (characterization of mutants, analyses of reporter genes...), biochemical assays (activity tests, protein-RNA interaction studies...) as well as high-throughput analyses (transcriptomic, ribosome profiling). It will provide a new understanding of the mechanisms regulating protein production.

Keywords: mRNA, regulation of gene expression, RNA decay, translation, ribosome, diseases

Relevant publications:

Caulier G, Siblini J, Sène L, Mauxion F, and Séraphin B. The CCR4-NOT complex: a multifaceted sensor of molecular signals instructing eukaryotic mRNA translation and stability. Nucleic Acids Research (2025).

Mauxion F, Séraphin B. An RNA-Ligation-Based RACE-PAT Assay to Monitor Poly(A) Tail Length of mRNAs of Interest. Methods Mol Biol. (2024) 2723:113-123. doi: 10.1007/978-1-0716-3481-3_7.

Huntzinger E, Sinteff J, Morlet B, Séraphin B. HELZ2: a new, interferon-regulated, human 3'-5' exoribonuclease of the RNB family is expressed from a non-canonical initiation codon. Nucleic Acids Res. (2023) 51(17):9279-9293. doi: 10.1093/nar/gkad673.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

The intricate cognitive functions of the cerebral cortex stem from a diverse network of neurons and glial cells, all generated from a uniform pool of progenitors during corticogenesis. This project seeks to elucidate how these progenitors sequentially produce distinct neuronal and glial progeny over time, shaping brain development.

While transcriptional programs have been recognized as key drivers of neuronal diversity, emerging evidence indicates that certain neuronal mRNAs are present in progenitor cells long before their corresponding proteins appear. This observation suggests that translation mechanisms may play a pivotal role in defining cell identity, alongside transcription.

We propose that dynamic regulation of tRNA pools significantly influences translation during cortical patterning, affecting progenitor competency. Our preliminary findings indicate that tRNA availability varies across cell types and developmental stages in the mouse cortex. Through cutting-edge cell labelling and sequencing techniques (tRNA sequencing, quantitative measurement of translation efficiency), the PhD candidate will resolve the tRNAs repertoires in neurons as they migrate and mature and determine whether tRNA fluctuation correlates with specific change in translational programs during cortical lineage differentiation.

By uncovering these mechanisms, this project not only advances our understanding of neural diversity but also has potential implications for neurodevelopmental disorders.

Keywords: brain development, neuronal diversity, translation, omic analysis, transfer RNA

Relevant publications:

- Del-Pozo-Rodriguez J, et al. ADAT3 variants disrupt the activity of the ADAT tRNA deaminase complex and impair neuronal migration. Brain (2025) 10.1093/brain/awaf109

- Bayam E et al.  Bi-allelic variants in WDR47 cause a complex neurodevelopmental syndrome. EMBO Mol Med (2024) 10.1038/s44321-024-00178-z.

- Ramos-Morales E et al. The structure of the mouse ADAT2/ADAT3 complex reveals the molecular basis for mammalian tRNA wobble adenosine-to-inosine deamination. Nucleic Acids Res (2021) 49: 6529-6548

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Neuromuscular disorders are rare genetic diseases characterized by muscle weakness arising from structural and functional alterations of the peripheral nerves, the neuromuscular junction, or skeletal muscle fibers. Patients typically manifest progressive muscle weakness and respiratory distress, impacting on the quality of life, autonomy, and survival. There is currently no curative treatment for the vast majority of these devastating diseases, and the underlying pathological mechanisms are barely understood. Our team previously identified the genetic basis of several neuromuscular diseases and generated and characterized reliable cell and mouse models.

The PhD project involves both in vitro and in vivo work. The PhD student will establish novel cell systems to reproduce the cellular and molecular alterations observed in patients. In addition, he/she will analyze and characterize these alterations in mouse models already available in the lab. Methods and techniques include cell culture, photonic and electronic microscopy with morphometrics, immunofluorescence, histology, omics approaches (RNA, protein, lipids, metabolites), western blotting, quantitative PCR, and motor and sensory phenotyping. Overall, the PhD project is expected to reveal yet unknown mechanisms leading to the development of neuromuscular diseases. In parallel, the student will test and validate novel therapeutic approaches in these cell and animal models based on a couple of targets we previously identified, using viral vectors, oligonucleotides to modulate gene expression, or pharmacological compounds.

The PhD student will manage the different aspects of his/her project with regular inputs from the team, be responsible for the choice of strategies and presentation of data, and manage the collaborations with technical platforms and external collaborators. He/she will gain expertise in molecular biology, gene therapy, targeted drug delivery, and preclinical evaluation, contributing to precision medicine advancements. Overall, this PhD project should lead to a better understanding of neuromuscular disorders and the establishment of therapies with the perspective to treat patients. Our previous work led to the development of 3 clinical trials and the creation of a start-up company.

Keywords: neuromuscular disorder, therapy, genetic disease, omics, virus vector, pharmacological treatment, mouse, cell, imaging

Relevant publications:

- Silva-Rojas R, Pérez-Guàrdia L, Simon A, Djeddi S, Treves S, Ribes A, Silva-Hernández L, Tard C, Laporte J, Böhm J. ORAI1 inhibition as an efficient preclinical therapy for tubular aggregate myopathy and Stormorken syndrome. JCI Insight. 2024 Mar 5;9(6):e174866. doi: 10.1172/jci.insight.174866.

- Goret M, Edelweiss E, Jehl J, Reiss D, Aguirre-Pineda P, Friant S, Laporte J. Combining dynamin 2 myopathy and neuropathy mutations rescues both phenotypes. Nat Commun. 2025 May 20;16(1):4667. doi: 10.1038/s41467-025-59925-6

- Moschovaki-Filippidou F, de Carvalho Neves J, Diedhiou N, Jad Y, Böhm J, Wood MJA, Varela MA, Laporte J. Exon skipping peptide-conjugated morpholinos downregulate dynamin 2 to rescue centronuclear myopathy. Brain. 2025 Jul 3:awaf249. doi: 10.1093/brain/awaf249.

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

World-class athletes display extraordinary physiological adaptations allowing them to perform at the limits of human endurance. These capabilities are driven not only by training and environment but also by genetic factors influencing muscle metabolism, oxygen utilization, and hypoxia tolerance, for example. The ‘Athlome’ project aims to identify and characterize genetic variants associated with enhanced skeletal muscle performance under hypoxic conditions, by analyzing the genomes of elite freedivers and ski mountaineers.

The PhD candidate will manage the ‘Athlome’ project aiming at identifying and characterizing genetic variants associated with enhanced skeletal muscle performance under hypoxia using advanced bioinformatics and genomic tools. Whole genomic sequences from about 60 athletes, including world champions and record holders, are already available for analysis. Additional cohorts will be retrieved through collaboration with researchers, federations and coaches. The candidate will develop and optimize bioinformatic pipelines for variant calling and rank best candidate variants. Correlation with athletic performance, and biological and physiological data will assess the importance of these novel genetic variants. Functional validation of the effect of chosen genetic variants will be performed by the candidate or in collaboration in in vitro models (cell culture, microscopy, omics).

Understanding the genetic determinants of outstanding athletic performance in these unique cohorts of athletes offers the opportunity to uncover the biological basis of exceptional human performance. This work also aims to identify therapeutic targets for severe diseases linked to muscle weakness and respiratory distress, that other team members study in our laboratory.

Keywords: genomics, bioinformatics, sequencing, sports, genetic disease

Relevant publications:

- Goret M, Edelweiss E, Jehl J, Reiss D, Aguirre-Pineda P, Friant S, Laporte J. Combining dynamin 2 myopathy and neuropathy mutations rescues both phenotypes. Nat Commun. 2025 May 20;16(1):4667. doi: 10.1038/s41467-025-59925-6 (M Goret = previous PhD student) 

- Goret M, Thomas M, Edelweiss E, Messaddeq N, Laporte J. BIN1 reduction ameliorates DNM2-related Charcot-Marie-Tooth neuropathy. Proc Natl Acad Sci U S A. 2025 Mar 11;122(10):e2419244122. doi: 10.1073/pnas.2419244122 (M Goret = previous PhD student) 

 - Gómez-Oca R, Edelweiss E, Djeddi S, Gerbier M, Massana-Muñoz X, Oulad-Abdelghani M, Crucifix C, Spiegelhalter C, Messaddeq N, Poussin-Courmontagne P, Koebel P, Cowling BS^, Laporte J^. Differential impact of ubiquitous and muscle dynamin 2 isoforms in muscle physiology and centronuclear myopathy. Nature Commun. 2022 Nov 11;13(1):6849. doi: 10.1038/s41467-022-34490-4. (R Gomez-Oca = previous PhD student) 

This project is self-funded by the team proposing the project.

Down Syndrome (DS) is the most common genetic cause of intellectual disability, affecting 1 in 1,000 births. Beyond cognitive and physical impairments, DS is a multi-organ condition with increased susceptibility to obesity, diabetes, and metabolic dysfunction-associated steatohepatitis (MASH), the severe form of steatotic liver disease. MASH, previously termed NAFLD, is characterized by lobular inflammation and hepatocyte ballooning, leading to fibrosis and systemic complications driven by insulin resistance, lipotoxicity, dysbiosis, and chronic inflammation. Alarmingly, MASH occurs in 82% of DS individuals with obesity and 45% with normal BMI.

Within the EU-funded GO-DS21 project, MASH was identified in Dp(16)1Yey DS mouse models, accompanied by bile acid accumulation, reduced cholesterol, and increased bilirubin, indicating cholestasis. Gut microbiota analysis revealed intestinal dysbiosis triggering inflammatory pathways across liver, muscle, adipose tissue, and brain. These findings mirror human DS hallmarks of peripheral and neuroinflammation, which likely contribute to cortico-hippocampal cognitive deficits via the gut–liver–brain axis.

We hypothesize that BA/cholesterol dysregulation, driven by triplicated genes on Mmu16 homologous to Hsa21, underlies MASH in DS. This project aims to dissect developmental liver dysfunction, identify genetic determinants, and explore their metabolic and cognitive consequences to uncover therapeutic targets.

Keywords: Liver disease, Gut-liver-brain axis, cognition, inflammation, OMICS

Relevant publications:

- Lanzillotta C, Baniowska MR, Prestia F, Sette C, Nalesso V, Perluigi M, Barone E, Duchon A, Tramutola A, Herault Y, Di Domenico F. Shaping down syndrome brain cognitive and molecular changes due to aging using adult animals from the Ts66Yah murine model. Neurobiol Dis. 2024 Jun 15;196:106523. doi: 10.1016/j.nbd.2024.106523.

- Hinckelmann MV, Dubos A, Artot V, Rudolf G, Nguyen TL, Tilly P, Nalesso V, Muniz Moreno MDM, Birling MC, Godin JD, Brault V, Herault Y. Interneuron migration defects during corticogenesis contribute to Dyrk1a haploinsufficiency syndrome pathogenesis. Mol Psychiatry. 2025 30:5227-5244. doi: 10.1038/s41380-025-03109-7

- Ahumada Saavedra JT, Chevalier C, Bloch Zupan A, Herault Y. Ripply3 overdosage induces mid-face shortening through Tbx1 downregulation in Down syndrome models. PLoS Genet. 2025 21:e1011873. doi: 10.1371/journal.pgen.1011873

Financial support of this subject is allocated by the Research Cluster / LabEx INRT based on applicant's merit.

Membrane proteins (MPs) play crucial roles at the interface between the cell and its external environment and constitute important target for drug discovery. However, their structural characterization by crystallography or electron microscopy (EM) is complex because it requires the extraction of MPs from lipid bilayers and their stabilization using detergents. This project aims to test and validate (novel) experimental procedures allowing the study of MPs in conditions closer to their natural environment using lipid nanotubes. It associates a research team interested in protein:RNA interactions, some involving MPs responsible for tRNA transport, with a cryoEM platform developing new protocols to facilitate the imaging of challenging biological samples, such as MPs or large biomolecular complexes. The proposed strategies will be tested on the tRNA import protein (tRip) from Plasmodium falciparum, the malaria vector. From a technical standpoint, the use of nanotubes should allow for better spatial distribution of MPs and their complexes with tRNAs or other cellular partners to facilitate the reconstruction of a 3D model at high resolution. From a functional standpoint, they will also facilitate the reconstitution and visualization of these biomolecular assemblies in a membrane environment and help understand their organization and the mechanism of tRNA import, thus opening new avenues to fight the malaria parasite.

Keywords: electron microscopy and tomography, methodology, membrane proteins, lipid nanotubes, tRNA import, Plasmodium

Relevant publications:

- Solution x-ray scattering highlights discrepancies in Plasmodium multi-aminoacyl-tRNA synthetase complexes. Jaramillo Ponce et al. Protein Science (2023) https://doi.org/10.1002/pro.4564

- Apicomplexa-specific tRip facilitates import of exogenous tRNAs into malaria parasites. Bour et al. PNAS (2016) https://doi.org/10.1073/pnas.1600476113

- Molecular basis for the differential interaction of plant mitochondrial VDAC proteins with tRNAs. Salinas et al. Nucleic Acids Res. (2014) https://doi.org/10.1093/nar/gku728

- Mechanism of DNA entrapment by a loop-extruding Wadjet SMC motor. Roisné-Hamelin et al. Molecular Cell (2025) https://doi.org/10.1016/j.molcel.2025.09.015

- Structural basis of DNA crossover capture by Escherichia coli DNA gyrase. Vayssières et al. Science (2024) https://doi.org/10.1126/science.adl5899

- Structural and mechanistic analysis of a tripartite ATP-independent periplasmic TRAP transporter. Peter et al. Nat Commun (2022) https://doi.org/10.1038/s41467-022-31907-y

Financial support of this subject is allocated by the IMCBio Graduate School based on applicant's merit.

Chikungunya virus (CHIKV) is an emerging mosquito-borne virus responsible for severe and persistent musculoskeletal pain. Although skeletal muscle has been identified as a key target tissue where the virus establishes pathology, how individual CHIKV proteins interact with and perturb host muscle factors remains poorly understood.

This PhD project aims to investigate the direct impact of individual CHIKV proteins on skeletal muscle in the absence of infection, enabling the identification of host pathways targeted by these viral factors without the confounding effects of viral replication. To do so, the PhD student will acquire broad training at the interface of cell biology and infection biology by a) generating and characterizing mouse models expressing individual CHIKV proteins in vivo using muscle-specific AAV delivery and b) validating key findings in primary cells infected with CHIKV.

The project is linked to an ANRS-funded study coordinated by Dr. Kim, who will provide expertise in muscle biology and in vivo model development. Dr. Pfeffer/Dr Girardi’s team will contribute with a complementary expertise in molecular virology and provide BSL3 infrastructure to validate the most relevant findings using primary murine cells for CHIKV infections.

Building on this collaborative framework, this interdisciplinary PhD project aims to:
(i) comprehensively map the interactome of CHIKV proteins with host factors in skeletal muscle,
(ii) characterize the localization and pathogenic impact of individual viral proteins, and (iii) integrate bioinformatics to identify key host pathways and therapeutic targets.

Keywords: Skeletal muscle, chikungunya virus, host-pathogen interaction

Relevant publications:

- Kim, M*., Franke, V*., Brandt, B., Lowenstein, E.D., Schowel, V., Spuler S., Akaline, A., and Birchmeier, C. (2020) Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells. Nature Communications. 11, 6375. *, co-first authors.

- Cristofer Calvo*, Coalesco Smith*, Taejeong Song, Sakthivel Sadayappan, Douglas P. Millay# and Minchul Kim#. Loss of Ufsp1 does not cause major changes at the neuromuscular junction. Plos One. *, co-first authors. #, co-correspondence.

- Kim, M*., Wende, H.,*, Walcher, J., Cheret, C., Kempa, S., Lewin, G., and Birchmeier, C. (2018) Maf links Neuregulin1 signaling to cholesterol synthesis in myelinating Schwann cells. Genes & Development. 2018. May 1;32(9-10):645-657. (Cover paper). *, co-first authors.

- Messmer M, Pierson L, Pasquier C, Djordjevic N, Chicher J, Hammann P, Pfeffer S, Girardi E (2024). DEAD box RNA helicase 5 is a new pro-viral host factor for Sindbis virus infection. Virol J. 21(1):76.

- Girardi E#, Messmer M, Lopez P, Fender A, Chicher J, Chane-Woon-Ming B, Hammann P, Pfeffer S# (2023). Proteomics-based determination of double-stranded RNA interactome reveals known and new factors involved in Sindbis virus infection. RNA 29(3):361-375. #, co-correspondence.

- López, P.*, Girardi, E.*, #, Mounce, B.C., Weiss, A., Chane-Woon-Ming, B., Messmer, M., Kaukinen, P., Kopp, A., Bortolamiol-Becet, D., Fendri, A., Vignuzzi M, Brino L, Pfeffer S#. (2020). High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection. J. Virol. 94, e02145-19. *, co-first authors. #, co-correspondence.

Financial support of this subject is allocated by the IMCBio Graduate School based on applicant's merit.

HIV-1, like all retroviruses, must select and encapsidate two copies of its genomic RNA (gRNA) to ensure successful replication. The viral precursor Pr55Gag (Gag) drives both the specific recognition of the gRNA and the assembly of the nascent viral particle at the plasma membrane (PM). Despite the central role of this step, the molecular mechanisms underlying selective gRNA recognition and packaging remain poorly understood. Gaining structural and functional insight into these early events is essential for improving antiretroviral strategies and optimizing retroviral vector design. This project aims to determine the first high-resolution structure of the complex made of Gag and gRNA fragments containing the packaging signal (Psi), in the context of PM-mimicking lipids by cryo-EM, thereby elucidating the earliest steps of HIV-1 genome selection and encapsidation.

Gag proteins will be produced in mammalian expression systems, while Psi RNA fragments will be generated by in vitro transcription, benefiting from our long-standing expertise. To maximize the chances of success, we will combine two complementary cryo-EM approaches: single-particle analysis and sub-tomogram averaging using cryo-electron tomography (cryo-ET). EM grids functionalized with a lipid monolayer mimicking the inner leaflet of the PM will be used to assemble lipid–Gag and lipid–Gag–Psi RNA complexes. In parallel, biotinylated liposomes will be immobilized on streptavidin-coated grids to stabilize liposome-bound complexes for cryo-ET. These strategies will be developed collaboratively between our teams, leveraging our expertise in HIV-1 assembly and state-of-the-art structural biology platforms.

Keywords: HIV-1, gRNA encapsidation, Gag precursor, Psi RNA, cryo-EM, cryo-ET, protein–RNA interactions, protein–lipid interactions, viral assembly, plasma membrane mimetics, structural biology

Relevant publications:

- Serrano T, Casartelli N, Ghasemi F, Wioland H, Cuvelier F, Salles A, Moya-Nilges M, Welker L, Bernacchi S, Ruff M, Jégou A, Romet-Lemonne G, Schwartz O, Frémont S, Echard A. HIV-1 budding requires cortical actin disassembly by the oxidoreductase MICAL1. Proc Natl Acad Sci U S A. 2024 Nov 26;121(48):e2407835121. doi: 10.1073/pnas.2407835121. Epub 2024 Nov 18. PMID: 39556735; PMCID: PMC11621841.

- Batisse C, Lapaillerie D, Humbert N, Real E, Zhu R, Mély Y, Parissi V, Ruff M, Batisse J. Integrase-LEDGF/p75 complex triggers the formation of biomolecular condensates that modulate HIV-1 integration efficiency in vitro. J Biol Chem. 2024 Jun;300(6):107374. doi: 10.1016/j.jbc.2024.107374. Epub 2024 May 16. PMID: 38762180; PMCID: PMC11208922.

- Drillien R, Pradeau-Aubreton K, Batisse J, Mezher J, Schenckbecher E, Marguin J, Ennifar E, Ruff M. Efficient production of protein complexes in mammalian cells using a poxvirus vector. PLoS One. 2022 Dec 15;17(12):e0279038. doi: 10.1371/journal.pone.0279038. PMID: 36520869; PMCID: PMC9754296.

Financial support of this subject is allocated by the IMCBio Graduate School based on applicant's merit.

Elucidating the causes of the awesome phenotypic diversity observed in natural populations is a major challenge in biology. To date quantitative genetics has mainly been focused on the identification of the nuclear determinants of complex trait, leaving mitochondrial DNA aside. The mitochondrial genome has been considered to study specific mitochondrial traits, but its contribution to common complex traits has been largely ignored. There is a growing number of evidence that genetic variations of the mitochondrion (considered alone or through interactions with nuclear variations) account for much of the heritability of complex traits. In this context, we would like to identify mitochondrial genetic determinants of multiple complex traits (including organismal as well as molecular traits like gene expression levels). Moreover, we will characterize the genetic architecture of the interaction between the mitochondrial and nuclear genomes, with respect with those traits. Beyond the description of mitochondrial genetic associations, we want to uncover the molecular mechanisms underlying them, i.e. what are the genes/proteins involved and how are they contribute together to a phenotype. To achieve this, we will develop genetic and genomic approaches (experimental and computational). Reaching a system comprehension of the genetic and molecular mechanisms underlying the nuclear-mitochondrial interactions requires a deep understanding of both molecular and computational biology. Therefore, we will work at the interface between genetics, genomics and computational biology.

Keywords: genetics, population genomics, phenotypic variation, mitochondrion, yeast

Relevant publications:

- From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes. Loegler V, Thiele P, Teyssonnière E, Tsouris A, Brach G, Cruaud C, Payen E, Engelen S, Dunham MJ, Hou J, Friedrich A, Schacherer J. Nature, 2025. doi: 10.1038/s41586-025-09637-0

- Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast. Caudal É, Loegler V, Dutreux F, Vakirlis N, Teyssonnière É, Caradec C, Friedrich A, Hou J, Schacherer J. Nature Genetics, 2024 Jun;56(6):1278-1287. doi: 10.1038/s41588-024-01769-9.

- Genome evolution across 1,011 Saccharomyces cerevisiae isolates. Peter J, De Chiara M, Friedrich A, Yue JX, Pflieger D, Bergström A, Sigwalt A, Barre B, Freel K, Llored A, Cruaud C, Labadie K, Aury JM, Istace B, Lebrigand K, Barbry P, Engelen S, Lemainque A, Wincker P, Liti G, Schacherer J. Nature, 2018, 7701:339-344. doi: 10.1038/s41586-018-0030-5.

Financial support of this subject is guaranteed by the Research Cluster / LabEx MitoCross.

Mitochondria are ancient endosymbiotic organelles that emerged nearly two billion years ago, profoundly shaping eukaryotic evolution. Beyond their iconic role as the cell’s “powerhouses,” producing ATP, they contain specialized gene expression systems that vary widely across species. Chlamydomonas reinhardtii, a unicellular green alga, offers a unique model because its mitochondrial genome combines plant-like features with an architecture reminiscent of mammals.

Our laboratory resolved the structure of the Chlamydomonas mitoribosome, revealing proteins that may facilitate the assembly of its unusually fragmented ribosomal RNAs. We also discovered that Chlamydomonas mitochondrial mRNAs initiate translation directly at AUG codons without leader sequences, an unconventional mechanism distinct from those described in mammals and still mechanistically unexplained.

The proposed doctoral project aims to build on these findings to unravel how translation is initiated in Chlamydomonas mitochondria. This multidisciplinary work will integrate genetic tools, next-generation sequencing, biochemical analyses, and advanced structural approaches (i.e., immunoprecipitation, Ribo-Seq, and cryo-EM). By identifying novel factors involved in mitochondrial translation initiation and defining their interplay with universal components, the project will clarify how mRNA and tRNA are recruited to the mitoribosome and how protein synthesis is triggered.

Ultimately, this research will expand our understanding of the diversity of translation mechanisms across eukaryotes.

Keywords: Chlamydomonas, algae, mitochondria, translational machinery, RNA, transcriptomics, proteomics

Relevant publications:

- Waltz, F., Salinas-Giegé, T., Englmeier, R. et al. (2021) How to build a ribosome from RNA fragments in Chlamydomonas mitochondria. Nat Commun 12, 7176. https://doi.org/10.1038/s41467-021-27200-z

- Salinas-Giegé, T., Cavaiuolo, M., Cognat, V. et al. (2017) Polycytidylation of mitochondrial mRNAs in Chlamydomonas reinhardtii, Nucleic Acids Research, Volume 45, Issue 22, Pages 12963–12973, https://doi.org/10.1093/nar/gkx903

- Salinas, T., Duby, F., Larosa, V. et al. (2012) Co-Evolution of mitochondrial tRNA import and codon usage determines translational efficiency in the green alga Chlamydomonas. PLoS Genet, 8(9):e1002946, https://doi.org/10.1371/journal.pgen.1002946

Financial support of this subject is guaranteed by the Research Cluster / LabEx MitoCross.

The goal of the PhD is to fill a knowledge gap in chloroplast RNA quality control (QC). Transcriptomics data suggest that the full chloroplast genome is transcribed, which, coupled to inefficient termination, leads to a highly complex primary transcriptome. Moreover, it is now clear that chloroplast also possess abundant non coding RNAs (ncRNAs) that can form RNA duplexes with genic transcripts (dsRNA) although the amplitude and biological meaning are unknown. The chloroplast therefore relies on RNA quality control (QC) to sort through this initial transcript pool for those segments to be preserved and in some cases subdivided, while the remainder is rapidly degraded. It is performed by an assortment of ribonucleases (RNases) described to have low sequence specificity. We have recently showed that at least two ribonucleases, PNPase and RNaseJ, have a major role in maintaining the sense/antisense RNA homeostasis and we are now exploring the role of another RNase, RNaseE which preliminary data suggest to be involved in transcription termination.

The project aims to (1) precisely define the role of RnaseE in transcription and transcript degradation, with a particular focus on the metabolism of RNA-RNA duplexes and (2) identify and initiate the characterization of new proteins factors interacting with RnaseE and involved in dsRNA metabolism.

Keywords: Chloroplast, Arabidopsis, RNA quality control, RNases, RNA-Seq, Nanopore, double stranded RNA

Relevant publications:

- Baudry et al., bioRxiv 2025.10.15.682605. LINK The GT1 domain of RNase J ensures RNA quality control through dsRNA binding in Arabidopsis plastids

- Liehrmnn et al., NAR Genom and Bioinform, 2023, Nov 6; 5(4):lqad098. LINK DiffSegR: An RNA-Seq data driven method for differential expression analysis using changepoint detection

- MacIntosh GC and Castandet B. Plant Physiology. 2020; 183(4):1438-1452. LINK Organellar and secretory ribonucleases, major players in RNA homeostasis

Financial support of this subject is guaranteed by the Research Cluster / LabEx MitoCross

Shigella is a facultative intracellular bacterium that invades colonic epithelial cells and manipulates host cellular processes to promote infection. While its protein-targeting virulence strategies are well described, the impact of Shigella infection on the host transcriptome—particularly at the post-transcriptional level—remains poorly explored. Preliminary data indicate that Shigella affects host RNA metabolism at both transcriptional and post-transcriptional stages, highlighting RNA regulation as a key but underexplored aspect of infection biology.
This PhD project aims to identify and characterize host and bacterial trans-acting factors involved in post-transcriptional RNA regulation during Shigella infection. The future PhD candidate will first select and identify post-transcriptionally deregulated mRNA targets using cultured epithelial cells infected with Shigella flexneri 2a. Next, proteomics approaches such as TurboID will be employed to identify RNA-binding proteins associated with the selected transcripts. These transcripts will be specifically targeted using CRISPR–dCas13 or the MS2 stem-loop system to dissect RNA–protein interactions and validate the underlying regulatory mechanisms. Finally, gain- or loss-of-function studies will assess the
contribution of these factors to Shigella pathogenesis.
Combining RNA-seq, RIP-seq, CRISPR-based RNA targeting, and global proteomics, this exploratory project will uncover novel post-transcriptional mechanisms shaping host responses during bacterial infection.

Keywords: RNA-binding proteins, post-transcriptional regulation, Shigella infection, RNAseq, RIP-seq, TurboID, CRISPR–dCas13, MS2

Relevant publications:

- Shigella-mediated oxygen depletion is essential for intestinal mucosa colonization. Tinevez JY, Arena ET, Anderson M, Nigro G, Injarabian L, André A, Ferrari M, Campbell-Valois FX, Devin A, Shorte SL, Sansonetti PJ, Marteyn BS. Nat Microbiol. 2019 Nov;4(11):2001-2009. doi: 10.1038/s41564-019-0525-3.
- Shigella Diversity and Changing Landscape: Insights for the Twenty-First Century. Anderson M, Sansonetti PJ, Marteyn BS. Front Cell Infect Microbiol. 2016 Apr 19;6:45. doi: 10.3389/fcimb.2016.00045. eCollection 2016.

- The interactome of CLUH reveals its association to SPAG5 and its co-translational proximity to mitochondrial proteins. Hémono M, Haller A, Chicher J, Duchêne AM, Ngondo RP.BMC Biol. 2022 Jan 10;20(1):13. doi: 10.1186/s12915-021-01213-y.

Financial support of this subject is guaranteed by the Research Cluster / LabEx NetRNA.

RNA degradation is a major regulator of gene expression, ensuring transcriptome plasticity essential for growth and adaptation. However, how RNA degradation varies between tissues of multicellular organisms remains poorly understood. In plants, most current insights in RNA decay come from studies in young seedlings using transcriptional block assays, which obscure tissue-specific differences in mRNA turnover at later developmental stages. Understanding these differences is crucial to reveal how RNA stability contributes to gene regulatory networks in mature plant tissues, especially under stress conditions.
This PhD project will explore RNA degradation in mature plant organs exposed to abiotic stresses. The student will employ a method called global mRNA molecular recording, which uses a molecular recorder that introduces specific nucleotide edits in the 3′UTR of all mRNAs in vivo. The edit frequency, detectable by Illumina and Nanopore sequencing, is proportional to poly(A) tail length and can reflect the time spent by the mRNA in the cytosol. The student will optimize this system by generating Arabidopsis transgenic lines expressing improved  molecular recorders. Sequencing analyses under stress conditions such as heat
or prolonged darkness will yield edit scores serving as proxies for mRNA stability, providing insights into RNA decay–mediated stress responses. Training will cover mRNA metabolism, plant genetics, Illumina and Nanopore sequencing, and bioinformatics.

Keywords: mRNA degradation; Nanopore sequencing; Illumina sequencing; Arabidopsis; abiotic stresses

Relevant publications:

- Peter J, Roignant J, Sacharowski S, Ubrig E, Lefèvre B, Swiezewski S, Gagliardi D and Zuber H (2024) The TUTase URT1 regulates the transcriptome of seeds and their primary dormancy. bioRxiv 2024.12.19.629392; doi: 10.1101/2024.12.19.629392v1 (in revision at The Plant Cell)
- Pouclet A, David Pflieger D, Merret R, Carpentier M-C, Schiaffini M, Zuber H, Gagliardi D and Garcia D (2024) Multi-transcriptomics identifies targets of the endoribonuclease DNE1 and highlights its coordination with decapping. The Plant Cell, 36(9):3674-3688, doi: 10.1093/plcell/koae175
- Joly AC, Garcia S, Hily J-M, Koechler S, Demangeat G, Garcia D, Vigne E, Lemaire O, Zuber H, Gagliardi D (2023) An extensive survey of phytoviral RNA 3' uridylation identifies extreme variations and virusspecific patterns. Plant Physiology 193(1):271-290, doi: 10.1093/plphys/kiad278

Financial support of this subject is guaranteed by the Research Cluster / LabEx NetRNA.

RNA viruses establish membrane-bound viral factories in host cells to replicate their genomes, relying on a complex interplay of viral and host-encoded proteins. This process generates double-stranded RNA (dsRNA) intermediates which serve as a danger signal, triggering both sequence-specific and broad-spectrum antiviral defenses. In plants, dsRNA is primarily detected by the RNA interference (RNAi) pathway in which long dsRNA is processed by the RNase-III Dicer enzymes into small interfering RNAs (siRNAs).  siRNA then guide the RNA-induced silencing complex (RISC) to degrade complementary viral RNA in a sequence-specific manner.

Our recent studies in Arabidopsis, have identified a dsRNA-binding protein that is predicted to bind to DCL4 and DCL2, the main RNase III enzymes for antiviral defense. This PhD project seeks to unravel the biological role of this protein under normal conditions and during viral infections. Using CRISPR-Cas9-generated mutants, phenotypic screens will be conducted under various environmental conditions, alongside spatio-temporal analyses. RNA-seq and small RNA profiling will be used to investigate changes in gene expression and small RNA pathways. Biochemical studies will aim are purifying the dsRNA/protein complexes for structural analyses.

To explore molecular mechanisms, the project will integrate advanced techniques, co-immunoprecipitation, and purification of native dsRNA-protein complexes for structural studies. This interdisciplinary project offers a unique opportunity to delve into plant immunity and antiviral defense using state-of-the-art molecular, genetic, and structural biology approaches.

 Keywords: RNA virus replication, Host-virus interactions, dsRNA-binding proteins, plant virology

Relevant publications:

- Incarbone, M., Clavel, M., Monsion, B., Kuhn, L., Scheer, H., Vantard, E., Poignavent, V., Dunoyer, P., Genschik, P., and Ritzenthaler, C. (2021). Immunocapture of dsRNA-bound proteins provides insight into Tobacco rattle virus replication complexes and reveals Arabidopsis DRB2 to be a wide-spectrum antiviral effector. Plant Cell 33, 3402-3420. https://www.ncbi.nlm.nih.gov/pubmed/34436604

- Incarbone, M., Scheer, H., Hily, J.M., Kuhn, L., Erhardt, M., Dunoyer, P., Altenbach, D., and Ritzenthaler, C. (2020). Characterization of a DCL2-Insensitive Tomato Bushy Stunt Virus Isolate Infecting Arabidopsis thaliana. Viruses 12, 1121. https://www.ncbi.nlm.nih.gov/pubmed/33023227

- Monsion, B., Incarbone, M., Hleibieh, K., Poignavent, V., Ghannam, A., Dunoyer, P., Daeffler, L., Tilsner, J., and Ritzenthaler, C. (2018). Efficient Detection of Long dsRNA in Vitro and in Vivo Using the dsRNA Binding Domain from FHV B2 Protein. Front Plant Sci 9, 70. https://www.ncbi.nlm.nih.gov/pubmed/29449856

Financial support of this subject is guaranteed by the Research Cluster / LabEx NetRNA.

Deadenylation - the shortening of the mRNA poly(A) tail - is the key initiating step of mRNA decay and a major regulator of gene expression. Because poly(A) tail length affects virtually every aspect of mRNA fate, understanding how deadenylation complexes are assembled and regulated is essential. Interestingly,
our recent analyses revealed dynamic changes of poly(A) tail lengths in Arabidopsis across developmental stages. Notably, we observed striking shifts in poly(A) tail patterns during seed development and germination, indicating tight regulation of poly(A) tail length at these stages. Investigating how changes
in the composition and activity of CCR4–NOT, the main deadenylation complex, can contribute to the regulation of poly(A)-tail length during developmental transitions is an important open question.

The objective of this thesis project is to investigate the molecular deadenylation machinery in Arabidopsis, focusing on developing and germinating seeds, where poly(A) tail length is highly regulated.
The student will:
i) characterize the composition of deadenylation complexes during seed development and
germination using affinity purification coupled with mass spectrometry and yeast two-hybrid assays;
ii) characterize the in vitro enzymatic activity of Arabidopsis deadenylases;
iii) use reverse genetics and Nanopore sequencing to assess the impact of major deadenylase mutations on poly(A) tail length regulation in seeds.
This project will provide significant insights into deadenylation mechanisms in plants. The student will gain theoretical and practical expertise in mRNA metabolism, reverse genetics, biochemistry, mass spectrometry and Nanopore sequencing, as well as associated bioinformatic skills.

Keywords: Gene expression - Deadenylation - Mass spectrometry – Biochemistry - Nanopore

Relevant publications:

- Peter J, Roignant J, Sacharowski S, Ubrig E, Lefèvre B, Swiezewski S, Gagliardi D., Zuber H. The TUTase URT1 regulates the transcriptome of seeds and their primary dormancy. (2024) bioRxiv 2024.12.19.629392; doi: 10.1101/2024.12.19.629392v1 (in revision at the Plant Cell)
- Giraudo P, Simonnot Q, Pflieger D, Peter J, Gagliardi D, Zuber H. Nano3'RACE: A Method to Analyze Poly(A) Tail Length and Nucleotide Additions at the 3' Extremity of Selected mRNAs Using Nanopore Sequencing. Methods in Molecular Biology. (2024) 2723: 233-252, doi: 10.1007/978-1-0716-3481-3_14
- Scheer H, de Almeida C, Ferrier E, Simonnot Q, Poirier L, Pflieger D, Sement FM, Koechler S, Piermaria C, Krawczyk P, Mroczek S, Chicher J, Kuhn L, Dziembowski A, Hammann P, Zuber H and Gagliardi D. The TUTase
URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis. (2021) Nature Communications. 12: 1298. doi: 10.1038/s41467-021-21382-2

Financial support of this subject is allocated by the IMCBio Graduate School based on applicant's merit.