IMCBio International PhD Program

This PhD project aims to predict transcription factor binding in cell types where it has never been measured, using only the DNA sequence and the cell’s gene expression profile. The student will combine pre-trained foundation models of DNA sequence and of single-cell gene expression into a model that learns how cellular context changes which DNA sites are bound. They will benchmark it rigorously against existing methods, extend it to single-cell data, and use interpretability methods to reveal which transcription factors cooperate to bind together. The PhD is co-supervised between the Institut Pasteur (machine learning) and the IGBMC (regulatory genomics). It is suited to students with a strong background in machine learning and deep learning.

Keywords: Computational biology, Deep learning, Foundation models, Interpretability, Transcription factors, Gene regulation

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

- Leporcq C, Spill Y, Balaramane D, Toussaint C, Weber M, Bardet AF#. TFmotifView: a webserver for the visualization of transcription factor motifs in genomic regions. Nucleic Acid Research (2020) 48:W208-W217

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:

- Sara Monticelli, Alina Sommer, Zeinab Al Haj Hassan, Kémy Adé, Pierre B. Cattenoz, Elisa Gomez Perdiguero and Angela Giangrande, “Early-wave macrophages control late hematopoiesis”, Developmental Cell, 2024 Apr 1:S1534-5807(24)00182-5. DOI: 10.1016/j.devcel.2024.03.013.

- Wael Bazzi, Sara Monticelli, Claude Delaporte, Céline Riet, Angela Giangrande and Pierre B. Cattenoz, “Gcm counteracts Toll-induced inflammation and impacts hemocyte number through cholinergic signaling”, Front Immunol. 2023 Nov 15:14:1293766. doi: 10.3389/fimmu.2023.1293766.

- Pierre B. Cattenoz, Rosy Sakr, Alexia Pavlidaki, Claude Delaporte, Andrea Riba, Nacho Molina, Nivedita Hariharan, Tina Mukherjee and Angela Giangrande, “Temporal specificity and heterogeneity of the fly immune cells’ transcriptional landscape”, EMBO J, DOI 10.15252/embj.2020104486

INRT : 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 5600 residues long maturation factor Rea1 (also known as Midasin or Mdn1) is a complex molecular machine and 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 the structural and functional characterization of human Rea1. Preliminary data suggests an involvement of human Rea1 in neurodevelopmental diseases and potential roles beyond ribosome maturations. The PhD student will be trained in the recombinant expression and purification of human Rea1 and use cryoEM to determine a high-resolution structure.  These structural investigations will be complemented by in-vitro as well in-vivo activity assays to validate the structure and elucidate the consequences of diseases causing mutations. Potential roles beyond ribosome maturation will be assessed by interactome studies. 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/Midasin/Mdn1, 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.

Understanding the genetic basis of phenotypic diversity remains a major challenge in biology. While recent advances in population genomics have considerably improved our understanding of complex trait inheritance, most studies have focused on nuclear genetic variation, largely overlooking the contribution of mitochondrial genomes. Our recent work on more than 1,000 natural Saccharomyces cerevisiae isolates revealed the importance of considering the full spectrum of genetic variation to decipher complex traits.

Building on the extensive mitochondrial genomic diversity previously characterized in the 1,011 yeast collection, this PhD project aims to systematically investigate its contribution to phenotypic variation. By integrating mitochondrial genome variation with thousands of existing molecular and organismal phenotypes, we will identify mitochondrial genetic determinants of complex traits and quantify their contribution to phenotypic variance and heritability.

Furthermore, we will investigate how mitochondrial and nuclear genetic variants interact to shape phenotypic diversity and potentially explain part of the missing heritability. Combining population-scale association analyses with targeted experimental validation, this project will provide new insights into the genetic architecture of complex traits and reveal the contribution of mitochondrial genomes to natural phenotypic diversity.

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.

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

The human genome encodes well known catalytic RNAs (ribozymes) like the ribosome, the spliceosome, or the RNAse P. However, other ribozymes have been described that have been mostly overlooked, indicating that more remain to be discovered. These encompass several instances of the hammerhead ribozyme [1]. Another one is an HDV-like (Hepatitis Delta Virus) ribozyme found in an intron of the CPEB3 (cytoplasmic polyadenylation element binding) protein gene [2], the structure of which we have recently solved and partly motivate this research topic [3]. CPEB proteins are involved in senescence following mitochondrial dysfunction in aging [4]. Alu elements specific to the stress response have also been characterized as epigenetic ribozymes [5], and a ribozyme found in a very long non-coding RNA of the hominin clade, thus named the hovlinc ribozyme [6] was identified by a transcriptomic approach. The mechanisms of action of these ribozymes have not been explored, and their three-dimensional (3D) structures are mostly unknown. However, their maintenance in the genome, and their structural diversity, point to conserved mechanisms in which they are at stake. Solving the structures and studying the mechanism of action of these genuine ribozymes would uncover new RNA-based processes, with a strong potential for the development of new therapeutics.

Keywords: catalytic RNA, 3D structure, SAR

Relevant publications:

- Hammann C, Luptak A, Perreault J, & de la Pena M (2012) The ubiquitous hammerhead ribozyme. Rna 18(5):871-885.

- Salehi-Ashtiani K, Luptak A, Litovchick A, & Szostak JW (2006) A Genomewide Search for Ribozymes Reveals an HDV-Like Sequence in the Human CPEB3 Gene. Science 313(5794):1788-1792.

- Przytula-Mally A-I, et al. (2022) Anticodon-like loop-mediated dimerization in the crystal structures of HdV- like CPEB3 ribozymes. bioRxiv.

- Burns DM & Richter JD (2008) CPEB regulation of human cellular senescence, energy metabolism, and p53 mRNA translation. Genes & development 22(24):3449-3460.

- Hernandez AJ, et al. (2020) B2 and ALU retrotransposons are self-cleaving ribozymes whose activity is enhanced by EZH2. Proceedings of the National Academy of Sciences of the United States of America 117(1):415-425.

- Chen Y, et al. (2021) Hovlinc is a recently evolved class of ribozyme found in human lncRNA. Nat Chem Biol.

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

How are transcription, protein binding and epigenetic modifications coordinated across individual DNA or RNA molecules? Despite major advances in genomics, existing technologies largely investigate these processes separately, leaving their interplay and long-range coordination poorly understood.

This PhD project aims to develop a new single-molecule technology combining chemical probing with Oxford Nanopore long-read sequencing to simultaneously detect transcription bubbles, protein footprints and modifications across entire DNA molecules. The student will establish methods to directly identify chemically modified nucleotides from nanopore signals and validate the approach using well-characterised transcription systems.

The project brings together the Smyth laboratory's expertise in chemical probing and nucleic acid biology with Abdelmalek Alioua's Gene Expression Analysis platform at IBMP, specialising in nanopore sequencing. This collaboration will provide complementary expertise in experimental method development, sequencing technologies and computational analysis.

This project will suit a candidate with a strong interest in nucleic acid biology, genomics and a willingness to engage with both experimental and computational approaches.

Keywords: Single-molecule genomics; Oxford Nanopore sequencing; chemical probing; transcription; DNA–protein interactions; epigenetics; gene regulation; herpesvirus

Relevant publications:

- van der Toorn, W. et al. Demultiplexing and barcode-specific adaptive sampling for nanopore direct RNA sequencing. Nature Communications 16, 3742 (2025). https://doi.org/10.1038/s41467-025-59102-9

- Bohn, P. et al. Nano-DMS-MaP allows isoform-specific RNA structure determination. Nature Methods 20, 849–859 (2023). https://doi.org/10.1038/s41592-023-01862-7

- Ye, L. et al. Short- and long-range interactions in the HIV-1 5′ UTR regulate genome dimerization and packaging. Nature Structural & Molecular Biology 29, 306–319 (2022). https://doi.org/10.1038/s41594-022-00746-2

- Sall, S. O., Alioua, A. et al. Characterization of radiations-induced genomic structural variations in Arabidopsis thaliana. The Plant Journal 121, e17180 (2025). DOI: 10.1111/tpj.17180.

- Méteignier, L.-V., et al. The Arabidopsis mTERF-repeat MDA1 protein plays a dual function in transcription and stabilization of specific chloroplast transcripts within the psbE and ndhH operons. New Phytologist 227, 1376–1391 (2020). DOI: 10.1111/nph.16625.

- Sement, F. M., et al. Uridylation prevents 3′ trimming of oligoadenylated mRNAs. Nucleic Acids Research 41, 7115–7127 (2013).

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