Chromatin Structure and Epigenetics/ Structure de la chromatine et épigénétique

Seminar FSER organized by Jerome Déjardin (Institute of Human Genetics, Montpellier), June 5 – 10, 2023

Participants


Constance ALABERT (University of Dundee – Dundee, Royaume-Uni), Tuncay BEAUBEC (Universiteit van Utrecht – Copernicus Institute of Sustainable Development – Utrecht, Pays-Bas), Magda BIENKO (Human Technopole and Karolinska Institute – Milano, Suède), Maud BORENSZTEIN (Institut de Génétique Moléculaire de Montpellier (IGMM) – Montpellier, France), Bernard DE MASSY (Institut de Génétique Humaine CNRS Université de Montpellier – Montpellier, France), Pierre-Antoine DEFOSSEZ (CNRS Epigenetics and cell fate – Paris, France), Jérôme DEJARDIN (Institut de Génétique Humaine – Montpellier, France), Sandra DUHARCOURT (Institut Jacques Monod, CNRS Université Paris Cité – Paris, France), Fabian ERDEL (CBI – Toulouse, France), Petra HAJKOVA (MRC London Institute of Medical Sciences – London, Royaume-Uni), Doug HIGGS (University of Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, Royaume-Uni), Pablo NAVARRO GIL (Institut Pasteur – CNRS UMR3691 – Paris, France), Antoine PETERS (Friedrich Miescher Institute – Basel, Suisse), Oliver RANDO (UMass Chan Medical School – Worcester, MA, États-Unis), Oded RECHAVI (Tel Aviv University – Tel Aviv, Israël), Iva TCHASOVNIKAROVA (The Gurdon Institute – Cambridge, Royaume-Uni), Didier TRONO (Ecole Polytechnique Fédérale de Lausanne – Lausanne, Suisse), Michiel VERMEULEN (Radboud University Nijmegen – Nijmegen, Pays-Bas), Anton WUTZ (ETH Zurich – Zurich, Suisse).

Résumé 

FISH d’orientation chromosomique sur des chromosomes de cellules souches embryonnaires en métaphase (J. Dejardin, cercle FSER).

Du 5 au 10 juin 2023, dix-neuf scientifiques, dont deux jeunes chercheures (Maud Borensztein et Iva Tschasovnikarova), se sont réunis à la Fondation Les Treilles pour discuter de la régulation des chromosomes et de l’hérédité phénotypique à travers les générations lors de l’atelier “Structure de la chromatine et Épigénétique”. Chaque participant, tout en étudiant un aspect spécifique de la biologie du génome dans un contexte précis, a apporté un point de vue unique sur des sujets divers, allant de la biologie du développement à la biologie des systèmes moléculaires et à la physique. Le nombre réduit de participants et le style du séminaire, unique en son genre, ont permis de nombreuses discussions de haut niveau scientifique, mais aussi informelles entre les participants. Cette combinaison unique de scientifiques et de sujets abordés a généré de nouvelles idées et a suscité plusieurs initiatives de collaboration. Ci-dessous sont mis en évidence les sujets abordés lors de cette réunion exceptionnelle.

Abstract

From June 5th to June 10th, 2023, nineteen scientists including two junior principal investigators (Maud Borensztein and Iva Tschasovnikarova) gathered at the Fondation Les Treilles to discuss chromosome regulation and phenotypic inheritance through generations at the ‘Chromatin structure and Epigenetics’ workshop. Each participant, while studying a specific aspect of genome biology in a specific context, has brought a unique view on such diverse topics, ranging from developmental biology to molecular systems biology and physics. The small number of participants and the “unique in its kind” workshop style allowed for ample informal, yet high-level exchanges between participants. This unique combination of scientists and topics covered, provided novel ideas and sparked multiple initiatives to collaborate. Below are highlighted the topics that were covered during the meeting.

Report

The reactivation of the inactive X chromosome, an epigenetic hallmark of female cells, correlates with the acquisition of germline identity in females. Maud Borensztein’s team (Institute of Molecular Genetics, Montpellier) investigates the biological impact and significance of this specific epigenetic characteristic. Maud discussed the kinetics of X-chromosome reactivation at the transcriptomic (scRNA-seq) and epigenomic levels (using CUT & RUN and Whole Genome Bisulfite Sequencing) in vivo. Additionally, her team has developed an in vitro model of germ cell specification that mimics in vivo X-chromosome dynamics. This model aims to unravel the mechanisms behind female reprogramming and should allow the investigation of potential sex differences. Following up on the topic of X transcriptional control, Anton Wutz (ETH, Zurich) discussed the initiation of X inactivation. His laboratory has identified candidates for silencing factors through genetic screening. In addition to published results on the mammalian homolog of split ends, SPEN, two components of a nucleosome assembly complex have been identified: Hira and Ubn2. These contribute to the deposition and exchange of the histone variant H3.3 in the transcription unit and regulatory elements of genes. He presented new data on gene repression by the long non-coding RNA Xist. Consistent with a role in X inactivation, Hira, Ubn2, and the Ubn1/2 double mutation show increased severity of the phenotype in female compared to male mice. The work indicates that histone dynamics and nucleosome turnover contribute to establishing a repressed configuration on the inactive X chromosomes. Petra Hajkova (MRC, London) briefly reminded everyone about the waves of epigenetic reprogramming that occur in the context of mammalian development. She then discussed the requirements for effective maintenance of epigenetic information and how this is critical for the stability of cell fate. Petra presented data regarding the maintenance of DNA modifications in the context of replication in the developing germline and unpublished results suggesting that the stability of epigenetic information probably involves a novel mechanism that will be exciting to identify. Tuncay Baubec’s laboratory (Utrecht University) is trying to understand how multiple chromatin modifications influence each other and contribute to gene expression or silencing phenotypes. For instance, the positive feedback between DNA methylation and H3K9me3 at imprinting control regions creates stable repression and epigenetic memory. The current challenge is to understand how such cross-talk shapes genome-wide epigenetic regulation and robust silencing through development and life. Pierre-Antoine Defossez (Epigenetics and cell fate CNRS Unit, Paris) presented the results of two different axes of research on mammalian DNA methylation, a mark often linked to gene silencing. In the first one, the lab carried out systematic CRISPR screens in mouse ES cells to uncover new regulators of epigenetic silencing. In the other, a degron approach was used to clarify the relative roles of UHRF1 and DNMT1 in maintaining DNA methylation in cancer cells.

Whether biological rules determined from a handful of examples apply to the rest of the genome remains an open question. Iva Tchasovnikarova (The Gurdon Institute, Cambridge) described the development of two novel genetic technologies, TRACE and ChILI-seq, to interrogate the mechanism of action of epigenetic pathways. TRACE is a high-throughput, genome-wide assay in which genetically barcoded constructs integrated randomly across the genome report on the chromatin environment in which they are situated through GFP expression. This screen aims to evaluate position effects on transcription within the genome. This approach identifies phenotypic reporters for epigenetic factors, which can subsequently be subjected to a battery of genetic and biochemical assays to gain new insight into the underlying biology. On the other hand, ChILI-seq exploits lentiviral integrations to measure chromatin occupancy of proteins and domains of interest in an antibody- and sequence-independent manner. The wider application of genetic technologies such as TRACE and ChILI-seq has strong potential to further our mechanistic understanding of many epigenetic pathways.

Conversely, Doug Higgs’ laboratory (Oxford University) is studying a single locus to understand the mechanisms underlying gene expression control. To this aim, he uses the prototypical globin locus. He convincingly showed that it is now possible to study globin gene expression throughout lineage specification, commitment, and differentiation, providing a tractable model for analyzing with high precision the mechanisms underlying the regulation of mammalian gene expression. Although it is now well recognized that enhancer-promoter proximity is a common finding when specific genes are being activated, how this is achieved and the precise relationship between physical proximity and transcription remains unknown. Using extensive genome engineering at the endogenous globin locus, he described that cohesin-mediated loop extrusion plays a significant role in mediating the efficient interaction between the enhancers and promoters. Furthermore, at the globin locus, loop extrusion appears to originate predominantly at the enhancer and to reel in the promoters. In another model of gene expression control, Pablo Navarro (Institut Pasteur, Paris) focused his talk on post-mitotic gene reactivation in embryonic stem cells. Such reactivation is particularly fast and strong, undergoing a hyper-transcription phase. He then described that this relies on three overlapping mechanisms: (i) histone methylation, which allows the distinction between active and inactive gene regulatory elements; (ii) post-mitotic hyper-transcription relies on the capacity of the MAX transcription factor to bind active promoters during mitosis, enabling fast recruitment of MYC after mitosis, and (iii) prominent redundancy among nuclear receptors such as ESRRB and NR5A2 in binding key regulatory elements during mitosis ensures the efficient reactivation of the pluripotency network. Sandra Duharcourt (Institut Jacques Monod, Paris) showed that, in the ciliate Paramecium, small-RNA-guided strategies, similar to those used in fungi, plants, and animals, recruit histone methyltransferases to repeated sequences and transcriptionally silence them. Instead of H3K9 methyltransferases, Paramecium has apparently rewired the RNAi machinery toward a Polycomb protein, which has the ability to trimethylate both K9 and K27 of histone H3. Studying how gene silencing occurs in this ciliate may prove crucial to understanding how silencing by K9 or by K27 methylation occurs in other organisms where the two systems seem to function independently of each other. Gene control may also depend on more global nuclear organization. Magda Bienko (Karolinska Institute) presented her lab’s recent work on the interplay between chromatin-bound RNA and DNA during neuronal differentiation. Her lab collected various complementary omics and FISH data revealing a cross-talk between long and short neuronal genes mediated by long introns of highly expressed neuron-specific genes. Oded Rechavi (Tel-Aviv University) discussed unpublished results regarding RNAi inheritance in roundworms and flatworms. Intriguingly, they found that RNAi can also be inherited in Planaria, although flatworms don’t have RNA-dependent RNA polymerases, which are thought to be required for RNAi inheritance based on studies in C. elegans. The findings raise the exciting possibility that a novel epigenetic inheritance mechanism will be discovered.

Protein self-organization in membrane-less compartments is increasingly recognized as a powerful means to organize biochemical pathways within the cell, including on the genome, at the chromatin level. Fabian Erdel (CBI, Toulouse) uses physics to understand chromatin biology. His talk presented evidence that membrane-less sub-compartments in the cell nucleus can be formed by different mechanisms, including liquid-liquid phase separation, polymer-polymer phase separation, or “simple” interactions with clustered binding sites on chromosomes. He went on to show that sub-compartments formed by these different mechanisms have different properties in terms of their viscosity, interfacial barrier, and solution properties, which affect the biochemical reactions taking place in these sub-compartments. Finally, he presented a technique: Model-free calibrated half-FRAP (MOCHA-FRAP) as a novel approach to distinguish the different types of sub-compartments in living cells. Understanding how proteins self-organize is crucial to comprehend genome transactions. Transposable elements (TEs) have been linked to human cancer through a variety of mechanisms, including the promotion of chromosomal rearrangements due to their repetitiveness, the inactivation of tumor suppressor genes through insertional mutagenesis, and the production of chimeric gene transcripts through aberrant activation of TE-embedded regulatory sequences. Under certain conditions, TEs can thus be viewed as genetic threats. In his talk, Didier Trono (EPFL, Lausanne) demonstrated how TEs can also act as sentinels to alert the cell against epigenetic perturbations, and how cancer cells subvert TE-controlling KRAB zinc finger proteins to evade this surveillance mechanism. Ollie Rando (U.Mass) spoke about paternal environmental effects in mice. He described his lab’s ongoing work to understand the folding of the genome in sperm, arguing that many existing results suffer from cell-free DNA contamination. He then discussed evidence for molecular communication between the central nervous system and male reproductive tissues. Michiel Vermeulen’s lab (Nijmegen University) is integrating state-of-the-art quantitative mass-spectrometry-based (interaction) proteomics and next-generation DNA sequencing technology to decipher (epi)genetic regulation of gene expression in (differentiated) stem cells. In his lecture, he provided an overview of some of their recent results related to these topics. Constance Alabert (Dundee University) described the efforts of her lab to describe changes in chromatin composition during the cell cycle, and in particular the kinetics of protein re-association to chromatin after DNA replication. These are crucial steps to understand how chromatin features are stably maintained through cell division. Finally, my laboratory is interested in the biology of repetitive DNA sequences in mammals. I described a novel protein, able to form the t-loop structure at the extremity of chromosomes, the telomeres, in embryonic stem cells. I discussed how this discovery could change the way we think about chromosome protection in general, with implications for cancer and aging.

In conclusion, we felt very fortunate to meet and exchange ideas in this fantastic location. A special thanks to the Fondation des Treilles for making this seminar possible, and to all the team at Les Treilles for taking excellent care of us. We all agreed that it would be fantastic to meet again with the exact same group of scientists in several years.



Citer ce billet
ldiebold (2024, 4 avril). Chromatin Structure and Epigenetics/ Structure de la chromatine et épigénétique. Les carnets de la Fondation des Treilles. Consulté le 14 juin 2024, à l’adresse https://lestreilles.hypotheses.org/9122

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