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Accueil > Départements > Biologie des Génomes > Daan NOORDERMEER : Dynamique de la Chromatine

Publications

2019


  • M. V. C. Greenberg, A. Teissandier, M. Walter, D. Noordermeer, et D. Bourc'his, « Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency », eLife, vol. 8, avr. 2019.
    Résumé : During early mammalian development, the chromatin landscape undergoes profound transitions. The Zdbf2 gene-involved in growth control-provides a valuable model to study this window: upon exit from naïve pluripotency and prior to tissue differentiation, it undergoes a switch from a distal to a proximal promoter usage, accompanied by a switch from polycomb to DNA methylation occupancy. Using an embryonic stem cell (ESC) system to mimic this period, we show here that four enhancers contribute to the Zdbf2 promoter switch, concomitantly with dynamic changes in chromatin architecture. In ESCs, the locus is partitioned to facilitate enhancer contacts with the distal Zdbf2 promoter. Relieving the partition enhances proximal Zdbf2 promoter activity, as observed during differentiation or with genetic mutants. Importantly, we show that 3D regulation occurs upstream of the polycomb and DNA methylation pathways. Our study reveals the importance of multi-layered regulatory frameworks to ensure proper spatio-temporal activation of developmentally important genes.
    Mots-clés : CHRODY, chromosomes, DBG, differentiation, DNA methylation, enhancers, epigenetics, gene expression, genetics, genomics, mouse, polycomb, stem cells.

  • T. B. Nesterova, G. Wei, H. Coker, G. Pintacuda, J. S. Bowness, T. Zhang, M. Almeida, B. Bloechl, B. Moindrot, E. J. Carter, I. Alvarez Rodrigo, Q. Pan, Y. Bi, C. - X. Song, et N. Brockdorff, « Systematic allelic analysis defines the interplay of key pathways in X chromosome inactivation », Nature Communications, vol. 10, nᵒ 1, p. 3129, juill. 2019.
    Résumé : Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome-wide silencing. Whilst recent studies have defined candidate silencing factors, their relative contribution to repressing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in mouse embryonic stem cell-based models. Using a machine learning approach we identify distance to the Xist locus and prior gene expression levels as key determinants of silencing efficiency. We go on to show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of weakly expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15/m6A-methyltransferase complex make only minor contributions to gene silencing. Together our results provide a comprehensive model for Xist-mediated chromosome silencing.
    Mots-clés : CHRODY, DBG.
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  • O. Shukron, V. Piras, D. Noordermeer, et D. Holcman, « Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers », Nature Communications, vol. 10, nᵒ 1, p. 2626, juin 2019.
    Résumé : Chromatin of mammalian nucleus folds into discrete contact enriched regions such as Topologically Associating Domains (TADs). Folding hierarchy and internal organization of TADs is highly dynamic throughout cellular differentiation, and are correlated with gene activation and silencing. To account for multiple interacting TADs, we developed a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency Hi-C encounters within and between TADs into direct loci interactions using cross-links at a given base-pair resolution. We reconstruct three TADs of the mammalian X chromosome for three stages of differentiation. We compute the radius of gyration of TADs and the encounter probability between genomic segments. We found 1) a synchronous compaction and decompaction of TADs throughout differentiation and 2) high order organization into meta-TADs resulting from weak inter-TAD interactions. Finally, the present framework allows to infer transient properties of the chromatin from steady-state statistics embedded in the Hi-C/5C data.
    Mots-clés : CHRODY, DBG.

2018



  • L. Li, Q. Zeng, A. Bhutkar, J. A. Galván, E. Karamitopoulou, D. Noordermeer, M. - W. Peng, A. Piersigilli, A. Perren, I. Zlobec, H. Robinson, M. L. Iruela-Arispe, et D. Hanahan, « GKAP Acts as a Genetic Modulator of NMDAR Signaling to Govern Invasive Tumor Growth », Cancer Cell, vol. 33, nᵒ 4, p. 736-751.e5, 2018.

  • B. Moindrot et N. Brockdorff, « Unbiased Genetic Screen to Identify Factors Involved in X-Chromosome Inactivation Using a Pooled Bar-Coded shRNA Library », Methods in Molecular Biology (Clifton, N.J.), vol. 1861, p. 19-36, 2018.
    Résumé : In mammals, a dosage compensation mechanism exists to equalize gene expression levels between male and female. This process is initiated by Xist RNA, a long noncoding RNA that mediates the transcriptional silencing of a complete chromosome. The kinetics of events occurring on the future inactive X-chromosome has been described in detail over the last 20 years. More recently, parallel studies using advanced biochemical assays and genetic screens identified key factors critical for the silencing cascade. Here, we describe the procedure adopted in one of these studies, an shRNA-based loss-of-function screen in mouse embryonic stem cells (mESCs).The screen made use of a reporter cell line in which Xist-mediated silencing could be monitored by changes in GFP fluorescence. Loss of function was achieved using a custom made bar-coded pooled shRNA library. The screen aimed to identify shRNAs that lessen Xist mediated repression of the GFP reporter. The methods that were applied are of potential relevance for the development of related screens, for example to better understand how specific repressors silence one or several genes.
    Mots-clés : CHRODY, DBG, Genetic screen, GFP reporter, shRNA, X-chromosome inactivation, Xist.

  • M. Sobecki, C. Souaid, J. Boulay, V. Guerineau, D. Noordermeer, et L. Crabbe, « MadID, a Versatile Approach to Map Protein-DNA Interactions, Highlights Telomere-Nuclear Envelope Contact Sites in Human Cells », Cell Reports, vol. 25, nᵒ 10, p. 2891-2903.e5, déc. 2018.
    Résumé : Mapping the binding sites of DNA- or chromatin-interacting proteins is essential to understanding biological processes. DNA adenine methyltransferase identification (DamID) has emerged as a comprehensive method to map genome-wide occupancy of proteins of interest. A caveat of DamID is the specificity of Dam methyltransferase for GATC motifs that are not homogenously distributed in the genome. Here, we developed an optimized method named MadID, using proximity labeling of DNA by the methyltransferase M.EcoGII. M.EcoGII mediates N6-adenosine methylation in any DNA sequence context, resulting in deeper and unbiased coverage of the genome. We demonstrate, using m6A-specific immunoprecipitation and deep sequencing, that MadID is a robust method to identify protein-DNA interactions at the whole-genome level. Using MadID, we revealed contact sites between human telomeres, repetitive sequences devoid of GATC sites, and the nuclear envelope. Overall, MadID opens the way to identification of binding sites in genomic regions that were largely inaccessible.
    Mots-clés : CHRODY, DBG, LADs, lamina interactions, M.EcoGII, m6A, MadID, methylation, nuclear envelope, proximity labeling, telomeres, TENOR.


  • C. Souaid, S. Bloyer, et D. Noordermeer, « Promoter–Enhancer Looping and Regulatory Neighborhoods », in Nuclear Architecture and Dynamics, Elsevier, 2018, p. 435-456.

2017


  • P. J. Fabre, M. Leleu, B. H. Mormann, L. Lopez-Delisle, D. Noordermeer, L. Beccari, et D. Duboule, « Large scale genomic reorganization of topological domains at the HoxD locus », Genome Biology, vol. 18, nᵒ 1, p. 149, août 2017.
    Résumé : BACKGROUND: The transcriptional activation of HoxD genes during mammalian limb development involves dynamic interactions with two topologically associating domains (TADs) flanking the HoxD cluster. In particular, the activation of the most posterior HoxD genes in developing digits is controlled by regulatory elements located in the centromeric TAD (C-DOM) through long-range contacts. RESULTS: To assess the structure-function relationships underlying such interactions, we measured compaction levels and TAD discreteness using a combination of chromosome conformation capture (4C-seq) and DNA FISH. We assessed the robustness of the TAD architecture by using a series of genomic deletions and inversions that impact the integrity of this chromatin domain and that remodel long-range contacts. We report multi-partite associations between HoxD genes and up to three enhancers. We find that the loss of native chromatin topology leads to the remodeling of TAD structure following distinct parameters. CONCLUSIONS: Our results reveal that the recomposition of TAD architectures after large genomic re-arrangements is dependent on a boundary-selection mechanism in which CTCF mediates the gating of long-range contacts in combination with genomic distance and sequence specificity. Accordingly, the building of a recomposed TAD at this locus depends on distinct functional and constitutive parameters.
    Mots-clés : CHRODY, Chromatin organization, CTCF, DBG, Enhancer, Gene regulation, Hox, Limb development, Regulatory landscape, TAD, Topologically associating domains.


  • G. Pintacuda, G. Wei, C. Roustan, B. A. Kirmizitas, N. Solcan, A. Cerase, A. Castello, S. Mohammed, B. Moindrot, T. B. Nesterova, et N. Brockdorff, « hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing », Molecular Cell, vol. 68, nᵒ 5, p. 955-969.e10, 2017.

  • E. Thierion, J. Le Men, S. Collombet, C. Hernandez, F. Coulpier, P. Torbey, M. Thomas-Chollier, D. Noordermeer, P. Charnay, et P. Gilardi-Hebenstreit, « Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements », PLoS genetics, vol. 13, nᵒ 7, p. e1006903, juill. 2017.
    Résumé : Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes a transcription factor required for the specification of two segments (rhombomeres) of the developing hindbrain. In rhombomere 3, Krox20 is subject to direct positive feedback governed by an autoregulatory enhancer, element A. In contrast, a second enhancer, element C, distant by 70 kb, is active from the initiation of transcription independent of the presence of the KROX20 protein. Here, using both enhancer knock-outs and investigations of chromatin organisation, we show that element C possesses a dual activity: besides its classical enhancer function, it is also permanently required in cis to potentiate the autoregulatory activity of element A, by increasing its chromatin accessibility. This work uncovers a novel, asymmetrical, long-range mode of cooperation between cis-acting elements that might be essential to avoid promiscuous activation of positive autoregulatory elements.
    Mots-clés : Animals, Body Patterning, CHRODY, Chromatin, DBG, Early Growth Response Protein 1, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Mice, Knockout, Mutation, Regulatory Elements, Transcriptional, Rhombencephalon, Sequence Homology, Nucleic Acid.

2016


  • M. Matelot et D. Noordermeer, « Determination of High-Resolution 3D Chromatin Organization Using Circular Chromosome Conformation Capture (4C-seq) », Methods in Molecular Biology (Clifton, N.J.), vol. 1480, p. 223-241, 2016.
    Résumé : 3D chromatin organization is essential for many aspects of transcriptional regulation. Circular Chromosome Conformation Capture followed by Illumina sequencing (4C-seq) is among the most powerful techniques to determine 3D chromatin organization. 4C-seq, like other modifications of the original 3C technique, uses the principle of "proximity ligation" to identify and quantify ten thousands of genomic interactions at a kilobase scale in a single experiment for predefined loci in the genome.In this chapter we focus on the experimental steps in the 4C-seq protocol, providing detailed descriptions on the preparation of cells, the construction of the circularized 3C library and the generation of the Illumina high throughput sequencing library. This protocol is particularly suited for the use of mammalian tissue samples, but can be used with minimal changes on circulating cells and cell lines from other sources as well. In the final section of this chapter, we provide a brief overview of data analysis approaches, accompanied by links to publicly available analysis tools.
    Mots-clés : 3D chromatin organization, 4C-seq, CHRODY, Chromatin compartmentalization, Chromatin loops, Circular Chromosome Conformation Capture, DBG, DNA interactions, High-throughput sequencing, nuclear organization.
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Publications majeures avant 2016

- Vieux-Rochas, M., Fabre, P.J., Leleu, M., Duboule, D. and Noordermeer, D. (2015) Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain. PNAS 112, 4672-4677
http://www.ncbi.nlm.nih.gov/pubmed/25825760

- Ghavi-Helm, Y., Klein, F., Pakozdi, T., Ciglar, L., Noordermeer, D., Huber, W. and Furlong, E.E.M. (2014) Enhancer loops appear stable during development and are associated with paused polymerase. Nature 512, 96-100
http://www.ncbi.nlm.nih.gov/pubmed/25043061

- Noordermeer, D., Leleu, M., Schorderet, P., Joye, E., Chabaud, F. and Duboule, D. (2014) Temporal dynamics and developmental memory of 3D chromatin architecture at Hox gene loci. eLife 3, e02557
http://www.ncbi.nlm.nih.gov/pubmed/24843030

- Andrey, G., Montavon, T., Mascrez, B., Gonzalez, F., Noordermeer D., Leleu, M., Trono, D., Spitz, F. and Duboule D. (2013) A functional switch between topological domains underlies HoxD genes collinearity in limbs. Science 340, 1195
http://www.ncbi.nlm.nih.gov/pubmed/23744951

- Coléno-Costes, A., Jang, S.M., de Vanssay, A., Rougeot, J., Bouceba, T., Randsholt, N.B., Gibert, J.M., Le Crom, S., Mouchel-Vielh, E., Bloyer, S. and Peronnet, F. (2012) New partners in regulation of gene expression : the enhancer of Trithorax and Polycomb Corto interacts with methylated ribosomal protein l12 via its chromodomain. PLoS Genet 8, e1003006
http://www.ncbi.nlm.nih.gov/pubmed/23071455

- Debat, V., Bloyer, S., Faradji, F., Gidaszewski, N., Navarro, N., Orozco-Terwengel, P., Ribeiro, V., Schlötterer, C., Deutsch, J.S. and Peronnet, F. (2011) Developmental stability : a major role for cyclin G in drosophila melanogaster. PLoS Genet 7, e1002314
http://www.ncbi.nlm.nih.gov/pubmed/21998598

- Noordermeer, D., Leleu, M., Splinter, E., Rougemont, J., De Laat, W. and Duboule, D. (2011) The dynamic architecture of Hox gene clusters. Science 334, 222-225
http://www.ncbi.nlm.nih.gov/pubmed/21998387

- Noordermeer, D., De Wit, E., Klous, P., Van De Werken, H., Simonis, M., Lopez-Jones, M., Eussen, B., De Klein, A., Singer, R. H. and De Laat, W. (2011) Variegated gene expression caused by cell-specific long-range DNA interactions. Nature Cell Biology 13, 944-951
http://www.ncbi.nlm.nih.gov/pubmed/21706023

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