Suchergebnisse

The 3D genome is characterized by a complex organization made of genomic and epigenomic layers with profound implications on gene regulation and cell function. However, the understanding of the fundamental mechanisms driving the crosstalk between nuclear architecture and (epi)genomic information is still lacking. The plant Arabidopsis thaliana is a powerful model organism to address these questions owing to its compact genome for which we have a rich collection of microscopy, chromosome conformation capture (Hi-C) and ChIP-seq experiments. Using polymer modelling, we investigate the roles of nucleolus formation and epigenomics-driven interactions in shaping the 3D genome of A. thaliana. By validation of several predictions with published data, we demonstrate that self-attracting nucleolar organizing regions and repulsive constitutive heterochromatin are major mechanisms to regulate the organization of chromosomes. Simulations also suggest that interphase chromosomes maintain a partial structural memory of the V-shapes, typical of (sub)metacentric chromosomes in anaphase. Additionally, self-attraction between facultative heterochromatin regions facilitates the formation of Polycomb bodies hosting H3K27me3-enriched gene-clusters. Since nucleolus and heterochromatin are highly-conserved in eukaryotic cells, our findings pave the way for a comprehensive characterization of the generic principles that are likely to shape and regulate the 3D genome in many species. ; Funding: European Union's H2020 Framework Programme through the ERC [609989 to M.A.M.-R.]; Spanish Ministry of Science and Innovation [BFU2017-85926-P to M.A.M.-R.]; Spanish Ministry of Science and Innovation to the EMBL [to C.R.G.]; Centro de Excelencia Severo Ochoa 2013–2017 [SEV-2012 0208]; CERCAProgramme/Generalitat de Catalunya, Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III; Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement; Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014–2020 Smart Growth Operating Program; Agence Nationale de la Recherche [ANR-18-CE12-0006-03, ANR-18-CE45-0022-01 to D.J.]; Royal Society [University Research Fellowship UF160138 to H.W.N.]; STSM Grant from COST Action CA17139. Funding for open access charge: COSTAction INC (CA18127), supported by COST(European Cooperation in Science and Technology)

Mètodes computacionals; Genòmica ; Métodos computacionales; Genómica ; Computational Methods; Genomics ; The rapid development of Chromosome Conformation Capture (3C-based techniques), as well as imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear as nested patterns in the 3C-based interaction matrices, the vast majority of available TAD callers are based on the hypothesis that TADs are individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to identify and analyze the entire hierarchy of TADs in intra-chromosomal interaction matrices. TADpole combines principal component analysis and constrained hierarchical clustering to provide a set of significant hierarchical chromatin levels in a genomic region of interest. TADpole is robust to data resolution, normalization strategy and sequencing depth. Domain borders defined by TADpole are enriched in main architectural proteins (CTCF and cohesin complex subunits) and in the histone mark H3K4me3, while their domain bodies, depending on their activation-state, are enriched in either H3K36me3 or H3K27me3, highlighting that TADpole is able to distinguish functional TAD units. Additionally, we demonstrate that TADpole's hierarchical annotation, together with the new DiffT score, allows for detecting significant topological differences on Capture Hi-C maps between wild-type and genetically engineered mouse. ; European Research Council under the Seventh Framework Program FP7/2007-2013 [609989, in part]; European Union's Horizon 2020 Research and Innovation Programme [676556]; Spanish Ministry of Science and Innovation [BFU2013-47736-P, BFU2017-85926-P to M.A.M-R., IJCI-2015-23352 to I.F., BES-2014-070327 to P.S-V.]; 'Centro de Excelencia Severo Ochoa 2013–2017', SEV-2012-0208; CERCA Programme/Generalitat de Catalunya (to C.R.G.). Funding for open access charge: European Research Council under the Seventh Framework Program FP7/2007-2013 [609989]. We also acknowledge the support of the Spanish Ministry of Science and Innovation to the EMBL partnership, the 'Centro de Excelencia Severo Ochoa 2013-2017', SEV-2012-0208, the CERCA Programme/Generalitat de Catalunya, Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program to the CRG.

Chromosome structure is a crucial regulatory factor for a wide range of nuclear processes. Chromosome conformation capture (3C)-based experiments combined with computational modelling are pivotal for unveiling 3D chromosome structure. Here, we introduce TADdyn, a tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements of genomic loci in a completely data-driven way. We apply TADdyn on in situ Hi-C time-course experiments studying the reprogramming of murine B cells to pluripotent cells, and characterize the structural rearrangements that take place upon changes in the transcriptional state of 21 genomic loci of diverse expression dynamics. By measuring various structural and dynamical properties, we find that during gene activation, the transcription starting site contacts with open and active regions in 3D chromatin domains. We propose that these 3D hubs of open and active chromatin may constitute a general feature to trigger and maintain gene transcription. ; This work was partially supported by the European Research Council under the 7th Framework Program FP7/2007-2013 (ERC grant agreement 609989 to M.A.M-R. and T.G.), the European Union's Horizon 2020 research and innovation programme (grant agreement 676556 to M.A.M-R.) and the Spanish Ministerio de Ciencia e Innovación (BFU2013-47736-P and BFU2017-85926-P to M.A.M-R. as well as IJCI-2015-23352 to I.F.). R.S. is supported by the Netherlands Organization for Scientific Research (VENI 91617114) and an Erasmus MC Fellowship. We also knowledge support from "Centro de Excelencia Severo Ochoa 2013-2017", SEV-2012-0208 the Spanish ministry of Science and Innovation to the EMBL partnership and the CERCA Programme/Generalitat de Catalunya to the CRG. We also acknowledge support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III, the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement and the Co-financing by the Spanish Ministry of Science and Innovation with funds from the European Regional Development Fund (ERDF) corresponding to the 2014-2020 Smart Growth Operating Program to CNAG

At the kilo- to megabase pair scales, eukaryotic genomes are partitioned into self-interacting modules or topologically associated domains (TADs) that associate to form nuclear compartments. Here, we combine high-content super-resolution microscopies with state-of-the-art DNA-labeling methods to reveal the variability in the multiscale organization of the Drosophila genome. We find that association frequencies within TADs and between TAD borders are below ~10%, independently of TAD size, epigenetic state, or cell type. Critically, despite this large heterogeneity, we are able to visualize nanometer-sized epigenetic domains at the single-cell level. In addition, absolute contact frequencies within and between TADs are to a large extent defined by genomic distance, higher-order chromosome architecture, and epigenetic identity. We propose that TADs and compartments are organized by multiple, small-frequency, yet specific interactions that are regulated by epigenetics and transcriptional state. ; This research was supported by funding from the European Research Council under the 7th Framework Program (FP7/2010-2015, ERC grant agreement 260787 to M.N. and FP7/2007-2013, and ERC grant agreement 609989 to M.A.M.-R.). M.A.M.-R. and G.C. acknowledge support from the European Union's Horizon 2020 research and innovation program under grant agreement 676556. This work has also benefited from support by the Labex EpiGenMed, an «Investments for the future» program, reference ANR-10-LABX-12-01, the Spanish Ministry of Economy and Competitiveness (BFU2013-47736-P to M.A.M.-R.), and from "Centro de Excelencia Severo Ochoa 2013-2017", SEV-2012-0208 to the CRG. 3D-SIM experiments were performed at Montpellier Resource Imaging. We acknowledge the France-BioImaging infrastructure supported by the French National Research Agency (ANR-10-INBS-04, «Investments for the future»).

To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we integrate in situ Hi-C and nine additional omics layers. Beyond conventional active (A) and inactive (B) compartments, we uncover a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, 28% of the compartments change, mostly involving a widespread chromatin activation from naive to germinal center B cells and a reversal to the naive state upon further maturation into memory B cells. B cell neoplasms are characterized by both entity and subtype-specific alterations in 3D genome organization, including large chromatin blocks spanning key disease-specific genes. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture. ; This research was funded by the European Union's Seventh Framework Programme through the Blueprint Consortium (grant agreement 282510), the World Wide Cancer Research Foundation Grant No. 16-1285 (to J.I.M.-S.), the ERC (grant agreement 609989 to M.A.M.-R.), European Union's Horizon 2020 research and innovation programme (grant agreement 676556 to M.A.M.-R.). We also knowledge the support of Spanish Ministerio de Ciencia, Innovación y Universidades through SAF2012-31138 and SAF2017-86126-R to J.I.M.-S., SAF2015-64885-R to E.C., BFU2017-85926-P to M.A.M.-R. and PMP15/00007 to E.C. which is part of Plan Nacional de I + D + I and co-financed by the ISCIII-Sub-Directorate General for Evaluation and the European Regional Development Fund (FEDER-"Una manera de Hacer Europa") (to E.C.), the International Cancer Genome Consortium (Chronic Lymphocytic Leukemia Genome consortium to E.C.), La Caixa Foundation (CLLEvolution-HE17-00221, to E.C.). Furthermore, the authors would like to thank the support of the Generalitat de Catalunya Suport Grups de Recerca AGAUR 2017-SGR-736 (to J.I.M.-S.), 2017-SGR-1142 (to E.C.) and 2017-SGR-468 (to E.C.), the Accelerator award CRUK/AIRC/AECC joint funder-partnership, the CERCA Programme/Generalitat de Catalunya and CIBERONC (CB16/12/00225, CB16/12/00334, and CB16/12/00489). R.V.-B. (BES-2013-064328) and P.S.-V. (BES-2014-070327) were supported by a predoctoral FPI Fellowship from the Spanish Government. CRG acknowledges support from 'Centro de Excelencia Severo Ochoa 2013-2017', SEV-2012-0208 and the CERCA Programme/Generalitat de Catalunya as well as support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the EMBL partnership, the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement, and the Cofinancing with funds from the European Regional Development Fund (ERDF) by the Spanish Ministry of Science and Innovation coresponding to the Programa Opertaivo FEDER Plurirregional de España (POPE) 2014-2020 and by the Secretaria d'Universitats i Recerca, Departament d'Empresa i Coneixement of the Generalitat de Catalunya corresponding to the programa Operatiu FEDER Catalunya 2014-2020