Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments

Chromosome conformation capture approaches have shown that interphase chromatin is partitioned into spatially segregated Mb-sized compartments and sub-Mb-sized topological domains. This compartmentalization is thought to facilitate the matching of genes and regulatory elements, but its precise function and mechanistic basis remain unknown. Cohesin controls chromosome topology to enable DNA repair and chromosome segregation in cycling cells. In addition, cohesin associates with active enhancers and promoters and with CTCF to form long-range interactions important for gene regulation. Although these findings suggest an important role for cohesin in genome organization, this role has not been assessed on a global scale. Unexpectedly, we find that architectural compartments are maintained in non-cycling mouse thymocytes after genetic depletion of cohesin in vivo. Cohesin was however required for specific long-range interactions within compartments where cohesin-regulated genes reside. Cohesin depletion diminished interactions between cohesin-bound sites, while alternative interactions between chromatin features associated with transcriptional activation and repression became more prominent, with corresponding changes in gene expression. Our findings indicate that cohesin-mediated long-range interactions facilitate discrete gene expression states within pre-existing chromosomal compartments

The role of cohesin in long-range gene regulation

The cohesin complex holds together sister chromatids after DNA replication: this is vital for correct segregation of chromosomes into daughter cells at mitosis. As well as this cell cycle role, cohesin has been implicated in regulating gene expression during interphase, through cohesin-mediated interactions between genes and regulatory elements. Such regulatory interactions tend to take place within topological domains. Topological domains are genomic regions which have preferential self-interactions in the 3D organisation of chromatin within the nucleus. Domain boundaries are enriched for cohesin and its frequent binding partner CTCF, and depletion of cohesin has been shown to affect genome organisation into topological domains, as well as causing the loss of enhancer–promoter interactions at some loci. However, it is unclear how cohesin-mediated interactions influence gene expression genome-wide. In this thesis, I use comparisons of control and cohesin-deficient mouse thymocytes to show that cohesin-mediated interactions between enhancers are important for the regulation of gene expression. Cohesin and CTCF are enriched at enhancers, and particularly at clusters of enhancer elements known as "super-enhancers". Cohesin mediates interactions between these enhancer elements, leading to their spatial clustering. While H3K27ac, H3K4me1, and transcription at enhancers are not affected by cohesin depletion, interactions between enhancer elements are lost. Enhancer-proximal genes are preferentially deregulated in cohesin-deficient cells, suggesting that these interactions are important for gene regulation. Deregulation of gene expression tends to occur in a coordinated manner within topological domains, which emphasises the importance of the structural organisation of the genome for gene regulation. Therefore, in this thesis I also consider models for the processes shaping genome organisation. I present evidence supporting key roles for cohesin and CTCF in these processes. Taken together, these results show that cohesin is important for both the organisation of topological domains and regulatory interactions within them.Open Acces

Base Classes for Storing Genomic Interaction Data

Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments

Additional file 1: of GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

R script used to generate figures, tables and numbers used in the described analysis of Hi-C data. (RMD 7 kb

Additional file 2: of GenomicInteractions: An R/Bioconductor package for manipulating and investigating chromatin interaction data

R script used to generate figures, tables and numbers used in the described analysis of ChIA-PET data. (RMD 14 kb

Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation

[EN] The differentiation of self-renewing progenitor cells requires not only the regulation of lineage- and developmental stage-specific genes but also the coordinated adaptation of housekeeping functions from a metabolically active, proliferative state toward quiescence. How metabolic and cell-cycle states are coordinated with the regulation of cell type-specific genes is an important question, because dissociation between differentiation, cell cycle, and metabolic states is a hallmark of cancer. Here, we use a model system to systematically identify key transcriptional regulators of Ikaros-dependent B cell-progenitor differentiation. We find that the coordinated regulation of housekeeping functions and tissue-specific gene expression requires a feedforward circuit whereby Ikaros down-regulates the expression of Myc. Our findings show how coordination between differentiation and housekeeping states can be achieved by interconnected regulators. Similar principles likely coordinate differentiation and housekeeping functions during progenitor cell differentiation in other cell lineages.EU FP7-Health STATegra project (grant number 36000). AG, VL, RR, AC, GP, ST, SF, PN, ME, JT, AM, MM, DGC. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Wellcome (grant number 099276/Z/12/Z). MM. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Medical Research Council, UK (grant number Institute Core Funding). AGF, BL, MM. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Bloodwise (grant number 09036). LC. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Wellcome (grant number). BL. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. European Research Council (grant number Repleniche). AGF. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. European Research Council (grant number 617393-CAUSALPATH). IT, VL, GP. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. MINECO (grant number BIO2015-71658-R). AC, ST. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Ferreiros-Vidal, I.; Carroll, T.; Zhang, T.; Lagani, V.; Ramirez, RN.; Ing-Simmons, E.; Gomez-Valades, AG.... (2019). Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during B cell progenitor cell differentiation. PLoS Biology. 17(4):1-28. https://doi.org/10.1371/journal.pbio.200650612817

Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation.

Cohesin is important for 3D genome organization. Nevertheless, even the complete removal of cohesin has surprisingly little impact on steady-state gene transcription and enhancer activity. Here we show that cohesin is required for the core transcriptional response of primary macrophages to microbial signals, and for inducible enhancer activity that underpins inflammatory gene expression. Consistent with a role for inflammatory signals in promoting myeloid differentiation of hematopoietic stem and progenitor cells (HPSCs), cohesin mutations in HSPCs led to reduced inflammatory gene expression and increased resistance to differentiation-inducing inflammatory stimuli. These findings uncover an unexpected dependence of inducible gene expression on cohesin, link cohesin with myeloid differentiation, and may help explain the prevalence of cohesin mutations in human acute myeloid leukemia