Cell type speci_city of chromatin organization mediated by CTCF and cohesin.

Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Proceedings of the National Academy of Sciences (Impact Factor: 9.67). 02/2010; 107(8):3651-6. DOI: 10.1073/pnas.0912087107
Source: PubMed


CTCF sites are abundant in the genomes of diverse species but their function is enigmatic. We used chromosome conformation capture to determine long-range interactions among CTCF/cohesin sites over 2 Mb on human chromosome 11 encompassing the beta-globin locus and flanking olfactory receptor genes. Although CTCF occupies these sites in both erythroid K562 cells and fibroblast 293T cells, the long-range interaction frequencies among the sites are highly cell type specific, revealing a more densely clustered organization in the absence of globin gene activity. Both CTCF and cohesins are required for the cell-type-specific chromatin conformation. Furthermore, loss of the organizational loops in K562 cells through reduction of CTCF with shRNA results in acquisition of repressive histone marks in the globin locus and reduces globin gene expression whereas silent flanking olfactory receptor genes are unaffected. These results support a genome-wide role for CTCF/cohesin sites through loop formation that both influences transcription and contributes to cell-type-specific chromatin organization and function.

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    • "The Human b-globin Locus Provides an Additional Example of CBS Orientation-Dependent Topological Chromatin Looping Based on the location and orientation of CBSs, as well as their CTCF/cohesin occupancy, we identified four CCDs (domains 1–4) in the well-characterized b-globin cluster (Figure 5A). The b-globin gene cluster is located between CBS3 (5 0 HS5) and CBS4 (3 0 HS1) in domain1 (Figure 5A) (Hou et al., 2010; Splinter et al., 2006). We generated a series of CBS4/5 mutant K562 cell lines using CRISPR/Cas9 with one or two sgRNAs (Li et al., "
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    ABSTRACT: CTCF and the associated cohesin complex play a central role in insulator function and higher-order chromatin organization of mammalian genomes. Recent studies identified a correlation between the orientation of CTCF-binding sites (CBSs) and chromatin loops. To test the functional significance of this observation, we combined CRISPR/Cas9-based genomic-DNA-fragment editing with chromosome-conformation-capture experiments to show that the location and relative orientations of CBSs determine the specificity of long-range chromatin looping in mammalian genomes, using protocadherin (Pcdh) and β-globin as model genes. Inversion of CBS elements within the Pcdh enhancer reconfigures the topology of chromatin loops between the distal enhancer and target promoters and alters gene-expression patterns. Thus, although enhancers can function in an orientation-independent manner in reporter assays, in the native chromosome context, the orientation of at least some enhancers carrying CBSs can determine both the architecture of topological chromatin domains and enhancer/promoter specificity. These findings reveal how 3D chromosome architecture can be encoded by linear genome sequences.
    Full-text · Article · Aug 2015
    • "H2AZ is known to be associated with nucleosome exchange and remodeling [13] [23] [108] [109], it thus likely contributes to the highly dynamic properties of pluripotent chromatin and its refractory character to HP1-associated constitutive heterochromatin extension [23] [27] [99] [101] [110]. This interpretation was further strengthened by the observation that unlike C4, EC4 is enriched in CTCF which besides its insulator properties [102] [103], is also known to mediate long-range intra-and inter-chromosomal interactions [111] [112] [113] [114] [115] [116]. The fact that H2AZ was also found to be broadly distributed in the bivalent state EC2 containing bivalent genes confirmed that the polycomb repressed state C2 resulted from the spreading of H3K27me3 in differentiated cells [23] [27] [99] [101] [110]. "
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    ABSTRACT: Recent analysis of genome-wide epigenetic modification data, mean replication timing (MRT) profiles and chromosome conformation data in mammals have provided increasing evidence that flexibility in replication origin usage is regulated locally by the epigenetic landscape and over larger genomic distances by the 3D chromatin architecture. Here, we review the recent results establishing some link between replication domains and chromatin structural domains in pluripotent and various differentiated cell types in human. We reconcile the originally proposed dichotomic picture of early and late constant timing regions that replicate by multiple rather synchronous origins in separated nuclear compartments of open and closed chromatins, with the U-shaped MRT domains bordered by "master" replication origins specified by a localized (∼200-300kb) zone of open and transcriptionally active chromatin from which a replication wave likely initiates and propagates toward the domain center via a cascade of origin firing. We discuss the relationships between these MRT domains, topologically associated domains and lamina-associated domains. This review sheds a new light on the epigenetically regulated global chromatin reorganization that underlies the loss of pluripotency and the determination of differentiation properties. Copyright © 2015 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
    No preview · Article · Apr 2015 · FEBS letters
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    • "In contrast, CTCF tends not to be present at enhancer-promoter loops. It is more commonly associated with constitutive, longer-range chromatin interactions (Phillips-Cremins et al., 2013; Sanyal et al., 2012), although some cell-type-specific CTCF-mediated interactions have been reported (Hou et al., 2010). CTCF is enriched at TAD borders (Dixon et al., 2012; Hou et al., 2012; Sexton et al., 2012), and CTCF-mediated loops are implicated in maintenance of TAD structure (Giorgetti et al., 2014) and are thus believed to play a more fundamental architectural role in chromosome folding. "
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    ABSTRACT: The genome must be highly compacted to fit within eukaryotic nuclei but must be accessible to the transcriptional machinery to allow appropriate expression of genes in different cell types and throughout developmental pathways. A growing body of work has shown that the genome, analogously to proteins, forms an ordered, hierarchical structure that closely correlates and may even be causally linked with regulation of functions such as transcription. This review describes our current understanding of how these functional genomic "secondary and tertiary structures" form a blueprint for global nuclear architecture and the potential they hold for understanding and manipulating genomic regulation. Copyright © 2015 Elsevier Inc. All rights reserved.
    Full-text · Article · Mar 2015 · Cell
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