A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
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ABSTRACT:
PROVIDER: PRJNA299708 | ENA |
REPOSITORIES: ENA
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Project description:We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ∼10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs "facing" one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.
| S-EPMC5635824 | biostudies-literature
Project description:A three-dimensional map of the human genome at kilobase resolution reveals prinicples of chromatin looping
| PRJNA268125 | ENA
Project description:We use in situ Hi-C to probe the three-dimensional architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1-kilobase resolution. We find that genomes are partitioned into local domains, which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ~10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs ‘facing’ one another. The inactive X-chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats. in situ Hi-C and dilution Hi-C were used to probe the three-dimensional structure of the genome in eight diverse human cell types and one mouse cell type
2014-12-11 | E-GEOD-63525 | biostudies-arrayexpress
Project description:We use in situ Hi-C to probe the three-dimensional architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1-kilobase resolution. We find that genomes are partitioned into local domains, which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ~10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs ‘facing’ one another. The inactive X-chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats.
2014-12-11 | GSE63525 | GEO
Project description:A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
| PRJNA299709 | ENA
Project description:The locations of chromatin loops in Drosophila were determined by Hi-C (chemical cross-linking, restriction digestion, ligation, and high-throughput DNA sequencing). Whereas most loop boundaries or “anchors” are associated with CTFC protein in mammals, loop anchors in Drosophila were found most often in association with the polycomb group (PcG) protein Polycomb (Pc), a subunit of Polycomb Repressive Complex 1 (PRC1). Loops were frequently located within domains of PcG-repressed chromatin. Promoters located at PRC1 loop anchors regulate some of the most important developmental genes and are less likely to be expressed than those not at PRC1 loop anchors. Although DNA looping has most commonly been associated with enhancer-promoter communication, our results indicate that loops are also associated with gene repression.
2017-01-11 | GSE89112 | GEO
Project description:The landscape of human epigenome undergoes extensive changes during development, leading to distinct transcription programs in different cell types. It is however still not clear how the high-order genome organization reshapes in cellular differentiation. Using Hi-C, we compared the comprehensive 3D genome maps in human embryonic stem cells (ESCs) and two differentiated cell types at kilobase resolution. Consistent with previous reports, we found that the CTCF protein anchors long-range constitutive interactions that are invariant between different cell types. The most stable DNA contacts in ESC are between a few hundred genomic loci with strongest histone H3 lysine 27 tri-methylation (H3K27me3) binding, which plays a key role maintaining pluripotency by inhibiting key development genes. These repressive 3D chromatin structures are resolved in differentiated cells, accompanied by redistribution of H3K27me3 mark. Most surprisingly, we found that in human ESCs, DNA looping interactions are not enriched at enhancers, suggesting a stochastic nature of DNA looping interactions at ESC enhancers. This is in sharp contrast to differentiated cells, in which a majority of cell type specific DNA looping interactions are at enhancers, regardless of whether the enhancers are co-occupied by CTCF. Taken together, our analysis revealed a primitive enhancer-independent genome architecture in ESCs, which is consistent with the stem cell pluripotency and differentiation plasticity. Most of the stable DNA looping interactions associated with lineage-governing enhancers are created only during cell fate commitment.
2017-08-31 | GSE85977 | GEO
Project description:The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has been the dominant hypothesis in the field for decades. However, a systematic testing of this hypothesis has not been conducted, primarily due to the absence of suitable experimental techniques. In this study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for the measurement of protein-mediated chromatin interactions at single-nucleosome resolution on a genome-wide scale. By applying MChIP-C to study H3K4me3 promoter-centered interactions in K562 cells, we found that it had greatly improved resolution and sensitivity compared to restriction endonuclease-based C-methods. This allowed us to identify EP300 histone acetyltransferase and the SWI/SNF remodelling complex as potential candidates for establishing and/or maintaining enhancer-promoter interactions. Finally, leveraging data from published CRISPRi screens, we found that most functionally-verified enhancers do physically interact with their cognate promoters, supporting the enhancer-promoter looping model.
2023-12-24 | GSE225087 | GEO
Project description:Genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model
| PRJNA933713 | ENA
Project description:A physical map of the Saccharomyces cerevisiae genome is presented. It was derived by mapping the sites for two restriction endonucleases, SfiI and NotI, each of which recognizes an 8-bp sequence. DNA-DNA hybridization probes for genetically mapped genes and probes that span particular SfiI and NotI sites were used to construct a map that contains 131 physical landmarks--32 chromosome ends, 61 SfiI sites and 38 NotI sites. These landmarks are distributed throughout the non-rDNA component of the yeast genome, which comprises 12.5 Mbp of DNA. The physical map suggests that those genes that can be detected and mapped by standard genetic methods are distributed rather uniformly over the full physical extent of the yeast genome. The map has immediate applications to the mapping of genes for which single-copy DNA-DNA hybridization probes are available.
| S-EPMC1204396 | biostudies-other