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      Genomic Views of Distant-Acting Enhancers

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      Nature

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          Preface

          In contrast to changes in protein-coding sequences, the significance of noncoding DNA variation in human disease has been minimally explored. A recent torrent of genome-wide association studies suggests that noncoding variation represents a significant risk factor for common disorders, but the mechanisms by which they contribute to disease remain largely obscure. Distant-acting transcriptional enhancers - a major category of functional noncoding DNA - are likely involved in many developmental and disease-relevant processes. Genome-wide approaches for their discovery and functional characterization are now available and provide a growing knowledgebase for the systematic exploration of their role in human biology and disease susceptibility.

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          Most cited references47

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          ChIP-seq accurately predicts tissue-specific activity of enhancers.

          A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover because they are scattered among the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases demonstrated reproducible enhancer activity in the tissues that were predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities, and suggest that such data sets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.
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            Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements.

            Physical interactions between genetic elements located throughout the genome play important roles in gene regulation and can be identified with the Chromosome Conformation Capture (3C) methodology. 3C converts physical chromatin interactions into specific ligation products, which are quantified individually by PCR. Here we present a high-throughput 3C approach, 3C-Carbon Copy (5C), that employs microarrays or quantitative DNA sequencing using 454-technology as detection methods. We applied 5C to analyze a 400-kb region containing the human beta-globin locus and a 100-kb conserved gene desert region. We validated 5C by detection of several previously identified looping interactions in the beta-globin locus. We also identified a new looping interaction in K562 cells between the beta-globin Locus Control Region and the gamma-beta-globin intergenic region. Interestingly, this region has been implicated in the control of developmental globin gene switching. 5C should be widely applicable for large-scale mapping of cis- and trans- interaction networks of genomic elements and for the study of higher-order chromosome structure.
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              Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains.

              Insulators are DNA elements that prevent inappropriate interactions between the neighboring regions of the genome. They can be functionally classified as either enhancer blockers or domain barriers. CTCF (CCCTC-binding factor) is the only known major insulator-binding protein in the vertebrates and has been shown to bind many enhancer-blocking elements. However, it is not clear whether it plays a role in chromatin domain barriers between active and repressive domains. Here, we used ChIP-seq to map the genome-wide binding sites of CTCF in three cell types and identified significant binding of CTCF to the boundaries of repressive chromatin domains marked by H3K27me3. Although we find an extensive overlapping of CTCF-binding sites across the three cell types, its association with the domain boundaries is cell-type-specific. We further show that the nucleosomes flanking CTCF-binding sites are well positioned. Interestingly, we found a complementary pattern between the repressive H3K27me3 and the active H2AK5ac regions, which are separated by CTCF. Our data indicate that CTCF may play important roles in the barrier activity of insulators, and this study provides a resource for further investigation of the CTCF function in organizing chromatin in the human genome.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                2 August 2010
                10 September 2009
                17 August 2010
                : 461
                : 7261
                : 199-205
                Affiliations
                Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA. U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
                Article
                NIHMS225119
                10.1038/nature08451
                2923221
                19741700
                7b091e7f-c3e3-4e15-b8fe-a7408ef05704
                History
                Funding
                Funded by: National Heart, Lung, and Blood Institute : NHLBI
                Award ID: U01 HL066681-08 || HL
                Funded by: National Heart, Lung, and Blood Institute : NHLBI
                Award ID: R21 HL098940-01 || HL
                Funded by: National Human Genome Research Institute : NHGRI
                Award ID: R01 HG003988-03 || HG
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