Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM) View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-03-08

AUTHORS

Robert A Beagrie, Antonio Scialdone, Markus Schueler, Dorothee C A Kraemer, Mita Chotalia, Sheila Q Xie, Mariano Barbieri, Inês de Santiago, Liron-Mark Lavitas, Miguel R Branco, James Fraser, Josée Dostie, Laurence Game, Niall Dillon, Paul A W Edwards, Mario Nicodemi, Ana Pombo

ABSTRACT

The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation). GAM also reveals an abundance of three-way contacts across the genome, especially between regions that are highly transcribed or contain super-enhancers, providing a level of insight into genome architecture that, owing to the technical limitations of current technologies, has previously remained unattainable. Furthermore, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian nuclei. More... »

PAGES

519-524

References to SciGraph publications

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  • Journal

    TITLE

    Nature

    ISSUE

    7646

    VOLUME

    543

    From Grant

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nature21411

    DOI

    http://dx.doi.org/10.1038/nature21411

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1084128543

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28273065


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