An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis.

Genome Research
Guanjue XiangRoss C Hardison

Abstract

Thousands of epigenomic data sets have been generated in the past decade, but it is difficult for researchers to effectively use all the data relevant to their projects. Systematic integrative analysis can help meet this need, and the VISION project was established for validated systematic integration of epigenomic data in hematopoiesis. Here, we systematically integrated extensive data recording epigenetic features and transcriptomes from many sources, including individual laboratories and consortia, to produce a comprehensive view of the regulatory landscape of differentiating hematopoietic cell types in mouse. By using IDEAS as our integrative and discriminative epigenome annotation system, we identified and assigned epigenetic states simultaneously along chromosomes and across cell types, precisely and comprehensively. Combining nuclease accessibility and epigenetic states produced a set of more than 200,000 candidate cis-regulatory elements (cCREs) that efficiently capture enhancers and promoters. The transitions in epigenetic states of these cCREs across cell types provided insights into mechanisms of regulation, including decreases in numbers of active cCREs during differentiation of most lineages, transitions from poise...Continue Reading

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Citations

Feb 23, 2020·Nucleic Acids Research·Guanjue XiangRoss C Hardison
Jul 31, 2020·Nature·UNKNOWN ENCODE Project ConsortiumZhiping Weng
Mar 21, 2021·Current Opinion in Hematology·Marlies P Rossmann, Leonard I Zon
Apr 1, 2021·G3 : Genes - Genomes - Genetics·Cheryl A KellerRoss C Hardison
Aug 29, 2021·Nature Communications·Haoyue ZhangGerd A Blobel
Oct 15, 2021·PLoS Computational Biology·Maxwell W LibbrechtMichael M Hoffman

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