RT Journal
A1 Xiang, Guanjue
A1 Keller, Cheryl A.
A1 Heuston, Elisabeth
A1 Giardine, Belinda M.
A1 An, Lin
A1 Wixom, Alexander Q.
A1 Miller, Amber
A1 Cockburn, April
A1 Sauria, Michael E.G.
A1 Weaver, Kathryn
A1 Lichtenberg, Jens
A1 Göttgens, Berthold
A1 Li, Qunhua
A1 Bodine, David
A1 Mahony, Shaun
A1 Taylor, James
A1 Blobel, Gerd A.
A1 Weiss, Mitchell J.
A1 Cheng, Yong
A1 Yue, Feng
A1 Hughes, Jim
A1 Higgs, Douglas R.
A1 Zhang, Yu
A1 Hardison, Ross C.
T1 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
JF Genome Research 
JO Genome Research 
YR 2020 
FD March 01 
VO 30 
IS 3 
SP 472 
OP 484 
DO 10.1101/gr.255760.119 
UL http://genome.cshlp.org/content/30/3/472.abstract 
AB 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 poised to active or inactive states, and shifts in nuclease accessibility of CTCF-bound elements. Regression modeling of epigenetic states at cCREs and gene expression produced a versatile resource to improve selection of cCREs potentially regulating target genes. These resources are available from our VISION website to aid research in genomics and hematopoiesis.