TY  - JOUR
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
Y1  - 2020/03/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 472 
EP  - 484 
DO  - 10.1101/gr.255760.119 
VL  - 30 
IS  - 3 
UR  - http://genome.cshlp.org/content/30/3/472.abstract 
N2  - 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. 
ER  -