RT Journal
A1 De Kumar, Bony
A1 Parrish, Mark E.
A1 Slaughter, Brian D.
A1 Unruh, Jay R.
A1 Gogol, Madelaine
A1 Seidel, Christopher
A1 Paulson, Ariel
A1 Li, Hua
A1 Gaudenz, Karin
A1 Peak, Allison
A1 McDowell, William
A1 Fleharty, Brian
A1 Ahn, Youngwook
A1 Lin, Chengqi
A1 Smith, Edwin
A1 Shilatifard, Ali
A1 Krumlauf, Robb
T1 Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells
JF Genome Research 
JO Genome Research 
YR 2015 
FD August 01 
VO 25 
IS 8 
SP 1229 
OP 1243 
DO 10.1101/gr.184978.114 
UL http://genome.cshlp.org/content/25/8/1229.abstract 
AB The clustered Hox genes, which are highly conserved across metazoans, encode homeodomain-containing transcription factors that provide a blueprint for segmental identity along the body axis. Recent studies have underscored that in addition to encoding Hox genes, the homeotic clusters contain key noncoding RNA genes that play a central role in development. In this study, we have taken advantage of genome-wide approaches to provide a detailed analysis of retinoic acid (RA)-induced transcriptional and epigenetic changes within the homeotic clusters of mouse embryonic stem cells. Although there is a general colinear response, our analyses suggest a lack of strict colinearity for several genes in the HoxA and HoxB clusters. We have identified transcribed novel noncoding RNAs (ncRNAs) and their cis-regulatory elements that function in response to RA and demonstrated that the expression of these ncRNAs from both strands represent some of the most rapidly induced transcripts in ES cells. Finally, we have provided dynamic analyses of chromatin modifications for the coding and noncoding genes expressed upon activation and suggest that active transcription can occur in the presence of chromatin modifications and machineries associated with repressed transcription state over the clusters. Overall, our data provide a resource for a better understanding of the dynamic nature of the coding and noncoding transcripts and their associated chromatin marks in the regulation of homeotic gene transcription during development.