home > bioproject > PRJDB2466
identifier PRJDB2466
type bioproject
sameAs
sra-study  DRP000383
organism Mus musculus
title Genome-wide profiling of PPARg and RXRa and CTCF and H3K4me3 in Adipocytes
description Genome-wide maps of PPARg and RXRa in 3T3-L1 adipocytes (on 36 hours and day 8 of differentiation), CTCF and H3K4me3 in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation), using ChIP-seq. We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes (on day 0 and day 8 of differentiation) and NIH-3T3 fibroblasts using formaldehyde-assisted isolation of regulatory elements coupled with high-throughput sequencing (FAIRE-seq). FAIRE peaks at the promoter were associated with active transcription and histone modifications of H3K4me3 and H3K27ac. Non-promoter FAIRE peaks were characterized by H3K4me1+/me3-, the signature of enhancers, and were largely located in distal regions. The non-promoter FAIRE peaks showed dynamic change during differentiation while the promoter FAIRE peaks were relatively constant. Functionally, the adipocyte- and preadipocyte-specific non-promoter FAIRE peaks were, respectively, associated with genes up-regulated and down-regulated by differentiation. Among the adipocyte-specific FAIRE peaks, 45.3% and 11.7% overlapped binding sites for, respectively, PPARg and C/EBPα, the master regulators of adipocyte differentiation. The adipocyte-specific FAIRE peaks were not evenly distributed in the genome but tended to form clusters. Genes highly up-regulated during differentiation were associated with multiple clustered adipocyte-specific FAIRE peaks. Neighboring genes were often co-regulated during differentiation. Our study demonstrates the utility of FAIRE-seq in providing a global view of cell-type-specific cis-regulatory elements in the genome and in identifying transcriptional regulators of adipocyte differentiation.
data type DDBJ SRA Study
publication
22028663
external link
properties 
{...}
dbXrefs
sra-run  DRR000986DRR000987DRR000988DRR000989DRR000990DRR000991DRR000992DRR000993DRR000994DRR000995 More
sra-submission  DRA000378
sra-analysis  DRZ000032DRZ000033DRZ000034DRZ000035DRZ000053DRZ000054DRZ000055DRZ000056
biosample  SAMD00012136SAMD00012138SAMD00012137
sra-study  DRP000383
sra-sample  DRS000646DRS000647DRS001284
sra-experiment  DRX000636DRX000637DRX000638DRX000639DRX001328DRX001329DRX001330DRX001331
distribution JSONJSON-LD
status public
visibility unrestricted-access
dateCreated 2014-05-12T00:46:27+0000
dateModified 2014-05-12T00:46:27+0000
datePublished 2014-05-12T00:46:27+0000