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Series GSE95533 Query DataSets for GSE95533
Status Public on Apr 26, 2017
Title Dynamic rewiring of promoter-anchored chromatin loops during adipocyte differentiation
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Interactions between transcriptional promoters and their distal regulatory elements play an important role in transcriptional regulation; however, the extent to which these interactions are subject to rapid modulations in response to signals is unknown. Here, we use promoter capture Hi-C to demonstrate a rapid reorganization of promoter anchored chromatin loops within four hours after induction of differentiation of 3T3-L1 preadipocytes. This reorganization is tightly coupled to dynamic changes in target gene expression. The formation of promoter-enhancer loops is tightly linked to the activation of poised (histone H3 lysine 4 mono- and dimethylated) enhancers, as evidenced by the acquisition of histone H3 lysine 27 acetylation and the binding of MED1, SMC1 and P300 proteins to these regions. Intriguingly, formation of loops connecting activated enhancers and promoters is also associated with extensive recruitment of corepressors such as NCoR and HDACs, indicating that this class of coregulators may play a previously unrecognized role during enhancer activation.
 
Overall design We performed Hi-C and promoter capture Hi-C (PCHi-C) to investigate the dynamics of the 3D chromatin structure during adipocyte differentiation. We used mRNA-seq to identify changes in gene expression and ChIP-seq to map the chromatin binding of transcriptional regulators and epigenomic marks.
 
Contributor(s) Rasmus S, Madsen J, Biola J, Nielsen R, K. Bagge E, Cairns J, Wingett S, Traynor S, Spivakov M, Fraser P, Mandrup S
Citation(s) 28475875
Submission date Feb 28, 2017
Last update date May 15, 2019
Contact name Susanne Mandrup
E-mail(s) s.mandrup@bmb.sdu.dk
Phone +45 6550 2340
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense M
ZIP/Postal code 5230
Country Denmark
 
Platforms (1)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
Samples (74)
GSM2515914 RNA_4h_Exp1
GSM2515915 RNA_4h_Exp2
GSM2515916 RNA_D0_Exp1
Relations
BioProject PRJNA377334
SRA SRP100871

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE95533_RAW.tar 22.9 Gb (http)(custom) TAR (of BEDGRAPH, TXT)
GSE95533_RNA_counts.txt.gz 554.2 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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