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| Status |
Public on Apr 17, 2014 |
| Title |
Transcription factor cooperativity in early adipogenic hotspots and super-enhancers |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Here we have used a combination of advanced proteomics and genomics approaches to investigate the extent and mechanisms of transcription factor cross-talk at genomic hotspots. We identify ~12,000 transcription factor hotspots in the early phase of adipogenesis, and we find evidence of both simultaneous and sequential binding of transcription factors at these regions. We demonstrate for the first time that hotspots are highly enriched in large super-enhancer regions and that these drive the early adipogenic reprogramming of gene expression. Our results indicate that cooperativity between transcription factors at the level of hotspots as well as super-enhancers is very important for enhancer activity and transcriptional reprogramming. Thus, hotspots and super-enhancers constitute important regulatory hubs integrating external stimuli on chromatin.
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| Overall design |
Genome-wide profiling of transcription factor and co-factor binding, epigenomic marks, and gene expression in 3T3-L1 pre-adipocytes.
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| Contributor(s) |
Siersbæk R, Rabiee A, Nielsen R, Sidoli S, Traynor S, Loft A, Poulsen LL, Rogowska-Wrzesinska A, Jensen ON, Mandrup S |
| Citation(s) |
24857652 |
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| Submission date |
Apr 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Susanne Mandrup |
| E-mail(s) |
s.mandrup@bmb.sdu.dk
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| Phone |
+45 6550 2340
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| Organization name |
University of Southern Denmark
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| Department |
Biochemistry and Molecular Biology
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| Street address |
Campusvej 55
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| City |
Odense M |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
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| Platforms (2) |
| GPL11002 |
Illumina Genome Analyzer IIx (Mus musculus) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
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| Samples (32)
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| GSM1370450 |
FOSL2 ChIP-seq, 3T3-L1 4h |
| GSM1370451 |
JunB ChIP-seq, 3T3-L1 4h |
| GSM1370452 |
KLF4 ChIP-seq, 3T3-L1 4h |
| GSM1370453 |
KLF5 ChIP-seq, 3T3-L1 4h |
| GSM1370454 |
PBX1 ChIP-seq, 3T3-L1 4h |
| GSM1370455 |
STAT1 ChIP-seq, 3T3-L1 4h |
| GSM1370456 |
VDR ChIP-seq, 3T3-L1 4h |
| GSM1370457 |
RXR ChIP-seq, 3T3-L1 4h |
| GSM1370458 |
MED1 ChIP-seq, 3T3-L1 4h, Scr_4h_exp1_MED1 |
| GSM1370459 |
MED1 ChIP-seq, 3T3-L1 4h, CEBPb_4h_exp1_MED1 |
| GSM1370460 |
MED1 ChIP-seq, 3T3-L1 4h, Scr_4h_exp2_MED1 |
| GSM1370461 |
MED1 ChIP-seq, 3T3-L1 4h, CEBPb_4h_exp2_MED1 |
| GSM1370462 |
MED1 ChIP-seq, 3T3-L1 4h, DMI_4h_exp1_MED1 |
| GSM1370463 |
MED1 ChIP-seq, 3T3-L1 4h, NoDex_4h_exp1_MED1 |
| GSM1370464 |
MED1 ChIP-seq, 3T3-L1 4h, DMI_4h_exp2_MED1 |
| GSM1370465 |
MED1 ChIP-seq, 3T3-L1 4h, NoDex_4h_exp2_MED1 |
| GSM1370466 |
MED1 ChIP-seq, 3T3-L1 4h |
| GSM1370467 |
p300 ChIP-seq, 3T3-L1 4h |
| GSM1370468 |
BRG1 ChIP-seq, 3T3-L1 4h |
| GSM1370469 |
H3K27ac ChIP-seq exp1, 3T3-L1 4h |
| GSM1370470 |
H3K27ac ChIP-seq exp2, 3T3-L1 4h |
| GSM1370471 |
H3K4me1 ChIP-seq exp1, 3T3-L1 4h |
| GSM1370472 |
H3K4me1 ChIP-seq exp2, 3T3-L1 4h |
| GSM1370473 |
H3K4me2 ChIP-seq exp1, 3T3-L1 4h |
| GSM1370474 |
H3K4me2 ChIP-seq exp2, 3T3-L1 4h |
| GSM1370475 |
4sU_RNA-seq exp2, 3T3-L1 D0 |
| GSM1370476 |
4sU_RNA-seq exp3, 3T3-L1 D0 |
| GSM1370477 |
4sU_RNA-seq exp2, 3T3-L1 4h |
| GSM1370478 |
4sU_RNA-seq exp3, 3T3-L1 4h |
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| Relations |
| BioProject |
PRJNA244848 |
| SRA |
SRP041249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56872_RAW.tar |
1.5 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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