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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 13, 2018 |
| Title |
Transcriptional repression by FACT is linked to regulation of chromatin accessibility at the promoter of ES cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
The conserved and essential histone chaperone FACT (Facilitates Chromatin Transcription) reorganizes nucleosomes during DNA transcription, replication and repair and ensures both, efficient elongation of RNA Pol II and nucleosome integrity. In mammalian cells, FACT is a heterodimer, consisting of SSRP1 and SUPT16. Here, we show that in contrast to yeast, FACT accumulates at the transcription start site of genes reminiscent of RNA Polymerase II profile. Depletion of FACT in mouse embryonic stem cells leads to de-regulation of developmental and pro-proliferative genes concomitant with hyper-proliferation of mES cells. Using MNase-, ATAC-, and Nascent Elongating Transcript Sequencing (NET-seq) we show that up-regulation of genes coincides with loss of nucleosomes upstream of the TSS and concomitant increase in antisense transcription, indicating that FACT impacts the promoter architecture to regulate expression of these genes. Finally, we demonstrate a role for FACT in cell fate determination and show that FACT depletion primes ES cells for the neuronal lineage.
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| Overall design |
ChIP-seq for FACT and RNA-seq, MNase-seq, ATAC-seq, and NET-seq profiles following knock-down of FACT were generated
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| Contributor(s) |
Mylonas C, Tessarz P |
| Citation(s) |
30456357 |
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| Submission date |
Dec 05, 2016 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Peter Tessarz |
| E-mail(s) |
ptessarz@age.mpg.de
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| Organization name |
Max Planck Institute
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| Street address |
Joseph-Stelzman-Str 9b
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| City |
Cologne |
| State/province |
Nordrhein-Westfalen |
| ZIP/Postal code |
50931 |
| Country |
Germany |
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| Platforms (3) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
| GPL21493 |
Illumina HiSeq 3000 (Mus musculus) |
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| Samples (28)
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| Relations |
| BioProject |
PRJNA356303 |
| SRA |
SRP094584 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE90906_ATAC.Control_merged.bw |
525.7 Mb |
(ftp)(http) |
BW |
| GSE90906_ATAC.Ssrp1KD_merged.bw |
434.9 Mb |
(ftp)(http) |
BW |
| GSE90906_MNase.Control_merged.bw |
1.6 Gb |
(ftp)(http) |
BW |
| GSE90906_MNase.Ssrp1KD_merged.bw |
1.5 Gb |
(ftp)(http) |
BW |
| GSE90906_NET-seq.Control.merged.fw.bw |
35.4 Mb |
(ftp)(http) |
BW |
| GSE90906_NET-seq.Control.merged.rv.bw |
34.7 Mb |
(ftp)(http) |
BW |
| GSE90906_NET-seq.Ssrp1KD.merged.fw.bw |
48.1 Mb |
(ftp)(http) |
BW |
| GSE90906_NET-seq.Ssrp1KD.merged.rv.bw |
46.9 Mb |
(ftp)(http) |
BW |
| GSE90906_Normalized.counts.RNA-seq.Control_vs_Ssrp1KD.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
| GSE90906_RAW.tar |
41.2 Gb |
(http)(custom) |
TAR (of BW, TAB) |
| GSE90906_RNAseq.diffsplice.exons.tab.gz |
74.1 Kb |
(ftp)(http) |
TAB |
| GSE90906_RNAseq.limma.NPC-WT.tab.gz |
935.5 Kb |
(ftp)(http) |
TAB |
| GSE90906_RNAseq.limma.allgenes.tab.gz |
2.0 Mb |
(ftp)(http) |
TAB |
| GSE90906_raw_counts_combined_chromatin_RNA-seq_samples.txt.gz |
2.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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