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| Status |
Public on Sep 05, 2017 |
| Title |
Gene expression changes upon deletion of CFP1 in mouse ES cells. [mESC_RNAseq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
Chromatin modifications and the promoter associated epigenome are thought to be important for the regulation of gene expression. However, the mechanisms by which chromatin modifying complexes are targeted to the appropriate gene promoters in vertebrates and how they influence gene expression have remained poorly defined. Here, using a combination of live cell imaging and functional genomics, we discover that the vertebrate SET1 complex is targeted to actively transcribed target gene promoters through CFP1 which engages in a unique form of multivalent chromatin reading that involves recognition of non-methylated DNA and histone H3 lysine 4 trimethylation (H3K4me3). CFP1 defines SET1 complex occupancy on chromatin and its multivalent interactions are required for the SET1 complex to place H3K4me3. In the absence of CFP1, gene expression is perturbed suggesting that the normal targeting and function of SET1 complex is central to creating an appropriately functioning vertebrate promoter associated epigenome.
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| Overall design |
CFP1 fl/fl mouse embryonic stem cells were treated with tamoxifen (TAM) for 96h to ablate CFP1 protein levels. Calibrated nuclear RNA-seq (nucRNA-seq) was performed to evaluate gene expression changes (4 biological replicates). 4-thiouridine-seq (4sU-seq) was used to measure the expression level of nascent transcripts in untreated CFP1 fl/fl cells (3 biological replicates).
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| Contributor(s) |
Brown DA, Di Cerbo V, Feldmann A, Klose R |
| Citation(s) |
28877467 |
| |
| Submission date |
Jan 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Vincenzo Di Cerbo |
| E-mail(s) |
vincenzo.dicerbo@bioch.ox.ac.uk
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| Organization name |
University of Oxford
|
| Street address |
South Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3QU |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (19)
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| This SubSeries is part of SuperSeries: |
| GSE93538 |
CFP1 engages in multivalent interactions with CpG island chromatin to recruit the SET1 complex and regulate gene expression. |
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| Relations |
| BioProject |
PRJNA361071 |
| SRA |
SRP096631 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE93537_4sU-Seq_raw_counts.txt.gz |
217.5 Kb |
(ftp)(http) |
TXT |
| GSE93537_4sUseq_MERGE_minusStrand.bw |
366.9 Mb |
(ftp)(http) |
BW |
| GSE93537_4sUseq_MERGE_plusStrand.bw |
376.0 Mb |
(ftp)(http) |
BW |
| GSE93537_nucRNA_TAM_MERGE_minusStrand.bw |
161.4 Mb |
(ftp)(http) |
BW |
| GSE93537_nucRNA_TAM_MERGE_plusStrand.bw |
165.9 Mb |
(ftp)(http) |
BW |
| GSE93537_nucRNA_UNT_MERGE_minusStrand.bw |
140.0 Mb |
(ftp)(http) |
BW |
| GSE93537_nucRNA_UNT_MERGE_plusStrand.bw |
143.1 Mb |
(ftp)(http) |
BW |
| GSE93537_nucRNA_seq_DeSEQ2_normalized_counts.txt.gz |
673.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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