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Series GSE53489 Query DataSets for GSE53489
Status Public on Aug 20, 2014
Title Cfp1 is required for gene expression dependent H3K4me3 and H3K9 acetylation in embryonic stem cells (RNA-Seq)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Trimethylation of histone H3 lysine 4 (H3K4me3) accumulates at promoters in a gene activity dependant manner. The Set1 complex is responsible for most H3K4me3 in somatic cells and contains the conserved subunit Cfp1, which is implicated in targeting the Set1 complex to CpG islands in mammals. In mouse embryonic stem cells, Cfp1 is necessary for H3K4me3 accumulation at constitutively active gene promoters, but is not required to maintain steady-state transcription of the associated gene. Here we show that Cfp1 is instrumental for targeting H3K4me3 at promoters upon rapid transcriptional induction in response to external stimuli. Surprisingly, H3K4me3 accumulation is not required to ensure appropriate transcriptional output but rather plays gene specific roles. We also show that Cfp1 dependant H3K4me3 deposition contributes to H3K9 acetylation genome wide; suggesting that Cfp1 dependant H3K4me3 regulates overall H3K9 acetylation dynamics and is necessary for histone acetyl transferase recruitment. Finally, we observe increased antisense transcription at start and end of genes that requires Cfp1 for accurate H3K4me3 and H3K9ac deposition. Our results assign a key role for Cfp1 in establishing a complex active promoter chromatin state and shed light on how chromatin signalling pathways provide context dependant outcomes.
 
Overall design wt (wtES) or Cfp1-/- (Cfp1null) ES cells were treated or not with doxorubicin (Dox) at 1uM for 6h and rRNA depleted total RNA was prepraed and analyzed by strand-specific RNA-Seq in 2 biological and 2 technical replicates per condition.
 
Contributor(s) Clouaire T, Webb S, Bird A
Citation(s) 25201068
Submission date Dec 19, 2013
Last update date May 15, 2019
Contact name Shaun Michael Webb
E-mail(s) shaun.webb@ed.ac.uk
Organization name University of Edinburgh
Department Wellcome Trust Centre for Cell Biology
Lab Bioinformatics Core Facility
Street address 2.21 Swann Building, Kings Buildings
City Edinburgh
ZIP/Postal code EH9 3JR
Country United Kingdom
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (16)
GSM1294846 m_wtES_RNA_1
GSM1294847 m_wtES_RNA_12
GSM1294848 m_wtES_RNA_2
This SubSeries is part of SuperSeries:
GSE53492 Cfp1 is required for gene expression dependent H3K4me3 and H3K9 acetylation in embryonic stem cells
Relations
BioProject PRJNA232119
SRA SRP034620

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
GSE53489_RNA_Seq_Normalized_Count_Table.txt.gz 999.6 Kb (ftp)(http) TXT
GSE53489_RNA_Seq_Raw_Count_Table.txt.gz 752.5 Kb (ftp)(http) TXT
GSE53489_m_Cfp1null_Dox_RNA_merged_forward.bigwig 314.8 Mb (ftp)(http) BIGWIG
GSE53489_m_Cfp1null_Dox_RNA_merged_reverse.bigwig 309.1 Mb (ftp)(http) BIGWIG
GSE53489_m_Cfp1null_RNA_merged_forward.bigwig 266.7 Mb (ftp)(http) BIGWIG
GSE53489_m_Cfp1null_RNA_merged_reverse.bigwig 247.3 Mb (ftp)(http) BIGWIG
GSE53489_m_wtES_Dox_RNA_merged_forward.bigwig 258.7 Mb (ftp)(http) BIGWIG
GSE53489_m_wtES_Dox_RNA_merged_reverse.bigwig 251.6 Mb (ftp)(http) BIGWIG
GSE53489_m_wtES_RNA_merged_forward.bigwig 264.5 Mb (ftp)(http) BIGWIG
GSE53489_m_wtES_RNA_merged_reverse.bigwig 252.8 Mb (ftp)(http) BIGWIG
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Processed data are available on Series record

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