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Series GSE57609 Query DataSets for GSE57609
Status Public on Dec 31, 2014
Title Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The pluripotent mammalian epiblast undergoes unusually fast cell proliferation. This rapid growth is expected to generate a high transcriptional demand, but the underlying mechanisms remain unknown. We report that the chromatin remodeler Chd1, which binds the activating histone mark H3K4me3 and is associated with transcription, is required for development of the mouse epiblast. Chd1-/- embryos exhibit proliferation defects and increased apoptosis, are smaller than controls by E5.5, and fail to grow, become patterned or gastrulate. We show that Chd1-/- ES cells have a self-renewal defect and a genome-wide reduction in transcriptional output that is associated with losses in RNA Pol II elongation at growth-promoting genes, including ribosomal proteins. We also report that Chd1 directly regulates ribosomal RNA transcription and that both Chd1-/- epiblast cells in vivo and ES cells in vitro express significantly lower levels of ribosomal RNA. Single cell analyses reveal abnormal nucleolar morphology in mutants in vivo and in vitro. These data indicate that Chd1 promotes a globally elevated transcriptional output required to sustain the distinct rapid growth of the mouse epiblast.
Overall design Cell-number normalized RNA-seq from wild-type and Chd1-/- mouse embryonic stem cells.
Contributor(s) Guzman-Ayala M, Sachs M, Koh FM, Onodera CS, Bulut-Karslioglu A, Lin CJ, Wong P, Nitta R, Song JS, Ramalho-Santos M
Citation(s) 25480920
Submission date May 13, 2014
Last update date May 15, 2019
Contact name Courtney Onodera
Organization name University of California, San Francisco
Street address 1450 Third St, HD374
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (4)
GSM1385509 RNA-Seq, Control cells, Set 1
GSM1385510 RNA-Seq, Chd1-/- cells, Set 1
GSM1385511 RNA-Seq, Control cells, Set 2
BioProject PRJNA247363
SRA SRP041944

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE57609_set1_rnaseq_processed.txt.gz 457.1 Kb (ftp)(http) TXT
GSE57609_set2_rnaseq_processed.txt.gz 469.2 Kb (ftp)(http) TXT
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