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Series GSE58317 Query DataSets for GSE58317
Status Public on Dec 08, 2015
Title Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation [expression array]
Organism Mus musculus
Experiment type Expression profiling by array
Summary Transcription factor/enhancer interactions determine cell specific gene expression. Here, we followed enhancers during differentiations of embryonic stem (ESCs) to epiblast like cells (EpiLCs). There were highly dynamic changes in histone lysine 27 acetylation at enhancer sites throughout the genome. These sites were enriched for a Foxd3 binding motif, a forkhead transcription factor essential in early embryonic development. Surprisingly, Foxd3 occupied largely mutually exclusive sites in the ESCs versus EpiLCs. Foxd3 bound to nucleosome occupied regions, simultaneously evicting the histones while inhibiting full gene expression through the recruitment of histone deacetylases. Knockout of Foxd3 resulted in hyperacetylation and transcriptional upregulation of neighboring genes, many of which were further upregulated at later stages of differentiation. These data show that Foxd3 primes enhancer sites during pregastrulation by removing nucleosomes, yet suppresses neighboring histone hyperacetylation. Such a mechanism may be common to many transcription factors that prepare enhancers for later gene activation during development.
 
Overall design Total RNA obtained Foxd3 knockout embryonic stem cells (ESCs) and epiblast-like cells (EpiLCs) (treated with 1uM tamoxifen for 36h to induce knockout) compared to wild-type controls
 
Contributor(s) Krishnakumar R, Blelloch R
Citation(s) 26748757
Submission date Jun 09, 2014
Last update date Jun 14, 2018
Contact name Raga Krishnakumar
E-mail(s) raga.krishnakumar@gmail.com
Organization name UCSF
Lab Blelloch
Street address 912E RMB, 35 Medical Center Way
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platforms (1)
GPL6885 Illumina MouseRef-8 v2.0 expression beadchip
Samples (19)
GSM1406400 dY EtOH rep2 hyb1
GSM1406401 dY Tam rep2 hyb1
GSM1406402 dY EtOH rep3 hyb1
This SubSeries is part of SuperSeries:
GSE58408 Foxd3 binding at enhancers controls developmental timing of gene expression by regulation of histone acetylation
Relations
BioProject PRJNA251987

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
GSE58317_RAW.tar 3.1 Mb (http)(custom) TAR
GSE58317_non-normalized.txt.gz 5.6 Mb (ftp)(http) TXT
Processed data included within Sample table
Raw data are available on Series record

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