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Series GSE42209 Query DataSets for GSE42209
Status Public on Nov 20, 2013
Title Hdac6 regulates Tip60-p400 function in stem cells (sequencing)
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The Tip60 (also known as Kat5) lysine acetyltransferase functions broadly as a transcriptional co-activator that acetylates histones. In contrast, Tip60 functions in embryonic stem cells (ESCs) both to silence genes that promote differentiation and to activate genes required for proliferation. The mechanism by which Tip60 functions as a repressor is unknown. Here we show that the class II histone deacetylase Hdac6 co-purifies with Tip60-p400 complex from ESCs and is necessary for complete silencing of most differentiation genes targeted by Tip60. In contrast to differentiated cells, where Hdac6 is mainly cytoplasmic and does not interact with Tip60, Hdac6 is largely nuclear in ESCs and neural stem cells (NSCs) and interacts with Tip60-p400 in both cell types. Hdac6 is enriched at promoters bound by Tip60-p400 in ESCs, but while Tip60 binds on both sides of transcription start sites (TSSs), Hdac6 binding overlaps with only the downstream Tip60 peak. Surprisingly, Hdac6 does not deacetylate histones at these sites, but rather is required for Tip60 binding. These data suggest that nuclear exclusion of Hdac6 during differentiation plays a major role in modulation of Tip60-p400 function.
Overall design We determined the genome-wide localization of Tip60 and Hdac6 in mouse ES cells, and examined genomic binding profiles of Tip60 and Hdac6 upon indicated knockdown by ChIP-seq.
We examined genomic binding profiles of p400 upon indicated knockdown by ChIP-seq.
Contributor(s) Chen PB, Hung J, Hickman TL, Coles AH, Carey JF, Weng Z, Chu F, Fazzio TG
Citation(s) 24302573
Submission date Nov 09, 2012
Last update date May 15, 2019
Contact name Benson Chen
Organization name UC San Diego
Department Cellular and Molecular Medicine
Lab Bing Ren
Street address 9500 Gilman Dr. CMM East, Room 2071
City La Jolla
State/province CA
ZIP/Postal code 92093-0653
Country USA
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (7)
GSM1035414 GFPKD_Tip60ChIP
GSM1035415 Hdac6KD_Tip60ChIP
GSM1035416 GFPKD_Hdac6ChIP
This SubSeries is part of SuperSeries:
GSE42329 Hdac6 regulates Tip60-p400 function in stem cells
BioProject PRJNA181085
SRA SRP017200

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
GSE42209_RAW.tar 20.4 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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