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Series GSE128535 Query DataSets for GSE128535
Status Public on Jul 01, 2019
Title Histone 3 K9 and K27 acetylation of enhancers in response to thyroid hormone
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Hormone dependent activation of enhancers includes histone hyperacetylation and mediator recruitment. Histone hyperacetylation is often explained by a bimodal switch mod-el, where histone deacetylases (HDACs) disassociates from chromatin and histone acetyl transferases (HATs) are recruited. This model builds on decades of research on steroid re-ceptor regulation of transcription. We have used a genomics approach to study enhancer hyperacetylation by the thyroid hormone receptor (TR) and present a revised model. 1) at poised constitutively TR bound enhancers, HATs occupy chromatin irrespective of thyroid hormone (T3) levels, whereas HDAC occupancy is regulated by T3, suggesting that HDACs functions as a histone acetylation rheostat. 2) at enhancers established in a T3 dependent manner, TR is recruited to chromatin together with HATs. 3) a number of enhancers are hy-peracetylated secondary to TR activation. Collectively, this demonstrates various mechanisms controlling hormone dependent transcription and adds significant details to the otherwise simple bimodal switch model.
Overall design ChIP-seq was performed in replicates from a pool of four individual ChIPs from livers of four individual mice. Some ChIP-seq's were not performed in replicates. The RNA-seq was performed on four indepedent biological replicates.
Contributor(s) Grøntved L, Præstholm SM
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Submission date Mar 19, 2019
Last update date Apr 27, 2020
Contact name Lars Grøntved
Phone +45 24 60 14 06
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense
ZIP/Postal code 5230
Country Denmark
Platforms (2)
GPL18480 Illumina HiSeq 1500 (Mus musculus)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (56)
GSM3679089 PTU_WT_rep1_H3K27Ac
GSM3679090 PTU_T3_WT_rep1_H3K27Ac
GSM3679091 PTU_NCORdeltaID_rep1_H3K27Ac
BioProject PRJNA528027
SRA SRP188846

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Supplementary file Size Download File type/resource
GSE128535_Collected_H3K9Ac_H3K27Ac_domain_coordinates.bed.gz 315.8 Kb (ftp)(http) BED
GSE128535_RAW.tar 1.4 Gb (http)(custom) TAR (of BEDGRAPH)
GSE128535_RPKM_RNA_WT_PTU_T3_NCORdeltaID_PTU.txt.gz 1.5 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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