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Series GSE115964 Query DataSets for GSE115964
Status Public on Jan 22, 2019
Title TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells [TET2 ChIP-seq ES cells]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The epigenetic regulator TET2 is frequently mutated in hematological diseases. Mutations have been shown to arise in hematopoietic stem cells early in disease development, lead to altered DNA methylation landscapes and to an increased risk of hematopoietic malignancy. Here, we show by genome-wide mapping of TET2 binding sites in different cell types that TET2 localizes to regions of open chromatin and cell-type specific enhancers. We find that deletion of Tet2 in native hematopoiesis as well as fully transformed Acute Myeloid Leukemia (AML) results in changes in transcription factor (TF) activity within these regions, and we provide evidence that loss of TET2 leads to attenuation of chromatin binding of members of the basic helix-loop-helix (bHLH) TF family. Together, these findings demonstrate that TET2 activity shapes the local chromatin environment at enhancers to facilitate TF binding and provide a compelling example of how epigenetic dysregulation can affect gene expression patterns and drive disease development.
 
Overall design ChIP-seq analysis of embryonic stem cells expressing wildtype TET2 or a FLAG-tagged TET2 expressed from the endogenous Tet2 locus. TET2 binding sites were defined by enrichment over non-specific ChIP enriched regions identified in Tet2 knockout cells or parental cells without FLAG-tagged TET2.
 
Contributor(s) Rasmussen KD, Berest I, Kessler S, Nishimura K, Simón-Carrasco L, Vassiliou GS, Pedersen MT, Christensen J, Zaugg JB, Helin K
Citation(s) 30796038
Submission date Jun 18, 2018
Last update date Feb 26, 2019
Contact name Kasper Dindler Rasmussen
E-mail(s) k.d.rasmussen@dundee.ac.uk
Organization name School of Life Sciences, University of Dundee
Department Centre for Gene Regulation & Expression (GRE)
Street address Dow Street
City Dundee
ZIP/Postal code DD1 5EH
Country United Kingdom
 
Platforms (1)
GPL21626 NextSeq 550 (Mus musculus)
Samples (10)
GSM3196078 ES-WT_rep1
GSM3196079 ES-WT_rep2
GSM3196080 ES-Tet2KO_rep1
This SubSeries is part of SuperSeries:
GSE115972 TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells
Relations
BioProject PRJNA476604
SRA SRP150790

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Supplementary file Size Download File type/resource
GSE115964_RAW.tar 2.5 Gb (http)(custom) TAR (of BIGWIG, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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