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Series GSE70660 Query DataSets for GSE70660
Status Public on Jan 11, 2016
Title Dynamic control of enhancer repertoires drives lineage and developmental stage-specific transcription during human erythropoiesis
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcriptional enhancers are the primary determinants of tissue-specific gene expression and influence a variety of cellular phenotypes. The regulatory components controlling enhancer assembly and turnover during stem cell development remain largely unknown. Here we compared the similarities and differences in enhancer landscape, transcriptional factor (TF) occupancy and transcriptomic changes in human primary fetal and adult hematopoietic stem/progenitor cells (HSPCs) and committed erythroid progenitors. We find that enhancers are modulated dynamically and extensively, and direct lineage and developmental stage-specific transcriptional programs. GATA2-to-GATA1 switch is prevalent within transcriptionally dynamic enhancers and drives enhancer commissioning. Further examination of lineage-specific enhancers identified TFs and their combinatorial patterns with known and unknown roles as putative drivers of enhancer turnover during differentiation. Importantly, by site-directed loss-of-function analysis of individual lineage-selective enhancers within the SLC25A37 super-enhancer using CRISPR/Cas9-mediated genomic editing, we uncover unexpected functional hierarchy of constituent enhancers within the super-enhancer cluster. Despite the indistinguishable chromatin features between the GATA switch enhancers at the GATA2 gene, we reveal through genomic editing the functional diversity of GATA switch enhancers in which enhancers with opposing functions cooperate to coordinate gene expression during development. Thus, genome-wide enhancer profiling coupled with in-depth enhancer editing in situ provide critical insights into the functional hierarchy and complexity of enhancers during stem cell development.
Overall design Analysis of chromatin occupancy of hematopoietic transcription factors (GATA1, GATA2, TAL1, NFE2, IRF2, PU.1, and RUNX1,) and various histone marks (H3K4me1, H3K4me3, H3K27ac, and H3K27me3) in primary human fetal liver and adult bone marrow CD34+ HSPCs and differentiated proerythroblasts (ProEs) by ChIP-seq
Contributor(s) Huang J, Shao Z, Orkin SH, Xu J
Citation(s) 26766440
Submission date Jul 09, 2015
Last update date May 15, 2019
Contact name Jian Xu
Phone 214-648-6125
Organization name UT Southwestern Medical Center
Department Children's Research Institute
Street address 6000 Harry Hines Blvd. NL12.138B
City Dallas
State/province TX
ZIP/Postal code 75235
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (30)
GSM1816066 H3K4me1-F0
GSM1816067 H3K4me1-F5
GSM1816068 H3K4me1-A0
BioProject PRJNA289303
SRA SRP060558

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Supplementary file Size Download File type/resource
GSE70660_RAW.tar 595.5 Mb (http)(custom) TAR (of BED, WIG)
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Raw data are available in SRA
Processed data provided as supplementary file

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