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Series GSE109625 Query DataSets for GSE109625
Status Public on Mar 28, 2018
Title Dynamic and integrated transcriptional code orchestrates the angiogenic response [Seq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Epigenetic modifications and transcription factors form a chromatin code to regulate gene expression in many physiological and pathological processes. However, little is known about whether the environmental stimuli could interplay with this code and regulate the transcription and biological functions. Here, we interrogated the chromatin state of multiple epigenetic modifications and transcription factors during a time course of VEGF stimulation in the endothelial cells and found a broad change of transcriptome induced by VEGF. At the promoter-proximal regions, a unique epigenetic pattern of bivalent domain preferentially governed the part of transcriptome change by hijacking the EZH1 transcriptional activity. VEGF substantially altered the epigenetic landscape at enhancer regions and transcription factor chromatin occupancy across the genome, which significantly accounted for the change of VEGF-downstream gene expression. Moreover, by integrating a transcription-regulatory network of VEGF pathway, we discovered MAFs as a novel mater transcriptional factor controlling the VEGF transcriptional program and angiogenesis. Collectively, these results revealed the extracellular stimulus of VEGF in fact implements a significant reconfiguration of chromatin code that coordinately regulates the angiogenic response.
Overall design RNA-seq on HUVEC after VEGF stimulation at 0,1,4,12 hours. ChIP-seq of H3K27ac, H3K27me3, H3K4me1, 2, 3, H3K36me3, RNAPII, ETS1, ERG1, FLI, JUN, RBPJ, GATA2, p300 and EZH2 on HUVEC after VEGF stimulation at 0, 1, 4, 12 hour.
Contributor(s) Wang S, Chen J, Garcia S, Liang X, Zhang F, Fu Y, Yan P, Yu H, Wei W, wang J, Le H, Han Z, Day DS, Stevens SM, Zhang Y, Park PJ, Sun K, Yuan G, Pu WT, Zhang B
Citation(s) 30670628
Submission date Jan 25, 2018
Last update date Mar 27, 2019
Contact name bing zhang
Organization name Shanghai Jiao Tong University
Department Shanghai Center for Systems Biomedicine
Lab Bing Zhang Lab
Street address 800 Dong Chuan Road
City Minhang
State/province Shanghai
ZIP/Postal code 200240
Country China
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (65)
GSM2947409 VEGF-0hour
GSM2947410 VEGF-1hour
GSM2947411 VEGF-4hour
This SubSeries is part of SuperSeries:
GSE109626 Dynamic and integrated transcriptional code orchestrates the angiogenic response
BioProject PRJNA431557
SRA SRP131219

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
GSE109625_RAW.tar 10.6 Gb (http)(custom) TAR (of BED, TDF)
GSE109625_genes_fpkm.txt.gz 2.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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