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Series GSE112717 Query DataSets for GSE112717
Status Public on Aug 19, 2020
Title Enhancer-dependence of gene expression increases with developmental age
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
Summary How overall principles of gene regulation (the "logic") may change during ontogeny is largely unexplored. We compared transcriptomic, epigenomic and topological profiles in embryonic (EryP) and adult (EryD) erythroblasts. Despite reduced chromatin accessibility compared to EryP, distal chromatin of EryD is enriched in H3K27ac, Gata1 and Myb occupancy. In contrast to EryP-specific genes, which exhibit promoter-centric regulation through Gata1, EryD-specific genes employ distal enhancers for long-range regulation through enhancer-promoter looping, confirmed by Gata1 HiChIP. Genome editing demonstrated distal enhancers are required for gene expression in EryD but not in EryP. Applying a metric for enhancer-dependence of transcription, we observed a progressive reliance on enhancer control with increasing age of ontogeny among diverse primary cells and tissues of mouse and human origin. Our findings highlight fundamental and conserved differences in regulatory logic at distinct developmental stages, characterized by simpler promoter-centric regulation in embryonic cells and combinatorial enhancer-driven control in adult cells.
 
Overall design In order to profile chromatin structure and organization during the ontogeny of primitive and definitive erythroblasts, we used two cell surface-markers CD71 and Ter119, which were used in previous studies to define and distinguish erythroblasts, to FACS isolate CD71+/Ter119+ primitive (EryP) and definitive erythroblasts (EryD) from E10.5 embryonic peripheral blood and E13.5 fetal liver, respectively. FACS sorted cells were subsequently used for profiling of chromatin accessibility, histone modifications, master TFs occupancy and chromatin interactions profiles. The genome-wide transcriptome profilings were determined by RNA-seq, and were used throughout the whole study as reference to evaluate the association between chromatin features and transcription.
 
Contributor(s) Cai W, Huang J, Zhu Q
Citation(s) 32817427
Submission date Apr 04, 2018
Last update date Aug 21, 2020
Contact name Jialiang Huang
E-mail(s) jhuang@xmu.edu.cn
Organization name Dana-Farber Cancer Institute
Street address 450 Brookline Avenue
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platforms (3)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (39)
GSM3081986 RNAseq-EryP-Rep1
GSM3081987 RNAseq-EryP-Rep2
GSM3081988 RNAseq-EryP-Rep3
Relations
BioProject PRJNA448883
SRA SRP137692

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
GSE112717_ATACseq-EryD.bed.gz 605.4 Kb (ftp)(http) BED
GSE112717_ATACseq-EryD.bw 129.4 Mb (ftp)(http) BW
GSE112717_ATACseq-EryP.bed.gz 714.9 Kb (ftp)(http) BED
GSE112717_ATACseq-EryP.bw 99.6 Mb (ftp)(http) BW
GSE112717_Expression_Matrix_EryPEryD.txt.gz 594.1 Kb (ftp)(http) TXT
GSE112717_Gata1-EryD.bed.gz 782.5 Kb (ftp)(http) BED
GSE112717_Gata1-EryD.bw 313.5 Mb (ftp)(http) BW
GSE112717_Gata1-EryP.bed.gz 809.4 Kb (ftp)(http) BED
GSE112717_Gata1-EryP.bw 255.1 Mb (ftp)(http) BW
GSE112717_Gata1-Mel-CtrlshRNA.bed.gz 433.2 Kb (ftp)(http) BED
GSE112717_Gata1-Mel-CtrlshRNA.bw 266.3 Mb (ftp)(http) BW
GSE112717_Gata1-Mel-GSE112717_MybshRNA.bed.gz 89.8 Kb (ftp)(http) BED
GSE112717_Gata1-Mel-GSE112717_MybshRNA.bw 143.3 Mb (ftp)(http) BW
GSE112717_H3K27ac-EryD.bed.gz 541.3 Kb (ftp)(http) BED
GSE112717_H3K27ac-EryD.bw 249.2 Mb (ftp)(http) BW
GSE112717_H3K27ac-EryP.bed.gz 534.2 Kb (ftp)(http) BED
GSE112717_H3K27ac-EryP.bw 172.7 Mb (ftp)(http) BW
GSE112717_H3K27ac-Mel-CtrlshRNA.bed.gz 766.0 Kb (ftp)(http) BED
GSE112717_H3K27ac-Mel-CtrlshRNA.bw 112.8 Mb (ftp)(http) BW
GSE112717_H3K27ac-Mel-GSE112717_MybshRNA.bed.gz 439.2 Kb (ftp)(http) BED
GSE112717_H3K27ac-Mel-GSE112717_MybshRNA.bw 123.7 Mb (ftp)(http) BW
GSE112717_Input-EryD.bw 200.5 Mb (ftp)(http) BW
GSE112717_Input-EryP.bw 311.3 Mb (ftp)(http) BW
GSE112717_Input-FL-Fbbio.bw 617.1 Mb (ftp)(http) BW
GSE112717_Input-FL.bw 307.9 Mb (ftp)(http) BW
GSE112717_Input-Mel-CtrlshRNA.bw 272.1 Mb (ftp)(http) BW
GSE112717_Input-Mel-GSE112717_MybshRNA.bw 126.0 Mb (ftp)(http) BW
GSE112717_Myb-FL.bed.gz 23.8 Kb (ftp)(http) BED
GSE112717_Myb-FL.bw 661.3 Mb (ftp)(http) BW
GSE112717_P300-FL-Fbbio.bed.gz 840.9 Kb (ftp)(http) BED
GSE112717_P300-FL-Fbbio.bw 398.2 Mb (ftp)(http) BW
GSE112717_RAW.tar 11.6 Gb (http)(custom) TAR (of BED, BW, HIC, TXT)
GSE112717_Tal1-EryD.bed.gz 273.0 Kb (ftp)(http) BED
GSE112717_Tal1-EryD.bw 361.8 Mb (ftp)(http) BW
GSE112717_Tal1-EryP.bed.gz 220.4 Kb (ftp)(http) BED
GSE112717_Tal1-EryP.bw 380.4 Mb (ftp)(http) BW
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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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