NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Series GSE102184 Query DataSets for GSE102184
Status Public on Sep 18, 2017
Title Developmental stage specific chromosome architecture in human erythroid cells (ChIP-seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin structure is tightly intertwined with transcription regulation. Here we compared the chromosomal architectures of fetal and adult human erythroblasts and find that globally, chromatin structures and compartments A/B are highly similar at both developmental stages. At a finer scale, we detect distinct folding patterns at the developmentally controlled b-globin locus. Specifically, new fetal stage-specific contacts are uncovered between a region separating the fetal (g-) and adult (b-) globin genes (encompassing the HBBP1 and BGLT3 non-coding genes) and two distal chromosomal sites (HS5 and 3'HS1) that flank the locus. In contrast, in adult cells the HBBP1-BGLT3 region contacts the embryonic e-globin gene, physically separating the fetal globin genes from the enhancer (LCR). Removal of the HBBP1 gene strongly reactivates g-globin expression, accompanied by increased LCR-g-globin and decreased BGLT3-e-globin interactions, mimicking the effects of deleting the fetal globin repressor BCL11A. Our results uncover a new critical regulatory region as a potential target for therapeutic genome editing for hemoglobinopathies and highlight the power of chromosome conformation analysis in discovering new cis control elements.
 
Overall design We compared the genome wide CTCF binding profiles of fetal and adult human erythroblasts by ChIP-seq.
 
Contributor(s) Huang P, Blobel GA
Citation(s) 28916711
Submission date Aug 02, 2017
Last update date May 15, 2019
Contact name Peng Huang
E-mail(s) huangp1@email.chop.edu
Organization name The Children's Hospital of Philadelphia
Department Hematology
Lab Gerd Blobel
Street address 3615 Civic Center Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (6)
GSM2730053 Fetal_CTCF_ChIPSeq_r1
GSM2730054 Fetal_CTCF_ChIPSeq_r2
GSM2730055 Fetal_CTCF_input
This SubSeries is part of SuperSeries:
GSE102201 Developmental stage specific chromosome architecture in human erythroid cells
Relations
BioProject PRJNA396940
SRA SRP114699

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
GSE102184_RAW.tar 11.2 Gb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap