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Status |
Public on Jun 28, 2016 |
Title |
CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells [RNA-Seq] |
Organism |
Homo sapiens |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
CTCF and cohesinSA-1 are regulatory proteins involved in a number of critical cellular processes including transcription, maintenance of chromatin domain architecture, and insulator function. To assess changes in the CTCF and cohesinSA-1 interactomes during erythropoiesis, chromatin immunoprecipitation coupled with high throughput sequencing and mRNA transcriptome analyses via RNA-seq were performed in primary human HSPC hematopoietic stem and progenitor cells (HSPC) and primary human erythroid cells from single donors. Sites of CTCF and cohesinSA-1 co-occupancy were enriched in gene promoters in HSPC and erythroid cells compared to single CTCF or cohesin sites. Cell type-specific CTCF sites in erythroid cells were linked to highly expressed genes, with the opposite pattern observed in HSPCs. Chromatin domains were identified by ChIP-seq with antibodies against trimethylated lysine 27 histone 3, a modification associated with repressive chromatin. Repressive chromatin domains increased in both number and size during hematopoiesis, with many more repressive domains in erythroid cells than HSPCs. CTCF and cohesinSA-1 marked the boundaries of these repressive chromatin domains in a cell-type specific manner. These genomic data support the hypothesis that CTCF and cohesinSA-1 have multiple roles in the regulation of gene expression during erythropoiesis including transcriptional regulation at gene promoters and maintenance of chromatin architecture.
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Overall design |
CD34+-selected stem and progenitor cells were expanded for three days in the absence of EPO. The cells were further cultured in the presence of EPO, and cells differentiated into R3/R4 nucleated erythroid cells. RNA was isolated from three biological replicates of each cell type and sequencing libraries were prepared from poly A selected RNA.
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Contributor(s) |
Steiner LA, Schulz VP, Maksimova Y, Lezon-Geyda K, Gallagher PG |
Citation(s) |
27219007 |
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Submission date |
Apr 14, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Vince Schulz |
E-mail(s) |
vincent.schulz@yale.edu
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Organization name |
Yale University
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Department |
Department of Pediatrics
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Lab |
Gallagher
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Street address |
333 Cedar St. LMP 4085
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City |
New Haven |
State/province |
CT |
ZIP/Postal code |
06519 |
Country |
USA |
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Platforms (1) |
GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
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Samples (6)
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This SubSeries is part of SuperSeries: |
GSE67893 |
CTCF and CohesinSA-1 Mark Active Promoters and Boundaries of Repressive Chromatin Domains in Primary Human Erythroid Cells |
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Relations |
BioProject |
PRJNA281131 |
SRA |
SRP057177 |