GATA Switch Enhancers Mark Dynamically Regulated Chromatin Interaction Nodes during Erythroid Maturation
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ABSTRACT:
PROVIDER: PRJNA648420 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12319377_1.fastq.gz | Fastqsanger.gz | |||
| SRR12319377_2.fastq.gz | Fastqsanger.gz | |||
| SRR12319378_1.fastq.gz | Fastqsanger.gz | |||
| SRR12319378_2.fastq.gz | Fastqsanger.gz | |||
| SRR12319379_1.fastq.gz | Fastqsanger.gz |
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Project description:Erythropoiesis is among the best understood examples of cell differentiation. In a required step, GATA1 replaces GATA2 at genomic loci, termed GATA switch enhancers. Little is known about how this switch affects chromatin architecture. Here, we show that cohesin binds GATA1 and occupies most GATA switch enhancers. Cohesin-based chromatin interaction analysis demonstrated that the most dynamic and interactive enhancers are enriched for GATA switch sites/TAL1 occupancy and frequently lack super-enhancer features. A c-kit locus CRISPR/Cas9 screen identified GATA motifs within one such element as strongly impacting expression. These data highlight the role of developmentally exchanged transcription factors in modulating genomic folding.
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Project description:We employed a gene complementation strategy combined with microarray screening to identify miRNAs involved in the formation of erythroid (red blood) cells. To search for GATA-1-regulated erythroid miRNAs, we used the Gata-1– erythroblast line G1E. These cells proliferate in culture as immature erythroid precursors and undergo terminal maturation when GATA-1 activity is restored. G1E-ER4 is a sub-line stably expressing an estrogen-activated form of GATA-1 (GATA-1 fused to the ligand binding domain of the estrogen receptor). Treatment of G1E-ER4 cells with estradiol induces a GATA-1-regulated program of gene expression with concomitant cellular maturation. We used a microarray to evaluate the expression of 292 different miRNAs in G1E-ER4 cells at 0 versus 24 hours after GATA-1 activation. Affymetrix gene expression profiling has previously been deposited (GEO accession no. GSE628). Keywords: microRNA analysis of a cell-line model of erythroid maturation
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Project description:We employed a gene complementation strategy combined with microarray screening to identify miRNAs involved in the formation of erythroid (red blood) cells. To search for GATA-1-regulated erythroid miRNAs, we used the Gata-1– erythroblast line G1E. These cells proliferate in culture as immature erythroid precursors and undergo terminal maturation when GATA-1 activity is restored. G1E-ER4 is a sub-line stably expressing an estrogen-activated form of GATA-1 (GATA-1 fused to the ligand binding domain of the estrogen receptor). Treatment of G1E-ER4 cells with estradiol induces a GATA-1-regulated program of gene expression with concomitant cellular maturation. We used a microarray to evaluate the expression of 292 different miRNAs in G1E-ER4 cells at 0 versus 24 hours after GATA-1 activation. Affymetrix gene expression profiling has previously been deposited (GEO accession no. GSE628). Keywords: microRNA analysis of a cell-line model of erythroid maturation Two condition experiment, 3 replicates each (independently grown and harvested) of untreated and estradiol-treated (24hrs) G1E-ER4 cells, which express an estrogen-responsive form of the GATA-1 transcription factor. Each sample is compared to a common reference sample, comprised of an equal mixture of all 6 experimental samples.
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