Transcriptomics,Genomics

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Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation


ABSTRACT: Erythropoiesis is dependent on the activity of transcription factors, including the erythroid-specific erythroid Kruppel-like factor (EKLF). ChIP followed by massively parallel sequencing (ChIP-Seq) is a powerful, unbiased method to map transfactor occupancy. We used ChIP-Seq to study the interactome of EKLF in mouse erythroid progenitor cells and more differentiated erythroblasts. We correlated these results with the nuclear distribution of EKLF, RNA-Seq analysis of the transcriptome, and the occupancy of other erythroid transcription factors. In progenitor cells, EKLF is found predominantly at the periphery of the nucleus, where EKLF primarily occupies the promoter regions of genes and acts as a transcriptional activator. In erythroblasts, EKLF is distributed throughout the nucleus, and erythroblast-specific EKLF occupancy is predominantly in intragenic regions. In progenitor cells, EKLF modulates general cell growth and cell cycle regulatory pathways, whereas in erythroblasts EKLF is associated with repression of these pathways. The EKLF interactome shows very little overlap with the interactomes of GATA1, GATA2, or TAL1, leading to a model in which EKLF directs programs that are independent of those regulated by the GATA factors or TAL1. (Blood.2011;118(17):e139-e148) We used ChIP-Seq to study the interactome of EKLF in mouse erythroid progenitor cells and more differentiated erythroblasts and RNA-Seq analysis of the transcriptome.

ORGANISM(S): Mus musculus  

SUBMITTER: David M Bodine  Stacie M Anderson   Elliott H Margulies   Stephen Wincovitch   Laurie A Steiner   Ross C Hardison   James C Mullikin   Patrick G Gallagher   Andre M Pilon   Swathi A Kumar   Praveen F Cherukuri   Ross Hardison   Subramanian S Ajay    

PROVIDER: E-GEOD-48020 | ArrayExpress | 2013-06-17

SECONDARY ACCESSION(S): SRP026111GSE48020PRJNA208710

REPOSITORIES: GEO, ArrayExpress, ENA

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Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation.

Pilon Andre M AM   Ajay Subramanian S SS   Kumar Swathi Ashok SA   Steiner Laurie A LA   Cherukuri Praveen F PF   Wincovitch Stephen S   Anderson Stacie M SM   Mullikin James C JC   Gallagher Patrick G PG   Hardison Ross C RC   Margulies Elliott H EH   Bodine David M DM  

Blood 20110906 17


Erythropoiesis is dependent on the activity of transcription factors, including the erythroid-specific erythroid Kruppel-like factor (EKLF). ChIP followed by massively parallel sequencing (ChIP-Seq) is a powerful, unbiased method to map trans-factor occupancy. We used ChIP-Seq to study the interactome of EKLF in mouse erythroid progenitor cells and more differentiated erythroblasts. We correlated these results with the nuclear distribution of EKLF, RNA-Seq analysis of the transcriptome, and the  ...[more]

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