E-GEOD-48020 - Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation

Status
Released on 17 June 2013, last updated on 3 May 2014
Organism
Mus musculus
Samples (7)
Protocols (5)
Description
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.
Experiment types
ChIP-seq, RNA-seq of coding RNA 
Contacts
Ross Hardison <rch8@psu.edu>, Andre M Pilon, David M Bodine, Elliott H Margulies, James C Mullikin, Laurie A Steiner, Patrick G Gallagher, Praveen F Cherukuri, Ross C Hardison, Stacie M Anderson, Stephen Wincovitch, Subramanian S Ajay, Swathi A Kumar
Citation
Genome-wide ChIP-Seq reveals a dramatic shift in the binding of the transcription factor erythroid Kruppel-like factor during erythrocyte differentiation. Pilon AM, Ajay SS, Kumar SA, Steiner LA, Cherukuri PF, Wincovitch S, Anderson SM, NISC Comparative Sequencing Center, Mullikin JC, Gallagher PG, Hardison RC, Margulies EH, Bodine DM. , Europe PMC 21900194
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
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