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Gene expression analysis of Ets1-/- CD4+ CD8+ thymocytes

ABSTRACT: We performed ChIP-Seq for hallmark TFs (Ets1, Runx1), histone modification marks (H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3), total RNA Pol II, short RNA-Seq as well as nucleosome mapping mainly in murine Rag2 -/- thymocytes. We also performed ChIP-Seq for E47 as well as nucleosome mapping, gene expression microarray analysis in CD4+ CD8+ WT and Ets1-/- DP thymocytes. Overall, we find a key role for the transcription factor Ets1, contributing towards alpha beta T cell lineage commitment via differential transactivation of stage-specific genes orchestrated by dynamic, co-association -mediated chromatin remodeling, as well as transcription dependent generation of a specialized chromatin structure at the TCR beta locus. Genome-wide analysis via ChIP-Seq for Ets1, Runx1, total RNA Pol II binding, H3K4me1, H3K4me2, H3K4me3, H3K27me3, H3K36me3, short RNA-Seq, Mnase-Seq in murine Rag2 -/- thymocytes, ChIP-Seq for E47, Mnase-Seq and gene expression microarray analysis in DP thymocytes Gene expression analysis of Ets1-/- CD4+ CD8+ thymocytes

ORGANISM(S): Mus musculus

SUBMITTER: Pierre Cauchy 

PROVIDER: E-GEOD-73849 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation.

Cauchy Pierre P   Maqbool Muhammad A MA   Zacarias-Cabeza Joaquin J   Vanhille Laurent L   Koch Frederic F   Fenouil Romain R   Gut Marta M   Gut Ivo I   Santana Maria A MA   Griffon Aurélien A   Imbert Jean J   Moraes-Cabé Carolina C   Bories Jean-Christophe JC   Ferrier Pierre P   Spicuglia Salvatore S   Andrau Jean-Christophe JC  

Nucleic acids research 20151215 8

Ets1 is a sequence-specific transcription factor that plays an important role during hematopoiesis, and is essential for the transition of CD4(-)/CD8(-) double negative (DN) to CD4(+)/CD8(+) double positive (DP) thymocytes. Using genome-wide and functional approaches, we investigated the binding properties, transcriptional role and chromatin environment of Ets1 during this transition. We found that while Ets1 binding at distal sites was associated with active genes at both DN and DP stages, its  ...[more]

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