Unknown,Transcriptomics,Genomics,Proteomics

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Effect of Ets1 knockdown in the P5424 thymic cell line


ABSTRACT: We performed ChIP-Seq for Ets1 and histone modifications in P5424 thymic cells, without and with Ets1 knockdown via shRNA. Overall, we find that loss of Ets1 results in specific, higher occupancy of H3K4me1-marked nucleosomes at the Ets1 binding site, but not H3K4me3 nucleosomes. We verified the specificity of this mechanism as Ets1-dependent by also computing H3K4me1 and 3 nucleosome occupancy in hypersensitive, Ets1-depleted sites. This effect was also found in primary WT DN+DP Ets1 sites. Overall, this suggests that Ets1 induces chromatin remodeling and that its loss increases H3K4me1 nucleosome occupancy in bound sites, with levels of H3K4me3 comparatively unchanged, thus reducing the activation status of these enhancers Genome-wide analysis via ChIP-Seq for Ets1, H3K4me1 and H3K4me3 in WT, sh-scramble and sh-Ets1 the P5424 thymic cell line

ORGANISM(S): Mus musculus

SUBMITTER: Pierre Cauchy 

PROVIDER: E-GEOD-74042 | 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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