Determining the Enhancer Proteomes in Primary Cells and Native Tissue

Abstract

Enhancers play a critical role for gene expression, yet their cell‐type‐specific establishment and maintenance remains incompletely understood. To investigate this, we surveyed the proteomic composition of enhancers in naive mesenchymal stem cells, differentiating adipocytes, and liver tissue using ChIP with selective isolation of chromatin‐associated proteins (ChIP‐SICAP). ChIP‐SICAP revealed that H3K27ac‐marked chromatin is enriched for over 500 proteins, including sequence‐specific transcription factors (TFs), chromatin remodeling complexes, and histone variants that collectively define the landscape of active enhancers in differentiating adipocytes and hepatocytes. Moreover, we observe a pivotal role for CEBP TFs at enhancers in both settings. To gain further insight into the roles of CEBPs, we performed ChIP‐SICAP for CEBPb and identified a subset of the proteins comprising the H3K27ac enhancer proteome. Although CEBPb‐bound chromatin is commonly enriched for the nuclear receptor GR and PAR‐family bZip proteins, other co‐localizing TFs, such as TEADs and HNF1a, show strict cell‐type‐specificity. Moreover, we observe that chromatin remodelers and transcriptional co‐activators such as BRD2 and MED8 are selectively enriched at sites of CEBP occupancy in response to adipogenic stimuli, suggesting these factors may play important roles with CEBPs to establish active chromatin during cell differentiation. Collectively, these observations reveal both constitutive and tissue‐specific determinants of the enhancer landscape, and provide new insights into mechanisms employed by lineage‐determining TFs to direct gene programs controlling cell development and function.Support or Funding InformationNIH grant R01 DK098542This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.