Chromatin structure and 3D architecture define differential functions ofPU.1cis regulatory elements in human blood cell lineages

Abstract

ABSTRACTThe precise spatio-temporal expression of the hematopoietic ETS transcription factorPU.1that determines the hematopoietic cell fates is tightly regulated at the chromatin level. However, it remains elusive as to how chromatin signatures are linked to this dynamic expression patternof PU.1across blood cell lineages. Here we performed an unbiased and in-depth analysis of the relationship between humanPU.1expression, the presence of trans-acting factors, and 3D architecture at various cis-regulatory elements (CRE) proximal to thePU.1locus. We identified multiple novel CREs at the upstream region of the gene following an integrative inspection for conserved DNA elements at the chromatin-accessible regions in primary human blood lineages. We showed that a subset of CREs localize within a 10 kb-wide cluster that exhibits that exhibit molecular features of a myeloid-specific super-enhancer involved in mediatingPU.1autoregulation, including open chromatin, unmethylated DNA, histone enhancer marks, transcription of enhancer RNAs, and occupancy of the PU.1 protein itself. Importantly, we revealed the presence of common 35-kb-wide CTCF-bound insulated neighborhood that contains the CRE cluster, forming the chromatin territory for lineage-specific and CRE-mediated chromatin interactions. These include functional CRE-promoter interactions in myeloid and B cells but not in erythroid and T cells. Our findings also provide mechanistic insights into the interplay between dynamic chromatin structure and 3D architecture in defining certain CREs as enhancers or silencers in chromatin regulation ofPU.1expression. The study lays the groundwork for further examination ofPU.1CREs as well as epigenetic regulation in malignant hematopoiesis.