Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types.

Existing studies of chromatin conformation have primarily focused on potential enhancers interacting with gene promoters. By contrast, the interactivity of promoters per se, while equally critical to understanding transcriptional control, has been largely unexplored, particularly in a cell type-specific manner for blood lineage cell types. In this study, we leverage promoter capture Hi-C data across a compendium of blood lineage cell types to identify and characterize cell type-specific super-interactive promoters (SIPs). Notably, promoter-interacting regions (PIRs) of SIPs are more likely to overlap with cell type-specific ATAC-seq peaks and GWAS variants for relevant blood cell traits than PIRs of non-SIPs. Moreover, PIRs of cell-type-specific SIPs show enriched heritability of relevant blood cell trait (s), and are more enriched with GWAS variants associated with blood cell traits compared to PIRs of non-SIPs. Further, SIP genes tend to express at a higher level in the corresponding cell type. Importantly, SIP subnetworks incorporating cell-type-specific SIPs and ATAC-seq peaks help interpret GWAS variants. Examples include GWAS variants associated with platelet count near the megakaryocyte SIP gene EPHB3 and variants associated lymphocyte count near the native CD4 T-Cell SIP gene ETS1. Interestingly, around 25.7% ~ 39.6% blood cell traits GWAS variants residing in SIP PIR regions disrupt transcription factor binding motifs. Importantly, our analysis shows the potential of using promoter-centric analyses of chromatin spatial organization data to identify biologically important genes and their regulatory regions. Author summary: By analyzing pcHi-C data, we catalogue super-interactive promoters (SIPs) in five blood cell types. These SIPs and SIP genes in blood cells will be valuable not only for studying hematological traits but for many complex phenotypes. We provide mechanistic hypotheses regarding the formation of SIPs. To be identified as a SIP, a promoter can be driven by few super strong interactions or many significant (not necessarily all strong) interactions. Importantly, we find that the latter seems to be the norm. This finding sheds light regarding the formation of SIPs: to ensure the expression level of some critical gene (here a SIP gene), multiple regulatory regions are likely key for orchestrating fine transcriptional control. These multiple regulatory regions provide a level of "redundancy", ensuring that even in the presence of genetic variant (s) that disrupt some enhancer(s), appropriate transcriptional regulation can still be maintained in a given hematopoietic cell type. This finding also has important implications for the interpretation and functional follow-up of hundreds of thousands of GWAS findings. These multiple regulatory regions for one SIP gene help explain multiple independent GWAS signals at one locus. In summary, we believe our work presents important findings governing the orchestrated transcriptional control in blood lineage cell types, and provides valuable insights and resources for the interpretation and follow-up of GWAS findings of many complex traits. [ABSTRACT FROM AUTHOR]