Understanding Epo-dependent Enhancer-Promoter Interactions in the Regulation of Erythroid Gene Expression

Abstract

The hormone erythropoietin (Epo) is required for erythropoiesis, yet its molecular mechanism of action remains poorly understood. To investigate how Epo modulates the erythroid genome, I performed epigenetic profiling using an ex vivo murine cell system that undergoes synchronous erythroid maturation in response to Epo stimulation. These findings define the repertoire of Epo-modulated enhancers, illuminating a previously uncharacterized impact of Epo on the epigenome. Additionally, the dynamics of chromatin architecture in response to hormone stimulation has yet to be fully elucidated. To fill this gap in understanding, I showed that there are transcriptional and epigenetic changes in response to Epo within an invariant chromatin domain organization. Using HiChIP, I identified enhancer-promoter (E-P) interactions mediated by an activating histone modification and structural transcription factor, revealing a subset of invariant chromatin loops. These findings offer new insights into Epo-mediated gene regulation through chromatin organization. Finally, to study the interplay of transcription initiation and chromatin, I profiled the genome-wide locations for RNA polymerase II, the histone variant H2A.Z, and the histone modification H3K4me3 using ChIP-seq and ChIP-exo. These data investigate the relationship between the occupancy of Pol II and nucleosome positions in the erythroleukemic K562 cell line, providing a disease-state profile for comparison to normal erythroid cells. Together, the findings presented here examine the transcriptional and epigenetic responses to hormone stimulation in erythroid cells. Future research should aim to integrate various types of genomic data, as described here, to comprehensively understand gene regulatory mechanisms from multiple perspectives.