Dynamic control of enhancer repertoires drives lineage and developmental stage-specific transcription during human erythropoiesis

ABSTRACT: Transcriptional enhancers are the primary determinants of tissue-specific gene expression and influence a variety of cellular phenotypes. The regulatory components controlling enhancer assembly and turnover during stem cell development remain largely unknown. Here we compared the similarities and differences in enhancer landscape, transcriptional factor (TF) occupancy and transcriptomic changes in human primary fetal and adult hematopoietic stem/progenitor cells (HSPCs) and committed erythroid progenitors. We find that enhancers are modulated dynamically and extensively, and direct lineage and developmental stage-specific transcriptional programs. GATA2-to-GATA1 switch is prevalent within transcriptionally dynamic enhancers and drives enhancer commissioning. Further examination of lineage-specific enhancers identified TFs and their combinatorial patterns with known and unknown roles as putative drivers of enhancer turnover during differentiation. Importantly, by site-directed loss-of-function analysis of individual lineage-selective enhancers within the SLC25A37 super-enhancer using CRISPR/Cas9-mediated genomic editing, we uncover unexpected functional hierarchy of constituent enhancers within the super-enhancer cluster. Despite the indistinguishable chromatin features between the GATA switch enhancers at the GATA2 gene, we reveal through genomic editing the functional diversity of GATA switch enhancers in which enhancers with opposing functions cooperate to coordinate gene expression during development. Thus, genome-wide enhancer profiling coupled with in-depth enhancer editing in situ provide critical insights into the functional hierarchy and complexity of enhancers during stem cell development.

ORGANISM(S): Homo sapiens

PROVIDER: GSE70660 | GEO | 2016/01/11

SECONDARY ACCESSION(S): PRJNA289303

REPOSITORIES: GEO