Abstract
Lineage commitment and differentiation is driven by the concerted action of master transcriptional regulators at their target chromatin sites. Multiple efforts have characterized the key transcription factors (TFs) that determine the various hematopoietic lineages. However, the temporal interactions between individual TFs and their chromatin targets during differentiation and how these interactions dictate lineage commitment remains poorly understood. We performed dense, daily, temporal profiling of chromatin accessibility (DNase I-seq) and gene expression changes (total RNA-seq) along ex vivo human erythropoiesis to comprehensively define developmentally regulated DNase I hypersensitive sites (DHSs) and transcripts. We link both distal DHSs to their target gene promoters and individual TFs to their target DHSs, revealing that the regulatory landscape is organized in distinct sequential regulatory modules that regulate lineage restriction and maturation. Finally, direct comparison of transcriptional dynamics (bulk and single-cell) and lineage potential between erythropoiesis and megakaryopoiesis uncovers differential fate commitment dynamics between the two lineages as they exit pluripotency. Collectively, these data provide novel insights into the global regulatory landscape during hematopoiesis.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
This version of the manuscript has been revised to include the following updates: 1.Demonstration that our elastic net model assigning putative TF regulators to individual DHS is outperforms the typical TF motif enrichment methods in predicting the temporal profile of a DHS, suggesting that the associations presented represent a more accurate representation of the TF-DHS temporal interactions. 2.Integrative analysis of publicly available Hi-C data to orthogonally validate and characterize enhancer-promoter linking. 3.Deepened analysis of the single-cell data using numerous approaches for clustering and lineage trajectory inference. 4.Re-analysis of publicly available single-cell RNA-seq data derived from human bone marrow to confirm that the in vitro system used in this manuscript recapitulates in vivotranscriptional dynamics. 5.Results from additional clonal assays during megakaryocytic differentiation. 6.Flow-cytometric identification of myeloid populations along erythroid and megakaryocytic differentiation