Establishment of regulatory elements during erythro-megakaryopoiesis identifies hematopoietic lineage-commitment points

Abstract

BackgroundEnhancers and promoters are cis-acting regulatory elements associated with lineage-specific gene expression. Previous studies showed that different categories of active regulatory elements are in regions of open chromatin, and each category is associated with a specific subset of post-translationally marked histones. These regulatory elements are systematically activated and repressed to promote commitment of hematopoietic stem cells along separate differentiation paths, including the closely related erythrocyte (ERY) and megakaryocyte (MK) lineages. However, the order in which these decisions are made remains unclear.ResultsTo characterize the order of cell fate decisions during hematopoiesis, we collected primary cells from mouse bone marrow and isolated 10 hematopoietic populations to generate transcriptomes and genome-wide maps of chromatin accessibility and histone H3 acetylated at lysine 27 binding (H3K27ac). Principle component analysis of transcriptional and open chromatin profiles demonstrated that cells of the megakaryocyte lineage group closely with multipotent progenitor populations, whereas erythroid cells form a separate group distinct from other populations. Using H3K27ac and open chromatin profiles, we showed that 89% of immature MK (iMK)-specific active regulatory regions are present in the most primitive hematopoietic cells, 46% of which contain active enhancer marks. These candidate active enhancers are enriched for transcription factor binding site motifs for megakaryopoiesis-essential proteins, including ERG and ETS1. In comparison, only 64% of ERY-specific active regulatory regions are present in the most primitive hematopoietic cells, 20% of which containing active enhancer marks. These regions were not enriched for any transcription factor consensus sequences. Incorporation of genome-wide DNA methylation identified significant levels of de novo methylation in iMK, but not ERY.ConclusionsOur results demonstrate that megakaryopoietic profiles are established early in hematopoiesis and are present in the majority of the hematopoietic progenitor population. However, megakaryopoiesis does not constitute a “default” differentiation pathway, as extensive de novo DNA methylation accompanies megakaryopoietic commitment. In contrast, erythropoietic profiles are not established until a later stage of hematopoiesis, and require more dramatic changes to the transcriptional and epigenetic programs. These data provide important insights into lineage commitment and can contribute to ongoing studies related to diseases associated with differentiation defects.Electronic supplementary materialThe online version of this article (10.1186/s13072-018-0195-z) contains supplementary material, which is available to authorized users.

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

“…While this reduction in numbers of active genes and regulatory elements appears to occur in most lineages of blood cells, it was not observed in megakaryocytic cells, which retain aspects of the regulatory landscape and transcriptomes of multilineage progenitor cells. Similarity of MK to multilineage progenitor cells has been discerned previously from phenotypic similarities (Huang and Cantor 2009), transcriptome data (Sanjuan-Pla et al 2013;Psaila et al 2016), and global epigenetic profiles (Heuston et al 2018). Recent studies have shown that MK cells can be derived from multiple stages of progenitor cells, including HSC, CMP, and MEP (Sanjuan-Pla et al 2013;Psaila et al 2016).…”

“…Detailed information about the cell populations and cell lines analyzed is in Supplemental Material, section 1. The ChIP-seq and ATAC-seq procedures followed previously published methods (Wilson et al 2010;Buenrostro et al 2013;Wu et al 2014;Heuston et al 2018).…”

“…Our multi-lab project called VISION (for ValIdated Systematic IntegratiON of hematopoietic epigenomes) is endeavoring to meet this challenge by focusing on an important biological system, hematopoietic differentiation. Not only is hematopoietic differentiation an important biological and medical system with abundant epigenetic data available (e.g., Cheng et al 2009;Fujiwara et al 2009;Yu et al 2009;Wilson et al 2010;Pilon et al 2011;Tijssen et al 2011;Wong et al 2011;Wu et al 2011;Kowalczyk et al 2012;Su et al 2013;Lara-Astiaso et al 2014;Pimkin et al 2014;Wu et al 2014;Corces et al 2016;Huang et al 2016;Heuston et al 2018;Ludwig et al 2019), but it also provides a powerful framework for validation of the integrative modeling. Specifically, work over prior decades has established key concepts that a successful modeling effort should recapitulate, and predictions of the modeling can be tested genetically in animals and cell lines.…”

Systematic integration of GATA transcription factors and epigenomes via IDEAS paints the regulatory landscape of hematopoietic cells

“…Over the past decade, the amount of information about gene expression levels and epigenetic regulatory landscapes in mammalian hematopoietic cells has increased exponentially, both through the work of individual laboratories [13][14][15][16][17][18][19][20][21][22][23][24][25][26][27] as well as the work of major consortia such as ENCODE and Blueprint. These data currently are provided in differing formats from diverse resources, with no common data processing or analysis, for example, to find significant peaks of signals.…”

Hyperacetylated Chromatin Domains Mark Cell Type-Specific Genes and Suggest Distinct Modes of Enhancer Function

“…ATAC-Seq ATAC-seq was performed as previously described 39 . Briefly, 5 x 10 4 sorted proerythroblasts were lysed by gently pipetting in cold lysis buffer.…”