Dynamics of Chromatin Accessibility During Hematopoietic Stem Cell Differentiation Into Progressively Lineage-Committed Progeny

Abstract

SUMMARY Epigenetic mechanisms regulate the multilineage differentiation capacity of hematopoietic stem cells (HSCs) into a variety of blood and immune cells. Mapping the chromatin dynamics of functionally defined cell populations will shed mechanistic insight on two major, unanswered questions in stem cell biology: how does epigenetic identity contribute to a cell type’s lineage potential, and how do cascades of chromatin remodeling dictate ensuing fate decisions? Our recent work revealed evidence of multilineage gene priming in HSCs, where open cis-regulatory elements (CREs) exclusively shared between HSCs and unipotent lineage cells were enriched for DNA binding motifs of known lineage-specific transcription factors. Oligopotent progenitor populations operating between the HSCs and unipotent cells play essential roles in effecting hematopoietic homeostasis. To test the hypothesis that selective HSC-primed lineage-specific CREs remain accessible throughout differentiation, we used ATAC-seq to map the temporal dynamics of chromatin remodeling during progenitor differentiation. We observed epigenetic-driven clustering of oligopotent and unipotent progenitors into distinct erythromyeloid and lymphoid branches, with multipotent HSCs and MPPs associating with the erythromyeloid lineage. We mapped the dynamics of lineage-primed CREs throughout hematopoiesis and identified both unique and shared CREs as potential lineage reinforcement mechanisms at fate branch points. Additionally, quantification of genome-wide peak count and size revealed overall greater chromatin accessibility in HSCs, allowing us to identify HSC-unique peaks as putative regulators of self-renewal and multilineage potential. Finally, CRISPRi-mediated targeting of ATACseq- identified putative CREs in HSCs allowed us to demonstrate the functional role of selective CREs in lineage-specific gene expression. These findings provide insight into the regulation of stem cell multipotency and lineage commitment throughout hematopoiesis and serve as a resource to test functional drivers of hematopoietic lineage fate.

Step by step analysis on gene datasets of growth phases in hematopoietic stem cells

“…The single cell RNA-Seq and ATAC-Seq data could reveal better gene profiles as reported in the differentiated blood cell, myeloid, and lymphoid cell lineages [ [96] , [97] , [98] , [99] ], however, these data were not enough to analyze the cell cycle phases in GEO database, so that in this study, the transcriptomic data obtained from the gene expression profiling by the array. The high-throughput data analysis suggested the gene profiles that could predict the crucial roles of genes in signaling pathways, however, epigenetic changes, gene mutations, interactions with neighboring cells, and post-translational modifications can affect the functions of signaling pathways.…”

Single-cell mitochondrial variant enrichment resolved clonal tracking and spatial architecture in human embryonic hematopoiesis

“…The lineage mapping of hematopoiesis started from the robust reconstruction power of hematopoietic stem cells. Transplantation of retrovirally labelled HSCs determined lineage reconstruction capacity from a single cell (Lemischka et al, 1986), as well as defined lineage- bias and its associated epigenetic signatures in hematopoiesis at extreme stress condition, namely transplantation hematopoiesis (Challen et al, 2010; Lu et al, 2011; Martin et al, 2023). The lineage tracing with HSC-specific reporter animal models advanced the understanding of HSC commitment and locomotion in native hematopoiesis, however its application is limited to mouse, not human (Acar et al, 2015; Chen et al, 2016; Christodoulou et al, 2020; Gazit et al, 2014).…”