YY1-Mediated PcG Regulation Dictates Hematopoietic Stem Cell Fate

Hematopoietic stem cells (HSCs) are undifferentiated, pluripotent cells that can either self-renew or differentiate into any of the mature lineage-specific cells in adult blood. Physiological aging and hematological malignancies in humans and mice are associated with dysregulation of the epigenetic landscape leading to biased HSC differentiation. The mechanisms that maintain normal HSC differentiation and balanced lineage output are incompletely understood. Mammalian Polycomb Group (PcG) proteins are negative regulators of gene expression that bind as large complexes to chromatin regulatory regions. However, many questions remain unanswered regarding mechanisms underlying the locus-specific targeting of PcG complexes. Yin Yang 1 (YY1) is unique among mammalian PcG proteins as it recruits other PcG proteins to its target genes and coordinates extensive long-range chromatin interactions (LRCIs) in upstream promoter/enhancer regions to activate/repress transcription of these genes. We have mapped the PcG function of YY1 to a small motif (aa 201-226), known as the Recruitment of Polycomb (REPO) domain, and demonstrated that it is essential to recruit other PcG proteins, stably repress transcription and initiate chromatin remodeling in YY1 target genes. Our previous work established a new paradigm in the regulation of lymphopoiesis by discovering that the YY1 REPO domain is required for Vκ gene rearrangement in pro-B cells and early T-cell survival. These results suggest that YY1 may orchestrate other PcG proteins in hematopoiesis through its PcG domain, which would have broad implications for YY1 as a coordinator of higher-order chromatin remodeling during HSC differentiation.

Our prior studies in mice show that YY1-deficient HSCs fail to self-renew, do not remain quiescent, and have disrupted HSC metabolic regulatory networks. Ectopic expression of the YY1 PcG domain-deleted mutant (YY1ΔREPO) promotes the development of myeloid cells, indicating a requirement for YY1 PcG function to maintain HSC lineage balance. We further generated a YY1ΔREPO mouse model (Yy1^-/ΔREPO) using CRISPR-Cas9 gene editing. Deletion of the YY1 PcG function/REPO domain leads to expansion of CD61^high phenotypic LT-HSCs, but with reduced capacity to long-term self-renew. Yy1^-/ΔREPO HSCs display reduced quiescence, higher intracellular reactive oxygen species and increased mitochondrial membrane potential. The YY1 PcG domain deletion leads to HSC myeloid skew with expansion of myeloid primed multipotent progenitors (MPPs), increased myeloid specific colonies (CFU-G, M, GM) and increased myeloid / lymphoid ratio in peripheral blood. Thus, YY1ΔREPO mice show hallmarks of aging-related changes in hematopoiesis. In addition, N-terminally truncated YY1 201-414, which is sufficient for YY1-mediated long-range chromatin interactions, rescued hematologic defects in Yy1^-/- mice, when expressed via the endogenous ROSA 26 promoter. These results support a model in which YY1 PcG function in chromatin structural regulation is essential for balanced HSC differentiation. CUT&Tag analysis in hematopoietic stem progenitor cells support that YY1 co-occupies with essential chromatin structural regulator cohesin at a large cohort of promoters genome-wide. Gene promoters with YY1-dependent occupancy are enriched in HSC metabolic process. Consistently, RNA-seq analysis of Yy1^-/ΔREPO HSCs revealed the genetic network governing HSC metabolism were deregulated with down regulation of Hif1α and Hif3α indicating essential role of YY1 PcG function in HSC metabolism and differentiation.

Our study supports that YY1 PcG function/chromatin remodeling is critical for HSC metabolism and differentiation. Disruption of YY1 mediated PcG function leads to acceleration of HSC aging. Our studies have elucidated innovative mechanisms and pathways by which epigenetic mechanisms dictate cell fate decisions during normal hematopoiesis.