Effects of depletion of Mel18 on gene expression in lineage negative hematopoietic stem cells [RNAseq_Lin_neg_cell]

Polycomb group (PcG) proteins play important roles in hematopoietic stem cell (HSC) self-renewal. Mel18 and Bmi1 are homologs of the PCGF subunit within the Polycomb repressive complex 1 (PRC1). Bmi1 (PCGF4) enhances HSC self-renewal and promotes terminal differentiation. However, the role of Mel18 (PCGF2) in hematopoiesis is not fully understood and how Mel18 regulates gene transcription in HSCs remains elusive. We found that acute deletion of Mel18 in the hematopoietic compartment significantly increased the frequency of functional HSCs in the bone marrow. Furthermore, we demonstrate that Mel18 inhibits HSC self-renewal and proliferation. RNA-seq studies revealed that HSC self-renewal and proliferation gene signatures are enriched in Mel18-/- hematopoietic stem and progenitors (HSPCs) compared to Mel18+/+ HSPCs. Notably, ATAC-seq revealed increased chromatin accessibility at genes important for HSC self-renewal, whereas CUT&RUN showed decreased enrichment of H2AK119ub1 at genes important for proliferation, leading to increased expression of both Hoxb4 and Cdk4 in Mel18-/- HSPCs. Furthermore, leukemia stem cells and several types of acute leukemia gene signatures are enriched in Mel18-/- HSCs compared to WT HSCs. Thus, we demonstrate that Mel18 inhibits hematopoietic stem cell self-renewal through repressing the transcription of genes important for HSC self-renewal and proliferation. Overall design: To determine whether polycomb group protein Mel18 alters gene transcription in mouse HSPCs, we established constional Mel18 knock out mouse model in hematopoietic system. We then performed gene expression profilling analysis using data obtained from RNA-seq with sorted Lin- cells from either wildtype or Mel18-null mouse. Comparative gene expression profilling analysis of RNA-seq data was performed between wildtype and Mel18 knouck out HSCs.