Setd2 regulates quiescence and differentiation of adult hematopoietic stem cells by restricting RNA polymerase II elongation

Abstract

SET domain containing 2 (Setd2), encoding a histone methyltransferase, is associated with many hematopoietic diseases when mutated. By generating a novel exon 6 conditional knockout mouse model, we describe an essential role of Setd2 in maintaining the adult hematopoietic stem cells. Loss of Setd2 results in leukopenia, anemia, and increased platelets accompanied by hypocellularity, erythroid dysplasia, and mild fibrosis in bone marrow. Setd2 knockout mice show significantly decreased hematopoietic stem and progenitor cells except for erythroid progenitors. Setd2 knockout hematopoietic stem cells fail to establish long-term bone marrow reconstitution after transplantation because of the loss of quiescence, increased apoptosis, and reduced multiple-lineage terminal differentiation potential. Bioinformatic analysis revealed that the hematopoietic stem cells exit from quiescence and commit to differentiation, which lead to hematopoietic stem cell exhaustion. Mechanistically, we attribute an important Setd2 function in murine adult hematopoietic stem cells to the inhibition of the Nsd1/2/3 transcriptional complex, which recruits super elongation complex and controls RNA polymerase II elongation on a subset of target genes, including Myc. Our results reveal a critical role of Setd2 in regulating quiescence and differentiation of hematopoietic stem cells through restricting the NSDs/SEC mediated RNA polymerase II elongation.

Linking histone methylation, transcription rates, and stem cell robustness

“…A growing body of literature has demonstrated that the core transcriptional machinery is not a simple digital switch responding to upstream interactions of transcription factors, but rather a highly regulated, multi-step process that behaves differently within different cells and in different contexts (reviewed by Coulon et al, 3 Goodrich and Tjian, 4 and Jonkers and Lis 5 ). The study by Zhou et al 1 confirms those results in the context of hematopoiesis and stem cell biology, as well as prompts a number of important questions that must now be resolved. Why are erythroid cells more robust to changes in Setd2 activity?…”

“…Prior work integrating Global Run-On sequencing (Gro-Seq) and ChIP-seq of H3K36me3 has demonstrated substantial anticorrelation between this histone mark and polymerase elongation rates. 2 The study by Zhou et al 1 is, to our knowledge, the first to demonstrate in vivo evidence for a directional and putatively causal link of this mark with polymerase kinetics. Moreover, this study provides significant evidence for the importance of Setd2, and consequently H3K36me3, to hematopoietic stem cell function.…”

“…In this issue of the Journal, Zhou et al 1 study the hematopoietic stem cell defects associated with genetic deletion of the mammalian H3K36 tri-methyltransferase, Setd2. While embryonic deletion of Setd2 within the endothelial/hematopoietic lineages by a Tie2-Cre is lethal, deletion with Vav and the inducible Mx1-Cre systems permitted the study of this critical enzyme during hematopoiesis.…”

“…Next, Zhou et al 1 established the molecular mechanism underlying these dramatic phenotypic findings. First, they found significant changes in both the mRNA and protein levels of other H3K36 methyltransferases, with Ash11 decreasing and Nsd1/2/3 increasing.…”

“…Moreover, perturbation of the mono/di-to tri-methylation status of H3K36 also lead to changes in other histone marks correlated with active transcription, such as increased H3K79me2 and H3K4me3, and decreased H3K27me3. As both H3K36 and H3K79 have been strongly linked to polymerase processivity, Zhou et al 1 looked at the distribution and abundance of initiated and actively elongating polymerase, indicated by the presence of phosphorylation marks on the CTD at serine 5 and serine 2, respectively. Intriguingly, these Authors show robust increases in the Ser2P after deletion of Setd2, as well as increased ChIP signal within the exonic region of elongation complex sensitive genes such as Mycc.…”