Lysine acetyltransferase Tip60 is required for hematopoietic stem cell maintenance

Abstract

Hematopoietic stem cells (HSC) have the potential to replenish the blood system for the lifetime of the organism. Their two defining properties, self-renewal and differentiation, are tightly regulated by the epigenetic machineries. Here, using conditional gene knockout models, we demonstrate a critical requirement of lysine acetyltransferase 5 (Kat5, also known as Tip60) for murine HSC maintenance both in the embryonic and adult stages, which depends on its acetyltransferase activity. Genome-wide chromatin and transcriptome profiling in murine hematopoietic stem and progenitor cells revealed that Tip60 co-localizes with c-Myc and that Tip60 deletion suppress the expression of Myc target genes, which are associated with critical biological processes for HSC maintenance, cell-cycle and DNA repair. Notably, acetylated H2A.Z (acH2A.Z) was enriched at the Tip60-bound active chromatin and Tip60 deletion induced a robust reduction in the acH2A.Z / H2A.Z ratio. These results uncover a critical epigenetic regulatory layer for HSC maintenance at least in part through Tip60 dependent H2A.Z acetylation to activate Myc target genes.

ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function

“…On the other hand, deletion of cohesin binding component STAG2 but not STAG1 increased HSC self-renewal and reduced differentiation capacity, suggesting that the cohesin complex plays different roles in HSPCs driven by different STAG subunits 42 . Other than the cohesin complex, coactivators and mediators were also reported to be critical for HSPC function through facilitating active histone marks, such as H2A.Z/H3K27 acetylation on promoter/enhancer regions [43][44][45] . Although our studies of ZNF143 reveal another aspect of the regulation of HSPC chromatin organization through mediating the integrity of CTCFbound loops, it is not clear that whether ZNF143 is critical for all HSPCs or only in LT-HSCs.…”

Formation and recycling of an active epigenetic mark mediated by cell cycle-specific RNAs

“…Given the close proximity of promoter RNAs to TSS and the growing body of literature showing that highly expressed genes are marked by the acetylated form of the variant histone H2A.Z (acH2A.Z) (ref. 5 ), the possibilities of a link between early S-phase promoter RNAs and H2A.Z/acH2A.Z was investigated by: (i) Ribonucleoprotein (RNP) pull-down experiments followed by mass spectrometry; and (ii) RNA immunoprecipitations followed by RNA sequencing (RIP-Seq).…”

Enhancers regulate 3′ end processing activity to control expression of alternative 3′UTR isoforms

“…FASTQ files for bulk RNA-seq samples were obtained from the Sequence Read Archive. Mouse definitive erythroblasts: SRR6946157-9 64 , SRR8945139-41,44-45 66 , mouse hematopoietic stem cells: SRR7946616-7 89 , SRR6458998-9000 65 .…”

“…To investigate if enhancers are preferentially associated with cell type-specific changes in 3′UTR isoform expression at endogenous genes, we analyzed cell type-specific changes in gene-level mRNA abundance and 3′UTR isoform usage between hematopoietic stem cells (HSC) and erythrocytes (Ery) ( Figure 4F) (Ha et al, 2018;Numata et al, 2020;Cai et al, 2020).…”

“…The following GEO datasets were used: Ery (definitive erythrocytes, EryD): GSE112717 and HSC: GSE120705 (Numata et al, 2020;Cai et al, 2020). FASTQ samples were obtained from the Sequence Read Archive (Ery: GSM3081989-GSM3081991; HSC: GSM3408762-GSM3408764) and pseudoaligned for transcript quantification in Salmon v1.3.0 (`salmon quant --gcBias --validateMappings -l A`) to the pre-compiled QAPA v1.3.0 mm10 3' UTR annotation with the full mm10 genome as decoy (Patro et al, 2017;Ha et al, 2018).…”