Regulation of the positive transcriptional effect of PLZF through a non-canonical EZH2 activity

Abstract

The transcription factor PLZF (promyelocytic leukemia zinc finger protein) acts as an epigenetic regulator balancing self-renewal and differentiation of hematopoietic cells through binding to various chromatin-modifying factors. First described as a transcriptional repressor, PLZF is also associated with active transcription, although the molecular bases underlying the differences are unknown. Here, we reveal that in a hematopoietic cell line, PLZF is predominantly associated with transcribed genes. Additionally, we identify a new association between PLZF and the histone methyltransferase, EZH2 at the genomic level. We find that co-occupancy of PLZF and EZH2 on chromatin at PLZF target genes is not associated with SUZ12 or trimethylated lysine 27 of histone H3 (H3K27me3) but with the active histone mark H3K4me3 and active transcription. Removal of EZH2 leads to an increase of PLZF binding and increased gene expression. Our results suggest a new role of EZH2 in restricting PLZF positive transcriptional activity independently of its canonical PRC2 activity.

PLZF limits enhancer activity during hematopoietic progenitor aging

“…This stable cell line was first used to profile PLZF genomic occupancy using Flag antibody. In PLZF-Flag 416b cells, PLZF binds mostly intragenic regions (63.6%) with preference for intronic sequences and TSS regions, in accordance with previously reported genomic localization in human myeloid cells (27) (Figure 1B). Presence of PLZF on its previously described targeted genomic loci was confirmed by Integrative Genomics Viewer (IGV) visualization (Supplemental Figure S1A) and peak calling analysis.…”

“…Presence of PLZF on its previously described targeted genomic loci was confirmed by Integrative Genomics Viewer (IGV) visualization (Supplemental Figure S1A) and peak calling analysis. In line with our previous study (27), genes bound by PLZF-Flag in the myeloid progenitor cell line ( Table 1) were enriched for Gene Ontology (GO) terms relating to cell cycle, DNA integrity and immunity. Remarkably, genes involved in protein acetylation-related GO terms were also enriched within the genes targeted by PLZF ( Figure 1C), underlying a potential effect of PLZF on Histone lysine acetylation.…”

“…For instance, previous studies have shown that PLZF recruits HDAC complexes at targeted promoters and locally reduced histone acetylation (25,26). In addition, we previously showed that presence of PLZF at chromatin is associated with the tri-methylation of lysine 27 of histone H3 (H3K27me3) enrichment at developmental genes (24,27). Here, we reveal a new chromatin function of PLZF in myeloid progenitors.…”

“…PLZF transcriptional repression required the acetyltransferase activity of P300 (53). More recently, PLZF was shown to interact with the histone methyltransferase EZH2, which could methylate PLZF affecting its stability and its transcriptional activity (27,54). In addition, HDAC7, a key factor of the innate effector programming of iNKT cells, changes PLZF activity underlying the tight connection between specific transcription factor activity and post-translational modification of the epigenetic machinery (55).…”

“…Since enhancer activity is cell-type specific and context sensitive, we determined enhancer regulatory regions using our 416b cell-specific ChIP-seq data. Promoter regions were defined as previously performed on human cells (27) but using the murine (mm10) genome. Enhancer regions were defined by the presence of H3K4me1 and absence of H3K4me3 and their activity was defined depending on the presence of additional histone marks (H3K27ac and H3K27me3).…”