Deubiquitylation of histone H2A activates transcriptional initiation via trans-histone cross-talk with H3K4 di- and trimethylation

Abstract

Transcriptional initiation is a key step in the control of mRNA synthesis and is intimately related to chromatin structure and histone modification. Here, we show that the ubiquitylation of H2A (ubH2A) correlates with silent chromatin and regulates transcriptional initiation. The levels of ubH2A vary during hepatocyte regeneration, and based on microarray expression data from regenerating liver, we identified USP21, a ubiquitin-specific protease that catalyzes the hydrolysis of ubH2A. When chromatin is assembled in vitro, ubH2A, but not H2A, specifically represses the di-and trimethylation of H3K4. USP21 relieves this ubH2A-specific repression. In addition, in vitro transcription analysis revealed that ubH2A represses transcriptional initiation, but not transcriptional elongation, by inhibiting H3K4 methylation. Notably, ubH2A-mediated repression was not observed when H3 Lys 4 was changed to arginine. Furthermore, overexpression of USP21 in the liver up-regulates a gene that is normally down-regulated during hepatocyte regeneration. Our studies revealed a novel mode of trans-histone cross-talk, in which H2A ubiquitylation controls the di-and trimethylation of H3K4, resulting in regulation of transcriptional initiation.[Keywords: Nucleosome; ubiquitylation; histone code; transcription; USP21; H2A] Supplemental material is available at http://www.genesdev.org.

Histone Monoubiquitylation Position Determines Specificity and Direction of Enzymatic Cross-talk with Histone Methyltransferases Dot1L and PRC2

“…In fact, the balance between H3K4me and H3K27me at gene promoters may be an important mechanism of transcriptional regulation (38,39). Others have shown that the activity of MTases for H3K4 are stimulated or repressed by H2Bub and H2Aub, respectively (16,22). Given the opposing function of H3K4me and H3K27me in transcriptional regulation, we wondered whether H2Aub and H2Bub also directly and antagonistically regulate PRC2-mediated methylation of H3K27.…”

“…However, the discovery of the major E3 ligase for H2Aub in mammalian systems, Ring1B, a member of the PRC1 (Polycomb repressive complex 1) family (21), opened the door to studies implicating H2Aub in developmentally regulated transcriptional repression. Recently, using nucleosomes reconstituted with endogenous H2A or H2Aub, Nakagawa et al (22) showed that deubiquitylation of H2Aub allowed for efficient methylation of H3K4 by the MTase MLL3. This study provided mechanistic support for H2Aub involvement in transcriptional repression.…”

Protein monoubiquitylation: targets and diverse functions

“…Consistent with the function of these six ubiquitin ligase complexes as transcriptional repressors, monoubiquitylated H2A inhibits transcription by several mechanisms including down‐regulation of methylation of histone H3 at lysine 4 (H3K4) (Nakagawa et al . 2008), a mark of active promoters, and recruitment of PRC2 (Blackledge et al . 2014).…”

“…2007), USP21 (Nakagawa et al . 2008), BRCA1‐associated protein 1 (BAP1) (Scheuermann et al . 2010) and 2A‐DUB (Zhu et al .…”

The flip side of the coin: Role of ZRF1 and histone H2A ubiquitination in transcriptional activation

“…Several H2A-specific deubiquitinases have been identified and investigated with respect to their function in either cell cycle or gene activation. 2,32,33 It has recently been demonstrated that the deubiquitinase USP21 has an impact on the activation of transcription from ubiquitinated chromatin. In vitro transcription experiments utilizing nucleosomes that contained mono-ubiquitinated histone H2A showed that transcription only occurred after the complete removal of the ubiquitin residue by USP21.…”