Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing

Abstract

Increasing evidence suggests that chromatin modifications have important roles in modulating constitutive or alternative splicing. Here we demonstrate that the PWWP domain of the chromatin-associated protein Psip1/Ledgf can specifically recognize tri-methylated H3K36 and that, like this histone modification, the Psip1 short (p52) isoform is enriched at active genes. We show that the p52, but not the long (p75), isoform of Psip1 co-localizes and interacts with Srsf1 and other proteins involved in mRNA processing. The level of H3K36me3 associated Srsf1 is reduced in Psip1 mutant cells and alternative splicing of specific genes is affected. Moreover, we show altered Srsf1 distribution around the alternatively spliced exons of these genes in Psip1 null cells. We propose that Psip1/p52, through its binding to both chromatin and splicing factors, might act to modulate splicing.

Histone H3K36 methylation regulates pre-mRNA splicing inSaccharomyces cerevisiae

“…This observation suggests that H3K36me3 is mostly dispensable for splicing in S. cerevisiae, a scenario that is different from human cells where H3K36me3, catalyzed by SETD2, is a critical regulator of splicing. [31][32][33][34] However, we note it is formally possible that H3K36me1 may contribute to some splicing functions, as the H199L mutant still contain H3K36me1. Nevertheless, our data suggests that H3K36me2 largely drives most of the splicing phenotypes.…”

“…The idea of direct methyl binding is consistent with recent studies in mammals showing that H3K36me3 by SETD2 is recognized by adapter proteins, which in turn recruits the U2 snRNP or splicing regulatory proteins to pre-mRNA to modulate alternative RNA splicing. [31][32][33] Whether Set2 works directly to recruit the snRNPs via H3K36me or altered chromatin structure remains an interesting question for future studies.…”

“…In metazoa, depletion of SETD2, the chromatin modification enzyme that tri-methylates H3K36 (see below), changes alternative splicing patterns and both tri-methylated H3K4 and tri-methylated H3K36 interact with splicing proteins to recruit them during transcription. [31][32][33][34][35] Thus, histone modifications and the changing chromatin landscape constitute an exciting frontier for splicing regulation that has yet to be fully explored.…”

Multiple cellular proteins interact with LEDGF/p75 through a conserved unstructured consensus motif

“…L ens epithelium-derived growth factor (LEDGF/p75) is an epigenetic reader recognizing H3K36me3 histone marks via its N-terminal PWWP domain 1,2 . Knockout of the gene encoding LEDGF/p75 and its splice variant p52 (Psip1) leads to perinatal mortality and severe homeotic skeletal transformations reminiscent of those seen in mice with Hox mutations 3 .…”

“…Recent work has revealed that LEDGF/p75 is involved in DNA double-strand break (DSB) repair by the homologous recombination repair pathway, through recruitment of C-terminal binding protein interacting protein (CtIP) to DNA DSB 5 . In addition, LEDGF/p52 has been associated with splicing through its interaction with serine/arginine-rich splicing factor 1 (SRSF1) 1,5 . Currently it is not clear whether the previously proposed roles of LEDGF/p75 in apoptosis and stress response, as well as its increased expression levels in different cancer types, are related to one of these functions [6][7][8][9][10][11] .…”