The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing

Abstract

MacroH2A1 is a histone variant that is enriched on the inactive X chromosome (Xi) in mammals and is postulated to play an important, but unknown, role in the repression of gene expression. Here we show that, although macroH2A1 marks repressed autosomal chromatin, it positively regulates transcription when located in the transcribed regions of a subset of its target genes. We used chromatin immunoprecipitation (ChIP) coupled with tiling microarrays (ChIP–chip) to determine the genomic localization of macroH2A1 in IMR90 human primary lung fibroblasts and MCF-7 breast cancer cells. The patterns of macroH2A1 deposition are largely similar across the autosomes of both cell lines. Our studies revealed a genomic localization pattern unique among histone variants; namely, the occupation by macroH2A1 of large chromatin domains (>500 kb in some cases) that contain repressive chromatin marks (e.g., histone H3 Lys 27 trimethylation). The boundaries of macroH2A1-containing domains tend to occur in promoter-proximal regions. Not all promoters, however, serve as macroH2A1 boundaries; many macroH2A1-containing chromatin domains invade the transcribed regions of genes whose products play key roles in development and cell–cell signaling. Surprisingly, the expression of a subset of these genes is positively regulated by macroH2A1. MacroH2A1 also plays a role in augmenting signal-regulated transcription, specifically for genes responsive to serum starvation. Collectively, our results document an unexpected role for macroH2A1 in the escape from heterochromatin-associated silencing and the enhancement of autosomal gene transcription.

MacroH2A in Stem Cells: A Story Beyond Gene Repression

“…Both studies, however, also pointed out that a small number of genes are expressed while harboring macroH2A nucleosomes on the promoter and/or the transcription start site proximal transcribed region. Moreover, Gamble et al further demonstrated that macroH2A is required for inducible activation of a set of target genes [41], thereby corroborating and extending on the earlier observation that macroH2A1.1 was required for the heat shock-mediated activation of Hsp70.1 [42]. In addition, many of the differentiation genes that were not fully activated in macroH2A1-deficient ES cells were also enriched for macroH2A in undifferentiated cells.…”

“…In mouse liver chromatin, for instance, macroH2A1 was found to be depleted from the transcribed regions of most active genes [39,40]. Two other genome-wide studies later confirmed in other cell types that macroH2A occupancy had a general negative correlation with transcriptional future science group activity [28,41]. Both studies, however, also pointed out that a small number of genes are expressed while harboring macroH2A nucleosomes on the promoter and/or the transcription start site proximal transcribed region.…”

Histone variants: dynamic punctuation in transcription

“…In vivo, macroH2A is enriched on the transcriptionally inactivated female X chromosome, senescence-associated heterochromatic foci (SAHF), and large transcriptionally silent domains (Costanzi and Pehrson 1998;Zhang et al 2005;Gamble et al 2010;Tolstorukov et al 2012). macroH2A localization to the inactive X is disrupted when Xist RNA is deleted, suggesting a role for this essential cisregulatory RNA in macroH2A recruitment (Csankovszki et al 1999).…”

“…3). macroH2A macroH2A localization on the inactivated female X chromosome, silent SAHF, and large transcriptionally silent domains (Costanzi and Pehrson 1998;Zhang et al 2005;Gamble et al 2010;Tolstorukov et al 2012) suggests a role in transcriptional repression, although macroH2A is not required for X-chromosome inactivation (Changolkar et al 2007). Genome-wide studies in human NT2 cells have shown that macroH2A is enriched at developmentally regulated genes, including overlap with the PRC2 complex.…”

Random deposition of histone variants: A cellular mistake or a novel regulatory mechanism?

“…While macroH2A is highly enriched on the inactive X chromosome, 57 H2A-Bbd is depleted from this chromosome. In addition, macroH2A associates with several inactive promoters, 58,59 whether H2A-Bbd is expected to be found on active genes. 60 Because H2A.Z is found on active promoters, it will be very interesting to characterize the dynamics and interrelations between these three H2A variants.…”