Genome-Wide Distribution of MacroH2A1 Histone Variants in Mouse Liver Chromatin

Abstract

Studies of macroH2A histone variants indicate that they have a role in regulating gene expression. To identify direct targets of the macroH2A1 variants, we produced a genome-wide map of the distribution of macroH2A1 nucleosomes in mouse liver chromatin using high-throughput DNA sequencing. Although macroH2A1 nucleosomes are widely distributed across the genome, their local concentration varies over a range of 100-fold or more. The transcribed regions of most active genes are depleted of macroH2A1, often in sharply localized domains that show depletion of 4-fold or more relative to bulk mouse liver chromatin. We used macroH2A1 enrichment to help identify genes that appear to be directly regulated by macroH2A1 in mouse liver. These genes functionally cluster in the area of lipid metabolism. All but one of these genes has increased expression in macroH2A1 knockout mice, indicating that macroH2A1 functions primarily as a repressor in adult liver. This repressor activity is further supported by the substantial and relatively uniform macroH2A1 enrichment along the inactive X chromosome, which averages 4-fold. Genes that escape X inactivation stand out as domains of macroH2A1 depletion. The rarity of such genes indicates that few genes escape X inactivation in mouse liver, in contrast to what has been observed in human cells.Nucleosomes, as basic structural units of chromatin, are important targets for modifying chromatin structure and function. One source of nucleosomal functional diversity is the substitution of histone variants for conventional histones. The macroH2A core histone variants appear to be present in most or all vertebrates and some deuterostome invertebrates, such as sea urchins. Three macroH2A variants have been identified in mammals. The macroH2A1 variants, macroH2A1.1 and macroH2A1.2, are produced by alternate splicing, and macroH2A2 is produced by a separate gene (8,13,31,34). They all have a full-length histone H2A domain on their N terminus and a C-terminal nonhistone region that primarily consists of a conserved domain called a macrodomain. Macrodomains are found as stand-alone proteins in bacteria and are embedded in other eukaryotic proteins and in proteins involved in the replication of some RNA viruses (2, 32). Some macrodomains bind ADP-ribose and related molecules (26), and a recent study indicates that ADP-ribose binding by macroH2A1.1 can alter chromatin structure (36).We estimated that there is approximately 1 macroH2A for every 30 nucleosomes in rat liver, an organ with relatively high macroH2A1 content and very little macroH2A2 (13, 31). Fluorescence studies showed that these nucleosomes are not uniformly distributed across the chromatin. Notably, macroH2A1 is preferentially localized to the inactive X chromosome (8,13,14), to centromeric chromatin in some cell types (15,22), and to transcriptionally silent senescence-associated heterochromatic foci (39), which suggests a role in repression of gene expression. macroH2A1 knockout mice are viable and fertile and show no obvious pathology...

Mice without MacroH2A Histone Variants

“…These results reinforce our previous finding that macroH2A.1 has a role in regulating metabolism-related genes, especially genes related to lipid metabolism (23,24). Two of the other 5 new genes also have a clear connection to lipid metabolism: Lepr (1.9-fold increase) encodes the receptor for leptin, an adipokine that has a central role in energy homeostasis (37), and Rgs16 (2.3-fold increase) encodes a GTPase-activating protein that can regulate fatty acid and glucose metabolism in the liver (38).…”

“…Our previous study of macroH2A.1 distribution in adult liver found that macroH2A.1 is typically organized in relatively large domains that can be enriched, neutral, or depleted for macroH2A.1 nucleosomes. The transcribed regions of most active genes were strongly depleted of macroH2A.1, while inactive genes showed no strong bias toward depletion or enrichment (24). Our new fetal liver macroH2A.1 map appears consistent with these findings, showing domains of enrichment, neutral domains, and discrete domains of depletion that correspond to genes (Fig.…”

“…Based on the intensity of the core histone and nucleosomal DNA bands seen for these fractions with normal liver, we feel that we would have easily detected 10% contamination of this fraction by nonmacroH2A-containing chromatin fragments. As we have previously discussed (24,28), the presence of conventional H2A in these fractions reflects the interspersion of macroH2A-containing nucleosomes with nucleosomes that contain conventional H2As. In addition, in vitro reconstitution experiments indicate that macroH2A.1 preferentially pairs with conventional H2A in the nucleosome core (39).…”

“…Changes in liver gene expression were seen for a few genes that functionally cluster in the area of metabolism. Most of these genes showed macroH2A.1 enrichment (24), suggesting that they are direct targets of macroH2A.1 nucleosomes. Our results seemed to be inconsistent with the studies that showed dramatic effects on early development and stem cell differentiation.…”

MacroH2A in Stem Cells: A Story Beyond Gene Repression

“…Subsequently, this has been well established in vitro and in vivo by a large body of evidence (reviewed in [15,18]). 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].…”