Developmental Changes in Histone macroH2A1-Mediated Gene Regulation

Abstract

macroH2A histone variants have been implicated to function in gene silencing by several studies, including ones showing a preferential association of macroH2A on the inactive X chromosome. To examine macroH2A function in vivo, we knocked out macroH2A1. macroH2A1 knockout mice are viable and fertile. A broad screen of liver gene expression showed no evidence of defects in X inactivation but did identify genes that have increased expression levels in macroH2A1 knockouts. macroH2A1-containing nucleosomes are enriched on the coding and/or upstream regions of these genes, suggesting that their increased expression levels are a direct effect of the absence of macroH2A1. The concentrations of macroH2A1 nucleosomes on these genes are low in the livers of newborn mice, and the macroH2A1 knockout had little effect on the expression levels of these genes in newborn liver. Our results indicate that an increase in liver macroH2A1 during the transition from newborn to young-adult status contributes to a decrease in the expression levels of these genes. These genes cluster in the area of lipid metabolism, and we observed metabolic effects in macroH2A1 knockouts. Our results indicate that the function of macroH2A1 histones is not restricted to gene silencing but also involves fine tuning the expression of specific genes.The nucleosome is an important target for modifying chromatin functions, including transcription. One mechanism for modifying nucleosome function is the substitution of variant histones for the major or canonical histones. Genetic studies showed that histone variants H2A.X, H2A.Z, CENPA, and H3.3 have important functional properties that cannot be provided by their conventional counterparts (reviewed in reference 24). macroH2A histone variants have an unusual structure, consisting of a full-length H2A domain linked to a large nonhistone domain, producing proteins that are nearly three times the size of conventional core histones (Fig. 1A) (26). macroH2As are highly conserved among vertebrates (1, 27). They appear to be absent from most invertebrates but are present in the sea urchin. The H2A domain of macroH2As is ϳ65% identical to conventional H2As. Most of the nonhistone region appears to be derived from a domain that is found in many contexts (3,27). Recent studies showed that some "macrodomains," including the one from macroH2A1.1, bind ADP ribose (17). The significance of this binding for macroH2A function is not known. There are three macroH2A variants. macroH2A1.1 and 1.2 are formed by alternate splicing of macroH2A1 (gene symbol H2afy), while macroH2A2 is encoded by a separate gene (4,7,26,30). The distributions of macroH2A variants are different in different cell types and change during development (7, 25). The macroH2A1 (1.1 and 1.2) content of adult rat liver chromatin, a relatively rich source of macroH2A1, was estimated to be one for every 30 nucleosomes (26).The distribution of macroH2A in chromatin suggests a role in transcriptional repression. We recently mapped the distribution of macroH2A1, usi...

X chromosome inactivation: A silence that needs to be broken

“…Therefore, mH2A is dispensable in maintaining XCI in somatic cells. In corroboration with this notion, the gene knockout of mH2A1 showed no defects of X chromosome inactivation (Changolkar et al, 2007).…”

A phosphorylated subpopulation of the histone variant macroH2A1 is excluded from the inactive X chromosome and enriched during mitosis

“…Although mH2A is concentrated on the Xi, it is also widely distributed throughout chromatin and localizes to other nuclear domains, exists in vertebrate species that do not undergo X inactivation, and is expressed to similar degrees in males and females (9,33,34). Moreover, whereas mH2A1 knockout mice are viable, fertile, and do not display X inactivation defects (mH2A2 is still present), a set of genes does exhibit increased expression levels during the transition from newborn to young-adult animals (35). This finding suggests that mH2A1 is not restricted to large-scale gene silencing and chromosome inactivation, but it also fine tunes expression levels of specific genes through development.…”

Mammalian cytosine methylation at a glance

“…It is enriched on the inactive X chromosome. There are two macroH2A genes in the mammalian genome, and mice deficient for the more abundant form, MacroH2A1, are viable, fertile and have normal X chromosome inactivation (Changolkar et al, 2007). However, analysis of liver DNA from mutant animals revealed a slight demethylation and reactivation of an LTR retrotransposon (Changolkar et al, 2008).…”