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Histone variants replace the core histones in a substantial fraction of nucleosomes, affecting chromatin structure and impacting chromatin-templated processes. In many instances incorporation of histone variants results in formation of specialized regions of chromatin. Proper localization of histone variants to distinct regions of the genome is critical for their function, yet how this specific localization is achieved remains unclear. MacroH2A1 is enriched on the inactive X chromosome in female mammalian cells, where it functions to maintain gene silencing. MacroH2A1 consists of a histone H2A-like histone domain and a large, globular C-terminal macro domain that is not present in other histone proteins. The histone domain of macroH2A1 is alone sufficient to direct enrichment on the inactive X chromosome when expressed in female cells, indicating that sequences important for correct localization lie in this domain. Here we investigate whether divergent sequences of the H2A variant macroH2A1 contribute to its correct localization. We mapped the regions of the macroH2A1 histone domain that are sufficient for localization to the inactive X chromosome using chimeras between H2A and the histone domain of macroH2A1. Multiple short sequences dispersed along the macroH2A1 histone domain individually supported enrichment on the inactive X chromosome when introduced into H2A. These sequences map to the surface of the macroH2A1/H2B dimer, but are buried in the crystal structure of the macroH2A1 containing nucleosome, suggesting that they may contribute to recognition by macroH2A1/H2B deposition factors.
MacroH2A, H2A, chromatin assembly, histone variants, X inactivation
The histone domain of macroH2A1 contains several dispersed elements that are each sufficient to direct enrichment on the inactive X chromosome
Dmitri A. Nusinow,1 Judith A. Sharp,1 Alana Morris,1 Sonia Salas,1 Kathrin Plath,2 and Barbara Panning1,†
2009 Jun 25.
A gene encoding a protein that shows sequence similarity with the histone H1 family only was cloned in Ascobolus immersus. The deduced peptide sequence presents the characteristic three-domain structure of metazoan linker histones, with a central globular region, an N-terminal tail, and a long positively charged C-terminal tail. By constructing an artificial duplication of this gene, named H1, it was possible to methylate and silence it by the MIP (methylation induced premeiotically) process. This resulted in the complete loss of the Ascobolus H1 histone. Mutant strains lacking H1 displayed normal methylation-associated gene silencing, underwent MIP, and showed the same methylation-associated chromatin modifications as did wild-type strains. However, they displayed an increased accessibility of micrococcal nuclease to chromatin, whether DNA was methylated or not, and exhibited a hypermethylation of the methylated genome compartment. These features are taken to imply that Ascobolus H1 histone is a ubiquitous component of chromatin which plays no role in methylation-associated gene silencing. Mutant strains lacking histone H1 reproduced normally through sexual crosses and displayed normal early vegetative growth. However, between 6 and 13 days after germination, they abruptly and consistently stopped growing, indicating that Ascobolus H1 histone is necessary for long life span. This constitutes the first observation of a physiologically important phenotype associated with the loss of H1.
In mammals, methylation of CpG islands correlates with loss of gene expression (2). In plants, hypermethylation accompanies gene silencing (52), while silenced genes which recover expression in mutants unable to maintain silencing lose methylation (32). In the fungus Ascobolus immersus, repeated genes are methylated and silenced by a process named MIP (methylation induced premeiotically) that takes place during sexual reproduction (43). In Neurospora crassa, a related process, named RIP (repeat-induced point mutation), leads to a concomitant hypermethylation and hypermutation of the DNA repeats (47). In the latter situation, methylation may spread to an unmutated neighboring gene which becomes silenced as well, suggesting that methylation without mutation may be sufficient to initiate gene silencing (20). It has been shown that methyl-binding proteins recognizing methylated CpG’s play an important role in the methylation-associated silencing in vertebrates (33). The methyl-CpG-binding protein MeCP2 can nucleate a complex containing deacetylases which remove acetyl moieties from lysine residues in the core histones H3 and H4 (41), resulting in a repressive nucleosomal array. In Neurospora, a connection has also been established between methylation, deacetylation, and gene silencing (48).
Methylated groups may directly prevent the binding of transcription factors to DNA (23). Methylation could also induce the formation of a silenced higher-order chromatin structure. Methylated DNA was found to be preferentially assembled in nuclease-resistant chromatin after transfection of mouse L cells (24). A ubiquitous component of chromatin might interact preferentially with methylated DNA, thereby stabilizing the higher order of chromatin structure and preventing gene expression.
Linker histones, which bind to linker DNA extending between nucleosomes, have been proposed as potential candidates for playing that role. Linker histones, such as H1, are known to seal nucleosomes, therefore stabilizing a higher order of chromatin structure (54). Histone H1 is abundant in nuclease-resistant, inactive chromatin (57), and it inhibits in vitro transcription (7, 59). Metazoan linker histones have a three-domain structure, with a central globular domain flanked by N- and C-terminal tails rich in basic residues (18). The amino acid sequence of the globular domain is the most conserved region. The basic C-terminal tail is rich in lysine, serine, proline, and alanine and is likely to be involved in the interaction with linker DNA, neutralizing its charge and facilitating chromatin condensation (1). In animals, linker histones show extensive diversification. Various subtypes display different DNA and chromatin-condensing properties in vitro (25). In addition, they exhibit highly regulated patterns of expression during development and differentiation (26).
Several studies aimed at investigating the possibility of a preferential binding of linker histones to methylated DNA have been performed, but the overall results remain inconclusive. In the mouse, 5-methylcytosine was reported to be preferentially located in nucleosomes that contain histone H1 (3). A chicken H1-like protein, MDBP-2, was reported to selectively bind methylated DNA both in vivo and in vitro (21). Further in vitro studies led to contradictory results. While H1 was reported by McArthur and Thomas (31) to bind preferentially to methylated DNA, Campoy et al. (5) and Nightingale and Wolffe (35) concluded that binding of H1 was indifferent to methylation in chromatin reconstitution experiments. It is difficult to make decisive conclusions from these in vitro studies, since factors playing an important role in the assembly of cellular chromatin may be missing in these assays.
A major contribution to understanding the structural and functional roles of linker histones in vivo came from experiments with Xenopus laevis. Extracts from Xenopus eggs depleted of histone B4, the only linker histone present in these eggs, retained the capacity to assemble chromatin from sperm nuclei, to initiate replication, and to condense their chromosomes (36). This finding indicates that linker histones facilitate the in vitro folding of nucleosomal arrays but are not required for chromatin and chromosome assembly. In somatic cells of Xenopus, histone H1 was shown to function as a developmentally regulated gene repressor acting specifically on the set of embryonic 5S RNA genes (4, 22, 46) and mesoderm-specific genes (53). In the case of 5S RNA genes, molecular studies indicated that the repressive effect of histone H1 is related to differential nucleosome positioning (38, 49).
In the unicellular eukaryotes Saccharomyces cerevisiae and Tetrahymena thermophila, putative linker histone genes encoding unusual products have been characterized. The S. cerevisiae candidate H1 histone contains two globular domains (27, 56), while that from Tetrahymena lacks the globular domain (61). In contrast, Ramon et al. recently characterized an H1 gene encoding a canonic linker histone in the filamentous fungus Aspergillus nidulans (40). S. cerevisiae, Tetrahymena, and A. nidulans cells lacking linker histones are viable and display normal growth (37, 40, 61). In A. nidulans, the nucleosomal organization of a number of promoters was shown to be identical in a wild-type strain and in a strain harboring a complete deletion of the H1 gene (40). Knocking out the S. cerevisiae linker histone gene had little effect on gene expression (37, 56). In particular, genes silenced as a consequence of their telomeric location were not activated in mutants devoid of histone H1. Deletion of the H1 gene expressed in the macronucleus of Tetrahymena did not affect transcription, except for a small subset of genes that were either activated or repressed (50). This again suggests that linker histones do not play a general role in gene repression and gene silencing but can occasionally interact with some specific gene targets to modulate their expression. However, these data provide no information on a possible role of linker histone in methylation-associated gene silencing, since S. cerevisiae, Tetrahymena, and A. nidulans do not display cytosine methylation.
The filamentous fungus Ascobolus immersus represents an attractive, well-characterized experimental system with which to test in vivo by a genetic approach the possible interaction between linker histones, methylated DNA, and gene silencing. This organism displays DNA methylation, and MIP provides a convenient tool to methylate and silence at will endogenous genes (10, 13, 43). The cloning and characterization of the H1-like gene from Ascobolus, henceforth named H1, allowed us to inactivate the expression of this gene and to construct strains lacking Ascobolus histone H1. We showed that this histone is not required for methylation-associated gene silencing and protects methylated and unmethylated chromatin equally well against micrococcal nuclease (MNase) digestion. Its loss results in three clear-cut phenotypes: hypermethylation, increased accessibility of MNase to chromatin, and reduced life span.
Histone H1 Is Dispensable for Methylation-Associated Gene Silencing in Ascobolus immersus and Essential for Long Life Span
Jose L. Barra,† La?la Rhounim,‡ Jean-Luc Rossignol, and Godeleine Faugeron*
Chromatin assembly is required for the duplication of chromosomes. ACF (ATP-utilizing chromatin assembly and remodeling factor) catalyzes the ATP-dependent assembly of periodic nucleosome arrays in vitro, and consists of Acf1 and the ISWI ATPase. Acf1 and ISWI are also subunits of CHRAC (chromatin accessibility complex), whose biochemical activities are similar to those of ACF. Here we investigate the in vivo function of the Acf1 subunit of ACF/CHRAC in Drosophila. Although most Acf1 null animals die during the larval-pupal transition, Acf1 is not absolutely required for viability. The loss of Acf1 results in a decrease in the periodicity of nucleosome arrays as well as a shorter nucleosomal repeat length in bulk chromatin in embryos. Biochemical experiments with Acf1-deficient embryo extracts further indicate that ACF/CHRAC is a major chromatin assembly factor in Drosophila. The phenotypes of flies lacking Acf1 suggest that ACF/CHRAC promotes the formation of repressive chromatin. The acf1 gene is involved in the establishment and/or maintenance of transcriptional silencing in pericentric heterochromatin and in the chromatin-dependent repression by Polycomb group genes. Moreover, cells in animals lacking Acf1 exhibit an acceleration of progression through S phase, which is consistent with a decrease in chromatin-mediated repression of DNA replication. In addition, acf1 genetically interacts with nap1, which encodes the NAP-1 nucleosome assembly protein. These findings collectively indicate that ACF/CHRAC functions in the assembly of periodic nucleosome arrays that contribute to the repression of genetic activity in the eukaryotic nucleus.
ACF, ISWI, CHRAC, chromatin assembly, position-effect variegation, cell cycle
Acf1 confers unique activities to ACF/CHRAC and promotes the formation rather than disruption of chromatin in vivo
Dmitry V. Fyodorov,1,3,6 Michael D. Blower,2,4,6 Gary H. Karpen,2,5 and James T. Kadonaga1,7
2004 Jan 15