A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation

Nakanishi, Shima; Sanderson, Brian W.; Delventhal, Kym M.; Bradford, W. David; Staehling‐Hampton, Karen; Shilatifard, Ali

doi:10.1038/nsmb.1454

Cited by 179 publications

(236 citation statements)

References 60 publications

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“…Substitution of H3K56 with glutamic acid in yeast caused lethality (supplemental Fig. S9), whereas substitution of the site with alanine or arginine did not change yeast cell viability (19,23). Because histone H3K56 localizes near the nucleosome entry site and is proximate to the DNA double helix, the change of charge from positive to negative at the site by malonylation might interfere with its interaction with DNA, causing the loss of cell viability.…”

Section: Discussionmentioning

confidence: 99%

Lysine Succinylation and Lysine Malonylation in Histones

Xie

Dai

et al. 2012

Molecular & Cellular Proteomics

508

466

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Histone protein post-translational modifications (PTMs) are significant for gene expression and DNA repair. Here we report the identification and validation of a new type of PTM in histones, lysine succinylation. The identified lysine succinylated histone peptides were verified by MS/MS of synthetic peptides, HPLC co-elution, and isotopic labeling. We identified 13, 7, 10, and 7 histone lysine succinylation sites in HeLa, mouse embryonic fibroblast, Drosophila S2, and Saccharomyces cerevisiae cells, respectively. We demonstrated that this histone PTM is present in all eukaryotic cells we examined. Mutagenesis of succinylation sites followed by functional assays implied that histone lysine succinylation can cause unique functional consequences. We also identified one and two histone lysine malonylation sites in HeLa and S. cerevisiae cells, respectively. Our results therefore increase potential combinatorial diversity of histone PTMs and suggest possible new connections between histone biology and metabolism. Molecular & Cellular

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Section: Discussionmentioning

confidence: 99%

Lysine Succinylation and Lysine Malonylation in Histones

Xie

Dai

et al. 2012

Molecular & Cellular Proteomics

508

466

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“…Similarly, cells containing a mutation of any single lysine on the H4 N-tail do not display an obvious DNA replication or chromatin assembly defect (12,13), and prominent transcriptional phenotypes, with the exception of H4K16 (10,14). Furthermore, recent systematic mutagenesis studies demonstrate that, despite the extremely well conserved nature of histone residues throughout different organisms, only a few mutations on the individual residues (including nonmodifiable sites) bring about prominent phenotypic defects (10,15,16).…”

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confidence: 99%

Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast

Kim

Hsu

Smith

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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A large body of literature provides compelling evidence for the role of evolutionarily conserved core histone residues in various biological processes. However, site-directed mutagenesis of individual residues that are known to be sites of posttranslational modifications often does not result in clear phenotypic defects. In some cases, the combination of multiple mutations can give rise to stronger phenotypes, implying functional redundancy between distinct residues on histones. Here, we examined the “histone redundancy hypothesis” by characterizing double deletion of all pairwise combinations of amino-terminal tails (N-tails) from the four core histones encoded in budding yeast. First, we found that multiple lysine residues on the N-tails of both H2A and H4 are redundantly involved in cell viability. Second, simultaneous deletion of N-tails from H2A and H3 leads to a severe growth defect, which is correlated with perturbed gross chromatin structure in the mutant cells. Finally, by combining point mutations on H3 with deletion of the H2A N-tail, we revealed a redundant role for lysine 4 on H3 and the H2A N-tail in hydroxyurea-mediated response. Altogether, these data suggest that the N-tails of core histones share previously unrecognized, potentially redundant functions that, in some cases are different from those of the widely accepted H2A/H2B and H3/H4 dimer pairs.

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“…Studies have suggested that sprocket arginine-DNA contacts may play an important role in the rotational positioning of nucleosomes (Luger et al 1997;Harp et al 2000;Rohs et al 2009;Wang et al 2010;West et al 2010). For example, short poly(A) stretches narrow the DNA minor groove, potentially enhancing electrostatic interactions between the DNA phosphate backbone and the sprocket arginine (Rohs et al 2009;West et al 2010).While sprocket arginine residues appear to have unique and important roles in DNA binding and are highly conserved among eukaryotic species, mutational screens in yeast revealed that only one of these arginine residues, H4 R45, is essential for cell viability (Matsubara et al 2007;Dai et al 2008;Nakanishi et al 2008) (Figure 1B Mutations in the H4 R45 residue (H4 R45C and H4 R45H) were originally isolated from a yeast genetic screen for switch-independent (sin) mutants (Kruger et al 1995). Expression of the H4 R45C (or R45H) mutant partially alleviates the requirement for the SWI/SNF remodeling complex to activate the expression of the yeast homothallic switching endonuclease (HO) gene.…”

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confidence: 99%

Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability inSaccharomyces cerevisiae

Hodges

Gallegos

Laughery³

et al. 2015

Genetics

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A critical feature of the intermolecular contacts that bind DNA to the histone octamer is the series of histone arginine residues that insert into the DNA minor groove at each superhelical location where the minor groove faces the histone octamer. One of these "sprocket" arginine residues, histone H4 R45, significantly affects chromatin structure in vivo and is lethal when mutated to alanine or cysteine in Saccharomyces cerevisiae (budding yeast). However, the roles of the remaining sprocket arginine residues (H3 R63, H3 R83, H2A R43, H2B R36, H2A R78, H3 R49) in chromatin structure and other cellular processes have not been well characterized. We have genetically characterized mutations in each of these histone residues when introduced either singly or in combination to yeast cells. We find that pairs of arginine residues that bind DNA adjacent to the DNA exit/entry sites in the nucleosome are lethal in yeast when mutated in combination and cause a defect in histone occupancy. Furthermore, mutations in individual residues compromise repair of UV-induced DNA lesions and affect gene expression and cryptic transcription. This study reveals simple rules for how the location and structural mode of DNA binding influence the biological function of each histone sprocket arginine residue.KEYWORDS nucleotide excision repair; cryptic transcription; nucleosome; histone assembly T HE histone octamer, which is composed of two copies each of histones H2A, H2B, H3, and H4, binds with high affinity to $147 bp of DNA to form the nucleosome core particle. Histone-DNA binding is mediated by .100 histone main-chain and side-chain interactions with the DNA sugarphosphate backbone and a similar number of indirect water-mediated interactions (Davey et al. 2002;Muthurajan et al. 2003). These interactions occur primarily at 14 locations in the nucleosome structure where the DNA minor groove faces the histone octamer [superhelical locations (SHL) 26.5 to 6.5] (Luger et al. 1997). At each of these locations, an arginine side chain extends into the DNA minor groove and makes extensive contacts with the DNA backbone ( Figure 1A).We will refer to the arginine residues that insert into the DNA minor groove as "sprocket" arginines, since they engage the DNA "chain" like the teeth of a bicycle sprocket wheel. Sprocket arginine residues are highly conserved (Muthurajan et al. 2003;Sullivan and Landsman 2003), and the insertion of sprocket arginine side chains into the DNA minor groove comprises a significant fraction of the solvent accessible surface area that is buried upon histone-DNA binding (Davey et al. 2002). Studies have suggested that sprocket arginine-DNA contacts may play an important role in the rotational positioning of nucleosomes (Luger et al. 1997;Harp et al. 2000;Rohs et al. 2009;Wang et al. 2010;West et al. 2010). For example, short poly(A) stretches narrow the DNA minor groove, potentially enhancing electrostatic interactions between the DNA phosphate backbone and the sprocket arginine (Rohs et al. 2009;West et al. 201...

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A comprehensive library of histone mutants identifies nucleosomal residues required for H3K4 methylation

Cited by 179 publications

References 60 publications

Lysine Succinylation and Lysine Malonylation in Histones

Lysine Succinylation and Lysine Malonylation in Histones

Mutagenesis of pairwise combinations of histone amino-terminal tails reveals functional redundancy in budding yeast

Histone Sprocket Arginine Residues Are Important for Gene Expression, DNA Repair, and Cell Viability inSaccharomyces cerevisiae

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