Molecular Basis of the Interaction of Saccharomyces cerevisiae Eaf3 Chromo Domain with Methylated H3K36

Sun, Bingfa; Hong, Jing; Zhang, Peng; Dong, Xiao; Shen, Xu; Lin, Donghai; Ding, Jianping

doi:10.1074/jbc.m806564200

Cited by 60 publications

(65 citation statements)

References 45 publications

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“…H3K36me3 and H4K20me3, both of which are recognized by MRG15, were not changed by lack of MRG15, indicating that MRG15 is not essential for meiotic homologous recombination (SI Appendix, Fig. S3) (25,26).…”

Section: Spermatids (mentioning

confidence: 99%

MRG15 is required for pre-mRNA splicing and spermatogenesis

Iwamori

Tominaga

Sato

et al. 2016

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

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Splicing can be epigenetically regulated and involved in cellular differentiation in somatic cells, but the interplay of epigenetic factors and the splicing machinery during spermatogenesis remains unclear. To study these interactions in vivo, we generated a germline deletion of MORF-related gene on chromosome 15 (MRG15), a multifunctional chromatin organizer that binds to methylated histone H3 lysine 36 (H3K36) in introns of transcriptionally active genes and has been implicated in regulation of histone acetylation, homology-directed DNA repair, and alternative splicing in somatic cells. Conditional KO (cKO) males lacking MRG15 in the germline are sterile secondary to spermatogenic arrest at the round spermatid stage. There were no significant alterations in meiotic division and histone acetylation. Specific mRNA sequences disappeared from 66 germ cell-expressed genes in the absence of MRG15, and specific intronic sequences were retained in mRNAs of 4 genes in the MRG15 cKO testes. In particular, introns were retained in mRNAs encoding the transition proteins that replace histones during sperm chromatin condensation. In round spermatids, MRG15 colocalizes with splicing factors PTBP1 and PTBP2 at H3K36me3 sites between the exons and single intron of transition nuclear protein 2 (Tnp2). Thus, our results reveal that MRG15 is essential for premRNA splicing during spermatogenesis and that epigenetic regulation of pre-mRNA splicing by histone modification could be useful to understand not only spermatogenesis but also, epigenetic disorders underlying male infertile patients.infertility | fertility defects | splicing defects | epigenetics | spermiogenesis S permatogenesis is a complex process involving several biological events and dramatic changes of chromatin structure. Male germ cells undergo stem cell self-renewal, mitotic divisions in spermatogonial proliferation, genomic rearrangement by meiotic homologous recombination at the spermatocyte stage, and morphological changes of round spermatids into elongated spermatids to form mature spermatozoa (1-3). During spermiogenesis, nucleosomal histone proteins are replaced with transition nuclear proteins (TNPs) and subsequently, protamines, the major nucleosomal proteins in spermatozoa. Moreover, epigenetic modifications, such as histone methylation, dramatically change throughout spermatogenesis (3, 4).Pre-mRNA splicing generates protein diversity and is involved in the regulation of cellular differentiation (5, 6). Recent advances have shown that histone modifications regulate alternative splicing through recruitment of splicing regulators via chromatin binding proteins, such as MORF-related gene on chromosome 15 (MRG15) (7). Histone H3 lysine 36 (H3K36) is methylated proximal to tissuespecific splicing regions (8-12). MRG15 specifically recognizes the methylated H3K36 and recruits polypyrimidine tract binding protein (PTB) at intronic splicing silencer elements near an exon to suppress exon insertions into mRNA (7). MRG15 is also a component of histone acetyltransfe...

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Section: Spermatids (mentioning

confidence: 99%

MRG15 is required for pre-mRNA splicing and spermatogenesis

Iwamori

Tominaga

Sato

et al. 2016

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

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“…With the exception of the PHD finger, all of these domains are members of the Tudor domain "Royal Family," which are characterized by hydrophobic cavities made up of 2 to 4 aromatic residues that bind methylated ligands (17). In yeast, numerous proteins have been shown to specifically interact with methylated H3K4; however, only one protein, Eaf3, has been demonstrated to preferentially interact with methylated histone H3K36 (3,10,12,16,29,34). Thus, the downstream functions triggered by H3K36 methylation are largely unexplored.…”

mentioning

confidence: 99%

Histone H3 Lysine 36 Methylation Targets the Isw1b Remodeling Complex to Chromatin

Maltby

Martin

Schulze

et al. 2012

Molecular and Cellular Biology

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bHistone H3 lysine 36 methylation is a ubiquitous hallmark of productive transcription elongation. Despite the prevalence of this histone posttranslational modification, however, the downstream functions triggered by this mark are not well understood. In this study, we showed that H3K36 methylation promoted the chromatin interaction of the Isw1b chromatin-remodeling complex in Saccharomyces cerevisiae. Similar to H3K36 methylation, Isw1b was found at the mid-and 3= regions of transcribed genes genome wide, and its presence at active genes was dependent on H3K36 methylation and the PWWP domain of the Isw1b subunit, Ioc4. Moreover, purified Isw1b preferentially interacted with recombinant nucleosomes that were methylated at lysine 36, and this interaction also required the Ioc4 PWWP domain. While H3K36 methylation has been shown to regulate the binding of numerous factors, this is the first time that it has been shown to facilitate targeting of a chromatin-remodeling complex. Chromatin, a nucleoprotein structure that packages DNA in all eukaryotes, serves as a barrier to numerous nuclear processes, such as transcription, replication, and DNA repair. Numerous mechanisms exist for alteration of chromatin structure, including histone posttranslational modifications, the incorporation of histone variants, and the activity of chromatin-remodeling complexes. There are many examples of these processes functioning in the same pathway, such as histone acetylation, which promotes the binding of the RSC and SWI/SNF remodeling complexes to chromatin (7, 11).Chromatin-remodeling complexes are multisubunit complexes that use the hydrolysis of ATP to disrupt histone-DNA contacts, promoting octamer sliding and histone eviction. Isw1b, a chromatin-remodeling complex found in Saccharomyces cerevisiae, consists of three subunits: Isw1, Ioc2, and Ioc4 (31). This complex localizes to the transcribed regions of genes, where it has been implicated in transcription elongation, termination, and pre-mRNA processing (19). While there have been some insights into how the Isw1b complex functions, how it is targeted to specific regions of the genome is unknown.Transcriptionally active genes are packaged with histones that are mono-, di-, or trimethylated on lysines 4 and 36 of histone H3. Lysine 4 methylation is catalyzed by Set1 as part of the COMPASS complex, which is targeted to transcribed genes through interaction with RNA polymerase II (RNAP II) during the early stages of transcription elongation (26). Lysine 36 methylation is generated by the histone methyltransferase Set2, which similarly interacts with elongating RNAP II, albeit at later stages of elongation. Consistent with the differential interactions of Set1 and Set2 with the various forms of elongating RNAP II, lysine 4 trimethylation (H3K4me3) is predominantly found at the 5= ends of transcribed genes, while lysine 36 di-and trimethylation (H3K36me2 and H3K36me3) are found in the mid-and 3= regions (26).Histone methylation is proposed to act as a docking site for proteins that m...

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“…However, the CBD of hMRG15 was previously reported to bind H3K36Me 3 , although binding of methylated H4K20 peptides to MRG15 was not tested in that study (41). Similar binding studies on the related yeast Eaf3 CBD also reported preferential binding to H3K36Me 2 or H3K36Me 3 (56,57), but one of the studies also suggested that H4-based peptides bound nearly as well (57). Given the high degree of structural similarity between the hMSL3 and hMRG15 CBDs, we therefore measured the in vitro binding of methylated histone tail sequences to the dMRG15 CBD to see if there was any similarity with the MSL3 CBD binding profile.…”

Section: An Aromatic Cage Methyllysine Binding Pocket In Hmsl3-mentioning

confidence: 63%

“…S3). Similar to the CBD of MRG15 and other tudor and chromo-barrel domains (41,(53)(54)(55)(56)(57), a canonical methyllysine binding pocket is evident at one end of the hMSL3 ␤-barrel domain, with important residues coming from surface loops between strands ␤ 1 -␤ 2 and ␤ 3 -␤ 4 ( Figs. 1 and 2).…”

Section: Tertiary Structure Of the Hmsl3 Chromo-barrel Domain-mentioning

confidence: 99%

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Structural and Biochemical Studies on the Chromo-barrel Domain of Male Specific Lethal 3 (MSL3) Reveal a Binding Preference for Mono- or Dimethyllysine 20 on Histone H4

Moore

Ferhatoglu

Jia

et al. 2010

Journal of Biological Chemistry

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We have determined the human male specific lethal 3 (hMSL3) chromo-barrel domain structure by x-ray crystallography to a resolution of 2.5 Å (r ‫؍‬ 0.226, R free ‫؍‬ 0.270). hMSL3 contains a canonical methyllysine binding pocket made up of residues Tyr-31, Phe-56, Trp-59, and Trp-63. A six-residue insertion between strands ␤ 1 and ␤ 2 of the hMSL3 chromobarrel domain directs the side chain of Glu-21 into the methyllysine binding pocket where it hydrogen bonds to the NH group of a bound cyclohexylamino ethanesulfonate buffer molecule, likely mimicking interactions with a histone tail dimethyllysine residue. In vitro binding studies revealed that both the human and Drosophila MSL3 chromo-barrel domains bind preferentially to peptides representing the mono or dimethyl isoform of lysine 20 on the histone H4 N-terminal tail (H4K20Me 1 or H4K20Me 2 ). Mutation of Tyr-31 to Ala in the hMSL3 methyllysine-binding cage resulted in weaker in vitro binding to H4K20Me 1 . The same mutation in the msl3 gene compromised male survival in Drosophila. Combined mutation of Glu-21 and Pro-22 to Ala in hMSL3 resulted in slightly weaker in vitro binding to H4K20Me 1 , but the corresponding msl3 mutation had no effect on male survival in Drosophila. We propose MSL3 plays an important role in targeting the male specific lethal complex to chromatin in both humans and flies by binding to H4K20Me 1 . Binding studies on the related dMRG15 chromo-barrel domain revealed that MRG15 prefers binding to H4K20Me 3 . Nuclear histone acetyltransferase (HAT)3 enzymes are found in multiprotein complexes that acetylate specific lysine residues on the N-terminal tails of histone proteins, thereby regulating nucleosome structure, chromatin packaging, and gene expression (1-15). MOF, a conserved member of the MYST (Moz, Ysb2, Sas2, Tip60) family of HAT enzymes, functions as the catalytic subunit in a number of distinct HAT complexes that target gene promoters (8), large contiguous domains of chromatin (3, 4, 14, 15), or non-histone proteins such as p53 (5-7). The precise targeting and substrate specificity of MOF relies on the presence of components distinct from the catalytic subunit (3,4,7,8). Specifically, in the MOFcontaining Drosophila male specific lethal (MSL) complex, the MSL3 protein is required for chromatin targeting, nucleosome binding, histone tail substrate recognition, and maximal MOF HAT activity (16 -20).The most well studied MOF-containing complex is the Drosophila melanogaster male specific lethal or MSL complex that binds selectively to large regions of the X-chromosome in male flies (14,15,(21)(22)(23)(24)(25)(26) where it is enriched at the 3Ј ends of actively transcribed genes (27-30) and acetylates lysine 16 on histone H4 (H4K16Ac) (22, 31), thereby balancing male Xchromosomal gene expression. The Drosophila MSL complex contains the dMSL1, dMSL2, and dMSL3 proteins, the RNA/ DNA helicase MLE, the HAT enzyme MOF, and one of two apparently functionally redundant non-coding RNAs (roX1 and roX2) (reviewed in Refs. 14, 15, and 21). The...

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Molecular Basis of the Interaction of Saccharomyces cerevisiae Eaf3 Chromo Domain with Methylated H3K36

Cited by 60 publications

References 45 publications

MRG15 is required for pre-mRNA splicing and spermatogenesis

MRG15 is required for pre-mRNA splicing and spermatogenesis

Histone H3 Lysine 36 Methylation Targets the Isw1b Remodeling Complex to Chromatin

Structural and Biochemical Studies on the Chromo-barrel Domain of Male Specific Lethal 3 (MSL3) Reveal a Binding Preference for Mono- or Dimethyllysine 20 on Histone H4

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