Readout of Epigenetic Modifications

Patel, Dinshaw J.; Wang, Zhanxin

doi:10.1146/annurev-biochem-072711-165700

Cited by 297 publications

(322 citation statements)

References 131 publications

(185 reference statements)

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“…The trimethyl-lysine side chain of Lys4 was positioned within an aromatic-lined surface groove pocket formed by the Trp410 and Trp419 of the CW domain and stabilized by the cation-π interactions (Fig. 3E), similar to other classical methyl-lysine recognition modules (20). In addition, Thr6 of the peptide formed one hydrogen bond with Trp410 of the CW domain.…”

Section: Resultsmentioning

confidence: 70%

Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin

Yen

Pastor

et al. 2016

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

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Microrchidia (MORC) proteins are GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) ATPases that function in gene regulation in multiple organisms. Animal MORCs also contain CW-type zinc finger domains, which are known to bind to modified histones. We solved the crystal structure of the murine MORC3 ATPase-CW domain bound to the nucleotide analog AMPPNP (phosphoaminophosphonic acidadenylate ester) and in complex with a trimethylated histone H3 lysine 4 (H3K4) peptide (H3K4me3). We observed that the MORC3 N-terminal ATPase domain forms a dimer when bound to AMPPNP. We used native mass spectrometry to show that dimerization is ATPdependent, and that dimer formation is enhanced in the presence of nonhydrolyzable ATP analogs. The CW domain uses an aromatic cage to bind trimethylated Lys4 and forms extensive hydrogen bonds with the H3 tail. We found that MORC3 localizes to promoters marked by H3K4me3 throughout the genome, consistent with its binding to H3K4me3 in vitro. Our work sheds light on aspects of the molecular dynamics and function of MORC3.X-ray crystallography | histone mark reader | ATPase | native mass spectrometry T he Microrchidia (MORC) family of ATPase proteins has been shown to be an important regulator of gene silencing in multiple organisms. This family was first described in mice, when it was discovered that morc1 null males showed arrested spermatogenesis (1). This arrest was later shown to be associated with transposon derepression, implicating murine MORC1 as a crucial mediator of transposon silencing (2). Arabidopsis thaliana MORC1 and MORC6 were shown to mediate silencing of transposons in a manner largely independent of changes in DNA methylation (3)(4)(5). Studies in Caenorhabditis elegans, which lack DNA methylation, also concluded that the single MORC gene in this organism plays a role in transgene silencing (4). Although the biological importance of MORC ATPases in enforcing gene silencing across multiple organisms is clear, how they are targeted and how they function are poorly understood.The MORC ATPases share a similar domain arrangement. The N terminus contains a GHKL (gyrase, heat-shock protein 90, histidine kinase, MutL) type ATPase domain, and at the C terminus is a coiled-coil segment. MORCs have been reported to form functional homomultimers or heteromultimers, where multimerization is likely mediated by the N-and/or the C-terminal domains (4, 6, 7). The coiled-coil region has been proposed to promote constitutive dimerization, whereas N-terminal ATPase head dimerization occurs only on ATP binding (6). This is consistent with other GHKL ATPases described in the literature, many of which have been reported to undergo ATP-dependent dimerization (8-10). Both plant and animal MORCs are capable of forming nuclear bodies, and mutations that impair ATP binding and/or hydrolysis disrupt nuclear body formation of human MORC3 (6).Animal MORCs also carry a CW-type zinc finger domain, which has been proposed to read histone H3 lysine 4 (H3K4) dimethylation and trimethylation mark...

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Section: Resultsmentioning

confidence: 70%

Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin

Yen

Pastor

et al. 2016

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

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“…chromatin | ubiquitin | Dot1L | epigenetics | protein chemistry H istone posttranslational modifications (PTMs) modulate chromatin structure and function either by directly altering the intrinsic physical properties of the chromatin fiber or by nucleating the recruitment and activity of a host of transacting nuclear factors (1)(2)(3). The chemical diversity, differential dynamics, and sheer number (currently over 100) (4,5) of these PTMs, along with their combinatorial occurrence at the level of the nucleosome, create a complex and nonstatic molecular architecture in which all chromatin-related processes function.…”

mentioning

confidence: 99%

Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin

Holt

David

Pollock

et al. 2015

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

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Ubiquitylation of histone H2B at lysine 120 (H2B-Ub) plays a critical role in transcriptional elongation, chromatin conformation, as well as the regulation of specific histone H3 methylations. Herein, we report a strategy for the site-specific chemical attachment of ubiquitin to preassembled nucleosomes. This allowed expedited structure-activity studies into how H2B-Ub regulates H3K79 methylation by the methyltransferase human Dot1. Through an alanine scan of the ubiquitin surface, we identified a functional hotspot on ubiquitin that is required for the stimulation of human Dot1 in vitro. Importantly, this result was validated in chromatin from isolated nuclei by using a synthetic biology strategy that allowed selective incorporation of the hotspot-deficient ubiquitin mutant into H2B. The ubiquitin hotspot additionally impacted the regulation of ySet1-mediated H3K4 methylation but was not required for H2B-Ub-induced impairment of chromatin fiber compaction. These data demonstrate the utility of applying chemical ligation technologies to preassembled chromatin and delineate the multifunctionality of ubiquitin as a histone posttranslational modification.H istone posttranslational modifications (PTMs) modulate chromatin structure and function either by directly altering the intrinsic physical properties of the chromatin fiber or by nucleating the recruitment and activity of a host of transacting nuclear factors (1-3). The chemical diversity, differential dynamics, and sheer number (currently over 100) (4, 5) of these PTMs, along with their combinatorial occurrence at the level of the nucleosome, create a complex and nonstatic molecular architecture in which all chromatin-related processes function. A central challenge in the field of epigenetics is to disentangle how distinct chromatin states control biochemical outputs, which requires the elucidation of the critical determinants governing histone PTM readout.A particularly fascinating histone PTM is the ubiquitylation of H2B at lysine 120 (H2B-Ub). H2B-Ub is enriched near the 5′ end of highly expressed genes and has been implicated in transcriptional elongation, as well as chromatin structure definition (6-9). Moreover, H2B-Ub directly regulates the H3K4 and H3K79 methyltransferases Set1 and Dot1, respectively (10-13). The mechanistic principles underlying these various phenomena remain poorly understood. At 8.5 kDa, ubiquitin is nearly as large as the histone to which it is linked (13.8 kDa in the case of H2B), increasing the nucleosome surface by as much as 4,800 A 2 (14). Thus, compared with smaller PTMs such as acetylation and methylation, ubiquitin is "information rich" in that it alters the steric and electrostatic properties around its attachment site, as well as presenting a large surface area for the recruitment of binding factors. Structural and biochemical studies of ubiquitin-ligand complexes, including the ubiquitylation of histone H2A at lysine 15, have revealed a canonical binding hotspot on ubiquitin involving a hydrophobic patch centered on Leu8/I...

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“…It is thought that these writers, erasers, and readers work in concert to establish and regulate histone PTM-mediated functions. Finally, histone modifications can further act in combinations to recruit or repel different binding proteins, or cross-regulate one another through complex pathways [114][115][116]. In this review, we will focus on some of the most recent advances in both well-known and newly discovered histone PTMs (Table 1).…”

Section: Histone Modificationsmentioning

confidence: 99%

“…In this review, we will focus on some of the most recent advances in both well-known and newly discovered histone PTMs (Table 1). Given the broad and complex scope of this field and due to limited space for this review, we refer interested readers to additional reviews for further reading [114][115][116][137][138][139].…”

Section: Histone Modificationsmentioning

confidence: 99%

Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications

2015

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The eukaryotic genome is highly complex and compartmentalized into distinct physical and functional domains. Although the majority of genomic DNA is wrapped around histone proteins in the same manner to form repeating units of nucleosomes, the use of distinct histone variants and the myriad of posttranslational modifications (PTMs) on different histones and amino acid residues create great diversity among these nucleosomes. In this review, we summarize some of the most recent findings in the histone variant and PTM fields and update the readers on our current understanding of various histone-related pathways. Furthermore, we discuss how homotypic or heterotypic deposition of histone variants as well as symmetric or asymmetric histone PTMs within the nucleosome context can further expand the diversity and functionality of chromatin. Altogether, this review highlights the complexity of chromatin composition and organization and their regulatory functions within the eukaryotic genome.

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Readout of Epigenetic Modifications

Cited by 297 publications

References 131 publications

Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin

Mouse MORC3 is a GHKL ATPase that localizes to H3K4me3 marked chromatin

Identification of a functional hotspot on ubiquitin required for stimulation of methyltransferase activity on chromatin

Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications

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