Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate

Girish, Taverekere S.; McGinty, Robert K.; Tan, Song

doi:10.1016/j.jmb.2016.02.025

Cited by 29 publications

(58 citation statements)

References 45 publications

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“…Only a handful of chromatin-binding protein-NCP structures have been determined by X-ray crystallography (Barbera et al, 2006;Makde et al, 2010;Armache et al, 2011;McGinty et al, 2014;Girish et al, 2016;Morgan et al, 2016;Fang et al, 2016;Zhou et al, 2015). All structures to date utilize multiple elements of the surface of the NCP to garner nucleosomal specificity and affinity, engaging in a multivalent manner.…”

Section: Using Single-particle Em To Study Ncp Interactorsmentioning

confidence: 99%

Cryo-electron microscopy of chromatin biology

Wilson

Costa

2017

Acta Cryst Sect D Struct Biol

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The basic unit of chromatin, the nucleosome core particle (NCP), controls how DNA in eukaryotic cells is compacted, replicated and read. Since its discovery, biochemists have sought to understand how this protein-DNA complex can help to control so many diverse tasks. Recent electron-microscopy (EM) studies on NCP-containing assemblies have helped to describe important chromatin transactions at a molecular level. With the implementation of recent technical advances in single-particle EM, our understanding of how nucleosomes are recognized and read looks to take a leap forward. In this review, the authors highlight recent advances in the architectural understanding of chromatin biology elucidated by EM.

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Section: Using Single-particle Em To Study Ncp Interactorsmentioning

confidence: 99%

Cryo-electron microscopy of chromatin biology

Wilson

Costa

2017

Acta Cryst Sect D Struct Biol

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“…21 Together with structural models of the Set8-nucleosome complex 22 we conclude that Set8 accesses both faces of the nucleosome, and thus both H4 tails independently. Thus, Set8 has an intrinsic propensity to produce asH4K20me1 nucleosomes, as observed in ES cells (Fig.…”

Section: Suv39h1mentioning

confidence: 54%

Controlling the supramolecular assembly of nucleosomes asymmetrically modified on H4

2017

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In stem cells, H4 proteins carrying different modifications coexist within single nucleosomes. For functional studies, we report the synthesis of such asymmetric nucleosomes. Asymmetry is achieved by transiently crosslinking H4 by a traceless, protease-removable tag introduced via an isopeptide linkage. These nucleosomes are used to study Set8 activity, a key methyltransferase.Nucleosomes, the basic unit of chromatin, organize 147 bp of DNA wrapped around two of each core histone H3, H4, H2A and H2B.1 The histone proteins carry combinations of post-translational modifications (PTMs, or marks), which are implicated in regulating chromatin function. 2 In particular, methylation of lysine residues on H3 and H4 has clearly defined roles in gene activation and repression, with implication for cell differentiation, development and disease. 3Detailed MS studies found that key methyl-marks in embryonic stem cells (ESCs) exist in asymmetric nucleosomes, i.e. nucleosomes carrying two differently modified copies of H3 or H4. 4 These PTMs include H4 monomethylated at lysine 20 (H4K20me1), as well as H3K4me3, H3K36me3 and H3K27me3. 5 H4K20 methylation is a critical modification involved in heterochromatin silencing, and also in DNA replication and the DNA damage response. 6 The methyltransferase Set8 (also known as PR-Set7 or KMT5A) is responsible for H4K20 monomethylation, whereas two further methyltransferases, Suv4-20h1 and Suv4-20h2, catalyze di-and trimethylation of this residue. 6 Together, H4K20 methylation is involved in chromatin structure regulation, 7 and serves as a binding site for chromatin regulators, including 53BP1 8 and L3MBTL1. The establishment, maintenance and function of nucleosomes asymmetrically modified on H4 is not well understood. This is mainly due to the fact that such nucleosomes are not easily available for detailed in vitro mechanistic studies. Here, we thus developed a synthetic strategy enabling the traceless synthesis of nucleosomes containing differentially modified H4 proteins, with a focus on H4K20me1. While expressed protein ligation (EPL) methods readily enable the installation of combinations of marks on nucleosomes, 10 the reconstitution of asymmetric chromatin is not straightforward and is largely based on the attachment of affinity tags, followed by multi-step purification schemes. 4,11 We recently developed a chemical method to address this problem and control supramolecular nucleosome assembly. 12 Our synthetic approach was based on the inclusion of a link-and-cut (lnc)-tag that enabled transient crosslinking (by a disulfide bond) of H3 species during nucleosome reconstitution. This allowed us to synthesize asymmetrically modified nucleosomes, carrying H3K4me3 and H3K27me3 on different H3 copies. 12 After the formation of nucleosomes, the crosslink was reversed and the lnc-tag was removed using tobacco etch virus (TEV) protease (Scheme 1A-C).Based on these studies, we thus wondered if our synthetic method could be adapted to synthesize crosslinked versions of differentially mo...

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“…coli)b y using recombinanto ligonucleosomes (SETD8a nd EZH2) or octamers (G9a, SETD7, and PRMT1)a ss ubstrates. [9] 2.2. [19] Upon testing in human cervical carcinoma HeLa cells, Hacid did not cause any effect on cell proliferation up to 500 mm,probablya s ar esulto fi ts inability to enter cells.…”

Section: Hacid and Thymolphthaleinmentioning

confidence: 99%

“…However, the development of SETD8 inhibitors is still in its infancy. [9] Ab asic N-terminal domain (Figure 3, in blue) is the primary determinant of such binding and interacts with ac luster of eight acidic residues of the nucleosomal H2A/H2B (Figure 3, gold and orange, respectively) histoned imer (E56, E61, E64, D90, E91, and E92 of H2A and E102 and E110 of H2B, in dark magenta) that forms an egatively charged" acidicp atch" having the shape of an arrow groove. Figure 1.…”

Section: Introductionmentioning

confidence: 99%

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Progress in the Development of Lysine Methyltransferase SETD8 Inhibitors

et al. 2016

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SETD8/SET8/Pr-SET7/KMT5A is the only known lysine methyltransferase that monomethylates lysine 20 of histone H4 (H4K20) in vivo. The methyltransferase activity of SETD8 has been implicated in many essential cellular processes, including DNA replication, DNA damage response, transcription modulation, and cell cycle regulation. In addition to H4K20, SETD8 monomethylates non-histone substrates including proliferating cell nuclear antigen and p53. During the past decade, different structural classes of inhibitors targeting various lysine methyltransferases have been designed and developed. However, the development of SETD8 inhibitors is still in its infancy. This review covers the progress made to date in inhibiting the activity of SETD8 by small molecules, with an emphasis on their discovery, selectivity over other methyltransferases, and cellular activity.

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Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate

Cited by 29 publications

References 45 publications

Cryo-electron microscopy of chromatin biology

Cryo-electron microscopy of chromatin biology

Controlling the supramolecular assembly of nucleosomes asymmetrically modified on H4

Progress in the Development of Lysine Methyltransferase SETD8 Inhibitors

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