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McDevitt PJ, Schneck JL, Diaz E, Hou W, Huddleston MJ, Matico RE, McCormick PM, Kirkpatrick RB. A Scalable Platform for Producing Recombinant Nucleosomes with Codified Histone Methyltransferase Substrate Preferences. Protein Expr Purif 2019; 164:105455. [PMID: 31306746 DOI: 10.1016/j.pep.2019.105455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 11/15/2022]
Abstract
Wolf-Hirschhorn Syndrome Candidate 1 (WHSC1; also known as NSD2) is a SET domain-containing histone lysine methyltransferase. A chromosomal translocation occurs in 15-20% of multiple myeloma patients and is associated with increased production of WHSC1 and poor clinical prognosis. To define the substrate requirements of NSD2, we established a platform for the large-scale production of recombinant polynucleosomes, based on authentic human histone proteins, expressed in E. coli, and complexed with linearized DNA. A brief survey of methyltransferases whose substrate requirements are recorded in the literature yielded expected results, lending credence to the fitness of our approach. This platform was readily 'codified' with respect to both position and extent of methylation at histone 3 lysines 18 and 36 and led to the conclusion that the most readily discernible activity of NSD2 in contact with a nucleosome substrate is dimethylation of histone 3 lysine 36. We further explored reaction mechanism, and conclude a processive, rather than distributive mechanism best describes the interaction of NSD2 with intact nucleosome substrates. The methods developed feature scale and flexibility and are suited to thorough pharmaceutical-scale drug discovery campaigns.
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Affiliation(s)
- Patrick J McDevitt
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA.
| | - Jessica L Schneck
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Elsie Diaz
- Janssen Pharmaceutical Companies of Johnson and Johnson, Philadelphia, PA, USA
| | - Wangfang Hou
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Michael J Huddleston
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
| | - Rosalie E Matico
- Janssen Pharmaceutical Companies of Johnson and Johnson, Philadelphia, PA, USA
| | - Patricia M McCormick
- GlaxoSmithKline Pharmaceutical Company, 1250 South Collegeville Road, Collegeville, PA, 19426-0989, USA
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Poulin MB, Schneck JL, Matico RE, McDevitt PJ, Huddleston MJ, Hou W, Johnson NW, Thrall SH, Meek TD, Schramm VL. Transition state for the NSD2-catalyzed methylation of histone H3 lysine 36. Proc Natl Acad Sci U S A 2016; 113:1197-201. [PMID: 26787850 PMCID: PMC4747696 DOI: 10.1073/pnas.1521036113] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Nuclear receptor SET domain containing protein 2 (NSD2) catalyzes the methylation of histone H3 lysine 36 (H3K36). It is a determinant in Wolf-Hirschhorn syndrome and is overexpressed in human multiple myeloma. Despite the relevance of NSD2 to cancer, there are no potent, selective inhibitors of this enzyme reported. Here, a combination of kinetic isotope effect measurements and quantum chemical modeling was used to provide subangstrom details of the transition state structure for NSD2 enzymatic activity. Kinetic isotope effects were measured for the methylation of isolated HeLa cell nucleosomes by NSD2. NSD2 preferentially catalyzes the dimethylation of H3K36 along with a reduced preference for H3K36 monomethylation. Primary Me-(14)C and (36)S and secondary Me-(3)H3, Me-(2)H3, 5'-(14)C, and 5'-(3)H2 kinetic isotope effects were measured for the methylation of H3K36 using specifically labeled S-adenosyl-l-methionine. The intrinsic kinetic isotope effects were used as boundary constraints for quantum mechanical calculations for the NSD2 transition state. The experimental and calculated kinetic isotope effects are consistent with an SN2 chemical mechanism with methyl transfer as the first irreversible chemical step in the reaction mechanism. The transition state is a late, asymmetric nucleophilic displacement with bond separation from the leaving group at (2.53 Å) and bond making to the attacking nucleophile (2.10 Å) advanced at the transition state. The transition state structure can be represented in a molecular electrostatic potential map to guide the design of inhibitors that mimic the transition state geometry and charge.
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Affiliation(s)
- Myles B Poulin
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461
| | - Jessica L Schneck
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Rosalie E Matico
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Patrick J McDevitt
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Michael J Huddleston
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Wangfang Hou
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Neil W Johnson
- Cancer Epigenetics Discovery Performance Unit, GlaxoSmithKline, Collegeville, PA 19426
| | - Sara H Thrall
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Thomas D Meek
- Biological Sciences, Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426
| | - Vern L Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461;
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Ren J, Briones V, Barbour S, Yu W, Han Y, Terashima M, Muegge K. The ATP binding site of the chromatin remodeling homolog Lsh is required for nucleosome density and de novo DNA methylation at repeat sequences. Nucleic Acids Res 2015; 43:1444-55. [PMID: 25578963 PMCID: PMC4330352 DOI: 10.1093/nar/gku1371] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/16/2014] [Accepted: 12/21/2014] [Indexed: 12/19/2022] Open
Abstract
Lsh, a chromatin remodeling protein of the SNF2 family, is critical for normal heterochromatin structure. In particular, DNA methylation at repeat elements, a hallmark of heterochromatin, is greatly reduced in Lsh(-/-) (KO) cells. Here, we examined the presumed nucleosome remodeling activity of Lsh on chromatin in the context of DNA methylation. We found that dynamic CG methylation was dependent on Lsh in embryonic stem cells. Moreover, we demonstrate that ATP function is critical for de novo methylation at repeat sequences. The ATP binding site of Lsh is in part required to promote stable association of the DNA methyltransferase 3b with the repeat locus. By performing nucleosome occupancy assays, we found distinct nucleosome occupancy in KO ES cells compared to WT ES cells after differentiation. Nucleosome density was restored to wild-type level by re-expressing wild-type Lsh but not the ATP mutant in KO ES cells. Our results suggest that ATP-dependent nucleosome remodeling is the primary molecular function of Lsh, which may promote de novo methylation in differentiating ES cells.
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Affiliation(s)
- Jianke Ren
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Victorino Briones
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Samantha Barbour
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Weishi Yu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Minoru Terashima
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA Basic Science Program, Leidos Biomedical Research, Inc., Mouse Cancer Genetics Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
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Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes. Epigenetics Chromatin 2014; 7:34. [PMID: 25506399 PMCID: PMC4265496 DOI: 10.1186/1756-8935-7-34] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/04/2014] [Indexed: 12/21/2022] Open
Abstract
Background The interplay between epigenetic modifications and chromatin structure are integral to our understanding of genome function. Methylation of cytosine (5mC) at CG dinucleotides, traditionally associated with transcriptional repression, is the most highly studied chemical modification of DNA, occurring at over 70% of all CG dinucleotides in the genome. Hypomethylated regions (HMRs) often occur in CG islands (CGIs), however, they also occur outside of CGIs and function as cell-type specific enhancers. During the process of differentiation, reorganization of chromatin and nucleosome arrangement at regulatory regions is thought to occur in order for the establishment of cell-type specific transcriptional programs. However, the specifics regarding the organization of nucleosomes at HMRs and the potential mechanisms regulating nucleosome occupancy in these regions are unknown. Here, we have investigated nucleosome organization around hypomethylated regions (HMRs) identified in two mouse primary cells. Results Microccocal nuclease (MNase) digested mononucleosomes from primary cultures of new-born female mouse dermal fibroblasts and keratinocytes were mapped and compared to the HMRs obtained from single base-pair resolution methylomes. In both cell types, we find that nucleosomes are enriched at HMR boundaries. In contrast to the nucleosomes found at boundaries of HMRs in CGIs, HMRs outside of CGIs are calculated to be preferentially bound by nucleosomes, with phased nucleosomes propagating into the methylated region. Nucleosomes are enriched at the tissue-specific HMRs (TS-HMR) boundaries in both cell types suggesting that nucleosome organization surrounding HMR boundaries is independent of methylation status. In addition, we find potential transcription factor (TF) binding sites (E-box motifs) enriched in non-CGI TS-HMR boundaries. Conclusions Our results show that intrinsic nucleosome occupancy score (INOS) positively correlate with the nucleosome organization surrounding non-CGI TS-HMRs, suggesting that DNA sequence plays a role in the establishment of HMRs in the genome. Since nucleosomes impact all processes involving the genome, our results provide a link between epigenetic modifications, chromatin structure, and regulatory function. Electronic supplementary material The online version of this article (doi:10.1186/1756-8935-7-34) contains supplementary material, which is available to authorized users.
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Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell 2014; 156:1286-1297. [PMID: 24630728 DOI: 10.1016/j.cell.2014.01.029] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 10/25/2013] [Accepted: 01/10/2014] [Indexed: 11/24/2022]
Abstract
Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.
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Li S, Gu XJ, Hao Q, Fan H, Li L, Zhou S, Zhao K, Chan HM, Wang YK. A liquid chromatography/mass spectrometry-based generic detection method for biochemical assay and hit discovery of histone methyltransferases. Anal Biochem 2013; 443:214-21. [PMID: 24018340 DOI: 10.1016/j.ab.2013.08.029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Accepted: 08/30/2013] [Indexed: 11/19/2022]
Abstract
Epigenetic modifications of the genome, such as DNA methylation and posttranslational modifications of histone proteins, contribute to gene regulation. Growing evidence suggests that histone methyltransferases are associated with the development of various human diseases, including cancer, and are promising drug targets. High-quality generic assays will facilitate drug discovery efforts in this area. In this article, we present a liquid chromatography/mass spectrometry (LC/MS)-based S-adenosyl homocysteine (SAH) detection assay for histone methyltransferases (HMTs) and its applications in HMT drug discovery, including analyzing the activity of newly produced enzymes, developing and optimizing assays, performing focused compound library screens and orthogonal assays for hit confirmations, selectivity profiling against a panel of HMTs, and studying mode of action of select hits. This LC/MS-based generic assay has become a critical platform for our methyltransferase drug discovery efforts.
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Affiliation(s)
- Shu Li
- Novartis Institutes for BioMedical Research, Cambridge, MA, 02139, USA.
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Diaz E, Machutta CA, Chen S, Jiang Y, Nixon C, Hofmann G, Key D, Sweitzer S, Patel M, Wu Z, Creasy CL, Kruger RG, LaFrance L, Verma SK, Pappalardi MB, Le B, Van Aller GS, McCabe MT, Tummino PJ, Pope AJ, Thrall SH, Schwartz B, Brandt M. Development and validation of reagents and assays for EZH2 peptide and nucleosome high-throughput screens. ACTA ACUST UNITED AC 2012; 17:1279-92. [PMID: 22904200 DOI: 10.1177/1087057112453765] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Histone methyltransferases (HMT) catalyze the methylation of histone tail lysines, resulting in changes in gene transcription. Misregulation of these enzymes has been associated with various forms of cancer, making this target class a potential new area for the development of novel chemotherapeutics. EZH2 is the catalytic component of the polycomb group repressive complex (PRC2), which selectively methylates histone H3 lysine 27 (H3K27). EZH2 is overexpressed in prostate, breast, bladder, brain, and other tumor types and is recognized as a molecular marker for cancer progression and aggressiveness. Several new reagents and assays were developed to aid in the identification of EZH2 inhibitors, and these were used to execute two high-throughput screening campaigns. Activity assays using either an H3K27 peptide or nucleosomes as substrates for methylation are described. The strategy to screen EZH2 with either a surrogate peptide or a natural substrate led to the identification of the same tractable series. Compounds from this series are reversible, are [(3)H]-S-adenosyl-L-methionine competitive, and display biochemical inhibition of H3K27 methylation.
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Affiliation(s)
- Elsie Diaz
- Platform Technology and Science, GlaxoSmithKline, Collegeville, PA 19426, USA
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