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Ma R, Zhang Y, Zhang J, Zhang P, Liu Z, Fan Y, Wang HT, Zhang Z, Zhu B. Targeting pericentric non-consecutive motifs for heterochromatin initiation. Nature 2024; 631:678-685. [PMID: 38961301 DOI: 10.1038/s41586-024-07640-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 05/31/2024] [Indexed: 07/05/2024]
Abstract
Pericentric heterochromatin is a critical component of chromosomes marked by histone H3 K9 (H3K9) methylation1-3. However, what recruits H3K9-specific histone methyltransferases to pericentric regions in vertebrates remains unclear4, as does why pericentric regions in different species share the same H3K9 methylation mark despite lacking highly conserved DNA sequences2,5. Here we show that zinc-finger proteins ZNF512 and ZNF512B specifically localize at pericentric regions through direct DNA binding. Notably, both ZNF512 and ZNF512B are sufficient to initiate de novo heterochromatin formation at ectopically targeted repetitive regions and pericentric regions, as they directly recruit SUV39H1 and SUV39H2 (SUV39H) to catalyse H3K9 methylation. SUV39H2 makes a greater contribution to H3K9 trimethylation, whereas SUV39H1 seems to contribute more to silencing, probably owing to its preferential association with HP1 proteins. ZNF512 and ZNF512B from different species can specifically target pericentric regions of other vertebrates, because the atypical long linker residues between the zinc-fingers of ZNF512 and ZNF512B offer flexibility in recognition of non-consecutively organized three-nucleotide triplets targeted by each zinc-finger. This study addresses two long-standing questions: how constitutive heterochromatin is initiated and how seemingly variable pericentric sequences are targeted by the same set of conserved machinery in vertebrates.
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Affiliation(s)
- Runze Ma
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
| | - Jing Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
| | - Pinqi Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zeqi Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yiming Fan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hao-Tian Wang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
- Key Laboratory of Epigenetic Regulation and Intervention, Chinese Academy of Sciences, Beijing, China.
- New Cornerstone Science Laboratory, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
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Domain Model Explains Propagation Dynamics and Stability of Histone H3K27 and H3K36 Methylation Landscapes. Cell Rep 2020; 30:1223-1234.e8. [PMID: 31995760 DOI: 10.1016/j.celrep.2019.12.060] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 11/25/2019] [Accepted: 12/16/2019] [Indexed: 01/12/2023] Open
Abstract
Chromatin states must be maintained during cell proliferation to uphold cellular identity and genome integrity. Inheritance of histone modifications is central in this process. However, the histone modification landscape is challenged by incorporation of new unmodified histones during each cell cycle, and the principles governing heritability remain unclear. We take a quantitative computational modeling approach to describe propagation of histone H3K27 and H3K36 methylation states. We measure combinatorial H3K27 and H3K36 methylation patterns by quantitative mass spectrometry on subsequent generations of histones. Using model comparison, we reject active global demethylation and invoke the existence of domains defined by distinct methylation endpoints. We find that H3K27me3 on pre-existing histones stimulates the rate of de novo H3K27me3 establishment, supporting a read-write mechanism in timely chromatin restoration. Finally, we provide a detailed quantitative picture of the mutual antagonism between H3K27 and H3K36 methylation and propose that it stabilizes epigenetic states across cell division.
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Cheema MS, Good KV, Kim B, Soufari H, O’Sullivan C, Freeman ME, Stefanelli G, Casas CR, Zengeler KE, Kennedy AJ, Eirin Lopez JM, Howard PL, Zovkic IB, Shabanowitz J, Dryhurst DD, Hunt DF, Mackereth CD, Ausió J. Deciphering the Enigma of the Histone H2A.Z-1/H2A.Z-2 Isoforms: Novel Insights and Remaining Questions. Cells 2020; 9:cells9051167. [PMID: 32397240 PMCID: PMC7290884 DOI: 10.3390/cells9051167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
The replication independent (RI) histone H2A.Z is one of the more extensively studied variant members of the core histone H2A family, which consists of many replication dependent (RD) members. The protein has been shown to be indispensable for survival, and involved in multiple roles from DNA damage to chromosome segregation, replication, and transcription. However, its functional involvement in gene expression is controversial. Moreover, the variant in several groups of metazoan organisms consists of two main isoforms (H2A.Z-1 and H2A.Z-2) that differ in a few (3–6) amino acids. They comprise the main topic of this review, starting from the events that led to their identification, what is currently known about them, followed by further experimental, structural, and functional insight into their roles. Despite their structural differences, a direct correlation to their functional variability remains enigmatic. As all of this is being elucidated, it appears that a strong functional involvement of isoform variability may be connected to development.
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Affiliation(s)
- Manjinder S. Cheema
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Katrina V. Good
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Bohyun Kim
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Heddy Soufari
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, 2 rue Robert Escarpit, F-33607 Pessac, France; (H.S.); (C.D.M.)
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Connor O’Sullivan
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Melissa E. Freeman
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Gilda Stefanelli
- Department of Neurosciences & Mental Health, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (G.S.); (I.B.Z.)
| | - Ciro Rivera Casas
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL 33181, USA; (C.R.C.); (J.M.E.L.)
| | - Kristine E. Zengeler
- Department of Chemistry and Biochemistry, Bates College, 2 Andrews Road, Lewiston, ME 04240, USA; (K.E.Z.); (A.J.K.)
| | - Andrew J. Kennedy
- Department of Chemistry and Biochemistry, Bates College, 2 Andrews Road, Lewiston, ME 04240, USA; (K.E.Z.); (A.J.K.)
| | - Jose Maria Eirin Lopez
- Environmental Epigenetics Group, Department of Biological Sciences, Florida International UniversityNorth Miami, FL 33181, USA; (C.R.C.); (J.M.E.L.)
| | - Perry L. Howard
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Iva B. Zovkic
- Department of Neurosciences & Mental Health, the Hospital for Sick Children, Toronto, ON M5G 1X8, Canada; (G.S.); (I.B.Z.)
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Jeffrey Shabanowitz
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (J.S.); (D.F.H.)
| | - Deanna D. Dryhurst
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
| | - Donald F. Hunt
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; (J.S.); (D.F.H.)
- Department of Pathology, University of Virginia, Charlottesville, VA 22903, USA
| | - Cameron D. Mackereth
- Institut Européen de Chimie et Biologie, Univ. Bordeaux, 2 rue Robert Escarpit, F-33607 Pessac, France; (H.S.); (C.D.M.)
- Inserm U1212, CNRS UMR 5320, ARNA Laboratory, Univ. Bordeaux, 146 rue Léo Saignat, F-33076 Bordeaux, France
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada; (M.S.C.); (K.V.G.); (B.K.); (C.O.); (M.E.F.); (P.L.H.); (D.D.D.)
- Correspondence: ; Tel.: +1-250-721-8863; Fax: +1-250-721-8855
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van Pijkeren A, Bischoff R, Kwiatkowski M. Mass spectrometric analysis of PTM dynamics using stable isotope labeled metabolic precursors in cell culture. Analyst 2019; 144:6812-6833. [PMID: 31650141 DOI: 10.1039/c9an01258c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological organisms represent highly dynamic systems, which are continually exposed to environmental factors and always strive to restore steady-state homeostasis. Posttranslational modifications are key regulators with which biological systems respond to external stimuli. To understand how homeostasis is restored, it is important to study the kinetics of posttranslational modifications. In this review we discuss proteomic approaches using stable isotope labeled metabolic precursors to study dynamics of posttranslational modifications in cell culture.
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Affiliation(s)
- Alienke van Pijkeren
- Department of Analytical Biochemistry, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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Yuan ZF, Sidoli S, Marchione DM, Simithy J, Janssen KA, Szurgot MR, Garcia BA. EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data. J Proteome Res 2018; 17:2533-2541. [PMID: 29790754 DOI: 10.1021/acs.jproteome.8b00133] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetics has become a fundamental scientific discipline with various implications for biology and medicine. Epigenetic marks, mostly DNA methylation and histone post-translational modifications (PTMs), play important roles in chromatin structure and function. Accurate quantification of these marks is an ongoing challenge due to the variety of modifications and their wide dynamic range of abundance. Here we present EpiProfile 2.0, an extended version of our 2015 software (v1.0), for accurate quantification of histone peptides based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. EpiProfile 2.0 is now optimized for data-independent acquisition through the use of precursor and fragment extracted ion chromatography to accurately determine the chromatographic profile and to discriminate isobaric forms of peptides. The software uses an intelligent retention time prediction trained on the analyzed samples to enable accurate peak detection. EpiProfile 2.0 supports label-free and isotopic labeling, different organisms, known sequence mutations in diseases, different derivatization strategies, and unusual PTMs (such as acyl-derived modifications). In summary, EpiProfile 2.0 is a universal and accurate platform for the quantification of histone marks via LC-MS/MS. Being the first software of its kind, we anticipate that EpiProfile 2.0 will play a fundamental role in epigenetic studies relevant to biology and translational medicine. EpiProfile is freely available at https://github.com/zfyuan/EpiProfile2.0_Family .
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Affiliation(s)
- Zuo-Fei Yuan
- Epigenetics Institute, Department of Biochemistry and Biophysics , Perelman School of Medicine University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics , Perelman School of Medicine University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Dylan M Marchione
- Department of Systems Pharmacology and Translational Therapeutics , Perelman School of Medicine University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Johayra Simithy
- Epigenetics Institute, Department of Biochemistry and Biophysics , Perelman School of Medicine University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Kevin A Janssen
- Epigenetics Institute, Department of Biochemistry and Biophysics , Perelman School of Medicine University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Mary R Szurgot
- Epigenetics Institute, Department of Biochemistry and Biophysics , Perelman School of Medicine University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics , Perelman School of Medicine University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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D'Urzo A, Boichenko AP, van den Bosch T, Hermans J, Dekker F, Andrisano V, Bischoff R. Site-specific quantification of lysine acetylation in the N-terminal tail of histone H4 using a double-labelling, targeted UHPLC MS/MS approach. Anal Bioanal Chem 2016; 408:3547-53. [PMID: 26968571 PMCID: PMC4837199 DOI: 10.1007/s00216-016-9431-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 02/04/2023]
Abstract
We developed a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the site-specific quantification of lysine acetylation in the N-terminal region of histone H4 by combining chemical derivatization at the protein and peptide levels with digestion using chymotrypsin and trypsin. Unmodified ε-amino groups were first modified with propionic acid anhydride and the derivatized protein digested with trypsin and chymotrypsin. The newly formed peptide N-termini were subjected to a second derivatization step with d6- (heavy) or d0- (light) acetic acid anhydride. Samples were mixed at different ratios and peptides monitored by multiple reaction monitoring (MRM) LC-MS/MS. The method was validated in terms of linearity (R2 ≥ 0.94), precision (RSD ≤ 10 %), and accuracy (≤27 %) and used to assess the effect of the histone deacetylase (HDAC) inhibitors SAHA and MS-275 in the murine macrophage-like cell line RAW 264.7. SAHA and MS-275 showed site-specific effects on the acetylation levels of K5 and K8 with the K5(Ac)–K8 and K5–K8(Ac) peptides increasing 2.5-fold and 5-fold upon treatment with SAHA and MS-275, respectively. Assessing lysine acetylation in a site-specific manner is important for gaining a better understanding of the effects of HDAC inhibitors and for clarifying disease mechanisms where lysine acetylation plays a role.
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Affiliation(s)
- Annalisa D'Urzo
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.,Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso di Augusto, 237-47921, Rimini, Italy
| | - Alexander P Boichenko
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Thea van den Bosch
- Department of Pharmaceutical Gene Modulation, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Jos Hermans
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Frank Dekker
- Department of Pharmaceutical Gene Modulation, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Vincenza Andrisano
- Department for Life Quality Studies, Alma Mater Studiorum-University of Bologna, Corso di Augusto, 237-47921, Rimini, Italy
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
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Zhang S, Wang XJ. Promote Connections of Young Computational Biologists in China. GENOMICS, PROTEOMICS & BIOINFORMATICS 2013; 11:253-6. [PMID: 23835348 PMCID: PMC4357815 DOI: 10.1016/j.gpb.2013.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 06/23/2013] [Accepted: 07/01/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Shihua Zhang
- National Center for Mathematics and Interdisciplinary Sciences, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- Corresponding authors.
| | - Xiu-Jie Wang
- Center for Molecular Systems Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Corresponding authors.
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Niu Y, Xia Y, Wang S, Li J, Niu C, Li X, Zhao Y, Xiong H, Li Z, Lou H, Cao Q. A prototypic lysine methyltransferase 4 from archaea with degenerate sequence specificity methylates chromatin proteins Sul7d and Cren7 in different patterns. J Biol Chem 2013; 288:13728-40. [PMID: 23530048 DOI: 10.1074/jbc.m113.452979] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND The origin of eukaryotic histone modification enzymes still remains obscure. RESULTS Prototypic KMT4/Dot1 from Archaea targets chromatin proteins (Sul7d and Cren7) and shows increased activity on Sul7d, but not Cren7, in the presence of DNA. CONCLUSION Promiscuous aKMT4 could be regulated by chromatin environment. SIGNIFICANCE This study supports the prokaryotic origin model of eukaryotic histone methyltransferases and sheds light on chromatin dynamics in Archaea. Histone methylation is one of the major epigenetic modifications even in early diverging unicellular eukaryotes. We show that a widespread lysine methyltransferase from Archaea (aKMT4), bears striking structural and functional resemblance to the core of distantly related eukaryotic KMT4/Dot1. aKMT4 methylates a set of various proteins, including the chromatin proteins Sul7d and Cren7, and RNA exosome components. Csl4- and Rrp4-exosome complexes are methylated in different patterns. aKMT4 can self-methylate intramolecularly and compete with other proteins for the methyl group. Automethylation is inhibited by suitable substrates or DNA in a concentration-dependent manner. The automethylated enzyme shows relatively compromised activity. aKMT4-8A mutant with abrogated automethylation shows a more than 150% increase in methylation of substrates, suggesting a possible mechanism to regulate methyltransferase activity. More interestingly, methylation of Sul7d, but not Cren7, by aKMT4 is significantly enhanced by DNA. MS/MS and kinetic analysis further suggest that aKMT4 methylates Sul7d in the chromatin context. These data provide a clue to the possible regulation of aKMT4 activity by the local chromatin environment, albeit as a promiscuous enzyme required for extensive and variegated lysine methylation in Sulfolobus. This study supports the prokaryotic origin model of eukaryotic histone modification enzymes and sheds light on regulation of archaeal chromatin.
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Affiliation(s)
- Yanling Niu
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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