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Sowd GA, Stivison EA, Chapagain P, Hale AT, Poland JC, Rameh LE, Blind RD. IPMK regulates HDAC3 activity and histone H4 acetylation in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.29.591660. [PMID: 38746349 PMCID: PMC11092501 DOI: 10.1101/2024.04.29.591660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Histone deacetylases (HDACs) repress transcription by catalyzing the removal of acetyl groups from histones. Class 1 HDACs are activated by inositol phosphate signaling molecules in vitro , but it is unclear if this regulation occurs in human cells. Inositol Polyphosphate Multikinase (IPMK) is required for production of inositol hexakisphosphate (IP6), pentakisphosphate (IP5) and certain tetrakisphosphate (IP4) species, all known activators of Class 1 HDACs in vitro . Here, we generated IPMK knockout (IKO) human U251 glioblastoma cells, which decreased cellular inositol phosphate levels and increased histone H4-acetylation by mass spectrometry. ChIP-seq showed IKO increased H4-acetylation at IKO-upregulated genes, but H4-acetylation was unchanged at IKO-downregulated genes, suggesting gene-specific responses to IPMK knockout. HDAC deacetylase enzyme activity was decreased in HDAC3 immunoprecipitates from IKO vs . wild-type cells, while deacetylase activity of other Class 1 HDACs had no detectable changes in activity. Wild-type IPMK expression in IKO cells fully rescued HDAC3 deacetylase activity, while kinase-dead IPMK expression had no effect. Further, the deficiency in HDAC3 activity in immunoprecipitates from IKO cells could be fully rescued by addition of synthesized IP4 (Ins(1,4,5,6)P4) to the enzyme assay, while control inositol had no effect. These data suggest that cellular IPMK-dependent inositol phosphates are required for full HDAC3 enzyme activity and proper histone H4-acetylation. Implications for targeting IPMK in HDAC3-dependent diseases are discussed.
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Rajado AT, Silva N, Esteves F, Brito D, Binnie A, Araújo IM, Nóbrega C, Bragança J, Castelo-Branco P. How can we modulate aging through nutrition and physical exercise? An epigenetic approach. Aging (Albany NY) 2023. [DOI: https:/doi.org/10.18632/aging.204668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Affiliation(s)
- Ana Teresa Rajado
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
| | - Nádia Silva
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
| | - Filipa Esteves
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
| | - David Brito
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
| | - Alexandra Binnie
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Department of Critical Care, William Osler Health System, Etobicoke, Ontario, Canada
| | - Inês M. Araújo
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Clévio Nóbrega
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - José Bragança
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Pedro Castelo-Branco
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
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Rajado AT, Silva N, Esteves F, Brito D, Binnie A, Araújo IM, Nóbrega C, Bragança J, Castelo-Branco P. How can we modulate aging through nutrition and physical exercise? An epigenetic approach. Aging (Albany NY) 2023; 15:3191-3217. [PMID: 37086262 DOI: 10.18632/aging.204668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/11/2023] [Indexed: 04/23/2023]
Abstract
The World Health Organization predicts that by 2050, 2.1 billion people worldwide will be over 60 years old, a drastic increase from only 1 billion in 2019. Considering these numbers, strategies to ensure an extended "healthspan" or healthy longevity are urgently needed. The present study approaches the promotion of healthspan from an epigenetic perspective. Epigenetic phenomena are modifiable in response to an individual's environmental exposures, and therefore link an individual's environment to their gene expression pattern. Epigenetic studies demonstrate that aging is associated with decondensation of the chromatin, leading to an altered heterochromatin structure, which promotes the accumulation of errors. In this review, we describe how aging impacts epigenetics and how nutrition and physical exercise can positively impact the aging process, from an epigenetic point of view. Canonical histones are replaced by histone variants, concomitant with an increase in histone post-translational modifications. A slight increase in DNA methylation at promoters has been observed, which represses transcription of previously active genes, in parallel with global genome hypomethylation. Aging is also associated with deregulation of gene expression - usually provided by non-coding RNAs - leading to both the repression of previously transcribed genes and to the transcription of previously repressed genes. Age-associated epigenetic events are less common in individuals with a healthy lifestyle, including balanced nutrition, caloric restriction and physical exercise. Healthy aging is associated with more tightly condensed chromatin, fewer PTMs and greater regulation by ncRNAs.
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Affiliation(s)
- Ana Teresa Rajado
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
| | - Nádia Silva
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
| | - Filipa Esteves
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
| | - David Brito
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
| | - Alexandra Binnie
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Department of Critical Care, William Osler Health System, Etobicoke, Ontario, Canada
| | - Inês M Araújo
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Clévio Nóbrega
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - José Bragança
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
| | - Pedro Castelo-Branco
- Algarve Biomedical Center, Research Institute (ABC-RI), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Algarve Biomedical Center (ABC), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve Campus Gambelas, Faro 8005-139, Portugal
- Champalimaud Research Program, Champalimaud Centre for the Unknown, Lisbon, Portugal
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Stransky S, Cutler R, Aguilan J, Nieves E, Sidoli S. Investigation of reversible histone acetylation and dynamics in gene expression regulation using 3D liver spheroid model. Epigenetics Chromatin 2022; 15:35. [PMID: 36411440 PMCID: PMC9677638 DOI: 10.1186/s13072-022-00470-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/04/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Three-dimensional (3D) cell culture has emerged as an alternative approach to 2D flat culture to model more accurately the phenotype of solid tissue in laboratories. Culturing cells in 3D more precisely recapitulates physiological conditions of tissues, as these cells reduce activities related to proliferation, focusing their energy consumption toward metabolism and homeostasis. RESULTS Here, we demonstrate that 3D liver spheroids are a suitable system to model chromatin dynamics and response to epigenetics inhibitors. To delay necrotic tissue formation despite proliferation arrest, we utilize rotating bioreactors that apply active media diffusion and low shearing forces. We demonstrate that the proteome and the metabolome of our model resemble typical liver functions. We prove that spheroids respond to sodium butyrate (NaBut) treatment, an inhibitor of histone deacetylases (HDACi), by upregulating histone acetylation and transcriptional activation. As expected, NaBut treatment impaired specific cellular functions, including the energy metabolism. More importantly, we demonstrate that spheroids reestablish their original proteome and transcriptome, including pre-treatment levels of histone acetylation, metabolism, and protein expression once the standard culture condition is restored after treatment. Given the slow replication rate (> 40 days) of cells in 3D spheroids, our model enables to monitor the recovery of approximately the same cells that underwent treatment, demonstrating that NaBut does not have long-lasting effects on histone acetylation and gene expression. These results suggest that our model system can be used to quantify molecular memory on chromatin. CONCLUSION Together, we established an innovative cell culture system that can be used to model anomalously decondensing chromatin in physiological cell growth and rule out epigenetics inheritance if cells recover the original phenotype after treatment. The transient epigenetics effects demonstrated here highlight the relevance of using a 3D culture model system that could be very useful in studies requiring long-term drug treatment conditions that would not be possible using a 2D cell monolayer system.
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Affiliation(s)
- Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Ronald Cutler
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA.,Department of Genetics, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Jennifer Aguilan
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Edward Nieves
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA.,Department of Developmental & Molecular Biology, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA.
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5
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Farrelly LA, Zheng S, Schrode N, Topol A, Bhanu NV, Bastle RM, Ramakrishnan A, Chan JC, Cetin B, Flaherty E, Shen L, Gleason K, Tamminga CA, Garcia BA, Li H, Brennand KJ, Maze I. Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia. Nat Commun 2022; 13:2195. [PMID: 35459277 PMCID: PMC9033776 DOI: 10.1038/s41467-022-29922-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Schizophrenia (SZ) is a psychiatric disorder with complex genetic risk dictated by interactions between hundreds of risk variants. Epigenetic factors, such as histone posttranslational modifications (PTMs), have been shown to play critical roles in many neurodevelopmental processes, and when perturbed may also contribute to the precipitation of disease. Here, we apply an unbiased proteomics approach to evaluate combinatorial histone PTMs in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons from individuals with SZ. We observe hyperacetylation of H2A.Z and H4 in neurons derived from SZ cases, results that were confirmed in postmortem human brain. We demonstrate that the bromodomain and extraterminal (BET) protein, BRD4, is a bona fide 'reader' of H2A.Z acetylation, and further provide evidence that BET family protein inhibition ameliorates transcriptional abnormalities in patient-derived neurons. Thus, treatments aimed at alleviating BET protein interactions with hyperacetylated histones may aid in the prevention or treatment of SZ.
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Affiliation(s)
- Lorna A Farrelly
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Shuangping Zheng
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Nadine Schrode
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aaron Topol
- Graduate School of Biomedical Science, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Natarajan V Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ryan M Bastle
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Jennifer C Chan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Bulent Cetin
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Erin Flaherty
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Kelly Gleason
- Department of Psychiatry, University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Carol A Tamminga
- Department of Psychiatry, University of Texas Southwestern Medical School, Dallas, TX, 75390, USA
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Haitao Li
- Beijing Advanced Innovation Center for Structural Biology, MOE Key Laboratory of Protein Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.
| | - Kristen J Brennand
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Pamela Sklar Division of Psychiatric Genomics, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Departments of Psychiatry and Genetics, Wu Tsai Institute, Yale School of Medicine, New Haven, CT, 065109, USA.
| | - Ian Maze
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Howard Hughes Medical Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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Richards AL, Chen KH, Wilburn DB, Stevenson E, Polacco BJ, Searle BC, Swaney DL. Data-Independent Acquisition Protease-Multiplexing Enables Increased Proteome Sequence Coverage Across Multiple Fragmentation Modes. J Proteome Res 2022; 21:1124-1136. [PMID: 35234472 PMCID: PMC9035370 DOI: 10.1021/acs.jproteome.1c00960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The use of multiple proteases has been shown to increase protein sequence coverage in proteomics experiments; however, due to the additional analysis time required, it has not been widely adopted in routine data-dependent acquisition (DDA) proteomic workflows. Alternatively, data-independent acquisition (DIA) has the potential to analyze multiplexed samples from different protease digests, but has been primarily optimized for fragmenting tryptic peptides. Here we evaluate a DIA multiplexing approach that combines three proteolytic digests (Trypsin, AspN, and GluC) into a single sample. We first optimize data acquisition conditions for each protease individually with both the canonical DIA fragmentation mode (beam type CID), as well as resonance excitation CID, to determine optimal consensus conditions across proteases. Next, we demonstrate that application of these conditions to a protease-multiplexed sample of human peptides results in similar protein identifications and quantitative performance as compared to trypsin alone, but enables up to a 63% increase in peptide detections, and a 45% increase in nonredundant amino acid detections. Nontryptic peptides enabled noncanonical protein isoform determination and resulted in 100% sequence coverage for numerous proteins, suggesting the utility of this approach in applications where sequence coverage is critical, such as protein isoform analysis.
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Affiliation(s)
- Alicia L Richards
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States.,J. David Gladstone Institutes, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Kuei-Ho Chen
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States.,J. David Gladstone Institutes, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Damien B Wilburn
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United States.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Erica Stevenson
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States.,J. David Gladstone Institutes, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States.,J. David Gladstone Institutes, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Brian C Searle
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio 43210, United States.,Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio 43210, United States
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, California 94158, United States.,J. David Gladstone Institutes, San Francisco, California 94158, United States.,Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
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7
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Agustinus AS, Bakhoum S. Biochemical, genomic, and epigenomic profiling of isolated cancer cell lines’ micronuclei. Methods Cell Biol 2022; 172:51-66. [DOI: 10.1016/bs.mcb.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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8
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Sheban D, Shani T, Maor R, Aguilera-Castrejon A, Mor N, Oldak B, Shmueli MD, Eisenberg-Lerner A, Bayerl J, Hebert J, Viukov S, Chen G, Kacen A, Krupalnik V, Chugaeva V, Tarazi S, Rodríguez-delaRosa A, Zerbib M, Ulman A, Masarwi S, Kupervaser M, Levin Y, Shema E, David Y, Novershtern N, Hanna JH, Merbl Y. SUMOylation of linker histone H1 drives chromatin condensation and restriction of embryonic cell fate identity. Mol Cell 2021; 82:106-122.e9. [PMID: 34875212 DOI: 10.1016/j.molcel.2021.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 11/08/2021] [Accepted: 11/10/2021] [Indexed: 12/12/2022]
Abstract
The fidelity of the early embryonic program is underlined by tight regulation of the chromatin. Yet, how the chromatin is organized to prohibit the reversal of the developmental program remains unclear. Specifically, the totipotency-to-pluripotency transition marks one of the most dramatic events to the chromatin, and yet, the nature of histone alterations underlying this process is incompletely characterized. Here, we show that linker histone H1 is post-translationally modulated by SUMO2/3, which facilitates its fixation onto ultra-condensed heterochromatin in embryonic stem cells (ESCs). Upon SUMOylation depletion, the chromatin becomes de-compacted and H1 is evicted, leading to totipotency reactivation. Furthermore, we show that H1 and SUMO2/3 jointly mediate the repression of totipotent elements. Lastly, we demonstrate that preventing SUMOylation on H1 abrogates its ability to repress the totipotency program in ESCs. Collectively, our findings unravel a critical role for SUMOylation of H1 in facilitating chromatin repression and desolation of the totipotent identity.
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Affiliation(s)
- Daoud Sheban
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel; Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tom Shani
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Roey Maor
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Nofar Mor
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bernardo Oldak
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Merav D Shmueli
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Jonathan Bayerl
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jakob Hebert
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Sergey Viukov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Guoyun Chen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Assaf Kacen
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Vladislav Krupalnik
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Valeriya Chugaeva
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Shadi Tarazi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Mirie Zerbib
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Adi Ulman
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Solaiman Masarwi
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Meital Kupervaser
- De Botton Institute for Protein Profiling, INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yishai Levin
- De Botton Institute for Protein Profiling, INCPM, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Efrat Shema
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Noa Novershtern
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel.
| | - Yifat Merbl
- Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
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9
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Leonen CJA, Shimada M, Weller CE, Nakadai T, Hsu PL, Tyson EL, Mishra A, Shelton PM, Sadilek M, Hawkins RD, Zheng N, Roeder RG, Chatterjee C. Sumoylation of the human histone H4 tail inhibits p300-mediated transcription by RNA polymerase II in cellular extracts. eLife 2021; 10:67952. [PMID: 34747692 PMCID: PMC8626089 DOI: 10.7554/elife.67952] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 11/06/2021] [Indexed: 01/22/2023] Open
Abstract
The post-translational modification of histones by the small ubiquitin-like modifier (SUMO) protein has been associated with gene regulation, centromeric localization, and double-strand break repair in eukaryotes. Although sumoylation of histone H4 was specifically associated with gene repression, this could not be proven due to the challenge of site-specifically sumoylating H4 in cells. Biochemical crosstalk between SUMO and other histone modifications, such as H4 acetylation and H3 methylation, that are associated with active genes also remains unclear. We addressed these challenges in mechanistic studies using an H4 chemically modified at Lys12 by SUMO-3 (H4K12su) and incorporated into mononucleosomes and chromatinized plasmids for functional studies. Mononucleosome-based assays revealed that H4K12su inhibits transcription-activating H4 tail acetylation by the histone acetyltransferase p300, as well as transcription-associated H3K4 methylation by the extended catalytic module of the Set1/COMPASS (complex of proteins associated with Set1) histone methyltransferase complex. Activator- and p300-dependent in vitro transcription assays with chromatinized plasmids revealed that H4K12su inhibits both H4 tail acetylation and RNA polymerase II-mediated transcription. Finally, cell-based assays with a SUMO-H4 fusion that mimics H4 tail sumoylation confirmed the negative crosstalk between histone sumoylation and acetylation/methylation. Thus, our studies establish the key role for histone sumoylation in gene silencing and its negative biochemical crosstalk with active transcription-associated marks in human cells.
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Affiliation(s)
| | - Miho Shimada
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States
| | - Caroline E Weller
- Department of Chemistry, University of Washington, Seattle, United States
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States.,Project for Cancer Epigenomics, Cancer Institute of JFCR, Tokyo, Japan
| | - Peter L Hsu
- Department of Pharmacology, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Elizabeth L Tyson
- Department of Chemistry, University of Washington, Seattle, United States
| | - Arpit Mishra
- Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, United States
| | - Patrick Mm Shelton
- Department of Chemistry, University of Washington, Seattle, United States
| | - Martin Sadilek
- Department of Chemistry, University of Washington, Seattle, United States
| | - R David Hawkins
- Department of Genome Sciences, Department of Medicine, University of Washington, Seattle, United States
| | - Ning Zheng
- Department of Pharmacology, University of Washington, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York City, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, United States
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10
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Lui KW, Ngai SM. PrSM-Level Side-by-Side Comparison of Online LC-MS Methods with Intact Histone H3 and H4 Proteoforms. J Proteome Res 2021; 20:4331-4345. [PMID: 34327993 DOI: 10.1021/acs.jproteome.1c00308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The heterogeneity of histone H3 proteoforms makes histone H3 top-down analysis challenging. To enhance the detection coverage of the proteoforms, performing liquid chromatography (LC) front-end to mass spectrometry (MS) detection is recommended. Here, using optimized electron-transfer/high-energy collision dissociation (EThcD) parameters, we have conducted a proteoform-spectrum match (PrSM)-level side-by-side comparison of reversed-phase LC-MS (RPLC-MS), "dual-gradient" weak cation-exchange/hydrophilic interaction LC-MS (dual-gradient WCX/HILIC-MS), and "organic-rich" WCX/HILIC-MS on the top-down analyses of H3.1, H3.2, and H4 proteins extracted from a HeLa cell culture. While both dual-gradient WCX/HILIC and organic-rich WCX/HILIC could resolve intact H3 and H4 proteoforms by the number of acetylations, the organic-rich method could enhance the separations of different trimethyl/acetyl near-isobaric H3 proteoforms. In comparison with RPLC-MS, both of the WCX/HILIC-MS methods enhanced the qualities of the H3 PrSMs and remarkably improved the range, reproducibility, and confidence in the identifications of H3 proteoforms.
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Affiliation(s)
- Kin-Wing Lui
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong 999077, P. R. China
| | - Sai-Ming Ngai
- School of Life Sciences, The Chinese University of Hong Kong, Sha Tin, Hong Kong 999077, P. R. China.,State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, P. R. China
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11
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Holt MV, Wang T, Young NL. Expeditious Extraction of Histones from Limited Cells or Tissue Samples and Quantitative Top-Down Proteomic Analysis. Curr Protoc 2021; 1:e26. [PMID: 33534192 DOI: 10.1002/cpz1.26] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Histones are the primary protein component of chromatin and are involved in virtually all DNA-templated processes. Histones are abundantly post-translationally modified by a variety of chromatin-modifying machinery. These post-translational modifications (PTMs) are recognized by a range of "reader" proteins, which recruit additional proteins to specific locations on chromatin and impart precise and powerful effects on gene regulation. Each PTM typically exerts a positive or negative effect on transcription, and recent studies have shown that histone PTMs function in a combinatorial histone code: that is, histone PTMs function in combination to exert precise DNA-templated regulation. Thus, there is a need to identify and understand proteoforms, or unambiguously defined single protein molecules with all combinations of modifications. Top-down proteomics is currently the only viable approach for identifying and quantitating histone proteoforms, and mass spectrometry instruments have become sufficiently powerful to perform these quantitative analyses in a robust and high-throughput fashion. These recent innovations have enabled new experimental directions in chromatin research but have also introduced temporal and other constraints. This has led us to develop the protocols described here, which increase throughput, reduce sample requirements, and maintain robust quantitation. Although originally designed for high-throughput quantitative top-down proteomics, the protocols described here are useful for a wide range of chromatin biology applications. Starting with small amounts of cells or tissue, we describe two basic protocols for exceptionally rapid and efficient nuclei isolation, acid extraction of histones, and high-performance liquid chromatography fractionation of histones into histone families. We additionally describe the quantitative top-down proteomic analysis of histone H4 proteoforms. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Nuclei isolation and acid extraction of histones from mammalian cells in culture/tissues Basic Protocol 2: HPLC fractionation of histones and histone H4 HPLC-MS/MS Support Protocol: Preparation of intact H3 histone tails by Glu-C digestion.
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Affiliation(s)
- Matthew V Holt
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Tao Wang
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas.,Current Address: Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
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12
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Zappacosta F, Wagner CD, Della Pietra A, Gerhart SV, Keenan K, Korenchuck S, Quinn CJ, Barbash O, McCabe MT, Annan RS. A Chemical Acetylation-Based Mass Spectrometry Platform for Histone Methylation Profiling. Mol Cell Proteomics 2021; 20:100067. [PMID: 33775892 PMCID: PMC8138768 DOI: 10.1016/j.mcpro.2021.100067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/11/2021] [Accepted: 02/18/2021] [Indexed: 12/18/2022] Open
Abstract
Histones are highly posttranslationally modified proteins that regulate gene expression by modulating chromatin structure and function. Acetylation and methylation are the most abundant histone modifications, with methylation occurring on lysine (mono-, di-, and trimethylation) and arginine (mono- and dimethylation) predominately on histones H3 and H4. In addition, arginine dimethylation can occur either symmetrically (SDMA) or asymmetrically (ADMA) conferring different biological functions. Despite the importance of histone methylation on gene regulation, characterization and quantitation of this modification have proven to be quite challenging. Great advances have been made in the analysis of histone modification using both bottom-up and top-down mass spectrometry (MS). However, MS-based analysis of histone posttranslational modifications (PTMs) is still problematic, due both to the basic nature of the histone N-terminal tails and to the combinatorial complexity of the histone PTMs. In this report, we describe a simplified MS-based platform for histone methylation analysis. The strategy uses chemical acetylation with d0-acetic anhydride to collapse all the differently acetylated histone forms into one form, greatly reducing the complexity of the peptide mixture and improving sensitivity for the detection of methylation via summation of all the differently acetylated forms. We have used this strategy for the robust identification and relative quantitation of H4R3 methylation, for which stoichiometry and symmetry status were determined, providing an antibody-independent evidence that H4R3 is a substrate for both Type I and Type II PRMTs. Additionally, this approach permitted the robust detection of H4K5 monomethylation, a very low stoichiometry methylation event (0.02% methylation). In an independent example, we developed an in vitro assay to profile H3K27 methylation and applied it to an EZH2 mutant xenograft model following small-molecule inhibition of the EZH2 methyltransferase. These specific examples highlight the utility of this simplified MS-based approach to quantify histone methylation profiles. Simplification of histone complexity for analysis of lysine and arginine methylation. Improved sensitivity for the analysis of dimethylarginine symmetry. Accurate ratio of symmetric and asymmetric H4R3 dimethylarginine in cancer cells. Catalog of accessible histone methyl marks to facilitate assay development.
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Affiliation(s)
- Francesca Zappacosta
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Craig D Wagner
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Sarah V Gerhart
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Kathryn Keenan
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Chad J Quinn
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | - Olena Barbash
- Oncology R&D, GlaxoSmithKline, Collegeville, Pennsylvania, USA
| | | | - Roland S Annan
- Discovery Analytical, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, Pennsylvania, USA.
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13
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De Benedittis S, Gaspari M, Magariello A, Spadafora P, Citrigno L, Romeo N, Qualtieri A. LC-MALDI-TOF ISD MS analysis is an effective, simple and rapid method of investigation for histones characterization: Application to EBV lymphoblastoid cell lines. JOURNAL OF MASS SPECTROMETRY : JMS 2021; 56:e4712. [PMID: 33851762 DOI: 10.1002/jms.4712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
This contribution is the result of our progressive engagement to develop and to apply a top-down liquid chromatography (LC) matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) (LC-MALDI-TOF) analysis for the histone post-translational modifications (PTMs) and variants characterization, mainly in order to provide comprehensive and fast results. The histone post-translational modifications and the differential expression of the histone variants play an essential role both in the DNA packaging mechanism in chromosomes and in the regulation of gene expression in different cellular processes, also in response to molecular agents of environmental origin. This epigenetic mechanism is widely studied in different field such as cellular differentiation, development and in the understanding of mechanisms underlying diseases. The characterization of histone PTMs has traditionally performed by antibodies-based assay, but immunological methods have significant limits, and today systems that use mass spectrometry are increasingly employed. We evaluated an in-source decay (ISD) analysis for the histone investigation on human lymphoblastoid cells, and by this approach, we were able to identify and quantify several PTMs such as the di-methylation in the lysine 20 and the acetylation in the lysine 16 in H4 and the mono-methylation, di-methylation and trimethylations at K9 of the histone H3.1. Moreover, we detected and quantified in the same H2B spectrum the prevalent H2B 1C/2E type but also the minor H2B 1D, 1M and 1B/1L/1N, 1O/2F, 1J/1K variants. In this work, we show that MALDI-ISD represents an excellent methodology to obtain global information on histone PTMs and variants from cells in culture, with rapidity and simplicity of execution. Finally, this is a useful approach to get label-free relative quantitative data of histone variants and PTMs.
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Affiliation(s)
- Selene De Benedittis
- National Research Council, Institute for Biomedical Research and Innovation (IRIB), Cosenza, Italy
- Department of Medical and Surgical Sciences, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Catanzaro, Italy
| | - Angela Magariello
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean (ISAFOM), Cosenza, Italy
| | - Patrizia Spadafora
- National Research Council, Institute for Biomedical Research and Innovation (IRIB), Cosenza, Italy
| | - Luigi Citrigno
- National Research Council, Institute for Biomedical Research and Innovation (IRIB), Cosenza, Italy
| | - Nelide Romeo
- National Research Council, Institute for Agricultural and Forest Systems in the Mediterranean (ISAFOM), Cosenza, Italy
| | - Antonio Qualtieri
- National Research Council, Institute for Biomedical Research and Innovation (IRIB), Cosenza, Italy
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14
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Willcockson MA, Healton SE, Weiss CN, Bartholdy BA, Botbol Y, Mishra LN, Sidhwani DS, Wilson TJ, Pinto HB, Maron MI, Skalina KA, Toro LN, Zhao J, Lee CH, Hou H, Yusufova N, Meydan C, Osunsade A, David Y, Cesarman E, Melnick AM, Sidoli S, Garcia BA, Edelmann W, Macian F, Skoultchi AI. H1 histones control the epigenetic landscape by local chromatin compaction. Nature 2021; 589:293-298. [PMID: 33299182 PMCID: PMC8110206 DOI: 10.1038/s41586-020-3032-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 10/06/2020] [Indexed: 01/29/2023]
Abstract
H1 linker histones are the most abundant chromatin-binding proteins1. In vitro studies indicate that their association with chromatin determines nucleosome spacing and enables arrays of nucleosomes to fold into more compact chromatin structures. However, the in vivo roles of H1 are poorly understood2. Here we show that the local density of H1 controls the balance of repressive and active chromatin domains by promoting genomic compaction. We generated a conditional triple-H1-knockout mouse strain and depleted H1 in haematopoietic cells. H1 depletion in T cells leads to de-repression of T cell activation genes, a process that mimics normal T cell activation. Comparison of chromatin structure in normal and H1-depleted CD8+ T cells reveals that H1-mediated chromatin compaction occurs primarily in regions of the genome containing higher than average levels of H1: the chromosome conformation capture (Hi-C) B compartment and regions of the Hi-C A compartment marked by PRC2. Reduction of H1 stoichiometry leads to decreased H3K27 methylation, increased H3K36 methylation, B-to-A-compartment shifting and an increase in interaction frequency between compartments. In vitro, H1 promotes PRC2-mediated H3K27 methylation and inhibits NSD2-mediated H3K36 methylation. Mechanistically, H1 mediates these opposite effects by promoting physical compaction of the chromatin substrate. Our results establish H1 as a critical regulator of gene silencing through localized control of chromatin compaction, 3D genome organization and the epigenetic landscape.
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Affiliation(s)
| | - Sean E Healton
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Cary N Weiss
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yair Botbol
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Laxmi N Mishra
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Dhruv S Sidhwani
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Tommy J Wilson
- Department of Neurology, Columbia University College of Physicians and Surgeons, Columbia University Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - Hugo B Pinto
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Maxim I Maron
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Karin A Skalina
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Laura Norwood Toro
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jie Zhao
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea
| | - Harry Hou
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nevin Yusufova
- Cell & Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology/Oncology, Department of Medicine, Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Adewola Osunsade
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Fernando Macian
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
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15
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Separovich RJ, Wong MWM, Chapman TR, Slavich E, Hamey JJ, Wilkins MR. Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential. J Biol Chem 2021; 296:100192. [PMID: 33334889 PMCID: PMC7948420 DOI: 10.1074/jbc.ra120.015995] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/06/2020] [Accepted: 12/15/2020] [Indexed: 12/15/2022] Open
Abstract
Histone methylation is central to the regulation of eukaryotic transcription. In Saccharomyces cerevisiae, it is controlled by a system of four methyltransferases (Set1p, Set2p, Set5p, and Dot1p) and four demethylases (Jhd1p, Jhd2p, Rph1p, and Gis1p). While the histone targets for these enzymes are well characterized, the connection of the enzymes with the intracellular signaling network and thus their regulation is poorly understood; this also applies to all other eukaryotes. Here we report the detailed characterization of the eight S. cerevisiae enzymes and show that they carry a total of 75 phosphorylation sites, 92 acetylation sites, and two ubiquitination sites. All enzymes are subject to phosphorylation, although demethylases Jhd1p and Jhd2p contained one and five sites respectively, whereas other enzymes carried 14 to 36 sites. Phosphorylation was absent or underrepresented on catalytic and other domains but strongly enriched for regions of disorder on methyltransferases, suggesting a role in the modulation of protein-protein interactions. Through mutagenesis studies, we show that phosphosites within the acidic and disordered N-terminus of Set2p affect H3K36 methylation levels in vivo, illustrating the functional importance of such sites. While most kinases upstream of the yeast histone methylation enzymes remain unknown, we model the possible connections between the cellular signaling network and the histone-based gene regulatory system and propose an integrated regulatory structure. Our results provide a foundation for future, detailed exploration of the role of specific kinases and phosphosites in the regulation of histone methylation.
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Affiliation(s)
- Ryan J Separovich
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Mandy W M Wong
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Tyler R Chapman
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Eve Slavich
- Stats Central, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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16
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Nicosia L, Bonaldi T. Native Chromatin Proteomics (N-ChroP) to Characterize Histone Post-translational Modification (PTM) Combinatorics at Distinct Genomic Regions. Methods Mol Biol 2021; 2351:251-274. [PMID: 34382194 DOI: 10.1007/978-1-0716-1597-3_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
In this chapter, we describe the proteomic approach named "Native Chromatin Proteomics" (N-ChroP) that couples a modified Chromatin ImmunoPrecipitation (ChIP) protocol with the mass spectrometry (MS) analysis of immunoprecipitated proteins to study the combinatorial enrichment or exclusion of histone post-translational modifications (PTMs) at specific genomic regions, such as promoters or enhancers. We describe the protocol steps from the digestion of chromatin and nucleosome immunoprecipitation to histone digestion and peptide enrichment prior to MS analysis, up to the MS raw data analysis. We also discuss current challenges and offer suggestions based on the direct hands-on experience acquired during the method setup.
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Affiliation(s)
- Luciano Nicosia
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
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17
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Lu C, Coradin M, Porter EG, Garcia BA. Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry-Based Approaches. Mol Cell Proteomics 2020; 20:100006. [PMID: 33203747 PMCID: PMC7950153 DOI: 10.1074/mcp.r120.002257] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 10/15/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
Histone post-translational modifications (PTMs) are one of the main mechanisms of epigenetic regulation. Dysregulation of histone PTMs leads to many human diseases, such as cancer. Because of its high throughput, accuracy, and flexibility, mass spectrometry (MS) has emerged as a powerful tool in the epigenetic histone modification field, allowing the comprehensive and unbiased analysis of histone PTMs and chromatin-associated factors. Coupled with various techniques from molecular biology, biochemistry, chemical biology, and biophysics, MS has been used to characterize distinct aspects of histone PTMs in the epigenetic regulation of chromatin functions. In this review, we will describe advancements in the field of MS that have facilitated the analysis of histone PTMs and chromatin biology. Middle–down is the most suitable to study histone combinatorial post-translational modifications. Crosslinking MS has a variety of potential applications in exploring histone post-translational modifications. Hydrogen–deuterium exchange MS holds great promise to study the compaction of nucleosome. Multi-omics approaches are useful to study complex regulatory networks.
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Affiliation(s)
- Congcong Lu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Elizabeth G Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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18
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Coradin M, Mendoza MR, Sidoli S, Alpert AJ, Lu C, Garcia BA. Bullet points to evaluate the performance of the middle-down proteomics workflow for histone modification analysis. Methods 2020; 184:86-92. [PMID: 32070774 PMCID: PMC7727281 DOI: 10.1016/j.ymeth.2020.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/14/2020] [Indexed: 02/07/2023] Open
Abstract
Middle-down proteomics has emerged as the method of choice to study combinatorial histone post translational modifications (PTMs). In the common bottom-up workflow, histones are digested into relatively short peptides (4-20 aa), separated using reversed-phase chromatography and analyzed using typical proteomics methods in mass spectrometry. In middle-down, histones are cleaved into longer polypeptides (50-60 aa) mostly corresponding to their N-terminal tails, resolved using weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) and analyzed with less conventional mass spectrometry, i.e. using Electron Transfer Dissociation (ETD) for analyte fragmentation. Middle-down is not nearly as utilized as bottom-up for PTM analysis, partially due to its limited reproducibility and robustness. This has also limited the establishment of rigorous benchmarks to discriminate good vs poor quality experiments. Here, we describe critical aspects of the middle-down workflow to assist the user in evaluating the presence of biased and misleading results. Specifically, we tested the use of porous graphitic carbon (PGC) during the desalting step, demonstrating that desalting using only C18 material leads to sample loss. We also tested different salts in the WCX-HILIC buffers for their effect on retention, selectivity, and reproducibility of analysis of variants of histone tail fragments, in particular replacing ammonium ion with ethylenediammonium ion in buffer A. These substitutions had marked effects on selectivity and retention. Our results provide a streamlined way to evaluate middle-down performance to identify and quantify combinatorial histone PTMs.
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Affiliation(s)
- Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Mariel R Mendoza
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Congcong Lu
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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19
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Zhou M, Malhan N, Ahkami AH, Engbrecht K, Myers G, Dahlberg J, Hollingsworth J, Sievert JA, Hutmacher R, Madera M, Lemaux PG, Hixson KK, Jansson C, Paša-Tolić L. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation. Methods 2020; 184:29-39. [DOI: 10.1016/j.ymeth.2019.10.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/10/2019] [Accepted: 10/21/2019] [Indexed: 12/30/2022] Open
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20
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Wang Z, Hausmann S, Lyu R, Li TM, Lofgren SM, Flores NM, Fuentes ME, Caporicci M, Yang Z, Meiners MJ, Cheek MA, Howard SA, Zhang L, Elias JE, Kim MP, Maitra A, Wang H, Bassik MC, Keogh MC, Sage J, Gozani O, Mazur PK. SETD5-Coordinated Chromatin Reprogramming Regulates Adaptive Resistance to Targeted Pancreatic Cancer Therapy. Cancer Cell 2020; 37:834-849.e13. [PMID: 32442403 PMCID: PMC8187079 DOI: 10.1016/j.ccell.2020.04.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 03/11/2020] [Accepted: 04/22/2020] [Indexed: 12/18/2022]
Abstract
Molecular mechanisms underlying adaptive targeted therapy resistance in pancreatic ductal adenocarcinoma (PDAC) are poorly understood. Here, we identify SETD5 as a major driver of PDAC resistance to MEK1/2 inhibition (MEKi). SETD5 is induced by MEKi resistance and its deletion restores refractory PDAC vulnerability to MEKi therapy in mouse models and patient-derived xenografts. SETD5 lacks histone methyltransferase activity but scaffolds a co-repressor complex, including HDAC3 and G9a. Gene silencing by the SETD5 complex regulates known drug resistance pathways to reprogram cellular responses to MEKi. Pharmacological co-targeting of MEK1/2, HDAC3, and G9a sustains PDAC tumor growth inhibition in vivo. Our work uncovers SETD5 as a key mediator of acquired MEKi therapy resistance in PDAC and suggests a context for advancing MEKi use in the clinic.
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Affiliation(s)
- Zhentian Wang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Simone Hausmann
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ruitu Lyu
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Tie-Mei Li
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Shane M Lofgren
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Natasha M Flores
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mary E Fuentes
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marcello Caporicci
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ze Yang
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | | | | | | | - Michael P Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anirban Maitra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huamin Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Cory Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Julien Sage
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
| | - Pawel K Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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21
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Gehre M, Bunina D, Sidoli S, Lübke MJ, Diaz N, Trovato M, Garcia BA, Zaugg JB, Noh KM. Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy. Nat Genet 2020; 52:273-282. [PMID: 32139906 DOI: 10.1038/s41588-020-0586-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 01/29/2020] [Indexed: 12/26/2022]
Abstract
Mutations in enzymes that modify histone H3 at lysine 4 (H3K4) or lysine 36 (H3K36) have been linked to human disease, yet the role of these residues in mammals is unclear. We mutated K4 or K36 to alanine in the histone variant H3.3 and showed that the K4A mutation in mouse embryonic stem cells (ESCs) impaired differentiation and induced widespread gene expression changes. K4A resulted in substantial H3.3 depletion, especially at ESC promoters; it was accompanied by reduced remodeler binding and increased RNA polymerase II (Pol II) activity. Regulatory regions depleted of H3.3K4A showed histone modification alterations and changes in enhancer activity that correlated with gene expression. In contrast, the K36A mutation did not alter H3.3 deposition and affected gene expression at the later stages of differentiation. Thus, H3K4 is required for nucleosome deposition, histone turnover and chromatin remodeler binding at regulatory regions, where tight regulation of Pol II activity is necessary for proper ESC differentiation.
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Affiliation(s)
- Maja Gehre
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between the European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Daria Bunina
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Marlena J Lübke
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Nichole Diaz
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Matteo Trovato
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between the European Molecular Biology Laboratory and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Kyung-Min Noh
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
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22
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Wang Y, Xu C, Zhong B, Zhan D, Liu M, Gao D, Wang Y, Qin J. Comparative Proteomic Analysis of Histone Modifications upon Acridone Derivative 8a-Induced CCRF-CEM Cells by Data Independent Acquisition. J Proteome Res 2020; 19:819-831. [PMID: 31887055 DOI: 10.1021/acs.jproteome.9b00650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The lead compound acridone derivative 8a showed potent antiproliferative activity by inducing DNA damage through direct stacking with DNA bases and triggering ROS in CCRF-CEM cells. To define the chromatin alterations during DNA damage sensing and repair, a detailed quantitative map of single and coexisting histone post-translational modifications (PTMs) in CCRF-CEM cells affected by 8a was performed by the Data Independent Acquisition (DIA) method on QE-plus. A total of 79 distinct and 164 coexisting histone PTMs were quantified, of which 16 distinct histone PTMs were significantly altered when comparing 8a-treated cells with vehicle control cells. The changes in histone PTMs were confirmed by Western blotting analysis for three H3 and one H4 histone markers. The up-regulated dimethylation on H3K9, H3K36, and H4K20 implied that CCRF-CEM cells might accelerate DNA damage repair to counteract the DNA lesion induced by 8a, which was verified by an increment in the 53BP1 foci localization at the damaged DNA. Most of the significantly altered PTMs were involved in transcriptional regulation, including down-regulated acetylation on H3K18, H3K27, and H3K122, and up-regulated di- and trimethylation on H3K9 and H3K27. This transcription-silencing phenomenon was associated with G2/M cell cycle arrest after 8a treatment by flow cytometry. This study shows that the DIA proteomics strategy provides a sensitive and accurate way to characterize the coexisting histone PTMs changes and their cross-talk in CCRF-CEM cells after 8a treatment. Specifically, histone PTMs rearrange transcription-silencing, and cell cycle arrest DNA damage repair may contribute to the mechanism of epigenetic response affected by 8a.
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Affiliation(s)
- Yini Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Caixia Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Bowen Zhong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Dongdong Zhan
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences , East China Normal University , Shanghai 200241 , China
| | - Mingwei Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206 , China
| | - Dan Gao
- The State Key Laboratory Breeding Base-Shenzhen Key Laboratory of Chemical Biology , Graduate School at Shenzhen, Tsinghua University , Shenzhen 518055 , China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206 , China.,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center , National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics , Beijing 102206 , China.,Alkek Center for Molecular Discovery, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Department of Molecular and Cellular Biology , Baylor College of Medicine , Houston , Texas 77030 , United States
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23
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Thomas SP, Haws SA, Borth LE, Denu JM. A practical guide for analysis of histone post-translational modifications by mass spectrometry: Best practices and pitfalls. Methods 2019; 184:53-60. [PMID: 31816396 DOI: 10.1016/j.ymeth.2019.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 11/23/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023] Open
Abstract
Advances in mass spectrometry (MS) have revolutionized the ability to measure global changes in histone post-translational modifications (PTMs). The method routinely quantifies over 60 modification states in a single sample, far exceeding the capabilities of traditional western blotting. Thus, MS-based histone analysis has become an increasingly popular tool for understanding how genetic and environmental factors influence epigenetic states. However, histone proteomics experiments exhibit unique challenges, such as batch-to-batch reproducibility, accurate peak integration, and noisy data. Here, we discuss the steps of histone PTM analysis, from sample preparation and peak integration to data analysis and validation. We outline a set of best practices for ensuring data quality, accurate normalization, and robust statistics. Using these practices, we quantify histone modifications in 5 human cell lines, revealing that each cell line exhibits a unique epigenetic signature. We also provide a reproducible workflow for histone PTM analysis in the form of an R script, which is freely available at https://github.com/DenuLab/HistoneAnalysisWorkflow.
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Affiliation(s)
- Sydney P Thomas
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, 420 Henry Mall, Madison, WI, USA
| | - Spencer A Haws
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, 420 Henry Mall, Madison, WI, USA
| | - Laura E Borth
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, 420 Henry Mall, Madison, WI, USA
| | - John M Denu
- Wisconsin Institute for Discovery, 330 N. Orchard Street, Madison, WI, USA; Department of Biomolecular Chemistry, University of Wisconsin, Madison, 420 Henry Mall, Madison, WI, USA.
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24
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Janssen KA, Coradin M, Lu C, Sidoli S, Garcia BA. Quantitation of Single and Combinatorial Histone Modifications by Integrated Chromatography of Bottom-up Peptides and Middle-down Polypeptide Tails. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2449-2459. [PMID: 31512222 DOI: 10.1007/s13361-019-02303-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 06/10/2023]
Abstract
The analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has been critical to the advancement of the field of epigenetics. The most sensitive and accurate workflow is similar to the canonical proteomics analysis workflow (bottom-up MS), where histones are digested into short peptides (4-20 aa) and quantitated in extracted ion chromatograms. However, this limits the ability to detect even very common co-occurrences of modifications on histone proteins, preventing biological interpretation of PTM crosstalk. By digesting with GluC rather than trypsin, it is possible to produce long polypeptides corresponding to intact histone N-terminal tails (50-60 aa), where most modifications reside. This middle-down MS approach is used to study distant PTM co-existence. However, the most sensitive middle-down workflow uses weak cation exchange-hydrophilic interaction chromatography (WCX-HILIC), which is less robust than conventional reversed-phase chromatography. Additionally, since the buffer systems for middle-down and bottom-up proteomics differ substantially, it is cumbersome to toggle back and forth between both experimental setups on the same LC system. Here, we present a new workflow using porous graphitic carbon (PGC) as a stationary phase for histone analysis where bottom-up and middle-down sized histone peptides can be analyzed simultaneously using the same reversed-phase buffer setup. By using this protocol for middle-down sized peptides, we identified 406 uniquely modified intact histone tails and achieved a correlation of 0.85 between PGC and WCX-HILIC LC methods. Together, our method facilitates the analysis of single and combinatorial histone PTMs with much simpler applicability for conventional proteomics labs than the state-of-the-art middle-down MS.
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Affiliation(s)
- Kevin A Janssen
- Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mariel Coradin
- Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Congcong Lu
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Benjamin A Garcia
- Biochemistry and Molecular Biophysics Graduate Group, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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25
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Holt MV, Wang T, Young NL. One-Pot Quantitative Top- and Middle-Down Analysis of GluC-Digested Histone H4. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2514-2525. [PMID: 31147891 DOI: 10.1007/s13361-019-02219-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/27/2019] [Accepted: 04/27/2019] [Indexed: 05/28/2023]
Abstract
Histone post-translational modifications (PTMs) have been intensively investigated due to their essential function in eukaryotic genome regulation. Histone modifications have been effectively studied using modified bottom-up proteomics approaches; however, the methods often do not capture single-molecule combinations of PTMs (proteoforms) that mediate known and expected biochemical mechanisms. Both middle-down mass spectrometry (MS) and top-down MS quantitation of H4 proteoforms present viable access to this important information. Histone H4 middle-down has previously avoided GluC digestion due to complex digestion products and interferences; however, the common AspN digestion cleaves at amino acid 23, disconnecting K31ac from other PTMs. Here, we demonstrate the effective use of GluC-based middle-down quantitation and compare it to top-down-based quantitation of proteoforms. Despite potential interferences in the m/z space, the proteoforms arising from all three GluC products (E52, E53, and E63) and intact H4 are chromatographically resolved and successfully analyzed in a single LC-MS analysis. Quantitative results and associated analytical metrics are compared between the different analytes of a single sample digested to different extents to reveal general concordance as well as the relative biases and complementarity of each approach. There is moderate proteoform discordance between digestion products (e.g., E52 and E53); however, each digestion product exhibits high concordance, regardless of digestion time. Under the conditions used, the GluC products are better chromatographically resolved yet show greater variance than the top-down quantitation that are more extensively sampled for MS2. GluC-based middle-down of H4 is thus viable. Both top-down and middle-down approaches have comparable quantitation capacity and are complementary.
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Affiliation(s)
- Matthew V Holt
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Tao Wang
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Nicolas L Young
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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26
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Sessa A, Fagnocchi L, Mastrototaro G, Massimino L, Zaghi M, Indrigo M, Cattaneo S, Martini D, Gabellini C, Pucci C, Fasciani A, Belli R, Taverna S, Andreazzoli M, Zippo A, Broccoli V. SETD5 Regulates Chromatin Methylation State and Preserves Global Transcriptional Fidelity during Brain Development and Neuronal Wiring. Neuron 2019; 104:271-289.e13. [DOI: 10.1016/j.neuron.2019.07.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/20/2019] [Accepted: 07/12/2019] [Indexed: 12/15/2022]
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27
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Histone H3K27 dimethyl loss is highly specific for malignant peripheral nerve sheath tumor and distinguishes true PRC2 loss from isolated H3K27 trimethyl loss. Mod Pathol 2019; 32:1434-1446. [PMID: 31175328 PMCID: PMC6763358 DOI: 10.1038/s41379-019-0287-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 02/06/2023]
Abstract
Malignant peripheral nerve sheath tumors contain loss of histone H3K27 trimethylation (H3K27me3) due to driver mutations affecting the polycomb repressive complex 2 (PRC2). Consequently, loss of H3K27me3 staining has served as a diagnostic marker for this tumor type. However, recent reports demonstrate H3K27me3 loss in numerous other tumors, including some in the differential diagnosis of malignant peripheral nerve sheath tumor. Since these tumors lose H3K27me3 through mechanisms distinct from PRC2 loss, we set out to determine whether loss of dimethylation of H3K27, which is also catalyzed by PRC2, might be a more specific marker of PRC2 loss and malignant peripheral nerve sheath tumor. Using mass spectrometry, we identify a near complete loss of H3K27me2 in malignant peripheral nerve sheath tumors and cell lines. Immunohistochemical analysis of 72 malignant peripheral nerve sheath tumors, seven K27M-mutant gliomas, 43 ependymomas, and 10 Merkel cell carcinomas demonstrates that while H3K27me3 loss is common across these tumor types, H3K27me2 loss is limited to malignant peripheral nerve sheath tumors and is highly concordant with H3K27me3 loss (33/34 cases). Thus, increased specificity does not come at the cost of greatly reduced sensitivity. To further compare H3K27me2 and H3K27me3 immunohistochemistry, we investigated 42 melanomas and 54 synovial sarcomas, histologic mimics of malignant peripheral nerve sheath tumor with varying degrees of H3K27me3 loss in prior reports. While global H3K27me3 loss was not seen in these tumors, weak and limited H3K27me3 staining was common. By contrast, H3K27me2 staining was more clearly retained in all cases, making it a superior binary classifier. This was confirmed by digital image analysis of stained slides. Our findings indicate that H3K27me2 loss is highly specific for PRC2 loss and that PRC2 loss is a rarer phenomenon than H3K27me3 loss. Consequently, H3K27me2 loss is a superior diagnostic marker for malignant peripheral nerve sheath tumor.
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28
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De Clerck L, Willems S, Noberini R, Restellini C, Van Puyvelde B, Daled S, Bonaldi T, Deforce D, Dhaenens M. hSWATH: Unlocking SWATH's Full Potential for an Untargeted Histone Perspective. J Proteome Res 2019; 18:3840-3849. [PMID: 31429292 DOI: 10.1021/acs.jproteome.9b00214] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Mass spectrometry (MS) has become the technique of choice for large-scale analysis of histone post-translational modifications (hPTMs) and their combinatorial patterns, especially in untargeted settings where novel discovery-driven hypotheses are being generated. However, MS-based histone analysis requires a distinct sample preparation, acquisition, and data analysis workflow when compared to traditional MS-based approaches. To this end, sequential window acquisition of all theoretical fragment ion spectra (SWATH) has great potential, as it allows for untargeted accurate identification and quantification of hPTMs. Here, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). We assess its validity on a technical dataset of time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e., acetylated substrate peptides reduce in intensity. We successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines.
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Affiliation(s)
- Laura De Clerck
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Sander Willems
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Roberta Noberini
- Department of Experimental Oncology, IEO , European Institute of Oncology IRCCS , 20141 Milan , Italy
| | - Camilla Restellini
- Department of Experimental Oncology, IEO , European Institute of Oncology IRCCS , 20141 Milan , Italy
| | - Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Simon Daled
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Tiziana Bonaldi
- Department of Experimental Oncology, IEO , European Institute of Oncology IRCCS , 20141 Milan , Italy
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology , Ghent University , 9000 Ghent , Belgium
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29
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Aubert Y, Egolf S, Capell BC. The Unexpected Noncatalytic Roles of Histone Modifiers in Development and Disease. Trends Genet 2019; 35:645-657. [PMID: 31301850 DOI: 10.1016/j.tig.2019.06.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 01/13/2023]
Abstract
Epigenetic regulation is critical for the precise control of cellular fate and developmental programs. Disruption of epigenetic information is increasingly appreciated as a potential driving mechanism in both developmental disorders as well as ubiquitous diseases such as cancer. Consistent with this, mutations in histone modifying enzymes are amongst the most frequent events in all of human cancer. While early studies have focused on the canonical enzymatic functions involved in catalyzing modifications to histones, more recent studies have uncovered a new layer of critical nonenzymatic roles in transcriptional regulation for these proteins. Here, we provide an overview of these surprising, yet exciting, noncanonical, noncatalytic roles, and highlight how these revelations may have important implications for understanding disease and the future of epigenome-targeting therapies.
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Affiliation(s)
- Yann Aubert
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shaun Egolf
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brian C Capell
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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30
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Sidoli S, Trefely S, Garcia BA, Carrer A. Integrated Analysis of Acetyl-CoA and Histone Modification via Mass Spectrometry to Investigate Metabolically Driven Acetylation. Methods Mol Biol 2019; 1928:125-147. [PMID: 30725455 DOI: 10.1007/978-1-4939-9027-6_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Acetylation is a highly abundant and dynamic post-translational modification (PTM) on histone proteins which, when present on chromatin-bound histones, facilitates the accessibility of DNA for gene transcription. The central metabolite, acetyl-CoA, is a substrate for acetyltransferases, which catalyze protein acetylation. Acetyl-CoA is an essential intermediate in diverse metabolic pathways, and cellular acetyl-CoA levels fluctuate according to extracellular nutrient availability and the metabolic state of the cell. The Michaelis constant (Km) of most histone acetyltransferases (HATs), which specifically target histone proteins, falls within the range of cellular acetyl-CoA concentrations. As a consequence, global levels of histone acetylation are often restricted by availability of acetyl-CoA. Such metabolic regulation of histone acetylation is important for cell proliferation, differentiation, and a variety of cellular functions. In cancer, numerous oncogenic signaling events hijack cellular metabolism, ultimately inducing an extensive rearrangement of the epigenetic state of the cell. Understanding metabolic control of the epigenome through histone acetylation is essential to illuminate the molecular mechanisms by which cells sense, adapt, and occasionally disengage nutrient fluctuations and environmental cues from gene expression. In particular, targeting metabolic regulators or even dietary interventions to impact acetyl-CoA availability and histone acetylation is a promising target in cancer therapy. Liquid chromatography coupled to mass spectrometry (LC-MS) is the most accurate methodology to quantify protein PTMs and metabolites. In this chapter, we present state-of-the-art protocols to analyze histone acetylation and acetyl-CoA. Histones are extracted and digested into short peptides (4-20 aa) prior to LC-MS. Acetyl-CoA is extracted from cells and analyzed using an analogous mass spectrometry-based procedure. Model systems can be fed with isotopically labeled substrates to investigate the metabolic preference for acetyl-CoA production and the metabolic dependence and turnover of histone acetylation. We also present an example of data integration to correlate changes in acetyl-CoA production with histone acetylation.
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Affiliation(s)
- Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Sophie Trefely
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.,A. J. Drexel Autism Institute, Drexel University, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Alessandro Carrer
- Department of Cancer Biology, Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA, USA.
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Lund PJ, Kori Y, Zhao X, Sidoli S, Yuan ZF, Garcia BA. Isotopic Labeling and Quantitative Proteomics of Acetylation on Histones and Beyond. Methods Mol Biol 2019; 1977:43-70. [PMID: 30980322 DOI: 10.1007/978-1-4939-9232-4_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Lysine acetylation is an important posttranslational modification (PTM) that regulates the function of proteins by affecting their localization, stability, binding, and enzymatic activity. Aberrant acetylation patterns have been observed in numerous diseases, most notably cancer, which has spurred the development of potential therapeutics that target acetylation pathways. Mass spectrometry (MS) has become the most adopted tool not only for the qualitative identification of acetylation sites but also for their large-scale quantification. By using heavy isotope labeling in cell culture combined with MS, it is now possible to accurately quantify newly synthesized acetyl groups and other PTMs, allowing differentiation between dynamically regulated and steady-state modifications. Here, we describe MS-based protocols to identify acetylation sites and quantify acetylation rates on both proteins in general and in the special case of histones. In the experimental approach for the former, 13C-glucose and D3-acetate are used to metabolically label protein acetylation in cells with stable isotopes, thus allowing isotope incorporation to be tracked over time. After protein extraction and digestion, acetylated peptides are enriched via immunoprecipitation and then analyzed by MS. For histones, a similar metabolic labeling approach is performed, followed by acid extraction, derivatization with propionic anhydride, and trypsin digestion prior to MS analysis. The procedures presented may be adapted to investigate acetylation dynamics in a broad range of experimental contexts, including different cell types and stimulation conditions.
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Affiliation(s)
- Peder J Lund
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Yekaterina Kori
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Xiaolu Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Simone Sidoli
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Zuo-Fei Yuan
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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Kuznetsov VI, Haws SA, Fox CA, Denu JM. General method for rapid purification of native chromatin fragments. J Biol Chem 2018; 293:12271-12282. [PMID: 29794135 PMCID: PMC6078465 DOI: 10.1074/jbc.ra118.002984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/10/2018] [Indexed: 11/06/2022] Open
Abstract
Biochemical, proteomic, and epigenetic studies of chromatin rely on the ability to efficiently isolate native nucleosomes in high yield and purity. However, isolation of native chromatin suitable for many downstream experiments remains a challenging task. This is especially true for the budding yeast Saccharomyces cerevisiae, which continues to serve as an important model organism for the study of chromatin structure and function. Here, we developed a time- and cost-efficient universal protocol for isolation of native chromatin fragments from yeast, insect, and mammalian cells. The resulting protocol preserves histone posttranslational modification in the native chromatin state and is applicable for both parallel multisample spin-column purification and large-scale isolation. This protocol is based on the efficient and stable purification of polynucleosomes and features a combination of optimized cell lysis and purification conditions, three options for chromatin fragmentation, and a novel ion-exchange chromatographic purification strategy. The procedure will aid chromatin researchers interested in isolating native chromatin material for biochemical studies and serve as a mild, acid- and detergent-free sample preparation method for MS analysis.
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Affiliation(s)
- Vyacheslav I Kuznetsov
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715; Wisconsin Institute for Discovery, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715
| | - Spencer A Haws
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715; Wisconsin Institute for Discovery, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715
| | - Catherine A Fox
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715.
| | - John M Denu
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715; Wisconsin Institute for Discovery, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715; Morgridge Institute for Research, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53715.
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Shastrula PK, Lund PJ, Garcia BA, Janicki SM. Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms. J Biol Chem 2018; 293:12360-12377. [PMID: 29921582 DOI: 10.1074/jbc.ra118.001845] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/30/2018] [Indexed: 01/26/2023] Open
Abstract
The histone H3 variant H3.3 is a highly conserved and dynamic regulator of chromatin organization. Therefore, fully elucidating its nucleosome incorporation mechanisms is essential to understanding its functions in epigenetic inheritance. We previously identified the RNase P protein subunit, Rpp29, as a repressor of H3.3 chromatin assembly. Here, we use a biochemical assay to show that Rpp29 interacts with H3.3 through a sequence element in its own N terminus, and we identify a novel interaction with histone H2B at an adjacent site. The fact that archaeal Rpp29 does not include this N-terminal region suggests that it evolved to regulate eukaryote-specific functions. Oncogenic H3.3 mutations alter the H3.3-Rpp29 interaction, which suggests that they could dysregulate Rpp29 function in chromatin assembly. We also used KNS42 cells, an H3.3(G34V) pediatric high-grade glioma cell line, to show that Rpp29 1) represses H3.3 incorporation into transcriptionally active protein-coding, rRNA, and tRNA genes; 2) represses mRNA, protein expression, and antisense RNA; and 3) represses euchromatic post-translational modifications (PTMs) and promotes heterochromatic PTM deposition (i.e. histone H3 Lys-9 trimethylation (H3K9me3) and H3.1/2/3K27me3). Notably, we also found that K27me2 is increased and K36me1 decreased on H3.3(G34V), which suggests that Gly-34 mutations dysregulate Lys-27 and Lys-36 methylation in cis The fact that Rpp29 represses H3.3 chromatin assembly and sense and antisense RNA and promotes H3K9me3 and H3K27me3 suggests that Rpp29 regulates H3.3-mediated epigenetic mechanisms by processing a transcribed signal that recruits H3.3 to its incorporation sites.
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Affiliation(s)
- Prashanth Krishna Shastrula
- From the Wistar Institute, Philadelphia, Pennsylvania 19104.,the Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania 19104, and
| | - Peder J Lund
- the Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Benjamin A Garcia
- the Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Susan M Janicki
- From the Wistar Institute, Philadelphia, Pennsylvania 19104,
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Tvardovskiy A, Schwämmle V, Kempf SJ, Rogowska-Wrzesinska A, Jensen ON. Accumulation of histone variant H3.3 with age is associated with profound changes in the histone methylation landscape. Nucleic Acids Res 2017; 45:9272-9289. [PMID: 28934504 PMCID: PMC5766163 DOI: 10.1093/nar/gkx696] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/26/2017] [Indexed: 12/20/2022] Open
Abstract
Deposition of replication-independent histone variant H3.3 into chromatin is essential for many biological processes, including development and reproduction. Unlike replication-dependent H3.1/2 isoforms, H3.3 is expressed throughout the cell cycle and becomes enriched in postmitotic cells with age. However, lifelong dynamics of H3 variant replacement and the impact of this process on chromatin organization remain largely undefined. Using quantitative middle-down proteomics we demonstrate that H3.3 accumulates to near saturation levels in the chromatin of various mouse somatic tissues by late adulthood. Accumulation of H3.3 is associated with profound changes in global levels of both individual and combinatorial H3 methyl modifications. A subset of these modifications exhibit distinct relative abundances on H3 variants and remain stably enriched on H3.3 throughout the lifespan, suggesting a causal relationship between H3 variant replacement and age-dependent changes in H3 methylation. Furthermore, the H3.3 level is drastically reduced in human hepatocarcinoma cells as compared to nontumoral hepatocytes, suggesting the potential utility of the H3.3 relative abundance as a biomarker of abnormal cell proliferation activity. Overall, our study provides the first quantitative characterization of dynamic changes in H3 proteoforms throughout lifespan in mammals and suggests a role for H3 variant replacement in modulating H3 methylation landscape with age.
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Affiliation(s)
- Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.,Center for Epigenetics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.,Center for Epigenetics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Stefan J Kempf
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.,Center for Epigenetics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark.,Center for Epigenetics, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
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Abstract
INTRODUCTION Analysis of histone post-translational modifications (PTMs) by mass spectrometry (MS) has become a fundamental tool for the characterization of chromatin composition and dynamics. Histone PTMs benchmark several biological states of chromatin, including regions of active enhancers, active/repressed gene promoters and damaged DNA. These complex regulatory mechanisms are often defined by combinatorial histone PTMs; for instance, active enhancers are commonly occupied by both marks H3K4me1 and H3K27ac. The traditional bottom-up MS strategy identifies and quantifies short (aa 4-20) tryptic peptides, and it is thus not suitable for the characterization of combinatorial PTMs. Areas covered: Here, we review the advancement of the middle-down MS strategy applied to histones, which consists in the analysis of intact histone N-terminal tails (aa 50-60). Middle-down MS has reached sufficient robustness and reliability, and it is far less technically challenging than PTM quantification on intact histones (top-down). However, the very few chromatin biology studies applying middle-down MS resulting from PubMed searches indicate that it is still very scarcely exploited, potentially due to the apparent high complexity of method and analysis. Expert commentary: We will discuss the state-of-the-art workflow and examples of existing studies, aiming to highlight its potential and feasibility for studies of cell biologists interested in chromatin and epigenetics.
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Affiliation(s)
- Simone Sidoli
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
| | - Benjamin A Garcia
- a Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine , University of Pennsylvania , Philadelphia , PA , USA
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