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Yang Y, Feng W, Zhou J, Zhang R, Lin X, Sooranna SR, Deng Y, Shi D. Epigenetic modifications of gonadotropin receptors can regulate follicular development. Anim Reprod Sci 2024; 268:107534. [PMID: 39047429 DOI: 10.1016/j.anireprosci.2024.107534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 05/14/2024] [Accepted: 06/11/2024] [Indexed: 07/27/2024]
Abstract
The spatiotemporal transcription of follicle-stimulating hormone receptor (FSHR) and luteinizing hormone/human chorionic gonadotropin receptor (LHCGR) are crucial events for follicular development. However, their regulatory mechanisms are unclear. DNA methylation and histone acetylation are the main epigenetic modifications, and play important roles in transcriptional expression, which regulate cell responses including cell proliferation, senescence and apoptosis. This review will discuss the dynamic epigenetic modifications of FSHR and LHCGR that occur during the process of follicular development and their response to gonadotropins. In addition, some alteration patterns that occur during these epigenetic modifications, as well as their retrospect retrotransposons, which regulate the gene expression levels of FSHR and LHCGR will be discussed.
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Affiliation(s)
- Yanyan Yang
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Wanyou Feng
- School of Environmental and Life Sciences, Nanning Normal University, Nanning 530023, China
| | - Jinhua Zhou
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Ruimen Zhang
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Xinyue Lin
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Suren Rao Sooranna
- Department of Metabolism, Digestion and Reproduction, Imperial College London, Chelsea and Westminster Hospital, London SW10 9NH, United Kingdom
| | - Yanfei Deng
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
| | - Deshun Shi
- Guangxi Key Laboratory of Animal Breeding and Disease Control, College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
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2
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Nacev BA, Dabas Y, Paul MR, Pacheco C, Mitchener M, Perez Y, Fang Y, Soshnev AA, Barrows D, Carroll T, Socci ND, St Jean SC, Tiwari S, Gruss MJ, Monette S, Tap WD, Garcia BA, Muir T, Allis CD. Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation. Nat Commun 2024; 15:5155. [PMID: 38886411 PMCID: PMC11183192 DOI: 10.1038/s41467-024-49486-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 06/06/2024] [Indexed: 06/20/2024] Open
Abstract
Dysregulated epigenetic states are a hallmark of cancer and often arise from genetic alterations in epigenetic regulators. This includes missense mutations in histones, which, together with associated DNA, form nucleosome core particles. However, the oncogenic mechanisms of most histone mutations are unknown. Here, we demonstrate that cancer-associated histone mutations at arginines in the histone H3 N-terminal tail disrupt repressive chromatin domains, alter gene regulation, and dysregulate differentiation. We find that histone H3R2C and R26C mutants reduce transcriptionally repressive H3K27me3. While H3K27me3 depletion in cells expressing these mutants is exclusively observed on the minor fraction of histone tails harboring the mutations, the same mutants recurrently disrupt broad H3K27me3 domains in the chromatin context, including near developmentally regulated promoters. H3K27me3 loss leads to de-repression of differentiation pathways, with concordant effects between H3R2 and H3R26 mutants despite different proximity to the PRC2 substrate, H3K27. Functionally, H3R26C-expressing mesenchymal progenitor cells and murine embryonic stem cell-derived teratomas demonstrate impaired differentiation. Collectively, these data show that cancer-associated H3 N-terminal arginine mutations reduce PRC2 activity and disrupt chromatin-dependent developmental functions, a cancer-relevant phenotype.
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Affiliation(s)
- Benjamin A Nacev
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA.
| | - Yakshi Dabas
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Matthew R Paul
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Christian Pacheco
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
| | - Michelle Mitchener
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - Yekaterina Perez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Yan Fang
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Alexey A Soshnev
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Douglas Barrows
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY, 10065, USA
| | - Nicholas D Socci
- Bioinformatics Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Samantha C St Jean
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sagarika Tiwari
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
| | - Michael J Gruss
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, 15213, USA
| | - Sebastien Monette
- Laboratory of Comparative Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - William D Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Tom Muir
- Department of Chemistry, Princeton University, Princeton, NJ, 08544, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, 10065, USA
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3
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Tibben BM, Rothbart SB. Mechanisms of DNA Methylation Regulatory Function and Crosstalk with Histone Lysine Methylation. J Mol Biol 2024; 436:168394. [PMID: 38092287 PMCID: PMC10957332 DOI: 10.1016/j.jmb.2023.168394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/20/2023]
Abstract
DNA methylation is a well-studied epigenetic modification that has key roles in regulating gene expression, maintaining genome integrity, and determining cell fate. Precisely how DNA methylation patterns are established and maintained in specific cell types at key developmental stages is still being elucidated. However, research over the last two decades has contributed to our understanding of DNA methylation regulation by other epigenetic processes. Specifically, lysine methylation on key residues of histone proteins has been shown to contribute to the allosteric regulation of DNA methyltransferase (DNMT) activities. In this review, we discuss the dynamic interplay between DNA methylation and histone lysine methylation as epigenetic regulators of genome function by synthesizing key recent studies in the field. With a focus on DNMT3 enzymes, we discuss mechanisms of DNA methylation and histone lysine methylation crosstalk in the regulation of gene expression and the maintenance of genome integrity. Further, we discuss how alterations to the balance of various sites of histone lysine methylation and DNA methylation contribute to human developmental disorders and cancers. Finally, we provide perspectives on the current direction of the field and highlight areas for continued research and development.
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Affiliation(s)
- Bailey M Tibben
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Scott B Rothbart
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
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4
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Harris RJ, Heer M, Levasseur MD, Cartwright TN, Weston B, Mitchell JL, Coxhead JM, Gaughan L, Prendergast L, Rico D, Higgins JMG. Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation. Nat Commun 2023; 14:7243. [PMID: 37945563 PMCID: PMC10636195 DOI: 10.1038/s41467-023-43115-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Histone modifications influence the recruitment of reader proteins to chromosomes to regulate events including transcription and cell division. The idea of a histone code, where combinations of modifications specify unique downstream functions, is widely accepted and can be demonstrated in vitro. For example, on synthetic peptides, phosphorylation of Histone H3 at threonine-3 (H3T3ph) prevents the binding of reader proteins that recognize trimethylation of the adjacent lysine-4 (H3K4me3), including the TAF3 component of TFIID. To study these combinatorial effects in cells, we analyzed the genome-wide distribution of H3T3ph and H3K4me2/3 during mitosis. We find that H3T3ph anti-correlates with adjacent H3K4me2/3 in cells, and that the PHD domain of TAF3 can bind H3K4me2/3 in isolated mitotic chromatin despite the presence of H3T3ph. Unlike in vitro, H3K4 readers are still displaced from chromosomes in mitosis in Haspin-depleted cells lacking H3T3ph. H3T3ph is therefore unlikely to be responsible for transcriptional downregulation during cell division.
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Affiliation(s)
- Rebecca J Harris
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Mark D Levasseur
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Bethany Weston
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jennifer L Mitchell
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jonathan M Coxhead
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Luke Gaughan
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Lisa Prendergast
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad Sevilla-Universidad Pablo de Olavide-Junta de Andalucía, 41092, Seville, Spain.
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
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5
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Graham-Paquin AL, Saini D, Sirois J, Hossain I, Katz MS, Zhuang QKW, Kwon SY, Yamanaka Y, Bourque G, Bouchard M, Pastor WA. ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development. Nucleic Acids Res 2023; 51:7314-7329. [PMID: 37395395 PMCID: PMC10415128 DOI: 10.1093/nar/gkad540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/24/2023] [Accepted: 06/09/2023] [Indexed: 07/04/2023] Open
Abstract
ZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found that Zmym2-/- mice show embryonic lethality by E10.5. Molecular characterization of Zmym2-/- embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice. Zmym2-/- embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. ZMYM2 homes to sites of PRC1.6 and TRIM28 complex binding, mediating repression of germline genes and transposons respectively. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation. ZMYM2-/- human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.
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Affiliation(s)
- Adda-Lee Graham-Paquin
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Deepak Saini
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jacinthe Sirois
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Ishtiaque Hossain
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Megan S Katz
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan
| | - Sin Young Kwon
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Yojiro Yamanaka
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan
- Canadian Center for Computational Genomics,McGill University, Montreal, Quebec, Canada
| | - Maxime Bouchard
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
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6
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Hamagami N, Wu DY, Clemens AW, Nettles SA, Li A, Gabel HW. NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons. Mol Cell 2023; 83:1412-1428.e7. [PMID: 37098340 PMCID: PMC10230755 DOI: 10.1016/j.molcel.2023.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 02/16/2023] [Accepted: 03/30/2023] [Indexed: 04/27/2023]
Abstract
During postnatal development, the DNA methyltransferase DNMT3A deposits high levels of non-CG cytosine methylation in neurons. This methylation is critical for transcriptional regulation, and loss of this mark is implicated in DNMT3A-associated neurodevelopmental disorders (NDDs). Here, we show in mice that genome topology and gene expression converge to shape histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. We show that NSD1, an H3K36 methyltransferase mutated in NDD, is required for the patterning of megabase-scale H3K36me2 and non-CG methylation in neurons. We find that brain-specific deletion of NSD1 causes altered DNA methylation that overlaps with DNMT3A disorder models to drive convergent dysregulation of key neuronal genes that may underlie shared phenotypes in NSD1- and DNMT3A-associated NDDs. Our findings indicate that H3K36me2 deposited by NSD1 is important for neuronal non-CG DNA methylation and suggest that the H3K36me2-DNMT3A-non-CG-methylation pathway is likely disrupted in NSD1-associated NDDs.
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Affiliation(s)
- Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Aidan Li
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St Louis, MO 63110-1093, USA.
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7
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Hamagami N, Wu DY, Clemens AW, Nettles SA, Gabel HW. NSD1 deposits histone H3 lysine 36 dimethylation to pattern non-CG DNA methylation in neurons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.17.528965. [PMID: 36824816 PMCID: PMC9949142 DOI: 10.1101/2023.02.17.528965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
During postnatal development the DNA methyltransferase DNMT3A deposits high levels of non-CG cytosine methylation in neurons. This unique methylation is critical for transcriptional regulation in the mature mammalian brain, and loss of this mark is implicated in DNMT3A-associated neurodevelopmental disorders (NDDs). The mechanisms determining genomic non-CG methylation profiles are not well defined however, and it is unknown if this pathway is disrupted in additional NDDs. Here we show that genome topology and gene expression converge to shape histone H3 lysine 36 dimethylation (H3K36me2) profiles, which in turn recruit DNMT3A and pattern neuronal non-CG methylation. We show that NSD1, the H3K36 methyltransferase mutated in the NDD, Sotos syndrome, is required for megabase-scale patterning of H3K36me2 and non-CG methylation in neurons. We find that brain-specific deletion of NSD1 causes alterations in DNA methylation that overlap with models of DNMT3A disorders and define convergent disruption in the expression of key neuronal genes in these models that may contribute to shared phenotypes in NSD1- and DNMT3A-associated NDD. Our findings indicate that H3K36me2 deposited by NSD1 is an important determinant of neuronal non-CG DNA methylation and implicates disruption of this methylation in Sotos syndrome. Highlights Topology-associated DNA methylation and gene expression independently contribute to neuronal gene body and enhancer non-CG DNA methylation patterns.Topology-associated H3K36me2 patterns and local enrichment of H3K4 methylation impact deposition of non-CG methylation by DNMT3A. Disruption of NSD1 in vivo leads to alterations in H3K36me2, DNA methylation, and gene expression that overlap with models of DNMT3A disorders.
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Affiliation(s)
- Nicole Hamagami
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- These authors contributed equally
| | - Dennis Y Wu
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- These authors contributed equally
| | - Adam W Clemens
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
| | - Sabin A Nettles
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
| | - Harrison W Gabel
- Department of Neuroscience, Washington University School of Medicine, St Louis MO 63110-1093, USA
- Lead contact
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8
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Characterizing crosstalk in epigenetic signaling to understand disease physiology. Biochem J 2023; 480:57-85. [PMID: 36630129 PMCID: PMC10152800 DOI: 10.1042/bcj20220550] [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: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Epigenetics, the inheritance of genomic information independent of DNA sequence, controls the interpretation of extracellular and intracellular signals in cell homeostasis, proliferation and differentiation. On the chromatin level, signal transduction leads to changes in epigenetic marks, such as histone post-translational modifications (PTMs), DNA methylation and chromatin accessibility to regulate gene expression. Crosstalk between different epigenetic mechanisms, such as that between histone PTMs and DNA methylation, leads to an intricate network of chromatin-binding proteins where pre-existing epigenetic marks promote or inhibit the writing of new marks. The recent technical advances in mass spectrometry (MS) -based proteomic methods and in genome-wide DNA sequencing approaches have broadened our understanding of epigenetic networks greatly. However, further development and wider application of these methods is vital in developing treatments for disorders and pathologies that are driven by epigenetic dysregulation.
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9
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Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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10
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de Mendoza A, Nguyen TV, Ford E, Poppe D, Buckberry S, Pflueger J, Grimmer MR, Stolzenburg S, Bogdanovic O, Oshlack A, Farnham PJ, Blancafort P, Lister R. Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability. Genome Biol 2022; 23:163. [PMID: 35883107 PMCID: PMC9316731 DOI: 10.1186/s13059-022-02728-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/06/2022] [Indexed: 12/22/2022] Open
Abstract
Background Cytosine DNA methylation is widely described as a transcriptional repressive mark with the capacity to silence promoters. Epigenome engineering techniques enable direct testing of the effect of induced DNA methylation on endogenous promoters; however, the downstream effects have not yet been comprehensively assessed. Results Here, we simultaneously induce methylation at thousands of promoters in human cells using an engineered zinc finger-DNMT3A fusion protein, enabling us to test the effect of forced DNA methylation upon transcription, chromatin accessibility, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that transcriptional responses to DNA methylation are highly context-specific, including lack of repression, as well as cases of increased gene expression, which appears to be driven by the eviction of methyl-sensitive transcriptional repressors. Furthermore, we find that some regulatory networks can override DNA methylation and that promoter methylation can cause alternative promoter usage. DNA methylation deposited at promoter and distal regulatory regions is rapidly erased after removal of the zinc finger-DNMT3A fusion protein, in a process combining passive and TET-mediated demethylation. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. Conclusions These findings have important implications for epigenome engineering and demonstrate that the response of promoters to DNA methylation is more complex than previously appreciated. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-022-02728-5.
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Affiliation(s)
- Alex de Mendoza
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia. .,School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.
| | - Trung Viet Nguyen
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Ethan Ford
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Daniel Poppe
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Sam Buckberry
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jahnvi Pflueger
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia
| | - Matthew R Grimmer
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA.,Integrated Genetics and Genomics, University of California, Davis, 451 Health Sciences Dr, Davis, CA, 95616, USA.,Department of Neurological Surgery, University of California, 1450 3rd St, San Francisco, CA, 94158, USA
| | - Sabine Stolzenburg
- School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia
| | - Ozren Bogdanovic
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia.,Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, 2052, Australia
| | - Alicia Oshlack
- The Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.,School of BioScience, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Peggy J Farnham
- Department of Biochemistry and Molecular Medicine, University of Southern California, 1450 Biggy St, Los Angeles, CA, 90089, USA
| | - Pilar Blancafort
- Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.,School of Anatomy, Physiology and Human Biology, The University of Western Australia, 35 Stirling Hwy, Crawley, WA, 6009, Australia.,The Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ryan Lister
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia. .,Harry Perkins Institute of Medical Research, QEII Medical Centre and Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
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11
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Sahoo OS, Pethusamy K, Srivastava TP, Talukdar J, Alqahtani MS, Abbas M, Dhar R, Karmakar S. The metabolic addiction of cancer stem cells. Front Oncol 2022; 12:955892. [PMID: 35957877 PMCID: PMC9357939 DOI: 10.3389/fonc.2022.955892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer stem cells (CSC) are the minor population of cancer originating cells that have the capacity of self-renewal, differentiation, and tumorigenicity (when transplanted into an immunocompromised animal). These low-copy number cell populations are believed to be resistant to conventional chemo and radiotherapy. It was reported that metabolic adaptation of these elusive cell populations is to a large extent responsible for their survival and distant metastasis. Warburg effect is a hallmark of most cancer in which the cancer cells prefer to metabolize glucose anaerobically, even under normoxic conditions. Warburg's aerobic glycolysis produces ATP efficiently promoting cell proliferation by reprogramming metabolism to increase glucose uptake and stimulating lactate production. This metabolic adaptation also seems to contribute to chemoresistance and immune evasion, a prerequisite for cancer cell survival and proliferation. Though we know a lot about metabolic fine-tuning in cancer, what is still in shadow is the identity of upstream regulators that orchestrates this process. Epigenetic modification of key metabolic enzymes seems to play a decisive role in this. By altering the metabolic flux, cancer cells polarize the biochemical reactions to selectively generate "onco-metabolites" that provide an added advantage for cell proliferation and survival. In this review, we explored the metabolic-epigenetic circuity in relation to cancer growth and proliferation and establish the fact how cancer cells may be addicted to specific metabolic pathways to meet their needs. Interestingly, even the immune system is re-calibrated to adapt to this altered scenario. Knowing the details is crucial for selective targeting of cancer stem cells by choking the rate-limiting stems and crucial branch points, preventing the formation of onco-metabolites.
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Affiliation(s)
- Om Saswat Sahoo
- Department of Biotechnology, National Institute of technology, Durgapur, India
| | - Karthikeyan Pethusamy
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Joyeeta Talukdar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Mohammed S. Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
- BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester, United Kingdom
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, Saudi Arabia
- Computers and communications Department, College of Engineering, Delta University for Science and Technology, Gamasa, Egypt
| | - Ruby Dhar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Subhradip Karmakar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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12
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Mattei AL, Bailly N, Meissner A. DNA methylation: a historical perspective. Trends Genet 2022; 38:676-707. [DOI: 10.1016/j.tig.2022.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
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13
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Janssen SM, Lorincz MC. Interplay between chromatin marks in development and disease. Nat Rev Genet 2022; 23:137-153. [PMID: 34608297 DOI: 10.1038/s41576-021-00416-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2021] [Indexed: 02/07/2023]
Abstract
DNA methylation (DNAme) and histone post-translational modifications (PTMs) have important roles in transcriptional regulation. Although many reports have characterized the functions of such chromatin marks in isolation, recent genome-wide studies reveal surprisingly complex interactions between them. Here, we focus on the interplay between DNAme and methylation of specific lysine residues on the histone H3 tail. We describe the impact of genetic perturbation of the relevant methyltransferases in the mouse on the landscape of chromatin marks as well as the transcriptome. In addition, we discuss the specific neurodevelopmental growth syndromes and cancers resulting from pathogenic mutations in the human orthologues of these genes. Integrating these observations underscores the fundamental importance of crosstalk between DNA and histone H3 methylation in development and disease.
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Affiliation(s)
- Sanne M Janssen
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matthew C Lorincz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, British Columbia, Canada.
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14
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Cedar H, Sabag O, Reizel Y. The role of DNA methylation in genome-wide gene regulation during development. Development 2022; 149:274050. [DOI: 10.1242/dev.200118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ABSTRACT
Although it is well known that DNA methylation serves to repress gene expression, precisely how it functions during the process of development remains unclear. Here, we propose that the overall pattern of DNA methylation established in the early embryo serves as a sophisticated mechanism for maintaining a genome-wide network of gene regulatory elements in an inaccessible chromatin structure throughout the body. As development progresses, programmed demethylation in each cell type then provides the specificity for maintaining select elements in an open structure. This allows these regulatory elements to interact with a large range of transcription factors and thereby regulate the gene expression profiles that define cell identity.
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Affiliation(s)
- Howard Cedar
- Department of Developmental Biology and Cancer Research, Hebrew University Medical School, P.O. Box 12272, 91120 Jerusalem, Israel
| | - Ofra Sabag
- Department of Developmental Biology and Cancer Research, Hebrew University Medical School, P.O. Box 12272, 91120 Jerusalem, Israel
| | - Yitzhak Reizel
- Faculty of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, 32000 Haifa, Israel
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15
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Tajima S, Suetake I, Takeshita K, Nakagawa A, Kimura H, Song J. Domain Structure of the Dnmt1, Dnmt3a, and Dnmt3b DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:45-68. [PMID: 36350506 PMCID: PMC11025882 DOI: 10.1007/978-3-031-11454-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In mammals, three major DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication. All Dnmts possess multiple domains. For instance, Dnmt3a and Dnmt3b each contain a Pro-Trp-Trp-Pro (PWWP) domain that recognizes the histone H3K36me2/3 mark, an Atrx-Dnmt3-Dnmt3l (ADD) domain that recognizes unmodified histone H3 tail, and a catalytic domain that methylates CpG sites. Dnmt1 contains an N-terminal independently folded domain (NTD) that interacts with a variety of regulatory factors, a replication foci-targeting sequence (RFTS) domain that recognizes the histone H3K9me3 mark and H3 ubiquitylation, a CXXC domain that recognizes unmodified CpG DNA, two tandem Bromo-Adjacent-homology (BAH1 and BAH2) domains that read the H4K20me3 mark with BAH1, and a catalytic domain that preferentially methylates hemimethylated CpG sites. In this chapter, the structures and functions of these domains are described.
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Affiliation(s)
- Shoji Tajima
- Institute for Protein Research, Osaka University, Osaka, Japan.
| | - Isao Suetake
- Department of Nutritional Sciences, Faculty of Nutritional Sciences, Nakamura Gakuen University, Fukuoka, Japan
| | | | - Atsushi Nakagawa
- Laboratory of Supramolecular Crystallography, Institute for Protein Research, Osaka University, Osaka, Japan
| | - Hironobu Kimura
- Institute for Protein Research, Osaka University, Osaka, Japan
| | - Jikui Song
- Department of Biochemistry, University of California Riverside, Riverside, CA, USA.
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16
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Jurkowska RZ, Jeltsch A. Enzymology of Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:69-110. [DOI: 10.1007/978-3-031-11454-0_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Li D, Guo J, Jia R. Histone code reader SPIN1 is a promising target of cancer therapy. Biochimie 2021; 191:78-86. [PMID: 34492335 DOI: 10.1016/j.biochi.2021.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/07/2021] [Accepted: 09/03/2021] [Indexed: 12/19/2022]
Abstract
SPIN1 is a histone methylation reader, which can epigenetically control multiple tumorigenesis-associated signaling pathways, including the Wnt, PI3K/AKT, and RET pathways. Considerable evidence has shown that SPIN1 is overexpressed in many cancers, which can promote cell proliferation, transformation, metastasis, and chemical or radiation resistance. With the growing understanding of the SPIN1 protein structure, some inhibitors have been developed to interfere with the recognition between SPIN1 and histone H3K4me3 and H3R8me2a methylation and block the oncogenic functions of SPIN1. Therefore, SPIN1 is a potential target of cancer therapy. However, the mechanism by which SPIN1-transformed cells overcome the significant mitotic spindle defects and the factors promoting SPIN1 overexpression in cancers remain unclear. In this review, we described the current understanding of the SPIN1 protein structure and its expression, functions, and regulatory mechanisms in carcinogenesis, and discussed the challenges faced in the mechanisms of SPIN1 overexpression and oncogenic functions, and the potential application of anti-SPIN1 treatment in human cancers.
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Affiliation(s)
- Di Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China; Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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18
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Naillat F, Saadeh H, Nowacka-Woszuk J, Gahurova L, Santos F, Tomizawa SI, Kelsey G. Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes. Clin Epigenetics 2021; 13:132. [PMID: 34183052 PMCID: PMC8240245 DOI: 10.1186/s13148-021-01116-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 06/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such techniques are used routinely in both rodent and human species. DNA methylation is a dynamic process that plays a role in epigenetic regulation of gametogenesis and development. In mammalian oocytes, DNA methylation establishment regulates gene expression in the embryos. This regulation is particularly important for a class of genes, imprinted genes, whose expression patterns are crucial for the next generation. The aim of this work was to establish an in vitro culture system for immature mouse oocytes that will allow manipulation of specific factors for a deeper analysis of regulatory mechanisms for establishing transcription regulation-associated methylation patterns. RESULTS An in vitro culture system was developed from immature mouse oocytes that were grown to germinal vesicles (GV) under two different conditions: normoxia (20% oxygen, 20% O2) and hypoxia (5% oxygen, 5% O2). The cultured oocytes were sorted based on their sizes. Reduced representative bisulphite sequencing (RRBS) and RNA-seq libraries were generated from cultured and compared to in vivo-grown oocytes. In the in vitro cultured oocytes, global and CpG-island (CGI) methylation increased gradually along with oocyte growth, and methylation of the imprinted genes was similar to in vivo-grown oocytes. Transcriptomes of the oocytes grown in normoxia revealed chromatin reorganisation and enriched expression of female reproductive genes, whereas in the 5% O2 condition, transcripts were biased towards cellular stress responses. To further confirm the results, we developed a functional assay based on our model for characterising oocyte methylation using drugs that reduce methylation and transcription. When histone methylation and transcription processes were reduced, DNA methylation at CGIs from gene bodies of grown oocytes presented a lower methylation profile. CONCLUSIONS Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo-grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex vivo culture condition. Our results shed light on epigenetic mechanisms for the development of oocytes from an immature to GV oocyte in an in vitro culture model.
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Affiliation(s)
- Florence Naillat
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Diseases Network Research Unit, Faculty of Biochemistry and Molecular Medicine, Oulu University, Oulu, Finland.
| | - Heba Saadeh
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Computer Science, King Abdullah II School of Information Technology, The University of Jordan, Amman, Jordan
| | - Joanna Nowacka-Woszuk
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznan, Poland
| | - Lenka Gahurova
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Early Mammalian Development, Department of Molecular Biology and Genetics, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Fatima Santos
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK
| | - Shin-Ichi Tomizawa
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK.,School of Medicine, Yokohama City University, Yokohama, Japan
| | - Gavin Kelsey
- Epigenetics Program, Babraham Institute, Cambridge, CB22 3AT, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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19
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Nishiyama A, Nakanishi M. Navigating the DNA methylation landscape of cancer. Trends Genet 2021; 37:1012-1027. [PMID: 34120771 DOI: 10.1016/j.tig.2021.05.002] [Citation(s) in RCA: 314] [Impact Index Per Article: 104.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/11/2022]
Abstract
DNA methylation is a chemical modification that defines cell type and lineage through the control of gene expression and genome stability. Disruption of DNA methylation control mechanisms causes a variety of diseases, including cancer. Cancer cells are characterized by aberrant DNA methylation (i.e., genome-wide hypomethylation and site-specific hypermethylation), mainly targeting CpG islands in gene expression regulatory elements. In particular, the early findings that a variety of tumor suppressor genes (TSGs) are targets of DNA hypermethylation in cancer led to the proposal of a model in which aberrant DNA methylation promotes cellular oncogenesis through TSGs silencing. However, recent genome-wide analyses have revealed that this classical model needs to be reconsidered. In this review, we will discuss the molecular mechanisms of DNA methylation abnormalities in cancer as well as their therapeutic potential.
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Affiliation(s)
- Atsuya Nishiyama
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
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20
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Li Y, Chen X, Lu C. The interplay between DNA and histone methylation: molecular mechanisms and disease implications. EMBO Rep 2021; 22:e51803. [PMID: 33844406 PMCID: PMC8097341 DOI: 10.15252/embr.202051803] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 02/16/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022] Open
Abstract
Methylation of cytosine in CpG dinucleotides and histone lysine and arginine residues is a chromatin modification that critically contributes to the regulation of genome integrity, replication, and accessibility. A strong correlation exists between the genome-wide distribution of DNA and histone methylation, suggesting an intimate relationship between these epigenetic marks. Indeed, accumulating literature reveals complex mechanisms underlying the molecular crosstalk between DNA and histone methylation. These in vitro and in vivo discoveries are further supported by the finding that genes encoding DNA- and histone-modifying enzymes are often mutated in overlapping human diseases. Here, we summarize recent advances in understanding how DNA and histone methylation cooperate to maintain the cellular epigenomic landscape. We will also discuss the potential implication of these insights for understanding the etiology of, and developing biomarkers and therapies for, human congenital disorders and cancers that are driven by chromatin abnormalities.
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Affiliation(s)
- Yinglu Li
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Xiao Chen
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
| | - Chao Lu
- Department of Genetics and Development and Herbert Irving Comprehensive Cancer CenterColumbia University Irving Medical CenterNew YorkNYUSA
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21
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Ferrer AI, Trinidad JR, Sandiford O, Etchegaray JP, Rameshwar P. Epigenetic dynamics in cancer stem cell dormancy. Cancer Metastasis Rev 2021; 39:721-738. [PMID: 32394305 DOI: 10.1007/s10555-020-09882-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cancer remains one of the most challenging diseases despite significant advances of early diagnosis and therapeutic treatments. Cancerous tumors are composed of various cell types including cancer stem cells capable of self-renewal, proliferation, differentiation, and invasion of distal tumor sites. Most notably, these cells can enter a dormant cellular state that is resistant to conventional therapies. Thereby, cancer stem cells have the intrinsic potential for tumor initiation, tumor growth, metastasis, and tumor relapse after therapy. Both genetic and epigenetic alterations are attributed to the formation of multiple tumor types. This review is focused on how epigenetic dynamics involving DNA methylation and DNA oxidations are implicated in breast cancer and glioblastoma multiforme. The emergence and progression of these cancer types rely on cancer stem cells with the capacity to enter quiescence also known as a dormant cellular state, which dictates the distinct tumorigenic aggressiveness between breast cancer and glioblastomas.
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Affiliation(s)
- Alejandra I Ferrer
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Jonathan R Trinidad
- Department of Biological Sciences, Rutgers University, Newark, NJ, 07102, USA
| | - Oleta Sandiford
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | | | - Pranela Rameshwar
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
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22
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Ren X, Zhou Y, Xue Z, Hao N, Li Y, Guo X, Wang D, Shi X, Li H. Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins. Nucleic Acids Res 2021; 49:114-126. [PMID: 33290558 PMCID: PMC7797077 DOI: 10.1093/nar/gkaa1130] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/24/2020] [Accepted: 11/07/2020] [Indexed: 02/01/2023] Open
Abstract
Histone modifications and their functional readout serve as an important mechanism for gene regulation. Lysine benzoylation (Kbz) on histones is a recently identified acylation mark associated with active transcription. However, it remains to be explored whether putative readers exist to recognize this epigenetic mark. Here, our systematic binding studies demonstrated that the DPF and YEATS, but not the Bromodomain family members, are readers for histone Kbz. Co-crystal structural analyses revealed a 'hydrophobic encapsulation' and a 'tip-sensor' mechanism for Kbz readout by DPF and YEATS, respectively. Moreover, the DPF and YEATS family members display subtle yet unique features to create somewhat flexible engagements of different acylation marks. For instance, YEATS2 but not the other YEATS proteins exhibits best preference for Kbz than lysine acetylation and crotonylation due to its wider 'tip-sensor' pocket. The levels of histone benzoylation in cultured cells or in mice are upregulated upon sodium benzoate treatment, highlighting its dynamic regulation. In summary, our work identifies the first readers for histone Kbz and reveals the molecular basis underlying Kbz recognition, thus paving the way for further functional dissections of histone benzoylation.
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Affiliation(s)
- Xiangle Ren
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yang Zhou
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhaoyu Xue
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ning Hao
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohuan Guo
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Daliang Wang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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23
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Ardehali MB, Damle M, Perea-Resa C, Blower MD, Kingston RE. Elongin A associates with actively transcribed genes and modulates enhancer RNA levels with limited impact on transcription elongation rate in vivo. J Biol Chem 2020; 296:100202. [PMID: 33334895 PMCID: PMC7948453 DOI: 10.1074/jbc.ra120.015877] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/06/2020] [Accepted: 12/16/2020] [Indexed: 01/08/2023] Open
Abstract
Elongin A (EloA) is an essential transcription factor that stimulates the rate of RNA polymerase II (Pol II) transcription elongation in vitro. However, its role as a transcription factor in vivo has remained underexplored. Here we show that in mouse embryonic stem cells, EloA localizes to both thousands of Pol II transcribed genes with preference for transcription start site and promoter regions and a large number of active enhancers across the genome. EloA deletion results in accumulation of transcripts from a subset of enhancers and their adjacent genes. Notably, EloA does not substantially enhance the elongation rate of Pol II in vivo. We also show that EloA localizes to the nucleoli and associates with RNA polymerase I transcribed ribosomal RNA gene, Rn45s. EloA is a highly disordered protein, which we demonstrate forms phase-separated condensates in vitro, and truncation mutations in the intrinsically disordered regions (IDR) of EloA interfere with its targeting and localization to the nucleoli. We conclude that EloA broadly associates with transcribed regions, tunes RNA Pol II transcription levels via impacts on enhancer RNA synthesis, and interacts with the rRNA producing/processing machinery in the nucleolus. Our work opens new avenues for further investigation of the role of this functionally multifaceted transcription factor in enhancer and ribosomal RNA biology.
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Affiliation(s)
- M Behfar Ardehali
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Manashree Damle
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Carlos Perea-Resa
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael D Blower
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA.
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24
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Johansson-Åkhe I, Mirabello C, Wallner B. InterPep2: global peptide-protein docking using interaction surface templates. Bioinformatics 2020; 36:2458-2465. [PMID: 31917413 PMCID: PMC7178396 DOI: 10.1093/bioinformatics/btaa005] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 12/16/2019] [Accepted: 01/03/2020] [Indexed: 12/23/2022] Open
Abstract
Motivation Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming and difficult because of the inherent flexibility of the peptide ligand. Although several prediction-methods exist, most are limited in performance or availability. Results InterPep2 is a freely available method for predicting the structure of peptide–protein interactions. Improved performance is obtained by using templates from both peptide–protein and regular protein–protein interactions, and by a random forest trained to predict the DockQ-score for a given template using sequence and structural features. When tested on 252 bound peptide–protein complexes from structures deposited after the complexes used in the construction of the training and templates sets of InterPep2, InterPep2-Refined correctly positioned 67 peptides within 4.0 Å LRMSD among top10, similar to another state-of-the-art template-based method which positioned 54 peptides correctly. However, InterPep2 displays a superior ability to evaluate the quality of its own predictions. On a previously established set of 27 non-redundant unbound-to-bound peptide–protein complexes, InterPep2 performs on-par with leading methods. The extended InterPep2-Refined protocol managed to correctly model 15 of these complexes within 4.0 Å LRMSD among top10, without using templates from homologs. In addition, combining the template-based predictions from InterPep2 with ab initio predictions from PIPER-FlexPepDock resulted in 22% more near-native predictions compared to the best single method (22 versus 18). Availability and implementation The program is available from: http://wallnerlab.org/InterPep2. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Isak Johansson-Åkhe
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Claudio Mirabello
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
| | - Björn Wallner
- Division of Bioinformatics, Department of Physics, Chemistry and Biology, Linköping University, Linköping, Sweden
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25
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Baumann C, Ma W, Wang X, Kandasamy MK, Viveiros MM, De La Fuente R. Helicase LSH/Hells regulates kinetochore function, histone H3/Thr3 phosphorylation and centromere transcription during oocyte meiosis. Nat Commun 2020; 11:4486. [PMID: 32900989 PMCID: PMC7478982 DOI: 10.1038/s41467-020-18009-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/23/2020] [Indexed: 12/31/2022] Open
Abstract
Centromeres are epigenetically determined nuclear domains strictly required for chromosome segregation and genome stability. However, the mechanisms regulating centromere and kinetochore chromatin modifications are not known. Here, we demonstrate that LSH is enriched at meiotic kinetochores and its targeted deletion induces centromere instability and abnormal chromosome segregation. Superresolution chromatin analysis resolves LSH at the inner centromere and kinetochores during oocyte meiosis. LSH knockout pachytene oocytes exhibit reduced HDAC2 and DNMT-1. Notably, mutant oocytes show a striking increase in histone H3 phosphorylation at threonine 3 (H3T3ph) and accumulation of major satellite transcripts in both prophase-I and metaphase-I chromosomes. Moreover, knockout oocytes exhibit centromere fusions, ectopic kinetochore formation and abnormal exchange of chromatin fibers between paired bivalents and asynapsed chromosomes. Our results indicate that loss of LSH affects the levels and chromosomal localization of H3T3ph and provide evidence that, by maintaining transcriptionally repressive heterochromatin, LSH may be essential to prevent deleterious meiotic recombination events at repetitive centromeric sequences.
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Affiliation(s)
- Claudia Baumann
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, 30602, USA
| | - Wei Ma
- School of Basic Medical Sciences, Capital Medical University, 100069, Beijing, China
| | - Xiaotian Wang
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, 30602, USA
| | | | - Maria M Viveiros
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, 30602, USA
| | - Rabindranath De La Fuente
- Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA, 30602, USA.
- Regenerative Biosciences Center (RBC), University of Georgia, Athens, GA, 30602, USA.
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26
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Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development. Nat Struct Mol Biol 2020; 27:706-716. [DOI: 10.1038/s41594-020-0445-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
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27
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The role and mechanisms of DNA methylation in the oocyte. Essays Biochem 2020; 63:691-705. [PMID: 31782490 PMCID: PMC6923320 DOI: 10.1042/ebc20190043] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 12/27/2022]
Abstract
Epigenetic information in the mammalian oocyte has the potential to be transmitted to the next generation and influence gene expression; this occurs naturally in the case of imprinted genes. Therefore, it is important to understand how epigenetic information is patterned during oocyte development and growth. Here, we review the current state of knowledge of de novo DNA methylation mechanisms in the oocyte: how a distinctive gene-body methylation pattern is created, and the extent to which the DNA methylation machinery reads chromatin states. Recent epigenomic studies building on advances in ultra-low input chromatin profiling methods, coupled with genetic studies, have started to allow a detailed interrogation of the interplay between DNA methylation establishment and chromatin states; however, a full mechanistic description awaits.
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28
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Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
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29
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Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y. Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion. Mol Cell 2020; 78:493-505.e8. [PMID: 32353257 DOI: 10.1016/j.molcel.2020.04.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/06/2019] [Accepted: 04/02/2020] [Indexed: 12/22/2022]
Abstract
The promyelocytic leukemia (PML) body is a phase-separated nuclear structure physically associated with chromatin, implying its crucial roles in genome functions. However, its role in transcriptional regulation is largely unknown. We developed APEX-mediated chromatin labeling and purification (ALaP) to identify the genomic regions proximal to PML bodies. We found that PML bodies associate with active regulatory regions across the genome and with ∼300 kb of the short arm of the Y chromosome (YS300) in mouse embryonic stem cells. The PML body association with YS300 is essential for the transcriptional activity of the neighboring Y-linked clustered genes. Mechanistically, PML bodies provide specific nuclear spaces that the de novo DNA methyltransferase DNMT3A cannot access, resulting in the steady maintenance of a hypo-methylated state at Y-linked gene promoters. Our study underscores a new mechanism for gene regulation in the 3D nuclear space and provides insights into the functional properties of nuclear structures for genome function.
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Affiliation(s)
- Misuzu Kurihara
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan
| | - Kagayaki Kato
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Center for Novel Science Initiatives (CNSI), National Institutes of Natural Sciences (NINS), Okazaki, 444-8787, Japan
| | - Chiaki Sanbo
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan
| | - Shuji Shigenobu
- National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, Hayama, 240-0193, Japan
| | - Yasuyuki Ohkawa
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-0054, Japan
| | - Takeshi Fuchigami
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8521, Japan
| | - Yusuke Miyanari
- Exploratory Research Center on Life and Living Systems (ExCELLS), Okazaki, 444-8787, Japan; National Institute for Basic Biology (NIBB), Okazaki, 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI, Hayama, 240-0193, Japan.
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30
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Lan Y, Pan H, Li C, Banks KM, Sam J, Ding B, Elemento O, Goll MG, Evans T. TETs Regulate Proepicardial Cell Migration through Extracellular Matrix Organization during Zebrafish Cardiogenesis. Cell Rep 2020; 26:720-732.e4. [PMID: 30650362 PMCID: PMC6366638 DOI: 10.1016/j.celrep.2018.12.076] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 10/30/2018] [Accepted: 12/18/2018] [Indexed: 12/22/2022] Open
Abstract
Ten-eleven translocation (Tet) enzymes (Tet1/2/3) mediate 5-methylcytosine (5mC) hydroxylation, which can facilitate DNA demethylation and thereby impact gene expression. Studied mostly for how mutant isoforms impact cancer, the normal roles for Tet enzymes during organogenesis are largely unknown. By analyzing compound mutant zebrafish, we discovered a requirement for Tet2/3 activity in the embryonic heart for recruitment of epicardial progenitors, associated with development of the atrial-ventricular canal (AVC). Through a combination of methylation, hydroxymethylation, and transcript profiling, the genes encoding the activin A subunit Inhbaa (in endocardium) and Sox9b (in myocardium) were implicated as demethylation targets of Tet2/3 and critical for organization of AVC-localized extracellular matrix (ECM), facilitating migration of epicardial progenitors onto the developing heart tube. This study elucidates essential DNA demethylation modifications that govern gene expression changes during cardiac development with striking temporal and lineage specificities, highlighting complex interactions in multiple cell populations during development of the vertebrate heart. Lan et al. show that zebrafish larvae mutant for tet2 and tet3 fail to demethylate genes encoding Inhbaa (in endocardium) and Sox9b (in myocardium), leading to defects in ECM needed to form valves and to recruit epicardial progenitors onto the heart tube.
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Affiliation(s)
- Yahui Lan
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Heng Pan
- Department of Physiology and Biophysics, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Cheng Li
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Program in Biochemistry and Structural Biology, Cell and Developmental Biology, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Kelly M Banks
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Jessica Sam
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA
| | - Bo Ding
- Bonacept, LLC, 7699 Palmilla Drive, Apt. 3312, San Diego, CA 92122, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Mary G Goll
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA.
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31
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Dunican DS, Mjoseng HK, Duthie L, Flyamer IM, Bickmore WA, Meehan RR. Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells. BMC Biol 2020; 18:25. [PMID: 32131813 PMCID: PMC7057567 DOI: 10.1186/s12915-020-0752-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/14/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Thousands of mammalian promoters are defined by co-enrichment of the histone tail modifications H3K27me3 (repressive) and H3K4me3 (activating) and are thus termed bivalent. It was previously observed that bivalent genes in human ES cells (hESC) are frequent targets for hypermethylation in human cancers, and depletion of DNA methylation in mouse embryonic stem cells has a marked impact on H3K27me3 distribution at bivalent promoters. However, only a fraction of bivalent genes in stem cells are targets of hypermethylation in cancer, and it is currently unclear whether all bivalent promoters are equally sensitive to DNA hypomethylation and whether H3K4me3 levels play a role in the interplay between DNA methylation and H3K27me3. RESULTS We report the sub-classification of bivalent promoters into two groups-promoters with a high H3K27me3:H3K4me3 (hiBiv) ratio or promoters with a low H3K27me3:H3K4me3 ratio (loBiv). HiBiv are enriched in canonical Polycomb components, show a higher degree of local intrachromosomal contacts and are highly sensitive to DNA hypomethylation in terms of H3K27me3 depletion from broad Polycomb domains. In contrast, loBiv promoters are enriched in non-canonical Polycomb components, show lower intrachromosomal contacts and are less sensitive to DNA hypomethylation at the same genomic resolution. Multiple systems reveal that hiBiv promoters are more depleted of Polycomb complexes than loBiv promoters following a reduction in DNA methylation, and we demonstrate that H3K27me3 re-accumulates at promoters when DNA methylation is restored. In human cancer, we show that hiBiv promoters lose H3K27me3 and are more susceptible to DNA hypermethylation than loBiv promoters. CONCLUSION We conclude that bivalency as a general term to describe mammalian promoters is an over-simplification and our sub-classification has revealed novel insights into the interplay between the largely antagonistic presence of DNA methylation and Polycomb systems at bivalent promoters. This approach redefines molecular pathologies underlying disease in which global DNA methylation is aberrant or where Polycomb mutations are present.
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Affiliation(s)
- Donnchadh S. Dunican
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Heidi K. Mjoseng
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Leanne Duthie
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Ilya M. Flyamer
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
| | - Richard R. Meehan
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU Scotland
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32
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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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33
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Lavery LA, Zoghbi HY. The distinct methylation landscape of maturing neurons and its role in Rett syndrome pathogenesis. Curr Opin Neurobiol 2019; 59:180-188. [PMID: 31542590 PMCID: PMC6892602 DOI: 10.1016/j.conb.2019.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 08/21/2019] [Indexed: 02/06/2023]
Abstract
Rett syndrome (RTT) is one of the most common causes of intellectual and developmental disabilities in girls, and is caused by mutations in the gene encoding methyl-CpG binding protein 2 (MECP2). Here we will review our current understanding of RTT, the landscape of pathogenic mutations and function of MeCP2, and culminate with recent advances elucidating the distinct DNA methylation landscape in the brain that may explain why disease symptoms are delayed and selective to the nervous system.
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Affiliation(s)
- Laura A Lavery
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Huda Y Zoghbi
- Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
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34
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Rajavelu A, Lungu C, Emperle M, Dukatz M, Bröhm A, Broche J, Hanelt I, Parsa E, Schiffers S, Karnik R, Meissner A, Carell T, Rathert P, Jurkowska RZ, Jeltsch A. Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2. Nucleic Acids Res 2019; 46:9044-9056. [PMID: 30102379 PMCID: PMC6158614 DOI: 10.1093/nar/gky715] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Despite their central importance in mammalian development, the mechanisms that regulate the DNA methylation machinery and thereby the generation of genomic methylation patterns are still poorly understood. Here, we identify the 5mC-binding protein MeCP2 as a direct and strong interactor of DNA methyltransferase 3 (DNMT3) proteins. We mapped the interaction interface to the transcriptional repression domain of MeCP2 and the ADD domain of DNMT3A and find that binding of MeCP2 strongly inhibits the activity of DNMT3A in vitro. This effect was reinforced by cellular studies where a global reduction of DNA methylation levels was observed after overexpression of MeCP2 in human cells. By engineering conformationally locked DNMT3A variants as novel tools to study the allosteric regulation of this enzyme, we show that MeCP2 stabilizes the closed, autoinhibitory conformation of DNMT3A. Interestingly, the interaction with MeCP2 and its resulting inhibition were relieved by the binding of K4 unmodified histone H3 N-terminal tail to the DNMT3A-ADD domain. Taken together, our data indicate that the localization and activity of DNMT3A are under the combined control of MeCP2 and H3 tail modifications where, depending on the modification status of the H3 tail at the binding sites, MeCP2 can act as either a repressor or activator of DNA methylation.
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Affiliation(s)
- Arumugam Rajavelu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Cristiana Lungu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Alexander Bröhm
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Julian Broche
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Ines Hanelt
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Edris Parsa
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Sarah Schiffers
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Rahul Karnik
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas Carell
- Center for Integrated Protein Science (CiPSM) at the Department of Chemistry, Ludwig-Maximilians-University, Butenandtstr. 5-13, 81377 Munich, Germany
| | - Philipp Rathert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Faculty of Chemistry, University Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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35
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Lu R, Wang J, Ren Z, Yin J, Wang Y, Cai L, Wang GG. A Model System for Studying the DNMT3A Hotspot Mutation (DNMT3A R882) Demonstrates a Causal Relationship between Its Dominant-Negative Effect and Leukemogenesis. Cancer Res 2019; 79:3583-3594. [PMID: 31164355 DOI: 10.1158/0008-5472.can-18-3275] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/03/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023]
Abstract
Mutation of DNA methyltransferase 3A at arginine 882 (DNMT3AR882mut) is prevalent in hematologic cancers and disorders. Recently, DNMT3AR882mut has been shown to have hypomorphic, dominant-negative, and/or gain-of-function effects on DNA methylation under different biological contexts. However, the causal role for such a multifaceted effect of DNMT3AR882mut in leukemogenesis remains undetermined. Here, we report TF-1 leukemia cells as a robust system useful for modeling the DNMT3AR882mut-dependent transformation and for dissecting the cause-effect relationship between multifaceted activities of DNMT3AR882mut and leukemic transformation. Ectopic expression of DNMT3AR882mut and not wild-type DNMT3A promoted TF-1 cell transformation characterized by cytokine-independent growth, and induces CpG hypomethylation predominantly at enhancers. This effect was dose dependent, acted synergistically with the isocitrate dehydrogenase 1 (IDH1) mutation, and resembled what was seen in human leukemia patients carrying DNMT3AR882mut. The transformation- and hypomethylation-inducing capacities of DNMT3AR882mut relied on a motif involved in heterodimerization, whereas its various chromatin-binding domains were dispensable. Mutation of the heterodimerization motif that interferes with DNMT3AR882mut binding to endogenous wild-type DNMT proteins partially reversed the CpG hypomethylation phenotype caused by DNMT3AR882mut, thus supporting a dominant-negative mechanism in cells. In mice, bromodomain inhibition repressed gene-activation events downstream of DNMT3AR882mut-induced CpG hypomethylation, thereby suppressing leukemogenesis mediated by DNMT3AR882mut. Collectively, this study reports a model system useful for studying DNMT3AR882mut, shows a requirement of the dominant-negative effect by DNMT3AR882mut for leukemogenesis, and describes an attractive strategy for the treatment of leukemias carrying DNMT3AR882mut. SIGNIFICANCE: These findings highlight a model system to study the functional impact of a hotspot mutation of DNMT3A at R882 in leukemia.
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Affiliation(s)
- Rui Lu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Zhihong Ren
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, California.,Department of Chemistry, University of California, Riverside, California
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California.,Department of Chemistry, University of California, Riverside, California
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina. .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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36
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Skvortsova K, Masle-Farquhar E, Luu PL, Song JZ, Qu W, Zotenko E, Gould CM, Du Q, Peters TJ, Colino-Sanguino Y, Pidsley R, Nair SS, Khoury A, Smith GC, Miosge LA, Reed JH, Kench JG, Rubin MA, Horvath L, Bogdanovic O, Lim SM, Polo JM, Goodnow CC, Stirzaker C, Clark SJ. DNA Hypermethylation Encroachment at CpG Island Borders in Cancer Is Predisposed by H3K4 Monomethylation Patterns. Cancer Cell 2019; 35:297-314.e8. [PMID: 30753827 DOI: 10.1016/j.ccell.2019.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 11/14/2018] [Accepted: 01/07/2019] [Indexed: 01/20/2023]
Abstract
Promoter CpG islands are typically unmethylated in normal cells, but in cancer a proportion are subject to hypermethylation. Using methylome sequencing we identified CpG islands that display partial methylation encroachment across the 5' or 3' CpG island borders. CpG island methylation encroachment is widespread in prostate and breast cancer and commonly associates with gene suppression. We show that the pattern of H3K4me1 at CpG island borders in normal cells predicts the different modes of cancer CpG island hypermethylation. Notably, genetic manipulation of Kmt2d results in concordant alterations in H3K4me1 levels and CpG island border DNA methylation encroachment. Our findings suggest a role for H3K4me1 in the demarcation of CpG island methylation borders in normal cells, which become eroded in cancer.
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Affiliation(s)
- Ksenia Skvortsova
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; Developmental Epigenomics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Etienne Masle-Farquhar
- Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Jenny Z Song
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Wenjia Qu
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Elena Zotenko
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Cathryn M Gould
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Qian Du
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Timothy J Peters
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Yolanda Colino-Sanguino
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Ruth Pidsley
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Shalima S Nair
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Amanda Khoury
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Grady C Smith
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Lisa A Miosge
- Immunogenomics Laboratory, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Joanne H Reed
- Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - James G Kench
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2010, Australia; Sydney Medical School, University of Sydney, Sydney, NSW 2010, Australia; Cancer Division, The Kinghorn Cancer Centre, Sydney, NSW 2010, Australia
| | - Mark A Rubin
- Caryl and Israel Englander Institute for Precision Medicine, New York Presbyterian Hospital-Weill Cornell Medicine, New York 10021, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York 10065, USA; Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine, New York 10065, USA; Department for Biomedical Research, University of Bern, Bern, CH-3012, Switzerland; Bern Center for Precision Medicine, Inselspital, Bern University Hospital, Bern, CH-3012, Switzerland
| | - Lisa Horvath
- Sydney Medical School, University of Sydney, Sydney, NSW 2010, Australia; St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia; Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW 2050, Australia; Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia; Cancer Division, The Kinghorn Cancer Centre, Sydney, NSW 2010, Australia
| | - Ozren Bogdanovic
- St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia; Developmental Epigenomics Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Sue Mei Lim
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Jose M Polo
- Department of Anatomy & Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Melbourne, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Christopher C Goodnow
- Immunogenomics Laboratory, Immunology Division, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia; St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia.
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics and Epigenetics Division, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; St Vincent's Clinical School, UNSW, Sydney, NSW 2010, Australia.
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37
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Laisné M, Gupta N, Kirsh O, Pradhan S, Defossez PA. Mechanisms of DNA Methyltransferase Recruitment in Mammals. Genes (Basel) 2018; 9:genes9120617. [PMID: 30544749 PMCID: PMC6316769 DOI: 10.3390/genes9120617] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 11/30/2018] [Accepted: 12/05/2018] [Indexed: 12/11/2022] Open
Abstract
DNA methylation is an essential epigenetic mark in mammals. The proper distribution of this mark depends on accurate deposition and maintenance mechanisms, and underpins its functional role. This, in turn, depends on the precise recruitment and activation of de novo and maintenance DNA methyltransferases (DNMTs). In this review, we discuss mechanisms of recruitment of DNMTs by transcription factors and chromatin modifiers—and by RNA—and place these mechanisms in the context of biologically meaningful epigenetic events. We present hypotheses and speculations for future research, and underline the fundamental and practical benefits of better understanding the mechanisms that govern the recruitment of DNMTs.
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Affiliation(s)
- Marthe Laisné
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | - Nikhil Gupta
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | - Olivier Kirsh
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
| | | | - Pierre-Antoine Defossez
- Epigenetics and Cell Fate, UMR7216 CNRS, University Paris Diderot, Sorbonne Paris Cité, 75013 Paris, France.
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38
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Jeltsch A, Broche J, Bashtrykov P. Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes. Genes (Basel) 2018; 9:genes9110566. [PMID: 30469440 PMCID: PMC6266221 DOI: 10.3390/genes9110566] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is an essential part of the epigenome chromatin modification network, which also comprises several covalent histone protein post-translational modifications. All these modifications are highly interconnected, because the writers and erasers of one mark, DNA methyltransferases (DNMTs) and ten eleven translocation enzymes (TETs) in the case of DNA methylation, are directly or indirectly targeted and regulated by other marks. Here, we have collected information about the genomic distribution and variability of DNA methylation in human and mouse DNA in different genomic elements. After summarizing the impact of DNA methylation on genome evolution including CpG depletion, we describe the connection of DNA methylation with several important histone post-translational modifications, including methylation of H3K4, H3K9, H3K27, and H3K36, but also with nucleosome remodeling. Moreover, we present the mechanistic features of mammalian DNA methyltransferases and their associated factors that mediate the crosstalk between DNA methylation and chromatin modifications. Finally, we describe recent advances regarding the methylation of non-CpG sites, methylation of adenine residues in human cells and methylation of mitochondrial DNA. At several places, we highlight controversial findings or open questions demanding future experimental work.
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Affiliation(s)
- Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Julian Broche
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
| | - Pavel Bashtrykov
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany.
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Gowher H, Jeltsch A. Mammalian DNA methyltransferases: new discoveries and open questions. Biochem Soc Trans 2018; 46:1191-1202. [PMID: 30154093 PMCID: PMC6581191 DOI: 10.1042/bst20170574] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 07/12/2018] [Accepted: 07/13/2018] [Indexed: 11/17/2022]
Abstract
As part of the epigenetic network, DNA methylation is a major regulator of chromatin structure and function. In mammals, it mainly occurs at palindromic CpG sites, but asymmetric methylation at non-CpG sites is also observed. Three enzymes are involved in the generation and maintenance of DNA methylation patterns. DNMT1 has high preference for hemimethylated CpG sites, and DNMT3A and DNMT3B equally methylate unmethylated and hemimethylated DNA, and also introduce non-CpG methylation. Here, we review recent observations and novel insights into the structure and function of mammalian DNMTs (DNA methyltransferases), including new structures of DNMT1 and DNMT3A, data on their mechanism, regulation by post-translational modifications and on the function of DNMTs in cells. In addition, we present news findings regarding the allosteric regulation and targeting of DNMTs by chromatin modifications and chromatin proteins. In combination, the recent publications summarized here impressively illustrate the intensity of ongoing research in this field. They provide a deeper understanding of key mechanistic properties of DNMTs, but they also document still unsolved issues, which need to be addressed in future research.
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Affiliation(s)
- Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, U.S.A
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, Department of Biochemistry, University of Stuttgart, Stuttgart, Germany
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40
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Relationship between PIWIL4-Mediated H3K4me2 Demethylation and piRNA-Dependent DNA Methylation. Cell Rep 2018; 25:350-356. [DOI: 10.1016/j.celrep.2018.09.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 06/22/2018] [Accepted: 09/07/2018] [Indexed: 11/22/2022] Open
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41
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Role of transcription complexes in the formation of the basal methylation pattern in early development. Proc Natl Acad Sci U S A 2018; 115:10387-10391. [PMID: 30257947 DOI: 10.1073/pnas.1804755115] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Following erasure in the blastocyst, the entire genome undergoes de novo methylation at the time of implantation, with CpG islands being protected from this process. This bimodal pattern is then preserved throughout development and the lifetime of the organism. Using mouse embryonic stem cells as a model system, we demonstrate that the binding of an RNA polymerase complex on DNA before de novo methylation is predictive of it being protected from this modification, and tethering experiments demonstrate that the presence of this complex is, in fact, sufficient to prevent methylation at these sites. This protection is most likely mediated by the recruitment of enzyme complexes that methylate histone H3K4 over a local region and, in this way, prevent access to the de novo methylation complex. The topological pattern of H3K4me3 that is formed while the DNA is as yet unmethylated provides a strikingly accurate template for modeling the genome-wide basal methylation pattern of the organism. These results have far-reaching consequences for understanding the relationship between RNA transcription and DNA methylation.
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42
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Chakraborty A, Viswanathan P. Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury. Anal Cell Pathol (Amst) 2018. [DOI: https://doi.org/10.1155/2018/8764384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Over the years, the epigenetic landscape has grown increasingly complex. Until recently, methylation of DNA and histones was considered one of the most important epigenetic modifications. However, with the discovery of enzymes involved in the demethylation process, several exciting prospects have emerged that focus on the dynamic regulation of methylation and its crucial role in development and disease. An interplay of the methylation-demethylation machinery controls the process of gene expression. Since acute kidney injury (AKI), a major risk factor for chronic kidney disease and death, is characterised by aberrant expression of genes, understanding the dynamics of methylation and demethylation will provide new insights into the intricacies of the disease. Research on epigenetics in AKI has only made its mark in the recent years but has provided compelling evidence that implicates the involvement of methylation and demethylation changes in its pathophysiology. In this review, we explore the role of methylation and demethylation machinery in cellular epigenetic control and further discuss the contribution of methylomic changes and histone modifications to the pathophysiology of AKI.
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Affiliation(s)
- Anubhav Chakraborty
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Pragasam Viswanathan
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
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43
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Boamah D, Lin T, Poppinga FA, Basu S, Rahman S, Essel F, Chakravarty S. Characteristics of a PHD Finger Subtype. Biochemistry 2018; 57:525-539. [PMID: 29253329 DOI: 10.1021/acs.biochem.7b00705] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the plant homeodomain (PHD) finger superfamily is known for its site-specific readouts of histone tails, the origins of the mechanistic differences in histone H3 readout by different PHD subtypes remain less clear. We show that sequences containing the xCDxCDx motif in the PHD treble clef (xCDxCDx-PHD) constitute a distinct subtype, based on the following observations: (i) the amino acid composition of the binding site is strikingly different from other subtypes due to position-specific enrichment of negatively charged and bulky nonpolar residues, (ii) the binding site positions are mutually and positively correlated, and this correlation is absent in other subtypes, and (iii) there are only small structural deviations, despite low sequence similarity. The xCDxCDx-PHD constitutes ∼20% of the PHD family, and the double PHD fingers (DPFs) are 10% of the total number of xCDxCDx-PHDs. This subtype originated early in the evolution of eukaryotes but has diversified within the metazoan lineage. Despite sequence diversification, the positions of the enriched nonpolar residues, in particular, show very small structural deviations, suggesting critical contributions of nonpolar residues in the binding mechanism of this subtype. Using mutagenesis, we probed the contributions of the binding-site positions enriched in nonpolar residues in four xCDxCDx-PHD proteins and found that they contribute to the tight packing of the H3 residues. This effect may potentially be exploited, as we observed affinity enhancement upon substituting a bulky nonpolar residue at the same binding site in another histone reader. Overall, we present a detailed characterization of PHD subtypes.
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Affiliation(s)
- Daniel Boamah
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Tao Lin
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Franchesca A Poppinga
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Shraddha Basu
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Shahariar Rahman
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Francisca Essel
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Suvobrata Chakravarty
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States.,BioSNTR, Brookings, South Dakota 57007, United States
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44
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Ravichandran M, Jurkowska RZ, Jurkowski TP. Target specificity of mammalian DNA methylation and demethylation machinery. Org Biomol Chem 2018; 16:1419-1435. [DOI: 10.1039/c7ob02574b] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review here the molecular mechanisms employed by DNMTs and TET enzymes that are responsible for shaping the DNA methylation pattern of a mammalian cell.
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Affiliation(s)
| | | | - T. P. Jurkowski
- Universität Stuttgart
- Abteilung Biochemie
- Institute für Biochemie und Technische Biochemie
- Stuttgart D-70569
- Germany
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45
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Chakraborty A, Viswanathan P. Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury. Anal Cell Pathol (Amst) 2018; 2018:8764384. [PMID: 30073137 PMCID: PMC6057397 DOI: 10.1155/2018/8764384] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/05/2018] [Accepted: 06/14/2018] [Indexed: 02/05/2023] Open
Abstract
Over the years, the epigenetic landscape has grown increasingly complex. Until recently, methylation of DNA and histones was considered one of the most important epigenetic modifications. However, with the discovery of enzymes involved in the demethylation process, several exciting prospects have emerged that focus on the dynamic regulation of methylation and its crucial role in development and disease. An interplay of the methylation-demethylation machinery controls the process of gene expression. Since acute kidney injury (AKI), a major risk factor for chronic kidney disease and death, is characterised by aberrant expression of genes, understanding the dynamics of methylation and demethylation will provide new insights into the intricacies of the disease. Research on epigenetics in AKI has only made its mark in the recent years but has provided compelling evidence that implicates the involvement of methylation and demethylation changes in its pathophysiology. In this review, we explore the role of methylation and demethylation machinery in cellular epigenetic control and further discuss the contribution of methylomic changes and histone modifications to the pathophysiology of AKI.
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Affiliation(s)
- Anubhav Chakraborty
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
| | - Pragasam Viswanathan
- Renal Research Lab, Centre for Bio-Medical Research, School of Bio-Sciences and Technology, Vellore Institute of Technology, Vellore 632014, India
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46
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King AD, Huang K, Rubbi L, Liu S, Wang CY, Wang Y, Pellegrini M, Fan G. Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells. Cell Rep 2017; 17:289-302. [PMID: 27681438 DOI: 10.1016/j.celrep.2016.08.083] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 07/16/2016] [Accepted: 08/24/2016] [Indexed: 01/18/2023] Open
Abstract
DNA methylation is one of a number of modes of epigenetic gene regulation. Here, we profile the DNA methylome, transcriptome, and global occupancy of histone modifications (H3K4me1, H3K4me3, H3K27me3, and H3K27ac) in a series of mouse embryonic stem cells (mESCs) with varying DNA methylation levels to study the effects of DNA methylation on deposition of histone modifications. We find that genome-wide DNA demethylation alters occupancy of histone modifications at both promoters and enhancers. This is reversed upon remethylation by Dnmt expression. DNA methylation promotes H3K27me3 deposition at bivalent promoters, while opposing H3K27me3 at silent promoters. DNA methylation also reversibly regulates H3K27ac and H3K27me3 at previously identified tissue-specific enhancers. These effects require DNMT catalytic activity. Collectively, our data show that DNA methylation is essential and instructive for deposition of specific histone modifications across regulatory regions, which together influences gene expression patterns in mESCs.
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Affiliation(s)
- Andrew D King
- Department of Human Genetics and Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Molecular Biology Interdepartmental Doctoral Program, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kevin Huang
- Department of Human Genetics and Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Division of Oral Biology and Medicine, School of Dentistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Liudmilla Rubbi
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Shuo Liu
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
| | - Cun-Yu Wang
- Division of Oral Biology and Medicine, School of Dentistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, CA 92521, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Guoping Fan
- Department of Human Genetics and Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.
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47
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Abstract
Information encoded in DNA is interpreted, modified, and propagated as chromatin. The diversity of inputs encountered by eukaryotic genomes demands a matching capacity for transcriptional outcomes provided by the combinatorial and dynamic nature of epigenetic processes. Advances in genome editing, visualization technology, and genome-wide analyses have revealed unprecedented complexity of chromatin pathways, offering explanations to long-standing questions and presenting new challenges. Here, we review recent findings, exemplified by the emerging understanding of crossregulatory interactions within chromatin, and emphasize the pathologic outcomes of epigenetic misregulation in cancer.
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48
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Ambrosi C, Manzo M, Baubec T. Dynamics and Context-Dependent Roles of DNA Methylation. J Mol Biol 2017; 429:1459-1475. [PMID: 28214512 DOI: 10.1016/j.jmb.2017.02.008] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/26/2017] [Accepted: 02/09/2017] [Indexed: 12/22/2022]
Abstract
DNA methylation is one of the most extensively studied epigenetic marks. It is involved in transcriptional gene silencing and plays important roles during mammalian development. Its perturbation is often associated with human diseases. In mammalian genomes, DNA methylation is a prevalent modification that decorates the majority of cytosines. It is found at the promoters and enhancers of inactive genes, at repetitive elements, and within transcribed gene bodies. Its presence at promoters is dynamically linked to gene activity, suggesting that it could directly influence gene expression patterns and cellular identity. The genome-wide distribution and dynamic behaviour of this mark have been studied in great detail in a variety of tissues and cell lines, including early embryonic development and in embryonic stem cells. In combination with functional studies, these genome-wide maps of DNA methylation revealed interesting features of this mark and provided important insights into its dynamic nature and potential functional role in genome regulation. In this review, we discuss how these recent observations, in combination with insights obtained from biochemical and functional genetics studies, have expanded our current knowledge about the regulation and context-dependent roles of DNA methylation in mammalian genomes.
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Affiliation(s)
- Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program of the Life Sciences Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Massimiliano Manzo
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Molecular Life Sciences PhD Program of the Life Sciences Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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49
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Abstract
DNA methylation plays important roles in development and disease. Yet, only recently has the dynamic nature of this epigenetic mark via oxidation and DNA repair-mediated demethylation been recognized. A major conceptual challenge to the model that DNA methylation is reversible is the risk of genomic instability, which may come with widespread DNA repair activity. Here, we focus on recent advances in mechanisms of TET-TDG mediated demethylation and cellular strategies that avoid genomic instability. We highlight the recently discovered involvement of NEIL DNA glycosylases, which cooperate with TDG in oxidative demethylation to accelerate substrate turnover and promote the organized handover of harmful repair intermediates to maintain genome stability.
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Affiliation(s)
| | - Christof Niehrs
- Institute of Molecular Biology (IMB), Mainz, Germany.,Division of Molecular Embryology, German Cancer Research Center-Zentrum für Molekulare Biologie der Universität Heidelberg (DKFZ-ZMBH) Alliance, Heidelberg, Germany
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50
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Abstract
Epigenetic modifications established during gametogenesis regulate transcription and other nuclear processes in gametes, but also have influences in the zygote, embryo and postnatal life. This is best understood for DNA methylation which, established at discrete regions of the oocyte and sperm genomes, governs genomic imprinting. In this review, we describe how imprinting has informed our understanding of de novo DNA methylation mechanisms, highlight how recent genome-wide profiling studies have provided unprecedented insights into establishment of the sperm and oocyte methylomes and consider the fate and function of gametic methylation and other epigenetic modifications after fertilization.
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Affiliation(s)
- Kathleen R Stewart
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Biotech Research & Innovation Centre (BRIC), University of Copenhagen, DK2200 Copenhagen, Denmark
| | - Lenka Veselovska
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Laboratory of Developmental Biology & Genetics, Department of Molecular Biology, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Gavin Kelsey
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
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