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Vergara X, Manjón AG, de Haas M, Morris B, Schep R, Leemans C, Friskes A, Beijersbergen RL, Sanders MA, Medema RH, van Steensel B. Widespread chromatin context-dependencies of DNA double-strand break repair proteins. Nat Commun 2024; 15:5334. [PMID: 38909016 PMCID: PMC11193718 DOI: 10.1038/s41467-024-49232-x] [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: 02/19/2024] [Accepted: 05/28/2024] [Indexed: 06/24/2024] Open
Abstract
DNA double-strand breaks are repaired by multiple pathways, including non-homologous end-joining (NHEJ) and microhomology-mediated end-joining (MMEJ). The balance of these pathways is dependent on the local chromatin context, but the underlying mechanisms are poorly understood. By combining knockout screening with a dual MMEJ:NHEJ reporter inserted in 19 different chromatin environments, we identified dozens of DNA repair proteins that modulate pathway balance dependent on the local chromatin state. Proteins that favor NHEJ mostly synergize with euchromatin, while proteins that favor MMEJ generally synergize with distinct types of heterochromatin. Examples of the former are BRCA2 and POLL, and of the latter the FANC complex and ATM. Moreover, in a diversity of human cancer types, loss of several of these proteins alters the distribution of pathway-specific mutations between heterochromatin and euchromatin. Together, these results uncover a complex network of proteins that regulate MMEJ:NHEJ balance in a chromatin context-dependent manner.
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Affiliation(s)
- Xabier Vergara
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Anna G Manjón
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Marcel de Haas
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Ben Morris
- NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ruben Schep
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Christ Leemans
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Anoek Friskes
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Roderick L Beijersbergen
- NKI Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mathijs A Sanders
- Department of Hematology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
- Cancer, Ageing and Somatic Mutation (CASM), Wellcome Sanger Institute, Hinxton, UK
| | - René H Medema
- Division of Cell Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands.
- Oncode Institute, Utrecht, The Netherlands.
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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2
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Tong J, Chen X, Wang X, Men S, Liu Y, Sun X, Yan D, Wang L. Novel KMT5B variant associated with neurodevelopmental disorder in a Chinese family: A case report. Heliyon 2024; 10:e28686. [PMID: 38571636 PMCID: PMC10988039 DOI: 10.1016/j.heliyon.2024.e28686] [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: 06/20/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/05/2024] Open
Abstract
Background We report here the clinical and genetic features of KMT5B-related neurodevelopmental disorder caused by a novel heterozygous frameshift variant in KMT5B in a Chinese family. Case presentation A 7-year-old Chinese boy with mild-to-moderate intellectual disability, significant language impairment, motor disability, and coordination difficulties presented to our hospital because he "could not speak and did not look at others." He was diagnosed with autism spectrum disorder previously owing to developmental delays in cognition, language expression, and understanding. The child also had variable nonspecific features including macrocephaly, wide button-hole space and nasal bridge, low ear, social behavior disorder, and foot deformities. Exome sequencing (ES) revealed that both the proband and his younger brother had inherited a novel heterozygous frameshift variant c.438_439ins[ASD; KT192064.1:1_310] of the KMT5B gene from their father. Bioinformatics analysis showed that the novel mutation affected the structure of the KMT5B pre-SET domain, mainly in the α-helix region. According to the American College of Medical Genetics and Genomics (ACMG) guidelines, this type of variant was eventually determined to be likely pathogenic (PVS1+PM2_P). Conclusions Our investigation expands the mutation spectrum of KMT5B to help us to better understand KMT5B-related neurodevelopmental disorder.
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Affiliation(s)
| | | | - Xin Wang
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Shuai Men
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Yuan Liu
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Xun Sun
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Dongmei Yan
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
| | - Leilei Wang
- Lianyungang Maternal and Child Health Hospital, Lianyungang, Jiangsu, China
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Arnold MR, Cohn GM, Oxe KC, Elliott SN, Moore C, Laraia PV, Shekoohi S, Brownell D, Meshul CK, Witt SN, Larsen DH, Unni VK. Alpha-synuclein regulates nucleolar DNA double-strand break repair in melanoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.13.575526. [PMID: 38260370 PMCID: PMC10802588 DOI: 10.1101/2024.01.13.575526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Although an increased risk of the skin cancer melanoma in people with Parkinson's Disease (PD) has been shown in multiple studies, the mechanisms involved are poorly understood, but increased expression of the PD-associated protein alpha-synuclein (αSyn) in melanoma cells may be important. Our previous work suggests that αSyn can facilitate DNA double-strand break (DSB) repair, promoting genomic stability. We now show that αSyn is preferentially enriched within the nucleolus in the SK-MEL28 melanoma cell line, where it colocalizes with DNA damage markers and DSBs. Inducing DSBs specifically within nucleolar ribosomal DNA (rDNA) increases αSyn levels near sites of damage. αSyn knockout increases DNA damage within the nucleolus at baseline, after specific rDNA DSB induction, and prolongs the rate of recovery from this induced damage. αSyn is important downstream of ATM signaling to facilitate 53BP1 recruitment to DSBs, reducing micronuclei formation and promoting cellular proliferation, migration, and invasion.
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Affiliation(s)
- Moriah R. Arnold
- Medical Scientist Training Program, Oregon Health and Science University, Portland, OR, USA
- Department of Neurology and Jungers Center for Neurosciences Research, Oregon Health and Science University, Portland, OR, USA
| | - Gabriel M. Cohn
- Department of Molecular and Medical Genetics, School of Medicine, Oregon Health and Science University, Portland, OR, USA
| | - Kezia Catharina Oxe
- Danish Cancer Institute, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Somarr N. Elliott
- Department of Neurology and Jungers Center for Neurosciences Research, Oregon Health and Science University, Portland, OR, USA
| | - Cynthia Moore
- Research Services, Neurocytology Laboratory, Veterans Affairs Medical Center, Portland, OR, USA
| | | | - Sahar Shekoohi
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Dillon Brownell
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
| | - Charles K. Meshul
- Research Services, Neurocytology Laboratory, Veterans Affairs Medical Center, Portland, OR, USA
- Departments of Behavioral Neuroscience and Pathology, Oregon Health and Science University, Portland, OR, USA
| | - Stephan N. Witt
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, USA
| | - Dorthe H. Larsen
- Danish Cancer Institute, Nucleolar Stress and Disease Group, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Vivek K. Unni
- Department of Neurology and Jungers Center for Neurosciences Research, Oregon Health and Science University, Portland, OR, USA
- OHSU Parkinson’s Center, Oregon Health and Science University, Portland, OR, USA
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4
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Lin F, Zhang R, Shao W, Lei C, Ma M, Zhang Y, Wen Z, Li W. Structural basis of nucleosomal H4K20 recognition and methylation by SUV420H1 methyltransferase. Cell Discov 2023; 9:120. [PMID: 38052811 DOI: 10.1038/s41421-023-00620-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/29/2023] [Indexed: 12/07/2023] Open
Abstract
Histone lysine methyltransferase SUV420H1, which is responsible for site-specific di-/tri-methylation of histone H4 lysine 20 (H4K20), has crucial roles in DNA-templated processes, including DNA replication, DNA damage repair, and chromatin compaction. Its mutations frequently occur in human cancers. Nucleosomes containing the histone variant H2A.Z enhance the catalytic activities of SUV420H1 on H4K20 di-methylation deposition, regulating early replication origins. However, the molecular mechanism by which SUV420H1 specifically recognizes and deposits H4K20 methyl marks on nucleosomes remains poorly understood. Here we report the cryo-electron microscopy structures of SUV420H1 associated with H2A-containing nucleosome core particles (NCPs), and H2A.Z-containing NCPs. We find that SUV420H1 makes extensive site-specific contacts with histone and DNA regions. SUV420H1 C-terminal domain recognizes the H2A-H2B acidic patch of NCPs through its two arginine anchors, thus enabling H4K20 insertion for catalysis specifically. We also identify important residues increasing the catalytic activities of SUV420H1 bound to H2A.Z NCPs. In vitro and in vivo functional analyses reveal that multiple disease-associated mutations at the interfaces are essential for its catalytic activity and chromatin state regulation. Together, our study provides molecular insights into the nucleosome-based recognition and methylation mechanisms of SUV420H1, and a structural basis for understanding SUV420H1-related human disease.
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Affiliation(s)
- Folan Lin
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Ruxin Zhang
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong, China
| | - Weihan Shao
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Cong Lei
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Mingxi Ma
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Ying Zhang
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Zengqi Wen
- School of Medicine, Shenzhen Campus of Sun Yat-Sen University, Sun Yat-Sen University, Shenzhen, Guangdong, China.
| | - Wanqiu Li
- Department of Pharmacology, Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China.
- Institute for Biological Electron Microscopy, Southern University of Science and Technology, Shenzhen, Guangdong, China.
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5
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Manohar S, Estrada ME, Uliana F, Vuina K, Alvarez PM, de Bruin RAM, Neurohr GE. Genome homeostasis defects drive enlarged cells into senescence. Mol Cell 2023; 83:4032-4046.e6. [PMID: 37977116 PMCID: PMC10659931 DOI: 10.1016/j.molcel.2023.10.018] [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: 09/12/2022] [Revised: 06/30/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Cellular senescence refers to an irreversible state of cell-cycle arrest and plays important roles in aging and cancer biology. Because senescence is associated with increased cell size, we used reversible cell-cycle arrests combined with growth rate modulation to study how excessive growth affects proliferation. We find that enlarged cells upregulate p21, which limits cell-cycle progression. Cells that re-enter the cell cycle encounter replication stress that is well tolerated in physiologically sized cells but causes severe DNA damage in enlarged cells, ultimately resulting in mitotic failure and permanent cell-cycle withdrawal. We demonstrate that enlarged cells fail to recruit 53BP1 and other non-homologous end joining (NHEJ) machinery to DNA damage sites and fail to robustly initiate DNA damage-dependent p53 signaling, rendering them highly sensitive to genotoxic stress. We propose that an impaired DNA damage response primes enlarged cells for persistent replication-acquired damage, ultimately leading to cell division failure and permanent cell-cycle exit.
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Affiliation(s)
- Sandhya Manohar
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Marianna E Estrada
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Federico Uliana
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Karla Vuina
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Patricia Moyano Alvarez
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Robertus A M de Bruin
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Gabriel E Neurohr
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland.
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6
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Hao L, Zhang M, Yang C, Pan X, Wu D, Lin H, Ma D, Yao Y, Fu W, Chang J, Yang Y, Zhuang Z. The epigenetic regulator Set9 harmonizes fungal development, secondary metabolism, and colonization capacity of Aspergillus flavus. Int J Food Microbiol 2023; 403:110298. [PMID: 37392609 DOI: 10.1016/j.ijfoodmicro.2023.110298] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/17/2023] [Accepted: 06/18/2023] [Indexed: 07/03/2023]
Abstract
As a widely distributed food-borne pathogenic fungus, Aspergillus flavus and its secondary metabolites, mainly aflatoxin B1 (AFB1), pose a great danger to humans. It is urgent to reveal the complex regulatory network of toxigenic and virulence of this fungus. The bio-function of Set9, a SET-domain-containing histone methyltransferase, is still unknown in A. flavus. By genetic engineering means, this study revealed that, through catalyzing H4K20me2 and -me3, Set9 is involved in fungal growth, reproduction, and mycotoxin production via the orthodox regulation pathway, and regulates fungal colonization on crop kernels through adjusting fungal sensitivity reactions to oxidation stress and cell wall integrity stress. Further domain deletion and point mutation inferred that the SET domain is the core element in catalyzing H4K20 methylation, and D200 site of the domain is the key amino acid in the active center of the methyltransferase. Combined with RNA-seq analysis, this study revealed that Set9 regulates the aflatoxin gene cluster by the AflR-like protein (ALP), other than traditional AflR. This study revealed the epigenetic regulation mechanism of fungal morphogenesis, secondary metabolism, and pathogenicity of A. flavus mediated by the H4K20-methyltransferase Set9, which might provide a potential new target for early prevention of contamination of A. flavus and its deadly mycotoxins.
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Affiliation(s)
- Ling Hao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mengjuan Zhang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chi Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Institute of Edible Mushroom, Fujian Academy of Agricultural Sciences, Fuzhou 350014, China
| | - Xiaohua Pan
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Fujian Key Laboratory of Propagated Sensation along Meridian, Fujian Academy of Chinese Medical Sciences, Fuzhou 350003, China
| | - Dandan Wu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Hong Lin
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dongmei Ma
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanfang Yao
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wangzhuo Fu
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiarui Chang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanling Yang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Zhenhong Zhuang
- Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Proteomic Research Center, and School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Möller M, Ridenour JB, Wright DF, Martin FA, Freitag M. H4K20me3 is important for Ash1-mediated H3K36me3 and transcriptional silencing in facultative heterochromatin in a fungal pathogen. PLoS Genet 2023; 19:e1010945. [PMID: 37747878 PMCID: PMC10553808 DOI: 10.1371/journal.pgen.1010945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 10/05/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023] Open
Abstract
Facultative heterochromatin controls development and differentiation in many eukaryotes. In metazoans, plants, and many filamentous fungi, facultative heterochromatin is characterized by transcriptional repression and enrichment with nucleosomes that are trimethylated at histone H3 lysine 27 (H3K27me3). While loss of H3K27me3 results in derepression of transcriptional gene silencing in many species, additional up- and downstream layers of regulation are necessary to mediate control of transcription in chromosome regions enriched with H3K27me3. Here, we investigated the effects of one histone mark on histone H4, namely H4K20me3, in the fungus Zymoseptoria tritici, a globally important pathogen of wheat. Deletion of kmt5, the gene encoding the sole methyltransferase responsible for H4K20 methylation, resulted in global derepression of transcription, especially in regions of facultative heterochromatin. Derepression in the absence of H4K20me3 not only affected known genes but also a large number of novel, previously undetected transcripts generated from regions of facultative heterochromatin on accessory chromosomes. Transcriptional activation in kmt5 deletion strains was accompanied by a complete loss of Ash1-mediated H3K36me3 and chromatin reorganization affecting H3K27me3 and H3K4me2 distribution in regions of facultative heterochromatin. Strains with H4K20L, M or Q mutations in the single histone H4 gene of Z. tritici recapitulated these chromatin changes, suggesting that H4K20me3 is important for Ash1-mediated H3K36me3. The ∆kmt5 mutants we obtained were more sensitive to genotoxic stressors than wild type and both, ∆kmt5 and ∆ash1, showed greatly increased rates of accessory chromosome loss. Taken together, our results provide insights into an unsuspected mechanism involved in the assembly and maintenance of facultative heterochromatin.
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Affiliation(s)
- Mareike Möller
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - John B. Ridenour
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Devin F. Wright
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Faith A. Martin
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
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Ma Z, Bolinger AA, Chen H, Zhou J. Drug Discovery Targeting Nuclear Receptor Binding SET Domain Protein 2 (NSD2). J Med Chem 2023; 66:10991-11026. [PMID: 37578463 PMCID: PMC11092389 DOI: 10.1021/acs.jmedchem.3c00948] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Nuclear receptor binding SET domain proteins (NSDs) catalyze the mono- or dimethylation of histone 3 lysine 36 (H3K36me1 and H3K36me2), using S-adenosyl-l-methionine (SAM) as a methyl donor. As a key member of the NSD family of proteins, NSD2 plays an important role in the pathogenesis and progression of various diseases such as cancers, inflammations, and infectious diseases, serving as a promising drug target. Developing potent and specific NSD2 inhibitors may provide potential novel therapeutics. Several NSD2 inhibitors and degraders have been discovered while remaining in the early stage of drug development. Excitingly, KTX-1001, a selective NSD2 inhibitor, has entered clinical trials. In this Perspective, the structures and functions of NSD2, its roles in various human diseases, and the recent advances in drug discovery strategies targeting NSD2 have been summarized. The challenges, opportunities, and future directions for developing NSD2 inhibitors and degraders are also discussed.
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Affiliation(s)
- Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Andrew A Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, Texas 77555, United States
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9
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Norton C, Clarke D, Holmstrom J, Stirland I, Reynolds PR, Jenkins TG, Arroyo JA. Altered Epigenetic Profiles in the Placenta of Preeclamptic and Intrauterine Growth Restriction Patients. Cells 2023; 12:1130. [PMID: 37190039 PMCID: PMC10136447 DOI: 10.3390/cells12081130] [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: 02/25/2023] [Revised: 03/30/2023] [Accepted: 04/08/2023] [Indexed: 05/17/2023] Open
Abstract
Intrauterine growth restriction (IUGR) and preeclampsia (PE) are placental pathologies known to complicate pregnancy and cause neonatal disorders. To date, there is a limited number of studies on the genetic similarity of these conditions. DNA methylation is a heritable epigenetic process that can regulate placental development. Our objective was to identify methylation patterns in placental DNA from normal, PE and IUGR-affected pregnancies. DNA was extracted, and bisulfite was converted, prior to being hybridized for the methylation array. Methylation data were SWAN normalized and differently methylated regions were identified using applications within the USEQ program. UCSC's Genome browser and Stanford's GREAT analysis were used to identify gene promoters. The commonality among affected genes was confirmed by Western blot. We observed nine significantly hypomethylated regions, two being significantly hypomethylated for both PE and IGUR. Western blot confirmed differential protein expression of commonly regulated genes. We conclude that despite the uniqueness of methylation profiles for PE and IUGR, the similarity of some methylation alterations in pathologies could explain the clinical similarities observed with these obstetric complications. These results also provide insight into the genetic similarity between PE and IUGR and suggest possible gene candidates plausibly involved in the onset of both conditions.
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Affiliation(s)
| | | | | | | | | | | | - Juan A. Arroyo
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
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Recent advances in nuclear receptor-binding SET domain 2 (NSD2) inhibitors: An update and perspectives. Eur J Med Chem 2023; 250:115232. [PMID: 36863225 DOI: 10.1016/j.ejmech.2023.115232] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 02/26/2023]
Abstract
Nuclear receptor-binding SET domain 2 (NSD2) is a histone lysine methyltransferase (HKMTase), which is mainly responsible for the di-methylation of lysine residues on histones, which are involved in the regulation of various biological pathways. The amplification, mutation, translocation, or overexpression of NSD2 can be linked to various diseases. NSD2 has been identified as a promising drug target for cancer therapy. However, relatively few inhibitors have been discovered and this field still needs further exploration. This review provides a detailed summary of the biological studies related to NSD2 and the current progress of inhibitors, research, and describes the challenges in the development of NSD2 inhibitors, including SET (su(var), enhancer-of-zeste, trithorax) domain inhibitors and PWWP1 (proline-tryptophan-tryptophan-proline 1) domain inhibitors. Through analysis and discussion of the NSD2-related crystal complexes and the biological evaluation of related small molecules, we hope to provide insights for future drug design and optimization methods that will stimulate the development of novel NSD2 inhibitors.
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11
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Zagelbaum J, Gautier J. Double-strand break repair and mis-repair in 3D. DNA Repair (Amst) 2023; 121:103430. [PMID: 36436496 PMCID: PMC10799305 DOI: 10.1016/j.dnarep.2022.103430] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
Abstract
DNA double-strand breaks (DSBs) are lesions that arise frequently from exposure to damaging agents as well as from ongoing physiological DNA transactions. Mis-repair of DSBs leads to rearrangements and structural variations in chromosomes, including insertions, deletions, and translocations implicated in disease. The DNA damage response (DDR) limits pathologic mutations and large-scale chromosome rearrangements. DSB repair initiates in 2D at DNA lesions with the stepwise recruitment of repair proteins and local chromatin remodeling which facilitates break accessibility. More complex structures are then formed via protein assembly into nanodomains and via genome folding into chromatin loops. Subsequently, 3D reorganization of DSBs is guided by clustering forces which drive the assembly of repair domains harboring multiple lesions. These domains are further stabilized and insulated into condensates via liquid-liquid phase-separation. Here, we discuss the benefits and risks associated with this 3D reorganization of the broken genome.
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Affiliation(s)
- Jennifer Zagelbaum
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Jean Gautier
- Institute for Cancer Genetics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Genetics and Development, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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12
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The Role of PARP1 and PAR in ATP-Independent Nucleosome Reorganisation during the DNA Damage Response. Genes (Basel) 2022; 14:genes14010112. [PMID: 36672853 PMCID: PMC9859207 DOI: 10.3390/genes14010112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/31/2022] Open
Abstract
The functioning of the eukaryotic cell genome is mediated by sophisticated protein-nucleic-acid complexes, whose minimal structural unit is the nucleosome. After the damage to genomic DNA, repair proteins need to gain access directly to the lesion; therefore, the initiation of the DNA damage response inevitably leads to local chromatin reorganisation. This review focuses on the possible involvement of PARP1, as well as proteins acting nucleosome compaction, linker histone H1 and non-histone chromatin protein HMGB1. The polymer of ADP-ribose is considered the main regulator during the development of the DNA damage response and in the course of assembly of the correct repair complex.
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13
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Hickenlooper SM, Davis K, Szulik MW, Sheikh H, Miller M, Valdez S, Bia R, Franklin S. Histone H4K20 Trimethylation Is Decreased in Murine Models of Heart Disease. ACS OMEGA 2022; 7:30710-30719. [PMID: 36092581 PMCID: PMC9453978 DOI: 10.1021/acsomega.2c00984] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Heart disease is the leading cause of death in the developed world, and its comorbidities such as hypertension, diabetes, and heart failure are accompanied by major transcriptomic changes in the heart. During cardiac dysfunction, which leads to heart failure, there are global epigenetic alterations to chromatin that occur concomitantly with morphological changes in the heart in response to acute and chronic stress. These epigenetic alterations include the reversible methylation of lysine residues on histone proteins. Lysine methylations on histones H3K4 and H3K9 were among the first methylated lysine residues identified and have been linked to gene activation and silencing, respectively. However, much less is known regarding other methylated histone residues, including histone H4K20. Trimethylation of histone H4K20 has been shown to repress gene expression; however, this modification has never been examined in the heart. Here, we utilized immunoblotting and mass spectrometry to quantify histone H4K20 trimethylation in three models of cardiac dysfunction. Our results show that lysine methylation at this site is differentially regulated in the cardiomyocyte, leading to increased H4K20 trimethylation during acute hypertrophic stress in cell models and decreased H4K20 trimethylation during sustained ischemic injury and cardiac dysfunction in animal models. In addition, we examined publicly available data sets to analyze enzymes that regulate H4K20 methylation and identified two demethylases (KDM7B and KDM7C) and two methyltransferases (KMT5A and SMYD5) that were all differentially expressed in heart failure patients. This is the first study to examine histone H4K20 trimethylation in the heart and to determine how this post-translational modification is differentially regulated in multiple models of cardiac disease.
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Affiliation(s)
- Samuel M. Hickenlooper
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Kathryn Davis
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Marta W. Szulik
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Hanin Sheikh
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Mickey Miller
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Steven Valdez
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan Bia
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
| | - Sarah Franklin
- Nora
Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah 84112, United States
- Division
of Cardiovascular Medicine, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah 84132, United States
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14
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Hernández-Reyes Y, Paz-Cabrera MC, Freire R, Smits VAJ. USP29 Deubiquitinates SETD8 and Regulates DNA Damage-Induced H4K20 Monomethylation and 53BP1 Focus Formation. Cells 2022; 11:cells11162492. [PMID: 36010569 PMCID: PMC9406528 DOI: 10.3390/cells11162492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/05/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
SETD8 is a histone methyltransferase that plays pivotal roles in several cellular functions, including transcriptional regulation, cell cycle progression, and genome maintenance. SETD8 regulates the recruitment of 53BP1 to sites of DNA damage by controlling histone H4K20 methylation. Moreover, SETD8 levels are tightly regulated in a cell cycle-dependent manner by ubiquitin-dependent proteasomal degradation. Here, we identified ubiquitin-specific peptidase 29, USP29, as a novel regulator of SETD8. Depletion of USP29 leads to decreased SETD8 protein levels, an effect that is independent of the cell cycle. We demonstrate that SETD8 binds to USP29 in vivo, and this interaction is dependent on the catalytic activity of USP29. Wildtype USP29 can deubiquitinate SETD8 in vivo, indicating that USP29 directly regulates SETD8 protein levels. Importantly, USP29 knockdown inhibits the irradiation-induced increase in H4K20 monomethylation, thereby preventing focus formation of 53BP1 in response to DNA damage. Lastly, depletion of USP29 increases the cellular sensitivity to irradiation. These results demonstrate that USP29 is critical for the DNA damage response and cell survival, likely by controlling protein levels of SETD8.
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Affiliation(s)
- Yeray Hernández-Reyes
- Unidad de Investigación, Hospital Universitario de Canarias, 38320 Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain
- Escuela de Doctorado y Estudio de Postgrado, Universidad de la Laguna, 38200 Santa Cruz de Tenerife, Spain
| | | | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, 38320 Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
| | - Veronique A. J. Smits
- Unidad de Investigación, Hospital Universitario de Canarias, 38320 Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200 Santa Cruz de Tenerife, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
- Correspondence: ; Tel.: +34-922-678107
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15
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Matsui M, Kajita S, Tsuchiya Y, Torii W, Tamekuni S, Nishi R. USP49 is a novel deubiquitylating enzyme for γ H2AX in DNA double-strand break repair. Gene 2022; 833:146599. [PMID: 35598681 DOI: 10.1016/j.gene.2022.146599] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/16/2022] [Indexed: 12/29/2022]
Abstract
DNA double-strand break (DSB) that is one of the most serious DNA lesions is mainly repaired by two mutually exclusive pathways, homologous recombination and non-homologous end-joining. Proper choice of DSB repair pathway, in which recruitment of 53BP1 to chromatin around DSB sites plays a pivotal role, is crucial for maintaining genome integrity. Ubiquitylations of histone H2A and H2AX on Lys15 are prerequisite for 53BP1 loading onto chromatin. Although ubiquitylation mechanism of H2A and H2AX had been extensively studied, mechanism regulating deubiquitylation of γH2AX that is a phosphorylated form of H2AX remains elusive. Here, we identified USP49 as a novel deubiquitylating enzyme targeting DSB-induced γH2AX ubiquitylation. Over-expressed USP49 suppressed ubiquitylation of γH2AX in an enzymatic activity-dependent manner. Catalytic dead mutant of USP49 interacted and colocalized with γH2AX. Consequently, over-expression of USP49 inhibited the DSB-induced foci formation of 53BP1 and resulted in higher cell sensitivity to DSB-inducing drug treatment. Furthermore, endogenous USP49 protein was degraded via the proteasome upon DSB induction, indicating the importance of modulating USP49 protein level for γH2AX deubiquitylation. Consistent with our cell-based data, kidney renal clear cell carcinoma patients with higher expression of USP49 showed poor survival rate in comparison to the patients with unaltered USP49 expression. In conclusion, these data suggest that fine tuning of protein level of USP49 and USP49-mediated deubiquitylation of γH2AX are important for genome integrity.
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Affiliation(s)
- Misaki Matsui
- Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan
| | - Shoki Kajita
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yuina Tsuchiya
- School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan
| | - Wakana Torii
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Shiori Tamekuni
- Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Ryotaro Nishi
- Graduate School of Bionics, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan; Department of Biomedical Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan; School of Bioscience and Biotechnology, Tokyo University of Technology, Hachioji, Tokyo 192-0982, Japan.
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16
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González-Bermúdez L, Genescà A, Terradas M, Martín M. Role of H4K16 acetylation in 53BP1 recruitment to double-strand break sites in in vitro aged cells. Biogerontology 2022; 23:499-514. [PMID: 35851632 PMCID: PMC9388460 DOI: 10.1007/s10522-022-09979-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Accepted: 06/29/2022] [Indexed: 12/20/2022]
Abstract
AbstractIncreased frequency of DNA double strand breaks (DSBs) with aging suggests an age-associated decline in DSB repair efficiency, which is also influenced by the epigenetic landscape. H4 acetylation at lysine 16 (H4K16Ac) has been related to DSB repair since deacetylation of this mark is required for efficient 53BP1 recruitment to DSBs. Although age-associated changes in H4K16Ac levels have been studied, their contribution to age-related DSB accumulation remains unknown. In vitro aged Human Dermal Fibroblasts (HDFs) display lower levels of H4K16A that correlate with reduced recruitment of 53BP1 to basal DSBs. Following DNA damage induction, early passage (EP) cells suffered from a transient H4K16 deacetylation that allowed proper 53BP1 recruitment to DSBs. In contrast, to reach this specific and optimum level, aged cells responded by increasing their overall lower H4K16Ac levels. Induced hyperacetylation of late passage (LP) cells using trichostatin A increased H4K16Ac levels but did not ameliorate 53BP1 recruitment. Instead, deacetylation induced by MOF silencing reduced H4K16Ac levels and compromised 53BP1 recruitment in both EP and LP cells. Age-associated decrease of H4K16Ac levels contributes to the repair defect displayed by in vitro aged cells. H4K16Ac responds to DNA damage in order to reach a specific, optimum level that allows proper 53BP1 recruitment. This response may be compromised with age, as LP cells depart from lower H4K16Ac levels. Variations in H4K16Ac following the activation of the DNA damage response and aging point at this histone mark as a key mediator between DNA repair and age-associated chromatin alterations.
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Affiliation(s)
- Lourdes González-Bermúdez
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Anna Genescà
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Mariona Terradas
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Spain
| | - Marta Martín
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
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17
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Chen Z, Tyler JK. The Chromatin Landscape Channels DNA Double-Strand Breaks to Distinct Repair Pathways. Front Cell Dev Biol 2022; 10:909696. [PMID: 35757003 PMCID: PMC9213757 DOI: 10.3389/fcell.2022.909696] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022] Open
Abstract
DNA double-strand breaks (DSBs), the most deleterious DNA lesions, are primarily repaired by two pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ), the choice of which is largely dependent on cell cycle phase and the local chromatin landscape. Recent studies have revealed that post-translational modifications on histones play pivotal roles in regulating DSB repair pathways including repair pathway choice. In this review, we present our current understanding of how these DSB repair pathways are employed in various chromatin landscapes to safeguard genomic integrity. We place an emphasis on the impact of different histone post-translational modifications, characteristic of euchromatin or heterochromatin regions, on DSB repair pathway choice. We discuss the potential roles of damage-induced chromatin modifications in the maintenance of genome and epigenome integrity. Finally, we discuss how RNA transcripts from the vicinity of DSBs at actively transcribed regions also regulate DSB repair pathway choice.
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Affiliation(s)
- Zulong Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York City, NY, United States
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18
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Meng S, Huang S, Liu J, Gai Y, Li M, Duan S, Zhang S, Sun X, Yang Q, Wang Y, Xu K, Ma H. Histone Methylation Is Required for Virulence, Conidiation, and Multi-Stress Resistance of Alternaria alternata. Front Microbiol 2022; 13:924476. [PMID: 35783406 PMCID: PMC9245015 DOI: 10.3389/fmicb.2022.924476] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/24/2022] [Indexed: 11/22/2022] Open
Abstract
Histone methylation, which is critical for transcriptional regulation and various biological processes in eukaryotes, is a reversible dynamic process regulated by histone methyltransferases (HMTs) and histone demethylases (HDMs). This study determined the function of 5 HMTs (AaDot1, AaHMT1, AaHnrnp, AaSet1, and AaSet2) and 1 HDMs (AaGhd2) in the phytopathogenic fungus Alternaria alternata by analyzing targeted gene deletion mutants. The vegetative growth, conidiation, and pathogenicity of ∆AaSet1 and ∆AaSet2 were severely inhibited indicating that AaSet1 and AaSet2 play critical roles in cell development in A. alternata. Multiple stresses analysis revealed that both AaSet1 and AaSet2 were involved in the adaptation to cell wall interference agents and osmotic stress. Meanwhile, ∆AaSet1 and ∆AaSet2 displayed serious vegetative growth defects in sole carbon source medium, indicating that AaSet1 and AaSet2 play an important role in carbon source utilization. In addition, ∆AaSet2 colony displayed white in color, while the wild-type colony was dark brown, indicating AaSet2 is an essential gene for melanin biosynthesis in A. alternata. AaSet2 was required for the resistance to oxidative stress. On the other hand, all of ∆AaDot1, ∆AaHMT1, and ∆AaGhd2 mutants displayed wild-type phenotype in vegetative growth, multi-stress resistance, pathogenicity, carbon source utilization, and melanin biosynthesis. To explore the regulatory mechanism of AaSet1 and AaSet2, RNA-seq of these mutants and wild-type strain was performed. Phenotypes mentioned above correlated well with the differentially expressed genes in ∆AaSet1 and ∆AaSet2 according to the KEGG and GO enrichment results. Overall, our study provides genetic evidence that defines the central role of HMTs and HDMs in the pathological and biological functions of A. alternata.
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Affiliation(s)
- Shuai Meng
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Suya Huang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Jinhua Liu
- Natural Medicine Institute of Zhejiang YangShengTang Co., LTD, Hangzhou, China
| | - Yunpeng Gai
- School of Grassland Science, Beijing Forestry University, Beijing, China
| | - Min Li
- China-USA Citrus Huanglongbing Joint Laboratory (GNU-UF Joint Lab), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Shuo Duan
- China-USA Citrus Huanglongbing Joint Laboratory (GNU-UF Joint Lab), National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, China
| | - Shuting Zhang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Qi Yang
- Linyi Inspection and Testing Center, Linyi, China
| | - Yuchun Wang
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Kai Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
| | - Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, China
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19
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Rang FJ, de Luca KL, de Vries SS, Valdes-Quezada C, Boele E, Nguyen PD, Guerreiro I, Sato Y, Kimura H, Bakkers J, Kind J. Single-cell profiling of transcriptome and histone modifications with EpiDamID. Mol Cell 2022; 82:1956-1970.e14. [PMID: 35366395 PMCID: PMC9153956 DOI: 10.1016/j.molcel.2022.03.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/24/2021] [Accepted: 03/02/2022] [Indexed: 12/25/2022]
Abstract
Recent advances in single-cell sequencing technologies have enabled simultaneous measurement of multiple cellular modalities, but the combined detection of histone post-translational modifications and transcription at single-cell resolution has remained limited. Here, we introduce EpiDamID, an experimental approach to target a diverse set of chromatin types by leveraging the binding specificities of single-chain variable fragment antibodies, engineered chromatin reader domains, and endogenous chromatin-binding proteins. Using these, we render the DamID technology compatible with the genome-wide identification of histone post-translational modifications. Importantly, this includes the possibility to jointly measure chromatin marks and transcription at the single-cell level. We use EpiDamID to profile single-cell Polycomb occupancy in mouse embryoid bodies and provide evidence for hierarchical gene regulatory networks. In addition, we map H3K9me3 in early zebrafish embryogenesis, and detect striking heterochromatic regions specific to notochord. Overall, EpiDamID is a new addition to a vast toolbox to study chromatin states during dynamic cellular processes.
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Affiliation(s)
- Franka J Rang
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Kim L de Luca
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Sandra S de Vries
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Christian Valdes-Quezada
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Ellen Boele
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Phong D Nguyen
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands
| | - Isabel Guerreiro
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Yuko Sato
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Jeroen Bakkers
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Department of Pediatric Cardiology, Division of Pediatrics, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, the Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands.
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20
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Etier A, Dumetz F, Chéreau S, Ponts N. Post-Translational Modifications of Histones Are Versatile Regulators of Fungal Development and Secondary Metabolism. Toxins (Basel) 2022; 14:toxins14050317. [PMID: 35622565 PMCID: PMC9145779 DOI: 10.3390/toxins14050317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/16/2022] [Accepted: 04/25/2022] [Indexed: 02/04/2023] Open
Abstract
Chromatin structure is a major regulator of DNA-associated processes, such as transcription, DNA repair, and replication. Histone post-translational modifications, or PTMs, play a key role on chromatin dynamics. PTMs are involved in a wide range of biological processes in eukaryotes, including fungal species. Their deposition/removal and their underlying functions have been extensively investigated in yeasts but much less in other fungi. Nonetheless, the major role of histone PTMs in regulating primary and secondary metabolisms of filamentous fungi, including human and plant pathogens, has been pinpointed. In this review, an overview of major identified PTMs and their respective functions in fungi is provided, with a focus on filamentous fungi when knowledge is available. To date, most of these studies investigated histone acetylations and methylations, but the development of new methodologies and technologies increasingly allows the wider exploration of other PTMs, such as phosphorylation, ubiquitylation, sumoylation, and acylation. Considering the increasing number of known PTMs and the full range of their possible interactions, investigations of the subsequent Histone Code, i.e., the biological consequence of the combinatorial language of all histone PTMs, from a functional point of view, are exponentially complex. Better knowledge about histone PTMs would make it possible to efficiently fight plant or human contamination, avoid the production of toxic secondary metabolites, or optimize the industrial biosynthesis of certain beneficial compounds.
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21
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Pal AS, Agredo A, Lanman NA, Son J, Sohal IS, Bains M, Li C, Clingerman J, Gates K, Kasinski AL. Loss of KMT5C Promotes EGFR Inhibitor Resistance in NSCLC via LINC01510-Mediated Upregulation of MET. Cancer Res 2022; 82:1534-1547. [PMID: 35404406 DOI: 10.1158/0008-5472.can-20-0821] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 12/03/2021] [Accepted: 01/05/2022] [Indexed: 11/16/2022]
Abstract
EGFR inhibitors (EGFRi) are standard-of-care treatments administered to patients with non-small cell lung cancer (NSCLC) that harbor EGFR alterations. However, development of resistance posttreatment remains a major challenge. Multiple mechanisms can promote survival of EGFRi-treated NSCLC cells, including secondary mutations in EGFR and activation of bypass tracks that circumvent the requirement for EGFR signaling. Nevertheless, the mechanisms involved in bypass signaling activation are understudied and require further elucidation. In this study, we identify that loss of an epigenetic factor, lysine methyltransferase 5C (KMT5C), drives resistance of NSCLC to multiple EGFRis, including erlotinib, gefitinib, afatinib, and osimertinib. KMT5C catalyzed trimethylation of histone H4 lysine 20 (H4K20), a modification required for gene repression and maintenance of heterochromatin. Loss of KMT5C led to upregulation of an oncogenic long noncoding RNA, LINC01510, that promoted transcription of the oncogene MET, a component of a major bypass mechanism involved in EGFRi resistance. These findings underscore the loss of KMT5C as a critical event in driving EGFRi resistance by promoting a LINC01510/MET axis, providing mechanistic insights that could help improve NSCLC treatment. SIGNIFICANCE Dysregulation of the epigenetic modifier KMT5C can drive MET-mediated EGFRi resistance, implicating KMT5C loss as a putative biomarker of resistance and H4K20 methylation as a potential target in EGFRi-resistant lung cancer.
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Affiliation(s)
- Arpita S Pal
- Department of Biological Sciences, West Lafayette, Indiana.,Purdue Life Sciences Interdisciplinary Program (PULSe), West Lafayette, Indiana
| | - Alejandra Agredo
- Department of Biological Sciences, West Lafayette, Indiana.,Purdue Life Sciences Interdisciplinary Program (PULSe), West Lafayette, Indiana
| | - Nadia A Lanman
- Purdue University Center for Cancer Research, West Lafayette, Indiana.,Department of Comparative Pathobiology, Purdue University, West Lafayette, Indiana
| | - Jihye Son
- Department of Biological Sciences, West Lafayette, Indiana
| | - Ikjot Singh Sohal
- Department of Biological Sciences, West Lafayette, Indiana.,Purdue University Center for Cancer Research, West Lafayette, Indiana
| | - Manvir Bains
- Department of Biological Sciences, West Lafayette, Indiana
| | - Chennan Li
- Department of Biological Sciences, West Lafayette, Indiana
| | - Jenna Clingerman
- Department of Biological Sciences, West Lafayette, Indiana.,Purdue Life Sciences Interdisciplinary Program (PULSe), West Lafayette, Indiana
| | - Kayla Gates
- Department of Biological Sciences, West Lafayette, Indiana
| | - Andrea L Kasinski
- Department of Biological Sciences, West Lafayette, Indiana.,Purdue University Center for Cancer Research, West Lafayette, Indiana
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22
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Tessadori F, Duran K, Knapp K, Fellner M, Smithson S, Beleza Meireles A, Elting MW, Waisfisz Q, O’Donnell-Luria A, Nowak C, Douglas J, Ronan A, Brunet T, Kotzaeridou U, Svihovec S, Saenz MS, Thiffault I, Del Viso F, Devine P, Rego S, Tenney J, van Haeringen A, Ruivenkamp CA, Koene S, Robertson SP, Deshpande C, Pfundt R, Verbeek N, van de Kamp JM, Weiss JM, Ruiz A, Gabau E, Banne E, Pepler A, Bottani A, Laurent S, Guipponi M, Bijlsma E, Bruel AL, Sorlin A, Willis M, Powis Z, Smol T, Vincent-Delorme C, Baralle D, Colin E, Revencu N, Calpena E, Wilkie AO, Chopra M, Cormier-Daire V, Keren B, Afenjar A, Niceta M, Terracciano A, Specchio N, Tartaglia M, Rio M, Barcia G, Rondeau S, Colson C, Bakkers J, Mace PD, Bicknell LS, van Haaften G, van Haaften G. Recurrent de novo missense variants across multiple histone H4 genes underlie a neurodevelopmental syndrome. Am J Hum Genet 2022; 109:750-758. [PMID: 35202563 PMCID: PMC9069069 DOI: 10.1016/j.ajhg.2022.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/03/2022] [Indexed: 12/12/2022] Open
Abstract
Chromatin is essentially an array of nucleosomes, each of which consists of the DNA double-stranded fiber wrapped around a histone octamer. This organization supports cellular processes such as DNA replication, DNA transcription, and DNA repair in all eukaryotes. Human histone H4 is encoded by fourteen canonical histone H4 genes, all differing at the nucleotide level but encoding an invariant protein. Here, we present a cohort of 29 subjects with de novo missense variants in six H4 genes (H4C3, H4C4, H4C5, H4C6, H4C9, and H4C11) identified by whole-exome sequencing and matchmaking. All individuals present with neurodevelopmental features of intellectual disability and motor and/or gross developmental delay, while non-neurological features are more variable. Ten amino acids are affected, six recurrently, and are all located within the H4 core or C-terminal tail. These variants cluster to specific regions of the core H4 globular domain, where protein-protein interactions occur with either other histone subunits or histone chaperones. Functional consequences of the identified variants were evaluated in zebrafish embryos, which displayed abnormal general development, defective head organs, and reduced body axis length, providing compelling evidence for the causality of the reported disorder(s). While multiple developmental syndromes have been linked to chromatin-associated factors, missense-bearing histone variants (e.g., H3 oncohistones) are only recently emerging as a major cause of pathogenicity. Our findings establish a broader involvement of H4 variants in developmental syndromes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gijs van Haaften
- Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, 3584 Utrecht, the Netherlands.
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23
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Xu L, Zhang L, Sun J, Hu X, Kalvakolanu DV, Ren H, Guo B. Roles for the methyltransferase SETD8 in DNA damage repair. Clin Epigenetics 2022; 14:34. [PMID: 35246238 PMCID: PMC8897848 DOI: 10.1186/s13148-022-01251-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/20/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetic posttranslational modifications are critical for fine-tuning gene expression in various biological processes. SETD8 is so far the only known lysyl methyltransferase in mammalian cells to produce mono-methylation of histone H4 at lysine 20 (H4K20me1), a prerequisite for di- and tri-methylation. Importantly, SETD8 is related to a number of cellular activities, impinging upon tissue development, senescence and tumorigenesis. The double-strand breaks (DSBs) are cytotoxic DNA damages with deleterious consequences, such as genomic instability and cancer origin, if unrepaired. The homology-directed repair and canonical nonhomologous end-joining are two most prominent DSB repair pathways evolved to eliminate such aberrations. Emerging evidence implies that SETD8 and its corresponding H4K20 methylation are relevant to establishment of DSB repair pathway choice. Understanding how SETD8 functions in DSB repair pathway choice will shed light on the molecular basis of SETD8-deficiency related disorders and will be valuable for the development of new treatments. In this review, we discuss the progress made to date in roles for the lysine mono-methyltransferase SETD8 in DNA damage repair and its therapeutic relevance, in particular illuminating its involvement in establishment of DSB repair pathway choice, which is crucial for the timely elimination of DSBs.
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Affiliation(s)
- Libo Xu
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China.,Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, People's Republic of China
| | - Ling Zhang
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China.,Key Laboratory of Pathobiology, Ministry of Education, and Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, People's Republic of China
| | - Jicheng Sun
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Xindan Hu
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China
| | - Dhan V Kalvakolanu
- Greenebaum NCI Comprehensive Cancer Center, Department of Microbiology and Immunology, University of Maryland School Medicine, Baltimore, MD, USA
| | - Hui Ren
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China.
| | - Baofeng Guo
- Department of Surgery, China-Japan Union Hospital of Jilin University, Changchun, People's Republic of China.
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24
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Phillips EO, Gunjan A. Histone Variants: The Unsung Guardians of the Genome. DNA Repair (Amst) 2022; 112:103301. [DOI: 10.1016/j.dnarep.2022.103301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 02/01/2022] [Accepted: 02/12/2022] [Indexed: 12/15/2022]
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25
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Karl LA, Peritore M, Galanti L, Pfander B. DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling. Front Genet 2022; 12:821543. [PMID: 35096025 PMCID: PMC8790285 DOI: 10.3389/fgene.2021.821543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
DNA double strand breaks (DSBs) are repaired in eukaryotes by one of several cellular mechanisms. The decision-making process controlling DSB repair takes place at the step of DNA end resection, the nucleolytic processing of DNA ends, which generates single-stranded DNA overhangs. Dependent on the length of the overhang, a corresponding DSB repair mechanism is engaged. Interestingly, nucleosomes-the fundamental unit of chromatin-influence the activity of resection nucleases and nucleosome remodelers have emerged as key regulators of DSB repair. Nucleosome remodelers share a common enzymatic mechanism, but for global genome organization specific remodelers have been shown to exert distinct activities. Specifically, different remodelers have been found to slide and evict, position or edit nucleosomes. It is an open question whether the same remodelers exert the same function also in the context of DSBs. Here, we will review recent advances in our understanding of nucleosome remodelers at DSBs: to what extent nucleosome sliding, eviction, positioning and editing can be observed at DSBs and how these activities affect the DSB repair decision.
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Affiliation(s)
- Leonhard Andreas Karl
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Martina Peritore
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Lorenzo Galanti
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- Resarch Group DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
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26
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Atanasoff-Kardjalieff AK, Studt L. Secondary Metabolite Gene Regulation in Mycotoxigenic Fusarium Species: A Focus on Chromatin. Toxins (Basel) 2022; 14:96. [PMID: 35202124 PMCID: PMC8880415 DOI: 10.3390/toxins14020096] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Fusarium is a species-rich group of mycotoxigenic plant pathogens that ranks as one of the most economically important fungal genera in the world. During growth and infection, they are able to produce a vast spectrum of low-molecular-weight compounds, so-called secondary metabolites (SMs). SMs often comprise toxic compounds (i.e., mycotoxins) that contaminate precious food and feed sources and cause adverse health effects in humans and livestock. In this context, understanding the regulation of their biosynthesis is crucial for the development of cropping strategies that aim at minimizing mycotoxin contamination in the field. Nevertheless, currently, only a fraction of SMs have been identified, and even fewer are considered for regular monitoring by regulatory authorities. Limitations to exploit their full chemical potential arise from the fact that the genes involved in their biosynthesis are often silent under standard laboratory conditions and only induced upon specific stimuli mimicking natural conditions in which biosynthesis of the respective SM becomes advantageous for the producer. This implies a complex regulatory network. Several components of these gene networks have been studied in the past, thereby greatly advancing the understanding of SM gene regulation and mycotoxin biosynthesis in general. This review aims at summarizing the latest advances in SM research in these notorious plant pathogens with a focus on chromatin structure.
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Affiliation(s)
| | - Lena Studt
- Department of Applied Genetics and Cell Biology, Institute of Microbial Genetics, University of Natural Resources and Life Sciences, Vienna (BOKU), 3430 Tulln an der Donau, Austria;
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27
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Zhang L, Geng X, Wang F, Tang J, Ichida Y, Sharma A, Jin S, Chen M, Tang M, Pozo FM, Wang W, Wang J, Wozniak M, Guo X, Miyagi M, Jin F, Xu Y, Yao X, Zhang Y. 53BP1 regulates heterochromatin through liquid phase separation. Nat Commun 2022; 13:360. [PMID: 35042897 PMCID: PMC8766474 DOI: 10.1038/s41467-022-28019-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/03/2022] [Indexed: 01/09/2023] Open
Abstract
Human 53BP1 is primarily known as a key player in regulating DNA double strand break (DSB) repair choice; however, its involvement in other biological process is less well understood. Here, we report a previously uncharacterized function of 53BP1 at heterochromatin, where it undergoes liquid-liquid phase separation (LLPS) with the heterochromatin protein HP1α in a mutually dependent manner. Deletion of 53BP1 results in a reduction in heterochromatin centers and the de-repression of heterochromatic tandem repetitive DNA. We identify domains and residues of 53BP1 required for its LLPS, which overlap with, but are distinct from, those involved in DSB repair. Further, 53BP1 mutants deficient in DSB repair, but proficient in LLPS, rescue heterochromatin de-repression and protect cells from stress-induced DNA damage and senescence. Our study suggests that in addition to DSB repair modulation, 53BP1 contributes to the maintenance of heterochromatin integrity and genome stability through LLPS.
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Affiliation(s)
- Lei Zhang
- Department of Pharmacology, Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA.
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, 430068, China.
| | - Xinran Geng
- Department of Pharmacology, Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Fangfang Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Jinshan Tang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Yu Ichida
- Department of Pharmacology, Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Arishya Sharma
- Department of Pharmacology, Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Sora Jin
- Department of Pharmacology, Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - Mingliang Tang
- College of Life Sciences, Wuhan University, Wuhan, Hubei, 430068, China
| | - Franklin Mayca Pozo
- Department of Pharmacology, Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Wenxiu Wang
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Michal Wozniak
- Department of Pharmacology and Toxicology, Wright State University, Dayton, OH, 45435, USA
- Department of Molecular Biology of Cancer, Medical University of Lodz, 6/8 Mazowiecka Street, 92-215, Lodz, Poland
| | - Xiaoxia Guo
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan, Hubei, 430068, China
| | - Masaru Miyagi
- Department of Pharmacology, Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Fulai Jin
- Department of Genetics and Genome Sciences, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA
| | - Yongjie Xu
- Department of Pharmacology and Toxicology, Wright State University, Dayton, OH, 45435, USA
| | - Xinsheng Yao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632, China
| | - Youwei Zhang
- Department of Pharmacology, Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH, 44106, USA.
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28
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Differentiation of fetal hematopoietic stem cells requires ARID4B to restrict autocrine KITLG/KIT-Src signaling. Cell Rep 2021; 37:110036. [PMID: 34818550 PMCID: PMC8722094 DOI: 10.1016/j.celrep.2021.110036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 07/15/2021] [Accepted: 11/01/2021] [Indexed: 11/26/2022] Open
Abstract
Balance between the hematopoietic stem cell (HSC) duality to either possess self-renewal capacity or differentiate into multipotency progenitors (MPPs) is crucial for maintaining homeostasis of the hematopoietic stem/progenitor cell (HSPC) compartment. To retain the HSC self-renewal activity, KIT, a receptor tyrosine kinase, in HSCs is activated by its cognate ligand KITLG originating from niche cells. Here, we show that AT-rich interaction domain 4B (ARID4B) interferes with KITLG/KIT signaling, consequently allowing HSC differentiation. Conditional Arid4b knockout in mouse hematopoietic cells blocks fetal HSC differentiation, preventing hematopoiesis. Mechanistically, ARID4B-deficient HSCs self-express KITLG and overexpress KIT. As to downstream pathways of KITLG/KIT signaling, inhibition of Src family kinases rescues the HSC differentiation defect elicited by ARID4B loss. In summary, the intrinsic ARID4B-KITLG/KIT-Src axis is an HSPC regulatory program that enables the differentiation state, while KIT stimulation by KITLG from niche cells preserves the HSPC undifferentiated pool. Hematopoietic stem cells (HSCs) at the top of the hematopoietic hierarchy are able to self-renew and differentiate to mature blood cells. Young et al. report that an HSC self-control mechanism established by ARID4B ensures HSC differentiation. ARID4B-deficient HSCs produce KITLG to stimulate KIT, leading to blockage of HSC differentiation and eventual hematopoietic failure.
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29
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Bachleitner S, Sulyok M, Sørensen JL, Strauss J, Studt L. The H4K20 methyltransferase Kmt5 is involved in secondary metabolism and stress response in phytopathogenic Fusarium species. Fungal Genet Biol 2021; 155:103602. [PMID: 34214671 DOI: 10.1016/j.fgb.2021.103602] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 02/08/2023]
Abstract
Fusarium fujikuroi and Fusarium graminearum are agronomically important plant pathogens, both infecting important staple food plants and thus leading to huge economic losses worldwide. F.fujikuroi belongs to the Fusarium fujikuroi species complex (FFSC) and causes bakanae disease on rice, whereas F.graminearum, a member of the Fusarium graminearum species complex (FGSC), is the causal agent of Fusarium Head Blight (FHB) disease on wheat, barley and maize. In recent years, the importance of chromatin regulation became evident in the plant-pathogen interaction. Several processes, including posttranslational modifications of histones, have been described as regulators of virulence and the biosynthesis of secondary metabolites. In this study, we have functionally characterised methylation of lysine 20 histone 4 (H4K20me) in both Fusarium species. We identified the respective genes solely responsible for H4K20 mono-, di- and trimethylation in F.fujikuroi (FfKMT5) and F.graminearum (FgKMT5). We show that loss of Kmt5 affects colony growth in F.graminearum while this is not the case for F.fujikuroi. Similarly, FgKmt5 is required for full virulence in F.graminearum as Δfgkmt5 is hypovirulent on wheat, whereas the F.fujikuroi Δffkmt5 strain did not deviate from the wild type during rice infection. Lack of Kmt5 had distinct effects on the secondary metabolism in both plant pathogens with the most pronounced effects on fusarin biosynthesis in F.fujikuroi and zearalenone biosynthesis in F.graminearum. Next to this, loss of Kmt5 resulted in an increased tolerance towards oxidative and osmotic stress in both species.
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Affiliation(s)
- Simone Bachleitner
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Michael Sulyok
- Institute of Bioanalytics and Agro-Metabolomics, Department for Agrobiotechnology (IFA-Tulln), University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Str. 20, Tulln 3430, Austria
| | - Jens Laurids Sørensen
- Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, DK-9000 Aalborg, Denmark
| | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria
| | - Lena Studt
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Konrad-Lorenz-Straße 24, 3430 Tulln an der Donau, Austria.
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30
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Ackerson SM, Romney C, Schuck PL, Stewart JA. To Join or Not to Join: Decision Points Along the Pathway to Double-Strand Break Repair vs. Chromosome End Protection. Front Cell Dev Biol 2021; 9:708763. [PMID: 34322492 PMCID: PMC8311741 DOI: 10.3389/fcell.2021.708763] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 06/17/2021] [Indexed: 01/01/2023] Open
Abstract
The regulation of DNA double-strand breaks (DSBs) and telomeres are diametrically opposed in the cell. DSBs are considered one of the most deleterious forms of DNA damage and must be quickly recognized and repaired. Telomeres, on the other hand, are specialized, stable DNA ends that must be protected from recognition as DSBs to inhibit unwanted chromosome fusions. Decisions to join DNA ends, or not, are therefore critical to genome stability. Yet, the processing of telomeres and DSBs share many commonalities. Accordingly, key decision points are used to shift DNA ends toward DSB repair vs. end protection. Additionally, DSBs can be repaired by two major pathways, namely homologous recombination (HR) and non-homologous end joining (NHEJ). The choice of which repair pathway is employed is also dictated by a series of decision points that shift the break toward HR or NHEJ. In this review, we will focus on these decision points and the mechanisms that dictate end protection vs. DSB repair and DSB repair choice.
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Affiliation(s)
- Stephanie M Ackerson
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Carlan Romney
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - P Logan Schuck
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
| | - Jason A Stewart
- Department of Biological Sciences, University of South Carolina, Columbia, SC, United States
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31
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Role of Histone Methylation in Maintenance of Genome Integrity. Genes (Basel) 2021; 12:genes12071000. [PMID: 34209979 PMCID: PMC8307007 DOI: 10.3390/genes12071000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/14/2022] Open
Abstract
Packaging of the eukaryotic genome with histone and other proteins forms a chromatin structure that regulates the outcome of all DNA mediated processes. The cellular pathways that ensure genomic stability detect and repair DNA damage through mechanisms that are critically dependent upon chromatin structures established by histones and, particularly upon transient histone post-translational modifications. Though subjected to a range of modifications, histone methylation is especially crucial for DNA damage repair, as the methylated histones often form platforms for subsequent repair protein binding at damaged sites. In this review, we highlight and discuss how histone methylation impacts the maintenance of genome integrity through effects related to DNA repair and repair pathway choice.
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32
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The nuclear kinesin KIF18B promotes 53BP1-mediated DNA double-strand break repair. Cell Rep 2021; 35:109306. [PMID: 34192545 DOI: 10.1016/j.celrep.2021.109306] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 04/29/2021] [Accepted: 06/03/2021] [Indexed: 12/13/2022] Open
Abstract
53BP1 is recruited to chromatin in the vicinity of DNA double-strand breaks (DSBs). We identify the nuclear kinesin, KIF18B, as a 53BP1-interacting protein and define its role in 53BP1-mediated DSB repair. KIF18B is a molecular motor protein involved in destabilizing astral microtubules during mitosis. It is primarily nuclear throughout the interphase and is constitutively chromatin bound. Our observations indicate a nuclear function during the interphase for a kinesin previously implicated in mitosis. We identify a central motif in KIF18B, which we term the Tudor-interacting motif (TIM), because of its interaction with the Tudor domain of 53BP1. TIM enhances the interaction between the 53BP1 Tudor domain and dimethylated lysine 20 of histone H4. TIM and the motor function of KIF18B are both required for efficient 53BP1 focal recruitment in response to damage and for fusion of dysfunctional telomeres. Our data suggest a role for KIF18B in efficient 53BP1-mediated end-joining of DSBs.
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33
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Cao X, Chen Y, Wu B, Wang X, Xue H, Yu L, Li J, Wang Y, Wang W, Xu Q, Mao H, Peng C, Han G, Chen CD. Histone H4K20 Demethylation by Two hHR23 Proteins. Cell Rep 2021; 30:4152-4164.e6. [PMID: 32209475 DOI: 10.1016/j.celrep.2020.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/12/2020] [Accepted: 02/28/2020] [Indexed: 02/06/2023] Open
Abstract
Histone methyl groups can be removed by demethylases. Although LSD1 and JmjC domain-containing proteins have been identified as histone demethylases, enzymes for many histone methylation states or sites are still unknown. Here, we perform a screening of a cDNA library containing 2,500 nuclear proteins and identify hHR23A as a histone H4K20 demethylase. Overexpression of hHR23A reduces the levels of H4K20me1/2/3 in cells. In vitro, hHR23A specifically demethylates H4K20me1/2/3 and generates formaldehyde. The enzymatic activity requires Fe(II) and α-ketoglutarate as cofactors and the UBA domains of hHR23A. hHR23B, a protein homologous to hHR23A, also demethylates H4K20me1/2/3 in vitro and in vivo. We further demonstrate that hHR23A/B activate the transcription of coding genes by demethylating H4K20me1 and the transcription of repetitive elements by demethylating H4K20me3. Nuclear magnetic resonance (NMR) analyses demonstrate that an HxxxE motif in the UBA1 domain is crucial for iron binding and demethylase activity. Thus, we identify two hHR23 proteins as histone demethylases.
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Affiliation(s)
- Xiongwen Cao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Yanran Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Bin Wu
- National Facility for Protein Science, Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Xiaoyun Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hongjuan Xue
- National Facility for Protein Science, Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Lu Yu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jie Li
- National Facility for Protein Science, Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yiqin Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Wei Wang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Qing Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hailei Mao
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Departments of Anaesthesiology and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Chao Peng
- National Facility for Protein Science, Shanghai, Zhangjiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Gang Han
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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34
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Kundu S, Ray MD, Sharma A. Interplay between genome organization and epigenomic alterations of pericentromeric DNA in cancer. J Genet Genomics 2021; 48:184-197. [PMID: 33840602 DOI: 10.1016/j.jgg.2021.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/07/2021] [Accepted: 02/20/2021] [Indexed: 12/16/2022]
Abstract
In eukaryotic genome biology, the genomic organization inside the three-dimensional (3D) nucleus is highly complex, and whether this organization governs gene expression is poorly understood. Nuclear lamina (NL) is a filamentous meshwork of proteins present at the lining of inner nuclear membrane that serves as an anchoring platform for genome organization. Large chromatin domains termed as lamina-associated domains (LADs), play a major role in silencing genes at the nuclear periphery. The interaction of the NL and genome is dynamic and stochastic. Furthermore, many genes change their positions during developmental processes or under disease conditions such as cancer, to activate certain sorts of genes and/or silence others. Pericentromeric heterochromatin (PCH) is mostly in the silenced region within the genome, which localizes at the nuclear periphery. Studies show that several genes located at the PCH are aberrantly expressed in cancer. The interesting question is that despite being localized in the pericentromeric region, how these genes still manage to overcome pericentromeric repression. Although epigenetic mechanisms control the expression of the pericentromeric region, recent studies about genome organization and genome-nuclear lamina interaction have shed light on a new aspect of pericentromeric gene regulation through a complex and coordinated interplay between epigenomic remodeling and genomic organization in cancer.
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Affiliation(s)
- Subhadip Kundu
- Laboratory of Chromatin and Cancer Epigenetics, Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - M D Ray
- Department of Surgical Oncology, IRCH, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Ashok Sharma
- Laboratory of Chromatin and Cancer Epigenetics, Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India.
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35
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Salimi-Jeda A, Badrzadeh F, Esghaei M, Abdoli A. The role of telomerase and viruses interaction in cancer development, and telomerase-dependent therapeutic approaches. Cancer Treat Res Commun 2021; 27:100323. [PMID: 33530025 DOI: 10.1016/j.ctarc.2021.100323] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/19/2021] [Accepted: 01/21/2021] [Indexed: 12/21/2022]
Abstract
Human telomerase reverse transcriptase (hTERT) is an enzyme that is critically involved in elongating and maintaining telomeres length to control cell life span and replicative potential. Telomerase activity is continuously expressed in human germ-line cells and most cancer cells, whereas it is suppressed in most somatic cells. In normal cells, by reducing telomerase activity and progressively shortening the telomeres, the cells progress to the senescence or apoptosis process. However, in cancer cells, telomere lengths remain constant due to telomerase's reactivation, and cells continue to proliferate and inhibit apoptosis, and ultimately lead to cancer development and human death due to metastasis. Studies demonstrated that several DNA and RNA oncoviruses could interact with telomerase by integrating their genome sequence within the host cell telomeres specifically. Through the activation of the hTERT promoter and lengthening the telomere, these cells contributes to cancer development. Since oncoviruses can activate telomerase and increase hTERT expression, there are several therapeutic strategies based on targeting the telomerase of cancer cells like telomerase-targeted peptide vaccines, hTERT-targeting dendritic cells (DCs), hTERT-targeting gene therapy, and hTERT-targeting CRISPR/Cas9 system that can overcome tumor-mediated toleration mechanisms and specifically apoptosis in cancer cells. This study reviews available data on the molecular structure of telomerase and the role of oncoviruses and telomerase interaction in cancer development and telomerase-dependent therapeutic approaches to conquest the cancer cells.
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Affiliation(s)
- Ali Salimi-Jeda
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Fariba Badrzadeh
- Faculti of Medicine, Golestan University of Medical sciences, Golestan, Iran.
| | - Maryam Esghaei
- Department of Virology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran.
| | - Asghar Abdoli
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran.
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36
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Bhat KP, Ümit Kaniskan H, Jin J, Gozani O. Epigenetics and beyond: targeting writers of protein lysine methylation to treat disease. Nat Rev Drug Discov 2021; 20:265-286. [PMID: 33469207 DOI: 10.1038/s41573-020-00108-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 02/07/2023]
Abstract
Protein lysine methylation is a crucial post-translational modification that regulates the functions of both histone and non-histone proteins. Deregulation of the enzymes or 'writers' of protein lysine methylation, lysine methyltransferases (KMTs), is implicated in the cause of many diseases, including cancer, mental health disorders and developmental disorders. Over the past decade, significant advances have been made in developing drugs to target KMTs that are involved in histone methylation and epigenetic regulation. The first of these inhibitors, tazemetostat, was recently approved for the treatment of epithelioid sarcoma and follicular lymphoma, and several more are in clinical and preclinical evaluation. Beyond chromatin, the many KMTs that regulate protein synthesis and other fundamental biological processes are emerging as promising new targets for drug development to treat diverse diseases.
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Affiliation(s)
- Kamakoti P Bhat
- Department of Biology, Stanford University, Stanford, CA, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA.
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37
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Anglada T, Genescà A, Martín M. Age-associated deficient recruitment of 53BP1 in G1 cells directs DNA double-strand break repair to BRCA1/CtIP-mediated DNA-end resection. Aging (Albany NY) 2020; 12:24872-24893. [PMID: 33361520 PMCID: PMC7803562 DOI: 10.18632/aging.202419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
DNA repair mechanisms play a crucial role in maintaining genome integrity. However, the increased frequency of DNA double-strand breaks (DSBs) and genome rearrangements in aged individuals suggests an age-associated DNA repair deficiency. Previous work from our group revealed a delayed firing of the DNA damage response in human mammary epithelial cells (HMECs) from aged donors. We now report a decreased activity of the main DSB repair pathways, the canonical non-homologous end-joining (c-NHEJ) and the homologous recombination (HR) in these HMECs from older individuals. We describe here a deficient recruitment of 53BP1 to DSB sites in G1 cells, probably influenced by an altered epigenetic regulation. 53BP1 absence at some DSBs is responsible for the age-associated DNA repair defect, as it permits the ectopic formation of BRCA1 foci while still in the G1 phase. CtIP and RPA foci are also formed in G1 cells from aged donors, but RAD51 is not recruited, thus indicating that extensive DNA-end resection occurs in these breaks although HR is not triggered. These results suggest an age-associated switch of DSB repair from canonical to highly mutagenic alternative mechanisms that promote the formation of genome rearrangements, a source of genome instability that might contribute to the aging process.
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Affiliation(s)
- Teresa Anglada
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Anna Genescà
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Marta Martín
- Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
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38
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Zhang J, Yan Z, Wang Y, Wang Y, Guo X, Jing J, Dong X, Dong S, Liu X, Yu X, Wu C. Cancer-associated 53BP1 mutations induce DNA damage repair defects. Cancer Lett 2020; 501:43-54. [PMID: 33359708 DOI: 10.1016/j.canlet.2020.12.033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/18/2020] [Accepted: 12/21/2020] [Indexed: 12/29/2022]
Abstract
TP53 binding protein 1 (53BP1) plays an important role in DNA damage repair and maintaining genomic stability. However, the mutations of 53BP1 in human cancers have not been systematically examined. Here, we have analyzed 541 somatic mutations of 53BP1 across 34 types of human cancer from databases of The Cancer Genome Atlas, International Cancer Genome Consortium and Catalogue of Somatic Mutations in Cancer. Among these cancer-associated 53BP1 mutations, truncation mutations disrupt the nuclear localization of 53BP1 thus abolish its biological functions in DNA damage repair. Moreover, with biochemical analyses and structural modeling, we have examined the detailed molecular mechanism by which missense mutations in the key domains causes the DNA damage repair defects. Taken together, our results reveal the functional defects of a set of cancer-associated 53BP1 mutations.
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Affiliation(s)
- Jiajia Zhang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Zhenzhen Yan
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Yukun Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Yaguang Wang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xin Guo
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Ju Jing
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xiangnan Dong
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Shasha Dong
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China
| | - Xiuhua Liu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China.
| | - Xiaochun Yu
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, 310024, China.
| | - Chen Wu
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, 071002, Hebei, China.
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39
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Schuh L, Loos C, Pokrovsky D, Imhof A, Rupp RAW, Marr C. H4K20 Methylation Is Differently Regulated by Dilution and Demethylation in Proliferating and Cell-Cycle-Arrested Xenopus Embryos. Cell Syst 2020; 11:653-662.e8. [PMID: 33296683 DOI: 10.1016/j.cels.2020.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/05/2020] [Accepted: 11/11/2020] [Indexed: 11/26/2022]
Abstract
DNA replication during cell division leads to dilution of histone modifications and can thus affect chromatin-mediated gene regulation, raising the question of how the cell-cycle shapes the histone modification landscape, particularly during embryogenesis. We tackled this problem by manipulating the cell cycle during early Xenopus laevis embryogenesis and analyzing in vivo histone H4K20 methylation kinetics. The global distribution of un-, mono-, di-, and tri-methylated histone H4K20 was measured by mass spectrometry in normal and cell-cycle-arrested embryos over time. Using multi-start maximum likelihood optimization and quantitative model selection, we found that three specific biological methylation rate constants were required to explain the measured H4K20 methylation state kinetics. While demethylation is essential for regulating H4K20 methylation kinetics in non-cycling cells, demethylation is very likely dispensable in rapidly dividing cells of early embryos, suggesting that cell-cycle-mediated dilution of H4K20 methylation is an essential regulatory component for shaping its epigenetic landscape during early development. A record of this paper's transparent peer review process is included in the Supplemental Information.
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Affiliation(s)
- Lea Schuh
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Mathematics, Technical University of Munich, Garching 85748, Germany
| | - Carolin Loos
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany; Department of Mathematics, Technical University of Munich, Garching 85748, Germany; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniil Pokrovsky
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Axel Imhof
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Ralph A W Rupp
- Department of Molecular Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Germany
| | - Carsten Marr
- Institute of Computational Biology, Helmholtz Zentrum München-German Research Center for Environmental Health, Neuherberg 85764, Germany.
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40
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Kurup JT, Han Z, Jin W, Kidder BL. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells. Development 2020; 147:dev.188516. [PMID: 33144397 DOI: 10.1242/dev.188516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 10/27/2020] [Indexed: 12/27/2022]
Abstract
Heterochromatin, a densely packed chromatin state that is transcriptionally silent, is a critical regulator of gene expression. However, it is unclear how the repressive histone modification H4K20me3 or the histone methyltransferase SUV420H2 regulates embryonic stem (ES) cell fate by patterning the epigenetic landscape. Here, we report that depletion of SUV420H2 leads to a near-complete loss of H4K20me3 genome wide, dysregulated gene expression and delayed ES cell differentiation. SUV420H2-bound regions are enriched with repetitive DNA elements, which are de-repressed in SUV420H2 knockout ES cells. Moreover, SUV420H2 regulation of H4K20me3-marked heterochromatin controls chromatin architecture, including fine-scale chromatin interactions in pluripotent ES cells. Our results indicate that SUV420H2 plays a crucial role in stabilizing the three-dimensional chromatin landscape of ES cells, as loss of SUV420H2 resulted in A/B compartment switching, perturbed chromatin insulation, and altered chromatin interactions of pericentric heterochromatin and surrounding regions, indicative of localized decondensation. In addition, depletion of SUV420H2 resulted in compromised interactions between H4K20me3 and gene-regulatory regions. Together, these findings describe a new role for SUV420H2 in regulating the chromatin landscape of ES cells.
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Affiliation(s)
- Jiji T Kurup
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA.,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Zhijun Han
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Wenfei Jin
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Benjamin L Kidder
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI 48201, USA .,Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48201, USA
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41
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Rehman S, Aatif M, Rafi Z, Khan MY, Shahab U, Ahmad S, Farhan M. Effect of non-enzymatic glycosylation in the epigenetics of cancer. Semin Cancer Biol 2020; 83:543-555. [DOI: 10.1016/j.semcancer.2020.11.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/09/2023]
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42
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Corvalan AZ, Coller HA. Methylation of histone 4's lysine 20: a critical analysis of the state of the field. Physiol Genomics 2020; 53:22-32. [PMID: 33197229 DOI: 10.1152/physiolgenomics.00128.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chromatin is a highly dynamic structure whose plasticity is achieved through multiple processes including the posttranslational modification of histone tails. Histone modifications function through the recruitment of nonhistone proteins to chromatin and thus have the potential to influence many fundamental biological processes. Here, we focus on the function and regulation of lysine 20 of histone H4 (H4K20) methylation in multiple biological processes including DNA repair, cell cycle regulation, and DNA replication. The purpose of this review is to highlight recent studies that elucidate the functions associated with each of the methylation states of H4K20, their modifying enzymes, and their protein readers. Based on our current knowledge of H4K20 methylation, we critically analyze the data supporting these functions and outline questions for future research.
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Affiliation(s)
- Adriana Z Corvalan
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California.,Department of Biological Chemistry, University of California, Los Angeles, California
| | - Hilary A Coller
- Molecular Biology Interdepartmental Program, University of California, Los Angeles, California.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, California.,Department of Biological Chemistry, University of California, Los Angeles, California
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43
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Sundaravinayagam D, Rahjouei A, Andreani M, Tupiņa D, Balasubramanian S, Saha T, Delgado-Benito V, Coralluzzo V, Daumke O, Di Virgilio M. 53BP1 Supports Immunoglobulin Class Switch Recombination Independently of Its DNA Double-Strand Break End Protection Function. Cell Rep 2020; 28:1389-1399.e6. [PMID: 31390554 PMCID: PMC6693562 DOI: 10.1016/j.celrep.2019.06.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/16/2019] [Accepted: 06/07/2019] [Indexed: 01/29/2023] Open
Abstract
Class switch recombination (CSR) is a DNA recombination reaction that diversifies the effector functions of antibodies. CSR occurs via the formation and non-homologous end joining (NHEJ) repair of programmed DNA double-strand breaks (DSBs) at the immunoglobulin heavy chain locus. The DNA repair factors 53BP1 and Rif1 promote NHEJ and CSR by protecting DSBs against resection. However, to what extent repression of DNA end resection contributes to CSR is unknown. Here, we show that B lymphocytes devoid of 53BP1-Rif1-dependent DSB end protection activity undergo robust CSR. Inactivation of specific sets of phospho-sites within 53BP1 N-terminal SQ/TQ motifs abrogates Rif1 recruitment and inhibition of resection but only mildly reduces CSR. Furthermore, mutations within 53BP1 oligomerization domain abolish CSR without substantially affecting DNA end processing. Thus, inhibition of DNA end resection does not correlate with CSR efficiency, indicating that regulation of DSB processing is not a key determinant step in CSR. 53BP1 oligomerization is largely dispensable for inhibition of DSB resection 53BP1 higher order oligomerization is a pre-requisite for CSR B lymphocytes devoid of 53BP1-Rif1 DSB end protection activity undergo robust CSR 53BP1-mediated DSB end mobility is dispensable for CSR
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Affiliation(s)
- Devakumar Sundaravinayagam
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Ali Rahjouei
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Matteo Andreani
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Dagnija Tupiņa
- Laboratory of Structural Biology of Membrane-Associated Processes, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Sandhya Balasubramanian
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Tannishtha Saha
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Verónica Delgado-Benito
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Violeta Coralluzzo
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Oliver Daumke
- Laboratory of Structural Biology of Membrane-Associated Processes, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Michela Di Virgilio
- Laboratory of DNA Repair and Maintenance of Genome Stability, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany.
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44
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Aleksandrov R, Hristova R, Stoynov S, Gospodinov A. The Chromatin Response to Double-Strand DNA Breaks and Their Repair. Cells 2020; 9:cells9081853. [PMID: 32784607 PMCID: PMC7464352 DOI: 10.3390/cells9081853] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cellular DNA is constantly being damaged by numerous internal and external mutagenic factors. Probably the most severe type of insults DNA could suffer are the double-strand DNA breaks (DSBs). They sever both DNA strands and compromise genomic stability, causing deleterious chromosomal aberrations that are implicated in numerous maladies, including cancer. Not surprisingly, cells have evolved several DSB repair pathways encompassing hundreds of different DNA repair proteins to cope with this challenge. In eukaryotic cells, DSB repair is fulfilled in the immensely complex environment of the chromatin. The chromatin is not just a passive background that accommodates the multitude of DNA repair proteins, but it is a highly dynamic and active participant in the repair process. Chromatin alterations, such as changing patterns of histone modifications shaped by numerous histone-modifying enzymes and chromatin remodeling, are pivotal for proficient DSB repair. Dynamic chromatin changes ensure accessibility to the damaged region, recruit DNA repair proteins, and regulate their association and activity, contributing to DSB repair pathway choice and coordination. Given the paramount importance of DSB repair in tumorigenesis and cancer progression, DSB repair has turned into an attractive target for the development of novel anticancer therapies, some of which have already entered the clinic.
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45
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Karakaidos P, Karagiannis D, Rampias T. Resolving DNA Damage: Epigenetic Regulation of DNA Repair. Molecules 2020; 25:molecules25112496. [PMID: 32471288 PMCID: PMC7321228 DOI: 10.3390/molecules25112496] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/18/2022] Open
Abstract
Epigenetic research has rapidly evolved into a dynamic field of genome biology. Chromatin regulation has been proved to be an essential aspect for all genomic processes, including DNA repair. Chromatin structure is modified by enzymes and factors that deposit, erase, and interact with epigenetic marks such as DNA and histone modifications, as well as by complexes that remodel nucleosomes. In this review we discuss recent advances on how the chromatin state is modulated during this multi-step process of damage recognition, signaling, and repair. Moreover, we examine how chromatin is regulated when different pathways of DNA repair are utilized. Furthermore, we review additional modes of regulation of DNA repair, such as through the role of global and localized chromatin states in maintaining expression of DNA repair genes, as well as through the activity of epigenetic enzymes on non-nucleosome substrates. Finally, we discuss current and future applications of the mechanistic interplays between chromatin regulation and DNA repair in the context cancer treatment.
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Affiliation(s)
| | - Dimitris Karagiannis
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA;
| | - Theodoros Rampias
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece;
- Correspondence: ; Tel.: +30-210-659-7469
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46
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Abstract
In the past decade, the study of the major DNA double strand break (DSB) repair pathways, homologous recombination (HR) and classical non-homologous end joining (C-NHEJ), has revealed a vast and intricate network of regulation. The choice between HR and C-NHEJ is largely controlled at the step of DNA end-resection. A pro-C-NHEJ cascade commencing with 53BP1 and culminating in the newly discovered REV7-Shieldin complex impedes end resection and therefore HR. Importantly, loss of any component of this pathway confers PARP inhibitor resistance in BRCA1-deficient cells; hence, their study is of great clinical importance. The newest entrant on the scene of end resection regulation is the ATPase TRIP13 that disables the pro-C-NHEJ cascade by promoting a novel conformational change of the HORMA protein REV7. Here, we tie these new findings and factors with previous research on the regulation of DSB repair and HORMA proteins, and suggest testable hypotheses for how TRIP13 could specifically inactivate REV7-Shieldin to promote HR. We also discuss these biological questions in the context of clinical therapeutics.
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Affiliation(s)
- Prabha Sarangi
- Department of Radiation Oncology, Dana-Farber Cancer Institute , Boston, MA, USA.,Center for DNA Damage and Repair, Dana-Farber Cancer Institute , Boston, MA, USA
| | - Connor S Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute , Boston, MA, USA.,Center for DNA Damage and Repair, Dana-Farber Cancer Institute , Boston, MA, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute , Boston, MA, USA.,Center for DNA Damage and Repair, Dana-Farber Cancer Institute , Boston, MA, USA
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47
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Gsell C, Richly H, Coin F, Naegeli H. A chromatin scaffold for DNA damage recognition: how histone methyltransferases prime nucleosomes for repair of ultraviolet light-induced lesions. Nucleic Acids Res 2020; 48:1652-1668. [PMID: 31930303 PMCID: PMC7038933 DOI: 10.1093/nar/gkz1229] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The excision of mutagenic DNA adducts by the nucleotide excision repair (NER) pathway is essential for genome stability, which is key to avoiding genetic diseases, premature aging, cancer and neurologic disorders. Due to the need to process an extraordinarily high damage density embedded in the nucleosome landscape of chromatin, NER activity provides a unique functional caliper to understand how histone modifiers modulate DNA damage responses. At least three distinct lysine methyltransferases (KMTs) targeting histones have been shown to facilitate the detection of ultraviolet (UV) light-induced DNA lesions in the difficult to access DNA wrapped around histones in nucleosomes. By methylating core histones, these KMTs generate docking sites for DNA damage recognition factors before the chromatin structure is ultimately relaxed and the offending lesions are effectively excised. In view of their function in priming nucleosomes for DNA repair, mutations of genes coding for these KMTs are expected to cause the accumulation of DNA damage promoting cancer and other chronic diseases. Research on the question of how KMTs modulate DNA repair might pave the way to the development of pharmacologic agents for novel therapeutic strategies.
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Affiliation(s)
- Corina Gsell
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Holger Richly
- Boehringer Ingelheim Pharma, Department of Molecular Biology, Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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48
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Li Z, Bao J, Qi Y, Zhang JZH. Computational approaches to studying methylated H4K20 recognition by DNA repair factor 53BP1. Phys Chem Chem Phys 2020; 22:6136-6144. [PMID: 32124883 DOI: 10.1039/c9cp05635a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Histone lysine methylation regulates the recruitment of mammalian DNA repair factor 53BP1 to the histone H4 lysine 20 (H4K20), through specific recognition of the tandem Tudor domain of 53BP1. The di- and mono-methylated H4K20 bind to 53BP1 with high affinity, but the non- and tri-methylated H4K20 do not. Here, we develop a new approach to carry out computational study to unravel the binding mechanism of methylated H4K20 by 53BP1 and to compute relative binding affinities of different methylations of H4K20 by 53BP1. First, hot spots in 53BP1 were predicted by computational alanine scanning and aromatic cages formed by W1495, Y1500, Y1502, and Y1523 are found to provide the dominant binding to di- and mono-methylated H4K20 in addition to D1521. Secondly, a de-methylation method is proposed to predict relative binding free energies between 53BP1 and different methylated states of H4K20. Finally, the tri-methylated and non-methylated H4K20/53BP1 complexes are found to be dynamically unstable, explaining the experimental finding that neither can bind to 53BP1. The present work provides an important theoretical basis for our understanding of histone methylations of H4K20 and their recognition mechanism by DNA repair factor 53BP1.
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Affiliation(s)
- Zhendong Li
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200062, China.
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49
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Wu F, Chen Y, Li G, Zhu D, Wang L, Wang J. Zinc oxide nanoparticles synthesized from Allium cepa prevents UVB radiation mediated inflammation in human epidermal keratinocytes (HaCaT cells). ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2020; 47:3548-3558. [PMID: 31456420 DOI: 10.1080/21691401.2019.1642905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The extensive relevance of nanoparticles arouses the requirement for manufacturing although the predictable technique are frequently perilous and energy saving. In the current study, zinc oxide nanoparticles manufactured from Allium cepa avert UVB radiation interceded irritation in human epidermal keratinocytes (HaCaT cells). In the current study, the zinc oxide nanoparticles (ZnO-NPs) was synthesized from the extract of A. cepa. The optimized ZnO-NPs hence attained and was enumerated and exemplified by UV visible spectroscopy, X-ray diffraction, Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM), scanning electron microscope (SEM) and EDAX impending analysis. In addition, amalgamated ZnO-NPs were experienced for cell viability (MTT), formation of reactive oxygen species (ROS), apoptosis, and antioxidant and lipid peroxidation (TBARS) levels. Also, we explored the effect of A. cepa ZnO-NPs in molecular level by evaluating the inflammatory and apoptotic markers, in which ZnO-NPs reinstated the interleukins 6, 10 and related signaling molecules like iNOS, COX-2 levels. Ultimately, ZnO-NPs induce apoptotic markers (Bax, Bcl-2) and also recommended that ZnO-NPs might aggravate cancer cell apoptosis in HaCaT cells.
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Affiliation(s)
- Fenglian Wu
- Department of Plastic Surgery, The First Hospital of Qin Huangdao Qinhuangdao , Hebei , China
| | - Yanxin Chen
- Department of Pathology, The First Hospital of Qin Huangdao Qinhuangdao , Hebei , China
| | - Guoliang Li
- Ever Care Medical and Beauty Hospital , Harbin , China
| | - Donglai Zhu
- Department of Plastic Surgery, The First Hospital of Qin Huangdao Qinhuangdao , Hebei , China
| | - Lianying Wang
- Department of Plastic Surgery, The First Hospital of Qin Huangdao Qinhuangdao , Hebei , China
| | - Jiaxin Wang
- The First Hospital of Qin Huangdao, Qinhuangdao , Hebei , China
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50
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Zheng R, Liang D, Jiang N, Zhou J, Long X, Wang X, Wu M, Wu C, Bao J. Computer-aided screening for suppressor of variegation 4-20 homolog 1 inhibitors and their preliminary activity validation in human osteosarcoma. J Biomol Struct Dyn 2020; 39:526-537. [PMID: 31902296 DOI: 10.1080/07391102.2019.1711187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Histone methylation/demethylation facilitate to maintain balanced histone methylation levels and underpin gene regulation, playing the key roles in epigenetic regulation. Suppressor of variegation 4-20 homolog 1 (SUV420H1), a member of class Histone Lysine Methyltransferase and a key enzyme in the epigenetic regulation of the pathways controlling metabolism and tumorigenesis, is crucial to maintain cell homeostasis. The inhibition of SUV420H1 has emerged as a promising candidate for drug development and cancer therapy. Herein, two potential and potent SUV420H1 inhibitors (ZINC08398384, ZINC08439608) were identified through in silico approach and in vitro biological experiments. In vitro biological tests demonstrated that these compounds can inhibit the proliferation of U2OS cells and restrict its migration ability. And the level of dimethylation of lysine 20 on histone H4 (H4K20me2) was markedly decreased by these compounds-treatment in a dose-dependent manner. These results indicated that ZINC08398384 and ZINC08439608 are potential SUV420H1 inhibitors and could be developed as promising drug candidates applied to cancer epigenetic therapy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ruxiao Zheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Danfeng Liang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Na Jiang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jing Zhou
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xin Long
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Xin Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Miaomiao Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Chuangfang Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jinku Bao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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