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Chen Z, Li C, Zhou Y, Li P, Cao G, Qiao Y, Yao Y, Su J. Histone 3 lysine 9 acetylation-specific reprogramming regulates esophageal squamous cell carcinoma progression and metastasis. Cancer Gene Ther 2024; 31:612-626. [PMID: 38291129 DOI: 10.1038/s41417-024-00738-y] [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: 08/08/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Dysregulation of histone acetylation is widely implicated in tumorigenesis, yet its specific roles in the progression and metastasis of esophageal squamous cell carcinoma (ESCC) remain unclear. Here, we profiled the genome-wide landscapes of H3K9ac for paired adjacent normal (Nor), primary ESCC (EC) and metastatic lymph node (LNC) esophageal tissues from three ESCC patients. Compared to H3K27ac, we identified a distinct epigenetic reprogramming specific to H3K9ac in EC and LNC samples relative to Nor samples. This H3K9ac-related reprogramming contributed to the transcriptomic aberration of targeting genes, which were functionally associated with tumorigenesis and metastasis. Notably, genes with gained H3K9ac signals in both primary and metastatic lymph node samples (common-gained gene) were significantly enriched in oncogenes. Single-cell RNA-seq analysis further revealed that the corresponding top 15 common-gained genes preferred to be enriched in mesenchymal cells with high metastatic potential. Additionally, in vitro experiment demonstrated that the removal of H3K9ac from the common-gained gene MSI1 significantly downregulated its transcription, resulting in deficiencies in ESCC cell proliferation and migration. Together, our findings revealed the distinct characteristics of H3K9ac in esophageal squamous cell carcinogenesis and metastasis, and highlighted the potential therapeutic avenue for intervening ESCC through epigenetic modulation via H3K9ac.
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Affiliation(s)
- Zhenhui Chen
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China
| | - Chenghao Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
| | - Yue Zhou
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China
| | - Pengcheng Li
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China
| | - Guoquan Cao
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yunbo Qiao
- Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200125, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
| | - Jianzhong Su
- School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, Zhejiang, China.
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, Zhejiang, China.
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2
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Wu D, Huang K, Shi J, Liu S, Wang W, Jiang J, Ren H, Chen T, Ye S, Chen J, Wei W, Li X. Genome-Wide 5-Formylcytosine Redistribution in KCl-Stimulated Mouse Primary Cortical Neurons is Associated with Neuronal Activity. ACS Chem Neurosci 2023; 14:4352-4362. [PMID: 38019771 DOI: 10.1021/acschemneuro.3c00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
An abundant accumulation of DNA demethylation intermediates has been identified in mammalian neurons. While the roles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in neuronal function have been extensively studied, little is known about 5-formylcytosine (5fC) in neurons. Therefore, this study was to investigate the genome-wide distribution and potential functions of 5fC in neurons. In an in vitro culture model of mouse primary cortical neurons, we observed a dynamic increase in the total 5fC level in the neuronal genome after potassium chloride (KCl) stimulation. Subsequently, we employed chemical-labeling-enabled C-to-T conversion sequencing (CLEVER-seq) to examine the 5fC distribution at a single-base resolution. Bioinformatic analysis revealed that 5fC was enriched in promoter regions, and gene ontology (GO) analysis indicated that the differential formylation positions (DFP) were correlated with neuronal activities. Additionally, integration with previously published nascent RNA-seq data revealed a positive correlation between gene formylation and mRNA expression levels. As well, 6 neuro-activity-related genes with a positive correlation were validated. Furthermore, we observed higher chromatin accessibility and RNA pol II binding signals near the 5fC sites through multiomics analysis. Motif analysis identified potential reader proteins for 5fC. In conclusion, our work provides a valuable resource for studying the dynamic changes and functional roles of 5fC in activated mammalian neurons.
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Affiliation(s)
- Du Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Kaixin Huang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Jichun Shi
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Sha Liu
- Department of General Practice, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Wenjing Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Jiazhi Jiang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Haobin Ren
- Cognitive Neuroepigenetics Laboratory, Queensland Brain Institute, The University of Queensland, Brisbane 4702, Australia
| | - Tongyu Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Shengda Ye
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Wei Wei
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
| | - Xiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Brain Research Center, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, 430071 Wuhan, China
- Medical Research Institute, Wuhan University, 430071 Wuhan, China
- Sino-Italian Ascula Brain Science Joint Laboratory, Zhongnan Hospital of Wuhan University, 430071 Wuhan, China
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3
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Fischer V, Kretschmer M, Germain PL, Kaur J, Mompart-Barrenechea S, Pelczar P, Schürmann D, Schär P, Gapp K. Sperm chromatin accessibility's involvement in the intergenerational effects of stress hormone receptor activation. Transl Psychiatry 2023; 13:378. [PMID: 38065942 PMCID: PMC10709351 DOI: 10.1038/s41398-023-02684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Dexamethasone is a stress hormone receptor agonist used widely in clinics. We and others previously showed that paternal administration of dexamethasone in mice affects the phenotype of their offspring. The substrate of intergenerational transmission of environmentally induced effects often involves changes in sperm RNA, yet other epigenetic modifications in the germline can be affected and are also plausible candidates. First, we tested the involvement of altered sperm RNAs in the transmission of dexamethasone induced phenotypes across generations. We did this by injecting sperm RNA into naïve fertilized oocytes, before performing metabolic and behavioral phenotyping of the offspring. We observed phenotypic changes in discordance with those found in offspring generated by in vitro fertilization using sperm from dexamethasone exposed males. Second, we investigated the effect of dexamethasone on chromatin accessibility using ATAC sequencing and found significant changes at specific genomic features and gene regulatory loci. Employing q-RT-PCR, we show altered expression of a gene in the tissue of offspring affected by accessibility changes in sperm. Third, we establish a correlation between specific DNA modifications and stress hormone receptor activity as a likely contributing factor influencing sperm accessibility. Finally, we independently investigated this dependency by genetically reducing thymine-DNA glycosylase levels and observing concomitant changes at the level of chromatin accessibility and stress hormone receptor activity.
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Affiliation(s)
- Vincent Fischer
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Miriam Kretschmer
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland
| | - Pierre-Luc Germain
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
- Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Department of Health Science and Technology, Zürich, Switzerland
- Computational Neurogenomics, Institute for Neuroscience, Department of Health Science and Technology, Zürich, Switzerland
- Laboratory of Statistical Bioinformatics, University of Zürich, Zürich, Switzerland
| | - Jasmine Kaur
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Sergio Mompart-Barrenechea
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
| | - Pawel Pelczar
- Center for Transgenic Models, University of Basel, Basel, Switzerland
| | - David Schürmann
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Primo Schär
- Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Katharina Gapp
- Laboratory of Epigenetics and Neuroendocrinology, Institute for Neuroscience, Department of Health Sciences and Technology, ETH Zürich, Zürich, Switzerland.
- Neuroscience Center Zurich, ETH Zürich and University of Zürich, Zürich, Switzerland.
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Jana A, Naga R, Saha S, Banerjee DR. 3D QSAR pharmacophore based lead identification of G9a lysine methyltransferase towards epigenetic therapeutics. J Biomol Struct Dyn 2023; 41:8635-8653. [PMID: 36264111 DOI: 10.1080/07391102.2022.2135600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/08/2022] [Indexed: 10/24/2022]
Abstract
The G9a, Lysine Methyltransferase that methylates the histone 3 lysine 9 (H3K9) of the nucleosome, is an excellent epigenetic target having no clinically passed inhibitor currently owing to adverse in vivo ADMET toxicities. In this work, we have carried out detailed computational investigations to find novel and safer lead against the target using advanced 3 D QSAR pharmacophore screening of databases containing more than 400000 entrees of natural compounds. The screening was conducted at different levels at increasing stringencies by employing pharmacophore mapping, druglikenesses and interaction profiles of the selected to identify potential hit compounds. The potential hits were further screened by advanced flexible docking, ADME and toxicity analysis to eight hit compounds. Based on the comparative analysis of the hits with the reference inhibitor, we identified one lead inhibitor against the G9a, having better binding efficacy and a safer ADMET profile than the reference inhibitor. Finally, the results were further verified using robust molecular dynamics simulation and MM-GBSA binding energy calculation. The natural compounds are generally considered benign due to their long human uses and this is the first attempt of in silico screening of a large natural compound library against G9a to our best knowledge. Therefore, the finding of this study may add value towards the development of epigenetic therapeutics against the G9a.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Abhisek Jana
- Department of Chemistry, National Institute of technology Durgapur, Durgapur, India
| | - Rahul Naga
- Department of Biotechnology, National Institute of technology Durgapur, Durgapur, India
| | - Sougata Saha
- Department of Biotechnology, National Institute of technology Durgapur, Durgapur, India
| | - Deb Ranjan Banerjee
- Department of Chemistry, National Institute of technology Durgapur, Durgapur, India
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5
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McGregor LA, Deckard CE, Smolen JA, Porter GM, Sczepanski JT. Thymine DNA glycosylase mediates chromatin phase separation in a DNA methylation-dependent manner. J Biol Chem 2023; 299:104907. [PMID: 37307918 PMCID: PMC10404674 DOI: 10.1016/j.jbc.2023.104907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 06/14/2023] Open
Abstract
Thymine DNA glycosylase (TDG) is an essential enzyme involved in numerous biological pathways, including DNA repair, DNA demethylation, and transcriptional activation. Despite these important functions, the mechanisms surrounding the actions and regulation of TDG are poorly understood. In this study, we demonstrate that TDG induces phase separation of DNA and nucleosome arrays under physiologically relevant conditions in vitro and show that the resulting chromatin droplets exhibited behaviors typical of phase-separated liquids, supporting a liquid-liquid phase separation model. We also provide evidence that TDG has the capacity to form phase-separated condensates in the cell nucleus. The ability of TDG to induce chromatin phase separation is dependent on its intrinsically disordered N- and C-terminal domains, which in isolation, promote the formation of chromatin-containing droplets having distinct physical properties, consistent with their unique mechanistic roles in the phase separation process. Interestingly, DNA methylation alters the phase behavior of the disordered domains of TDG and compromises formation of chromatin condensates by full-length TDG, indicating that DNA methylation regulates the assembly and coalescence of TDG-mediated condensates. Overall, our results shed new light on the formation and physical nature of TDG-mediated chromatin condensates, which have broad implications for the mechanism and regulation of TDG and its associated genomic processes.
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Affiliation(s)
- Lauren A McGregor
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Charles E Deckard
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Justin A Smolen
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Gabriela M Porter
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
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6
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Wang G, Zhou Y, Yi B, Long Y, Ma B, Zhang Y. Comprehensive analysis of the prognostic value and biological function of TDG in hepatocellular carcinoma. Cell Cycle 2023; 22:1478-1495. [PMID: 37224078 PMCID: PMC10281473 DOI: 10.1080/15384101.2023.2216501] [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: 12/19/2022] [Revised: 03/30/2023] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Epigenetics plays an important role in the malignant progression of tumors, in which DNA methylation can alter genetic performance without altering the DNA sequence. As a key regulator demethylation, thymine-DNA glycosylase (TDG) has been reported to participate in malignant progression of multiple tumors. In this study, we demonstrate that TDG is highly expressed in hepatocellular carcinoma (HCC) and its high expression is closely related to the poor prognosis of patients. Decreasing TDG expression can significantly inhibit the malignant biological behavior of HCC cells. ABL proto-oncogene 1(ABL1) was identified as a downstream gene regulated by TDG demethylation. In addition, TDG can affect the Hippo signaling pathway through ABL1 to regulate HCC cell proliferation, apoptosis, invasion and migration. Overall, our study demonstrated that TDG reduces DNA methylation of ABL1, increases ABL1 protein expression, and affects the Hippo signaling pathway to regulate the malignant progression of HCC.
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Affiliation(s)
- Guoliang Wang
- Department of Hepatobiliary Surgery, Department of Organ Transplantation, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Yinwen Zhou
- Department of Surgery, Zunyi Medical University, Zunyi, Guizhou, China
| | - Bin Yi
- Department of Hepatobiliary Surgery, Department of Organ Transplantation, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Yanli Long
- Department of Pathology, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Bo Ma
- Department of Hepatobiliary Surgery, Department of Organ Transplantation, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
| | - Yi Zhang
- Department of Hepatobiliary Surgery, Department of Organ Transplantation, Guizhou Provincial People’s Hospital, Guiyang, Guizhou, China
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7
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Rioux KL, Delaney S. Ionic strength modulates excision of uracil by SMUG1 from nucleosome core particles. DNA Repair (Amst) 2023; 125:103482. [PMID: 36931160 PMCID: PMC10073303 DOI: 10.1016/j.dnarep.2023.103482] [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: 12/20/2022] [Revised: 03/04/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023]
Abstract
Ionic strength affects many cellular processes including the packaging of genetic material in eukaryotes. For example, chromatin fibers are compacted in high ionic strength environments as are the minimal unit of packaging in chromatin, nucleosome core particles (NCPs). Furthermore, ionic strength is known to modulate several aspects of NCP dynamics including transient unwrapping of DNA from the histone protein core, nucleosome gaping, and intra- and internucleosomal interactions of the N-terminal histone tails. Changes in NCP structure may also impact interactions of transcriptional, repair, and other cellular machinery with nucleosomal DNA. One repair process, base excision repair (BER), is impacted by NCP structure and may be further influenced by changes in ionic strength. Here we examine the effects of ionic strength on the initiation of BER using biochemical assays. Using a population of NCPs containing uracil (U) at dozens of geometric locations, excision of U by single-strand selective monofunctional uracil DNA glycosylase (SMUG1) is assessed at higher and lower ionic strengths. SMUG1 has increased excision activity in the lower ionic strength conditions. On duplex DNA, however, SMUG1 activity is largely unaffected by ionic strength except at short incubation times, suggesting that changes in SMUG1 activity are likely due to alterations in NCP structure and dynamics. These results allow us to further understand the cellular role of SMUG1 in a changing ionic environment and broadly contribute to the understanding of BER on chromatin and genomic stability.
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Affiliation(s)
- Katelyn L Rioux
- Department of Chemistry, Brown University, Providence, RI, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, RI, USA.
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8
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McGregor LA, Zhu B, Goetz AM, Sczepanski JT. Thymine DNA Glycosylase is an RNA-Binding Protein with High Selectivity for G-Rich Sequences. J Biol Chem 2023; 299:104590. [PMID: 36889585 PMCID: PMC10124917 DOI: 10.1016/j.jbc.2023.104590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Thymine DNA glycosylase (TDG) is a multifaceted enzyme involved in several critical biological pathways, including transcriptional activation, DNA demethylation, and DNA repair. Recent studies have established regulatory relationships between TDG and RNA, but the molecular interactions underlying these relationships is poorly understood. Herein, we now demonstrate that TDG binds directly to RNA with nanomolar affinity. Using synthetic oligonucleotides of defined length and sequence, we show that TDG has a strong preference for binding G-rich sequences in single-stranded RNA but binds weakly to single-stranded DNA and duplex RNA. TDG also binds tightly to endogenous RNA sequences. Studies with truncated proteins indicate that TDG binds RNA primarily through its structured catalytic domain and that its disordered C-terminal domain plays a key role in regulating TDG's affinity and selectivity for RNA. Finally, we show that RNA competes with DNA for binding to TDG, resulting in inhibition of TDG-mediated excision in the presence of RNA. Together, this work provides support for and insights into a mechanism wherein TDG-mediated processes (e.g., DNA demethylation) are regulated through the direct interactions of TDG with RNA.
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Affiliation(s)
- Lauren A McGregor
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
| | - Baiyu Zhu
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
| | - Allison M Goetz
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, USA
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9
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Wen T, Yang K, Greenberg MM. Local Alteration of Ionic Strength in a Nucleosome Core Particle and Its Effect on N7-Methyl-2'-deoxyguanosine Depurination. Biochemistry 2022; 61:2221-2228. [PMID: 36136907 PMCID: PMC9670023 DOI: 10.1021/acs.biochem.2c00342] [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] [Indexed: 11/28/2022]
Abstract
Positively charged N-terminal histone tails play important roles in maintaining the nucleosome (and chromatin) structure and function. Charge alteration, including those imposed by post-translational modifications, impacts chromatin dynamics, protein binding, and the fate of DNA damage. There is evidence that N-terminal histone tails affect the local ionic environment within a nucleosome core particle (NCP), but this phenomenon is not well understood. Determining the modulation of the local ionic environment within an NCP by histone tails could help uncover the underlying mechanisms of their functions and effects. Utilizing bottom-up syntheses of NCPs containing wild-type or mutated histones and a fluorescent probe that is sensitive to the local ionic environment, we show that interaction with positively charged N-terminal tails increases the local ionic strength near nucleosomal DNA. The effect is diminished by replacing positively charged residues with neutral ones or deleting a tail in its entirety. Replacing the fluorescent probe with the major DNA methylation product, N7-methyl-2'-deoxyguanosine (MdG), revealed changes in the depurination rate constant varying inversely with local ionic strength. These data indicate that the MdG hydrolysis rates depend on and also inform on local ionic strength in an NCP. Overall, histone tail charge contributes to the complexity of the NCP structure and function by modulating the local ionic strength.
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Affiliation(s)
- Tingyu Wen
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Kun Yang
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
| | - Marc M Greenberg
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles Street, Baltimore, Maryland 21218, United States
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10
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Histone variants H3.3 and H2A.Z/H3.3 facilitate excision of uracil from nucleosome core particles. DNA Repair (Amst) 2022; 116:103355. [PMID: 35717761 PMCID: PMC9262417 DOI: 10.1016/j.dnarep.2022.103355] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/08/2022] [Indexed: 11/20/2022]
Abstract
At the most fundamental level of chromatin organization, DNA is packaged as nucleosome core particles (NCPs) where DNA is wound around a core of histone proteins. This ubiquitous sequestration of DNA within NCPs presents a significant barrier to many biological processes, including DNA repair. We previously demonstrated that histone variants from the H2A family facilitate excision of uracil (U) lesions by DNA base excision repair (BER) glycosylases. Here, we consider how the histone variant H3.3 and double-variant H2A.Z/H3.3 modulate the BER enzymes uracil DNA glycosylase (UDG) and single-strand selective monofunctional uracil DNA glycosylase (SMUG1). Using an NCP model system with U:G base pairs at a wide variety of geometric positions we generate the global repair profile for both glycosylases. Enhanced excision of U by UDG and SMUG1 is observed with the H3.3 variant. We demonstrate that these H3.3-containing NCPs form two species: (1) octasomes, which contain the full complement of eight histone proteins and (2) hexasomes which are sub-nucleosomal particles that contain six histones. Both the octasome and hexasome species facilitate excision activity of UDG and SMUG1, with the largest impacts observed at sterically-occluded lesion sites and in terminal regions of DNA of the hexasome that do not closely interact with histones. For the double-variant H2A.Z/H3.3 NCPs, which exist as octasomes, the global repair profile reveals that UDG but not SMUG1 has increased U excision activity. The enhanced glycosylase activity reveals potential functions for these histone variants to facilitate BER in packaged DNA and contributes to our understanding of DNA repair in chromatin and its significance regarding mutagenesis and genomic integrity.
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11
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Hindi NN, Elsakrmy N, Ramotar D. The base excision repair process: comparison between higher and lower eukaryotes. Cell Mol Life Sci 2021; 78:7943-7965. [PMID: 34734296 PMCID: PMC11071731 DOI: 10.1007/s00018-021-03990-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 09/08/2021] [Accepted: 10/14/2021] [Indexed: 01/01/2023]
Abstract
The base excision repair (BER) pathway is essential for maintaining the stability of DNA in all organisms and defects in this process are associated with life-threatening diseases. It is involved in removing specific types of DNA lesions that are induced by both exogenous and endogenous genotoxic substances. BER is a multi-step mechanism that is often initiated by the removal of a damaged base leading to a genotoxic intermediate that is further processed before the reinsertion of the correct nucleotide and the restoration of the genome to a stable structure. Studies in human and yeast cells, as well as fruit fly and nematode worms, have played important roles in identifying the components of this conserved DNA repair pathway that maintains the integrity of the eukaryotic genome. This review will focus on the components of base excision repair, namely, the DNA glycosylases, the apurinic/apyrimidinic endonucleases, the DNA polymerase, and the ligases, as well as other protein cofactors. Functional insights into these conserved proteins will be provided from humans, Saccharomyces cerevisiae, Drosophila melanogaster, and Caenorhabditis elegans, and the implications of genetic polymorphisms and knockouts of the corresponding genes.
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Affiliation(s)
- Nagham Nafiz Hindi
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Noha Elsakrmy
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar
| | - Dindial Ramotar
- Division of Biological and Biomedical Sciences, College of Health and Life Sciences, Hamad Bin Khalifa University, Education City, Doha, Qatar.
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12
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Abstract
The field of epigenetics has exploded over the last two decades, revealing an astonishing level of complexity in the way genetic information is stored and accessed in eukaryotes. This expansion of knowledge, which is very much ongoing, has been made possible by the availability of evermore sensitive and precise molecular tools. This review focuses on the increasingly important role that chemistry plays in this burgeoning field. In an effort to make these contributions more accessible to the nonspecialist, we group available chemical approaches into those that allow the covalent structure of the protein and DNA components of chromatin to be manipulated, those that allow the activity of myriad factors that act on chromatin to be controlled, and those that allow the covalent structure and folding of chromatin to be characterized. The application of these tools is illustrated through a series of case studies that highlight how the molecular precision afforded by chemistry is being used to establish causal biochemical relationships at the heart of epigenetic regulation.
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Affiliation(s)
- John D Bagert
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
| | - Tom W Muir
- Frick Chemistry Laboratory, Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA; ,
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Deckard CE, Sczepanski JT. Reversible chromatin condensation by the DNA repair and demethylation factor thymine DNA glycosylase. Nucleic Acids Res 2021; 49:2450-2459. [PMID: 33733652 PMCID: PMC7969020 DOI: 10.1093/nar/gkab040] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 11/23/2022] Open
Abstract
Chromatin structures (and modulators thereof) play a central role in genome organization and function. Herein, we report that thymine DNA glycosylase (TDG), an essential enzyme involved in DNA repair and demethylation, has the capacity to alter chromatin structure directly through its physical interactions with DNA. Using chemically defined nucleosome arrays, we demonstrate that TDG induces decompaction of individual chromatin fibers upon binding and promotes self-association of nucleosome arrays into higher-order oligomeric structures (i.e. condensation). Chromatin condensation is mediated by TDG’s disordered polycationic N-terminal domain, whereas its C-terminal domain antagonizes this process. Furthermore, we demonstrate that TDG-mediated chromatin condensation is reversible by growth arrest and DNA damage 45 alpha (GADD45a), implying that TDG cooperates with its binding partners to dynamically control chromatin architecture. Finally, we show that chromatin condensation by TDG is sensitive to the methylation status of the underlying DNA. This new paradigm for TDG has specific implications for associated processes, such as DNA repair, DNA demethylation, and transcription, and general implications for the role of DNA modification ‘readers’ in controlling chromatin organization.
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Affiliation(s)
- Charles E Deckard
- Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
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Prasad R, Yen TJ, Bellacosa A. Active DNA demethylation-The epigenetic gatekeeper of development, immunity, and cancer. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10033. [PMID: 36618446 PMCID: PMC9744510 DOI: 10.1002/ggn2.10033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/11/2023]
Abstract
DNA methylation is a critical process in the regulation of gene expression with dramatic effects in development and continually expanding roles in oncogenesis. 5-Methylcytosine was once considered to be an inherited and stably repressive epigenetic mark, which can be only removed by passive dilution during multiple rounds of DNA replication. However, in the past two decades, physiologically controlled DNA demethylation and deamination processes have been identified, thereby revealing the function of cytosine methylation as a highly regulated and complex state-not simply a static, inherited signature or binary on-off switch. Alongside these fundamental discoveries, clinical studies over the past decade have revealed the dramatic consequences of aberrant DNA demethylation. In this review we discuss DNA demethylation and deamination in the context of 5-methylcytosine as critical processes for physiological and physiopathological transitions within three states-development, immune maturation, and oncogenic transformation; and we describe the expanding role of DNA demethylating drugs as therapeutic agents in cancer.
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Affiliation(s)
- Rahul Prasad
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Timothy J. Yen
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
| | - Alfonso Bellacosa
- Cancer Epigenetics and Cancer Biology Programs, Fox Chase Cancer CenterPhiladelphiaPennsylvaniaUSA
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Pidugu LS, Dai Q, Malik SS, Pozharski E, Drohat AC. Excision of 5-Carboxylcytosine by Thymine DNA Glycosylase. J Am Chem Soc 2019; 141:18851-18861. [PMID: 31693361 DOI: 10.1021/jacs.9b10376] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
5-Methylcytosine (mC) is an epigenetic mark that is written by methyltransferases, erased through passive and active mechanisms, and impacts transcription, development, diseases including cancer, and aging. Active DNA demethylation involves TET-mediated stepwise oxidation of mC to 5-hydroxymethylcytosine, 5-formylcytosine (fC), or 5-carboxylcytosine (caC), excision of fC or caC by thymine DNA glycosylase (TDG), and subsequent base excision repair. Many elements of this essential process are poorly defined, including TDG excision of caC. To address this problem, we solved high-resolution structures of human TDG bound to DNA with cadC (5-carboxyl-2'-deoxycytidine) flipped into its active site. The structures unveil detailed enzyme-substrate interactions that mediate recognition and removal of caC, many involving water molecules. Importantly, two water molecules contact a carboxylate oxygen of caC and are poised to facilitate acid-catalyzed caC excision. Moreover, a substrate-dependent conformational change in TDG modulates the hydrogen bond interactions for one of these waters, enabling productive interaction with caC. An Asn residue (N191) that is critical for caC excision is found to contact N3 and N4 of caC, suggesting a mechanism for acid-catalyzed base excision that features an N3-protonated form of caC but would be ineffective for C, mC, or hmC. We also investigated another Asn residue (N140) that is catalytically essential and strictly conserved in the TDG-MUG enzyme family. A structure of N140A-TDG bound to cadC DNA provides the first high-resolution insight into how enzyme-substrate interactions, including water molecules, are impacted by depleting the conserved Asn, informing its role in binding and addition of the nucleophilic water molecule.
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Affiliation(s)
- Lakshmi S Pidugu
- Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States
| | - Qing Dai
- Department of Chemistry , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Shuja S Malik
- Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States.,Center for Biomolecular Therapeutics , Institute for Bioscience and Biotechnology Research , Rockville , Maryland 20850 , United States
| | - Alexander C Drohat
- Department of Biochemistry and Molecular Biology , University of Maryland School of Medicine , Baltimore , Maryland 21201 , United States
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Banerjee DR, Deckard CE, Zeng Y, Sczepanski JT. Acetylation of the histone H3 tail domain regulates base excision repair on higher-order chromatin structures. Sci Rep 2019; 9:15972. [PMID: 31685935 PMCID: PMC6828659 DOI: 10.1038/s41598-019-52340-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
Despite recent evidence suggesting that histone lysine acetylation contributes to base excision repair (BER) in cells, their exact mechanistic role remains unclear. In order to examine the influence of histone acetylation on the initial steps of BER, we assembled nucleosome arrays consisting of homogeneously acetylated histone H3 (H3K18 and H3K27) and measured the repair of a site-specifically positioned 2′-deoxyuridine (dU) residue by uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1). We find that H3K18ac and H3K27ac differentially influence the combined activities of UDG/APE1 on compact chromatin, suggesting that acetylated lysine residues on the H3 tail domain play distinct roles in regulating the initial steps of BER. In addition, we show that the effects of H3 tail domain acetylation on UDG/APE1 activity are at the nucleosome level and do not influence higher-order chromatin folding. Overall, these results establish a novel regulatory role for histone H3 acetylation during the initiation of BER on chromatin.
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Affiliation(s)
- Deb Ranjan Banerjee
- Department of Chemistry, National Institute of Technology, Durgapur, West Bengal, India
| | - Charles E Deckard
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, United States
| | - Yu Zeng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, Texas, 77843, United States
| | - Jonathan T Sczepanski
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, United States.
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