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Mu S, Wang W, Liu Q, Ke N, Li H, Sun F, Zhang J, Zhu Z. Autoimmune disease: a view of epigenetics and therapeutic targeting. Front Immunol 2024; 15:1482728. [PMID: 39606248 PMCID: PMC11599216 DOI: 10.3389/fimmu.2024.1482728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2024] [Accepted: 10/23/2024] [Indexed: 11/29/2024] Open
Abstract
Autoimmune diseases comprise a large group of conditions characterized by a complex pathogenesis and significant heterogeneity in their clinical manifestations. Advances in sequencing technology have revealed that in addition to genetic susceptibility, various epigenetic mechanisms including DNA methylation and histone modification play critical roles in disease development. The emerging field of epigenetics has provided new perspectives on the pathogenesis and development of autoimmune diseases. Aberrant epigenetic modifications can be used as biomarkers for disease diagnosis and prognosis. Exploration of human epigenetic profiles revealed that patients with autoimmune diseases exhibit markedly altered DNA methylation profiles compared with healthy individuals. Targeted cutting-edge epigenetic therapies are emerging. For example, DNA methylation inhibitors can rectify methylation dysregulation and relieve patients. Histone deacetylase inhibitors such as vorinostat can affect chromatin accessibility and further regulate gene expression, and have been used in treating hematological malignancies. Epigenetic therapies have opened new avenues for the precise treatment of autoimmune diseases and offer new opportunities for improved therapeutic outcomes. Our review can aid in comprehensively elucidation of the mechanisms of autoimmune diseases and development of new targeted therapies that ultimately benefit patients with these conditions.
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Affiliation(s)
- Siqi Mu
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Department of Skin Genetics, Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Hefei, Anhui, China
- Department of Dermatology, Shannan People's Hospital, Shannan, China
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Wanrong Wang
- Department of Skin Genetics, Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Hefei, Anhui, China
- Department of Dermatology, Shannan People's Hospital, Shannan, China
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Department of Pharmacology, Basic Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Qiuyu Liu
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Naiyu Ke
- Department of Ophthalmology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Hao Li
- Department of Urology, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Feiyang Sun
- First Clinical Medical College, Anhui Medical University, Hefei, Anhui, China
| | - Jiali Zhang
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Department of Skin Genetics, Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Hefei, Anhui, China
- Department of Dermatology, Shannan People's Hospital, Shannan, China
| | - Zhengwei Zhu
- Department of Dermatology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, Anhui, China
- Department of Skin Genetics, Anhui Province Laboratory of Inflammation and Immune Mediated Diseases, Hefei, Anhui, China
- Department of Dermatology, Shannan People's Hospital, Shannan, China
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2
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Gan Q, Fan C. Orthogonal Translation for Site-Specific Installation of Post-translational Modifications. Chem Rev 2024; 124:2805-2838. [PMID: 38373737 PMCID: PMC11230630 DOI: 10.1021/acs.chemrev.3c00850] [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: 02/21/2024]
Abstract
Post-translational modifications (PTMs) endow proteins with new properties to respond to environmental changes or growth needs. With the development of advanced proteomics techniques, hundreds of distinct types of PTMs have been observed in a wide range of proteins from bacteria, archaea, and eukarya. To identify the roles of these PTMs, scientists have applied various approaches. However, high dynamics, low stoichiometry, and crosstalk between PTMs make it almost impossible to obtain homogeneously modified proteins for characterization of the site-specific effect of individual PTM on target proteins. To solve this problem, the genetic code expansion (GCE) strategy has been introduced into the field of PTM studies. Instead of modifying proteins after translation, GCE incorporates modified amino acids into proteins during translation, thus generating site-specifically modified proteins at target positions. In this review, we summarize the development of GCE systems for orthogonal translation for site-specific installation of PTMs.
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Affiliation(s)
- Qinglei Gan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Chenguang Fan
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas 72701, United States
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3
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Wang Q, Wu Y, Wu W, Lyu L, Li W. A review of changes at the phenotypic, physiological, biochemical, and molecular levels of plants due to high temperatures. PLANTA 2024; 259:57. [PMID: 38307982 DOI: 10.1007/s00425-023-04320-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/23/2023] [Indexed: 02/04/2024]
Abstract
MAIN CONCLUSION This review summarizes the physiological, biochemical, and molecular regulatory network changes in plants in response to high temperature. With the continuous rise in temperature, high temperature has become an important issue limiting global plant growth and development, affecting the phenotype and physiological and biochemical processes of plants and seriously restricting crop yield and tree growth speed. As sessile organisms, plants inevitably encounter high temperatures and improve their heat tolerance by activating molecular networks related to heat stress, such as signal transduction, synthesis of metabolites, and gene expression. Heat tolerance is a polygenic trait regulated by a variety of genes, transcription factors, proteins, and metabolites. Therefore, this review summarizes the changes in physiological, biochemical and molecular regulatory networks in plants under high-temperature conditions to lay a foundation for an in-depth understanding of the mechanisms involved in plant heat tolerance responses.
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Affiliation(s)
- Que Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China.
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.
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Smolen P, Dash PK, Redell JB. Traumatic brain injury-associated epigenetic changes and the risk for neurodegenerative diseases. Front Neurosci 2023; 17:1259405. [PMID: 37795186 PMCID: PMC10546067 DOI: 10.3389/fnins.2023.1259405] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/04/2023] [Indexed: 10/06/2023] Open
Abstract
Epidemiological studies have shown that traumatic brain injury (TBI) increases the risk for developing neurodegenerative diseases (NDs). However, molecular mechanisms that underlie this risk are largely unidentified. TBI triggers widespread epigenetic modifications. Similarly, NDs such as Alzheimer's or Parkinson's are associated with numerous epigenetic changes. Although epigenetic changes can persist after TBI, it is unresolved if these modifications increase the risk of later ND development and/or dementia. We briefly review TBI-related epigenetic changes, and point out putative feedback loops that might contribute to long-term persistence of some modifications. We then focus on evidence suggesting persistent TBI-associated epigenetic changes may contribute to pathological processes (e.g., neuroinflammation) which may facilitate the development of specific NDs - Alzheimer's disease, Parkinson's disease, or chronic traumatic encephalopathy. Finally, we discuss possible directions for TBI therapies that may help prevent or delay development of NDs.
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Affiliation(s)
- Paul Smolen
- Department of Neurobiology and Anatomy, McGovern Medical School, University of Texas Health Science Center, Houston, TX, United States
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Zhao Y, Huang S, Tan X, Long L, He Q, Liang X, Bai J, Li Q, Lin J, Li Y, Liu N, Ma J, Chen Y. N 6 -Methyladenosine-Modified CBX1 Regulates Nasopharyngeal Carcinoma Progression Through Heterochromatin Formation and STAT1 Activation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2205091. [PMID: 36310139 PMCID: PMC9798977 DOI: 10.1002/advs.202205091] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Indexed: 05/16/2023]
Abstract
Epitranscriptomic remodeling such as N6 -methyladenosine (m6 A) modification plays a critical role in tumor development. However, little is known about the underlying mechanisms connecting m6 A modification and nasopharyngeal carcinoma (NPC) progression. Here, CBX1 is identified, a histone methylation regulator, to be significantly upregulated with m6 A hypomethylation in metastatic NPC tissues. The m6 A-modified CBX1 mRNA transcript is recognized and destabilized by the m6 A reader YTHDF3. Furthermore, it is revealed that CBX1 promotes NPC cell migration, invasion, and proliferation through transcriptional repression of MAP7 via H3K9me3-mediated heterochromatin formation. In addition to its oncogenic effect, CBX1 can facilitate immune evasion through IFN-γ-STAT1 signaling-mediated PD-L1 upregulation. Clinically, CBX1 serves as an independent predictor for unfavorable prognosis in NPC patients. The results reveal a crosstalk between epitranscriptomic and epigenetic regulation in NPC progression, and shed light on the functions of CBX1 in tumorigenesis and immunomodulation, which may provide an appealing therapeutic target in NPC.
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Affiliation(s)
- Yin Zhao
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Shengyan Huang
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Xirong Tan
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Liufen Long
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Qingmei He
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Xiaoyu Liang
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jiewen Bai
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Qingjie Li
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jiayi Lin
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Yingqin Li
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Na Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Jun Ma
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
| | - Yupei Chen
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center of Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy651 Dongfeng Road EastGuangzhouGuangdong510060China
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Weigle AT, Feng J, Shukla D. Thirty years of molecular dynamics simulations on posttranslational modifications of proteins. Phys Chem Chem Phys 2022; 24:26371-26397. [PMID: 36285789 PMCID: PMC9704509 DOI: 10.1039/d2cp02883b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/06/2023]
Abstract
Posttranslational modifications (PTMs) are an integral component to how cells respond to perturbation. While experimental advances have enabled improved PTM identification capabilities, the same throughput for characterizing how structural changes caused by PTMs equate to altered physiological function has not been maintained. In this Perspective, we cover the history of computational modeling and molecular dynamics simulations which have characterized the structural implications of PTMs. We distinguish results from different molecular dynamics studies based upon the timescales simulated and analysis approaches used for PTM characterization. Lastly, we offer insights into how opportunities for modern research efforts on in silico PTM characterization may proceed given current state-of-the-art computing capabilities and methodological advancements.
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Affiliation(s)
- Austin T Weigle
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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7
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Wang W, Shen Y, Zhang P, Liu L, Sha X, Li H, Wang S, Zhang H, Zhou Y, Shi J. Histone acetylation modification regulator-mediated tumor microenvironment infiltration characteristics and prognostic model of lung adenocarcinoma patients. J Thorac Dis 2022; 14:3886-3902. [PMID: 36389327 PMCID: PMC9641363 DOI: 10.21037/jtd-22-1000] [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: 07/18/2022] [Accepted: 09/16/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND The incidence rate of lung adenocarcinoma (LUAD) is rapidly increasing. Recent studies have reported that histone acetylation modification plays an important role in the occurrence and development of tumors. However, the potential role of modification of histone acetylation modification in the development of tumor immune microenvironment is still unclear. METHODS In this study, we comprehensively evaluated the acetylation modification patterns of LUAD samples obtained from various different databases based on 36 histone modification regulators, and constructed a prognostic model based on The Cancer Genome Atlas (TCGA) LUAD cohort using the Cox regression method. The close relationship between histone acetylation and tumor immune characteristics was further studied, including immune infiltration, immune escape and immunotherapy. Finally, we combined three cohort (GSE30219, GSE72094 and GSE50081) from Gene Expression Omnibus (GEO) database to verify the above results. RESULTS We analyzed the expression, mutation and interaction of 36 histone acetylation regulated genes. After Univariate Cox regression analysis and least absolute shrinkage and selection operator regression (LASSO), 5 genes (KAT2B, SIRT2, HDAC5, KAT8, HDAC2) were screened to establish the prognosis model and calculate the risk score. Then, patients in the TCGA cohort were divided into high- and low-risk groups based on the risk scores. Further analysis indicated that patients in the high-risk group exhibited significantly reduced overall survival (OS) compared with those in the low-risk group. The high- and low-risk groups exhibited significant differences in terms of tumor immune characteristics, such as immune infiltration, immune escape and immunotherapy. The high-risk group had lower immune score, less immune cell infiltration and higher clinical stage. Moreover, multivariate analysis revealed that this prognostic model might be a powerful prognostic predictor for LUAD. In addition, drugs sensitive for this classification were identified. Finally, the efficacy of the prognostic model was validated by cohort (GSE30219, GSE72094 and GSE50081) from GEO database. CONCLUSIONS Our study provided a robust signature for predicting changing prognosis of patients with LUAD. Thus, it appears to be a potentially useful prognostic tool. Moreover, the important relationship between histone acetylation and tumor immune microenvironment was revealed.
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Affiliation(s)
- Wenmiao Wang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Yao Shen
- School of Medicine, Nantong University, Nantong, China
| | - Peng Zhang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Lei Liu
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Xinyu Sha
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Houqiang Li
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Silin Wang
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Youlang Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiahai Shi
- Department of Thoracic Surgery, Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases in Affiliated Hospital of Nantong University, Nantong, China;,Graduate School, Dalian Medical University, Dalian, China;,School of Public Health, Nantong University, Nantong, China
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8
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Vincent SA, Kim JM, Pérez-Salamó I, To TK, Torii C, Ishida J, Tanaka M, Endo TA, Bhat P, Devlin PF, Seki M, Devoto A. Jasmonates and Histone deacetylase 6 activate Arabidopsis genome-wide histone acetylation and methylation during the early acute stress response. BMC Biol 2022; 20:83. [PMID: 35399062 PMCID: PMC8996529 DOI: 10.1186/s12915-022-01273-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Jasmonates (JAs) mediate trade-off between responses to both biotic and abiotic stress and growth in plants. The Arabidopsis thaliana HISTONE DEACETYLASE 6 is part of the CORONATINE INSENSITIVE1 receptor complex, co-repressing the HDA6/COI1-dependent acetic acid-JA pathway that confers plant drought tolerance. The decrease in HDA6 binding to target DNA mirrors histone H4 acetylation (H4Ac) changes during JA-mediated drought response, and mutations in HDA6 also cause depletion in the constitutive repressive marker H3 lysine 27 trimethylation (H3K27me3). However, the genome-wide effect of HDA6 on H4Ac and much of the impact of JAs on histone modifications and chromatin remodelling remain elusive. RESULTS We performed high-throughput ChIP-Seq on the HDA6 mutant, axe1-5, and wild-type plants with or without methyl jasmonate (MeJA) treatment to assess changes in active H4ac and repressive H3K27me3 histone markers. Transcriptional regulation was investigated in parallel by microarray analysis in the same conditions. MeJA- and HDA6-dependent histone modifications on genes for specialized metabolism; linolenic acid and phenylpropanoid pathways; and abiotic and biotic stress responses were identified. H4ac and H3K27me3 enrichment also differentially affects JAs and HDA6-mediated genome integrity and gene regulatory networks, substantiating the role of HDA6 interacting with specific families of transposable elements in planta and highlighting further specificity of action as well as novel targets of HDA6 in the context of JA signalling for abiotic and biotic stress responses. CONCLUSIONS The findings demonstrate functional overlap for MeJA and HDA6 in tuning plant developmental plasticity and response to stress at the histone modification level. MeJA and HDA6, nonetheless, maintain distinct activities on histone modifications to modulate genetic variability and to allow adaptation to environmental challenges.
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Affiliation(s)
- Stacey A Vincent
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Jong-Myong Kim
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Ac-Planta Inc., 2-16-9 Yushima, Bunkyo-ku, Tokyo, 113-0034, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Imma Pérez-Salamó
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Taiko Kim To
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
- Present address: Department of Biological Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Chieko Torii
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Junko Ishida
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maho Tanaka
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Takaho A Endo
- Bioinformatics and Systems Engineering Division, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
- Present address: Center for Integrative Medical Sciences, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Prajwal Bhat
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Paul F Devlin
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK
| | - Motoaki Seki
- Center for Sustainable Resource Science, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan.
- Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Alessandra Devoto
- Plant Molecular Science and Centre of Systems and Synthetic Biology, Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK.
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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10
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Gupta C, Salgotra RK. Epigenetics and its role in effecting agronomical traits. FRONTIERS IN PLANT SCIENCE 2022; 13:925688. [PMID: 36046583 PMCID: PMC9421166 DOI: 10.3389/fpls.2022.925688] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 07/11/2022] [Indexed: 05/16/2023]
Abstract
Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which underpins plant growth and dictates phenotypic responsiveness for extrinsic and intrinsic inputs. Epigenetic modifications, in addition to DNA sequence variation, improve breeding by giving useful markers. Also, it takes epigenome diversity into account to predict plant performance and increase crop production. In this review, emphasis has been given for summarising the role of epigenetic changes in epibreeding for crop improvement.
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11
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Kourani M, Mohareb F, Rezwan FI, Anastasiadi M, Hammond JP. Genetic and Physiological Responses to Heat Stress in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:832147. [PMID: 35449889 PMCID: PMC9016328 DOI: 10.3389/fpls.2022.832147] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/04/2022] [Indexed: 05/07/2023]
Abstract
Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.
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Affiliation(s)
- Mariam Kourani
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Fady Mohareb
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
- *Correspondence: Fady Mohareb,
| | - Faisal I. Rezwan
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Maria Anastasiadi
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
- John P. Hammond,
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12
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Rashid MM, Vaishnav A, Verma RK, Sharma P, Suprasanna P, Gaur RK. Epigenetic regulation of salinity stress responses in cereals. Mol Biol Rep 2021; 49:761-772. [PMID: 34773178 DOI: 10.1007/s11033-021-06922-9] [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: 07/06/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.
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Affiliation(s)
- Md Mahtab Rashid
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.,Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281121, India.,Agroecology and Environment, Agroscope (Reckenholz), 8046, Zürich, Switzerland
| | - Rakesh Kumar Verma
- Department of Biosciences, Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
| | - Pradeep Sharma
- Department of Biotechnology, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - P Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - R K Gaur
- Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, India.
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13
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Epigenetic control of abiotic stress signaling in plants. Genes Genomics 2021; 44:267-278. [PMID: 34515950 DOI: 10.1007/s13258-021-01163-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Although plants may be regularly exposed to various abiotic stresses, including drought, salt, cold, heat, heavy metals, and UV-B throughout their lives, it is not possible to actively escape from such stresses due to the immobile nature of plants. To overcome adverse environmental stresses, plants have developed adaptive systems that allow appropriate responses to diverse environmental cues; such responses can be achieved by fine-tuning or controlling genetic and epigenetic regulatory systems. Epigenetic mechanisms such as DNA or histone modifications and modulation of chromatin accessibility have been shown to regulate the expression of stress-responsive genes in struggles against abiotic stresses. OBJECTIVE Herein, the current progress in elucidating the epigenetic regulation of abiotic stress signaling in plants has been summarized in order to further understand the systems plants utilize to effectively respond to abiotic stresses. METHODS This review focuses on the action mechanisms of various components that epigenetically regulate plant abiotic stress responses, mainly in terms of DNA methylation, histone methylation/acetylation, and chromatin remodeling. CONCLUSIONS This review can be considered a basis for further research into understanding the epigenetic control system for abiotic stress responses in plants. Moreover, the knowledge of such systems can be effectively applied in developing novel methods to generate abiotic stress resistant crops.
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Nie F, Feng P, Song X, Wu M, Tang Q, Chen W. RNAWRE: a resource of writers, readers and erasers of RNA modifications. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2020:5865458. [PMID: 32608478 PMCID: PMC7327530 DOI: 10.1093/database/baaa049] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/25/2020] [Accepted: 05/29/2020] [Indexed: 12/12/2022]
Abstract
RNA modifications are involved in various kinds of cellular biological processes. Accumulated evidences have demonstrated that the functions of RNA modifications are determined by the effectors that can catalyze, recognize and remove RNA modifications. They are called ‘writers’, ‘readers’ and ‘erasers’. The identification of RNA modification effectors will be helpful for understanding the regulatory mechanisms and biological functions of RNA modifications. In this work, we developed a database called RNAWRE that specially deposits RNA modification effectors. The current version of RNAWRE stored 2045 manually curated writers, readers and erasers for the six major kinds of RNA modifications, namely Cap, m1A, m6A, m5C, ψ and Poly A. The main modules of RNAWRE not only allow browsing and downloading the RNA modification effectors but also support the BLAST search of the potential RNA modification effectors in other species. We hope that RNAWRE will be helpful for the researches on RNA modifications. Database URL: http://rnawre.bio2db.com
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Affiliation(s)
- Fulei Nie
- School of Life Sciences, Center for Genomics and Computational Biology, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan 063009, China
| | - Pengmian Feng
- School of Basic Medical Sciences, 1166 Liutai Avenue, Wenjiang District, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaoming Song
- School of Life Sciences, Center for Genomics and Computational Biology, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan 063009, China
| | - Meng Wu
- School of Life Sciences, Center for Genomics and Computational Biology, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan 063009, China
| | - Qiang Tang
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Wenjiang District, Chengdu 611137, China
| | - Wei Chen
- School of Life Sciences, Center for Genomics and Computational Biology, North China University of Science and Technology, 21 Bohai Road, Caofeidian Xincheng, Tangshan 063009, China.,Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, 1166 Liutai Avenue, Wenjiang District, Chengdu 611137, China
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15
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Chappell K, Graw S, Washam CL, Storey AJ, Bolden C, Peterson EC, Byrum SD. PTMViz: a tool for analyzing and visualizing histone post translational modification data. BMC Bioinformatics 2021; 22:275. [PMID: 34039258 PMCID: PMC8157737 DOI: 10.1186/s12859-021-04166-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 05/04/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Histone post-translational modifications (PTMs) play an important role in our system by regulating the structure of chromatin and therefore contribute to the regulation of gene and protein expression. Irregularities in histone PTMs can lead to a variety of different diseases including various forms of cancer. Histone modifications are analyzed using high resolution mass spectrometry, which generate large amounts of data that requires sophisticated bioinformatics tools for analysis and visualization. PTMViz is designed for downstream differential abundance analysis and visualization of both protein and/or histone modifications. RESULTS PTMViz provides users with data tables and visualization plots of significantly differentiated proteins and histone PTMs between two sample groups. All the data is packaged into interactive data tables and graphs using the Shiny platform to help the user explore the results in a fast and efficient manner to assess if changes in the system are due to protein abundance changes or epigenetic changes. In the example data provided, we identified several proteins differentially regulated in the dopaminergic pathway between mice treated with methamphetamine compared to a saline control. We also identified histone post-translational modifications including histone H3K9me, H3K27me3, H4K16ac, and that were regulated due to drug exposure. CONCLUSIONS Histone modifications play an integral role in the regulation of gene expression. PTMViz provides an interactive platform for analyzing proteins and histone post-translational modifications from mass spectrometry data in order to quickly identify differentially expressed proteins and PTMs.
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Affiliation(s)
- Kevin Chappell
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St. slot 516, Little Rock, AR, 72205, USA
| | - Stefan Graw
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St. slot 516, Little Rock, AR, 72205, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Charity L Washam
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St. slot 516, Little Rock, AR, 72205, USA.,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA
| | - Aaron J Storey
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St. slot 516, Little Rock, AR, 72205, USA
| | - Chris Bolden
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Eric C Peterson
- Department of Pharmacology and Toxicology, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Stephanie D Byrum
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, 4301 W Markham St. slot 516, Little Rock, AR, 72205, USA. .,Arkansas Children's Research Institute, Little Rock, AR, 72202, USA.
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16
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Seier JA, Reinhardt J, Saraf K, Ng SS, Layer JP, Corvino D, Althoff K, Giordano FA, Schramm A, Fischer M, Hölzel M. Druggable epigenetic suppression of interferon-induced chemokine expression linked to MYCN amplification in neuroblastoma. J Immunother Cancer 2021; 9:e001335. [PMID: 34016720 PMCID: PMC8141444 DOI: 10.1136/jitc-2020-001335] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Amplification of the MYCN oncogene is a molecular hallmark of aggressive neuroblastoma (NB), a childhood cancer of the sympathetic nervous system. There is evidence that MYCN promotes a non-inflamed and T-cell infiltration-poor ('cold') tumor microenvironment (TME) by suppressing interferon signaling. This may explain, at least in part, why patients with NB seem to have little benefit from single-agent immune checkpoint blockade (ICB) therapy. Targeting MYCN or its effectors could be a strategy to convert a cold TME into a 'hot' (inflamed) TME and improve the efficacy of ICB therapy. METHODS NB transcriptome analyses were used to identify epigenetic drivers of a T-cell infiltration-poor TME. Biological and molecular responses of NB cells to epigenetic drugs and interferon (IFN)-γ exposure were assessed by proliferation assays, immunoblotting, ELISA, qRT-PCR, RNA-seq and ChIP-qPCR as well as co-culture assays with T cells. RESULTS We identified H3K9 euchromatic histone-lysine methyltransferases EHMT2 and EHMT1, also known as G9a and GLP, as epigenetic effectors of the MYCN-driven malignant phenotype and repressors of IFN-γ transcriptional responses in NB cells. EHMT inhibitors enhanced IFN-γ-induced expression of the Th1-type chemokines CXCL9 and CXCL10, key factors of T-cell recruitment into the TME. In MYCN-amplified NB cells, co-inhibition of EZH2 (enhancer of zeste homologue 2), a H3K27 histone methyltransferase cooperating with EHMTs, was needed for strong transcriptional responses to IFN-γ, in line with histone mark changes at CXCL9 and CXCL10 chemokine gene loci. EHMT and EZH2 inhibitor response gene signatures from NB cells were established as surrogate measures and revealed high EHMT and EZH2 activity in MYCN-amplified high-risk NBs with a cold immune phenotype. CONCLUSION Our results delineate a strategy for targeted epigenetic immunomodulation of high-risk NBs, whereby EHMT inhibitors alone or in combination with EZH2 inhibitors (in particular, MYCN-amplified NBs) could promote a T-cell-infiltrated TME via enhanced Th1-type chemokine expression.
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Affiliation(s)
- Johanna A Seier
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Julia Reinhardt
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Kritika Saraf
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Susanna S Ng
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Julian P Layer
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, Bonn, Germany
- Department of Radiation Oncology, University Hospital Bonn, Bonn, Germany
| | - Dillon Corvino
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, Bonn, Germany
| | - Kristina Althoff
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Frank A Giordano
- Department of Radiation Oncology, University Hospital Bonn, Bonn, Germany
| | - Alexander Schramm
- Department of Medical Oncology, West German Cancer Center, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Michael Hölzel
- Institute of Experimental Oncology, Medical Faculty, University Hospital Bonn, Bonn, Germany
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17
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Arora I, Tollefsbol TO. Computational methods and next-generation sequencing approaches to analyze epigenetics data: Profiling of methods and applications. Methods 2021; 187:92-103. [PMID: 32941995 PMCID: PMC7914156 DOI: 10.1016/j.ymeth.2020.09.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/20/2022] Open
Abstract
Epigenetics is mainly comprised of features that regulate genomic interactions thereby playing a crucial role in a vast array of biological processes. Epigenetic mechanisms such as DNA methylation and histone modifications influence gene expression by modulating the packaging of DNA in the nucleus. A plethora of studies have emphasized the importance of analyzing epigenetics data through genome-wide studies and high-throughput approaches, thereby providing key insights towards epigenetics-based diseases such as cancer. Recent advancements have been made towards translating epigenetics research into a high throughput approach such as genome-scale profiling. Amongst all, bioinformatics plays a pivotal role in achieving epigenetics-related computational studies. Despite significant advancements towards epigenomic profiling, it is challenging to understand how various epigenetic modifications such as chromatin modifications and DNA methylation regulate gene expression. Next-generation sequencing (NGS) provides accurate and parallel sequencing thereby allowing researchers to comprehend epigenomic profiling. In this review, we summarize different computational methods such as machine learning and other bioinformatics tools, publicly available databases and resources to identify key modifications associated with epigenetic machinery. Additionally, the review also focuses on understanding recent methodologies related to epigenome profiling using NGS methods ranging from library preparation, different sequencing platforms and analytical techniques to evaluate various epigenetic modifications such as DNA methylation and histone modifications. We also provide detailed information on bioinformatics tools and computational strategies responsible for analyzing large scale data in epigenetics.
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Affiliation(s)
- Itika Arora
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Center for Healthy Aging, University of Alabama Birmingham, 1530 3rd Avenue South, Birmingham, AL 35294, USA; Comprehensive Cancer Center, University of Alabama Birmingham, 1802 6th Avenue South, Birmingham, AL 35294, USA; Nutrition Obesity Research Center, University of Alabama Birmingham, 1675 University Boulevard, Birmingham, AL 35294, USA; Comprehensive Diabetes Center, University of Alabama Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA.
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18
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Nishad A, Nandi AK. Recent advances in plant thermomemory. PLANT CELL REPORTS 2021; 40:19-27. [PMID: 32975635 DOI: 10.1007/s00299-020-02604-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/13/2020] [Indexed: 05/04/2023]
Abstract
This review summarizes the process of thermal acquired tolerance in plants and the knowledge gap compared to systemic acquired resistance that a plant shows after pathogen inoculation. Plants are continuously challenged by several biotic stresses such as pests and pathogens, or abiotic stresses like high light, UV radiation, drought, salt, and very high or low temperature. Interestingly, for most stresses, prior exposure makes plants more tolerant during the subsequent exposures, which is often referred to as acclimatization. Research of the last two decades reveals that the memory of most of the stresses is associated with epigenetic changes. Heat stress causes damage to membrane proteins, denaturation and inactivation of various enzymes, and accumulation of reactive oxygen species leading to cell injury and death. Plants are equipped with thermosensors that can recognize certain specific changes and activate protection machinery. Phytochrome and calcium signaling play critical roles in sensing sudden changes in temperature and activate cascades of signaling, leading to the production of heat shock proteins (HSPs) that keep protein-unfolding under control. Heat shock factors (HSFs) are the transcription factors that read the activation of thermosensors and induce the expression of HSPs. Epigenetic modifications of HSFs are likely to be the key component of thermal acquired tolerance (TAT). Despite the advances in understanding the process of thermomemory generation, it is not known whether plants are equipped with systemic activation thermal protection, as happens in the form of systemic acquired resistance (SAR) upon pathogen infection. This review describes the recent advances in the understanding of thermomemory development in plants and the knowledge gap in comparison with SAR.
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Affiliation(s)
- Anand Nishad
- School of Life Sciences, Jawaharlal Nehru University, 415, New Delhi, 110067, India
| | - Ashis Kumar Nandi
- School of Life Sciences, Jawaharlal Nehru University, 415, New Delhi, 110067, India.
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19
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Plant Responses to Heat Stress: Physiology, Transcription, Noncoding RNAs, and Epigenetics. Int J Mol Sci 2020; 22:ijms22010117. [PMID: 33374376 PMCID: PMC7795586 DOI: 10.3390/ijms22010117] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/20/2020] [Indexed: 01/05/2023] Open
Abstract
Global warming has increased the frequency of extreme high temperature events. High temperature is a major abiotic stress that limits the growth and production of plants. Therefore, the plant response to heat stress (HS) has been a focus of research. However, the plant response to HS involves complex physiological traits and molecular or gene networks that are not fully understood. Here, we review recent progress in the physiological (photosynthesis, cell membrane thermostability, oxidative damage, and others), transcriptional, and post-transcriptional (noncoding RNAs) regulation of the plant response to HS. We also summarize advances in understanding of the epigenetic regulation (DNA methylation, histone modification, and chromatin remodeling) and epigenetic memory underlying plant–heat interactions. Finally, we discuss the challenges and opportunities of future research in the plant response to HS.
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20
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Identification, expression, and artificial selection of silkworm epigenetic modification enzymes. BMC Genomics 2020; 21:740. [PMID: 33096977 PMCID: PMC7585183 DOI: 10.1186/s12864-020-07155-z] [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: 02/20/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
Background Understanding the genetic basis of phenotype variations during domestication and breeding is of great interest. Epigenetics and epigenetic modification enzymes (EMEs) may play a role in phenotypic variations; however, no comprehensive study has been performed to date. Domesticated silkworm (Bombyx mori) may be utilized as a model in determining how EMEs influence domestication traits. Results We identified 44 EMEs in the genome of silkworm (Bombyx mori) using homology searching. Phylogenetic analysis showed that genes in a subfamily among different animals were well clustered, and the expression pattern of EMEs is constant among Bombyx mori, Drosophila melanogaster, and Mus musculus. These are most highly expressed in brain, early embryo, and internal genitalia. By gene-related selective sweeping, we identified five BmEMEs under artificial selection during the domestication and breeding of silkworm. Among these selected genes, BmSuv4–20 and BmDNMT2 harbor selective mutations in their upstream regions that alter transcription factor-binding sites. Furthermore, these two genes are expressed higher in the testis and ovary of domesticated silkworm compared to wild silkworms, and correlations between their expression pattern and meiosis of the sperm and ova were observed. Conclusions The domestication of silkworm has induced artificial selection on epigenetic modification markers that may have led to phenotypic changes during domestication. We present a novel perspective to understand the genetic basis underlying animal domestication and breeding. Supplementary information Supplementary information accompanies this paper at 10.1186/s12864-020-07155-z.
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21
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Halaburkova A, Cahais V, Novoloaca A, Araujo MGDS, Khoueiry R, Ghantous A, Herceg Z. Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes. Genome Res 2020; 30:1517-1532. [PMID: 32963031 PMCID: PMC7605261 DOI: 10.1101/gr.268292.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
The recent identification of recurrently mutated epigenetic regulator genes (ERGs) supports their critical role in tumorigenesis. We conducted a pan-cancer analysis integrating (epi)genome, transcriptome, and DNA methylome alterations in a curated list of 426 ERGs across 33 cancer types, comprising 10,845 tumor and 730 normal tissues. We found that, in addition to mutations, copy number alterations in ERGs were more frequent than previously anticipated and tightly linked to expression aberrations. Novel bioinformatics approaches, integrating the strengths of various driver prediction and multi-omics algorithms, and an orthogonal in vitro screen (CRISPR-Cas9) targeting all ERGs revealed genes with driver roles within and across malignancies and shared driver mechanisms operating across multiple cancer types and hallmarks. This is the largest and most comprehensive analysis thus far; it is also the first experimental effort to specifically identify ERG drivers (epidrivers) and characterize their deregulation and functional impact in oncogenic processes.
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Affiliation(s)
- Andrea Halaburkova
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Vincent Cahais
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | | | - Rita Khoueiry
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), 69008 Lyon, France
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22
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Mass Spectrometry to Study Chromatin Compaction. BIOLOGY 2020; 9:biology9060140. [PMID: 32604817 PMCID: PMC7345930 DOI: 10.3390/biology9060140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/26/2022]
Abstract
Chromatin accessibility is a major regulator of gene expression. Histone writers/erasers have a critical role in chromatin compaction, as they “flag” chromatin regions by catalyzing/removing covalent post-translational modifications on histone proteins. Anomalous chromatin decondensation is a common phenomenon in cells experiencing aging and viral infection. Moreover, about 50% of cancers have mutations in enzymes regulating chromatin state. Numerous genomics methods have evolved to characterize chromatin state, but the analysis of (in)accessible chromatin from the protein perspective is not yet in the spotlight. We present an overview of the most used approaches to generate data on chromatin accessibility and then focus on emerging methods that utilize mass spectrometry to quantify the accessibility of histones and the rest of the chromatin bound proteome. Mass spectrometry is currently the method of choice to quantify entire proteomes in an unbiased large-scale manner; accessibility on chromatin of proteins and protein modifications adds an extra quantitative layer to proteomics dataset that assist more informed data-driven hypotheses in chromatin biology. We speculate that this emerging new set of methods will enhance predictive strength on which proteins and histone modifications are critical in gene regulation, and which proteins occupy different chromatin states in health and disease.
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23
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Tombline G, Gigas J, Macoretta N, Zacher M, Emmrich S, Zhao Y, Seluanov A, Gorbunova V. Proteomics of Long-Lived Mammals. Proteomics 2020; 20:e1800416. [PMID: 31737995 PMCID: PMC7117992 DOI: 10.1002/pmic.201800416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/25/2019] [Indexed: 12/29/2022]
Abstract
Mammalian species differ up to 100-fold in their aging rates and maximum lifespans. Long-lived mammals appear to possess traits that extend lifespan and healthspan. Genomic analyses have not revealed a single pro-longevity function that would account for all longevity effects. In contrast, it appears that pro-longevity mechanisms may be complex traits afforded by connections between metabolism and protein functions that are impossible to predict by genomic approaches alone. Thus, metabolomics and proteomics studies will be required to understand the mechanisms of longevity. Several examples are reviewed that demonstrate the naked mole rat (NMR) shows unique proteomic signatures that contribute to longevity by overcoming several hallmarks of aging. SIRT6 is also discussed as an example of a protein that evolves enhanced enzymatic function in long-lived species. Finally, it is shown that several longevity-related proteins such as Cip1/p21, FOXO3, TOP2A, AKT1, RICTOR, INSR, and SIRT6 harbor posttranslational modification (PTM) sites that preferentially appear in either short- or long-lived species and provide examples of crosstalk between PTM sites. Prospects of enhancing lifespan and healthspan of humans by altering metabolism and proteoforms with drugs that mimic changes observed in long-lived species are discussed.
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Affiliation(s)
- Gregory Tombline
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Jonathan Gigas
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Nicholas Macoretta
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Max Zacher
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Stephan Emmrich
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Yang Zhao
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Andrei Seluanov
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Vera Gorbunova
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
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24
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Swanson GM, Estill M, Diamond MP, Legro RS, Coutifaris C, Barnhart KT, Huang H, Hansen KR, Trussell JC, Coward RM, Zhang H, Goodrich R, Krawetz SA. Human chromatin remodeler cofactor, RNA interactor, eraser and writer sperm RNAs responding to obesity. Epigenetics 2020; 15:32-46. [PMID: 31354029 PMCID: PMC6961666 DOI: 10.1080/15592294.2019.1644880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/23/2022] Open
Abstract
In the United States almost 33% of adults are considered obese (BMI > 30 kg/m2). Both animal models and to a lesser extent human studies, have associated BMI, a measure of obesity, with alterations in sperm DNA methylation and RNAs. Sperm RNAs from the Assessment of Multiple Gestations from Ovarian Stimulation trial, were isolated and sequenced. A Generalized Linear Model identified 487 BMI associated human sperm RNA elements (short exon-sized sequences). They partitioned into four patterns; a continual increase with BMI, increase once obese (BMI>30 kg/m2); a steady decrease with BMI; and decrease once overweight (BMI 25 - 30 kg/m2). Gene Ontology revealed a unique relationship between BMI and transcripts associated with chromosome organization, adipogenesis, cellular stress and obesity-related inflammation. Coregulatory networks linked by Chromatin remodeler cofactors, RNA interactors, Erasers and Writers (CREWs) were uncovered to reveal a hierarchical epigenetic response pathway.
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Affiliation(s)
- Grace M. Swanson
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, USA
| | - Molly Estill
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, USA
| | - Michael P. Diamond
- Department of Obstetrics and Gynecology, Augusta University, Augusta, USA
| | - Richard S. Legro
- Department of Obstetrics and Gynecology, Pennsylvania State University, Hershey, USA
| | - Christos Coutifaris
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Kurt T. Barnhart
- Department of Obstetrics and Gynecology, University of Pennsylvania School of Medicine, Philadelphia, USA
| | - Hao Huang
- Department of Biostatistics, Yale University School of Public Health, New Haven, USA
| | - Karl R. Hansen
- Department of Obstetrics and Gynecology, University of Oklahoma College of Medicine, Oklahoma City, USA
| | - J. C. Trussell
- Urology Department, Upstate Medical University, Syracuse, USA
| | - R. Matthew Coward
- Department of Urology, University of North Carolina School of Medicine, Chapel Hill, USA
| | - Heping Zhang
- Department of Biostatistics, Yale University School of Public Health, New Haven, USA
| | - Robert Goodrich
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, USA
| | - Stephen A. Krawetz
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, USA
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25
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Ueda M, Seki M. Histone Modifications Form Epigenetic Regulatory Networks to Regulate Abiotic Stress Response. PLANT PHYSIOLOGY 2020; 182:15-26. [PMID: 31685643 PMCID: PMC6945856 DOI: 10.1104/pp.19.00988] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 10/22/2019] [Indexed: 05/19/2023]
Abstract
Epigenetic modifiers such as erasers, readers, writers, and recruiters control abiotic stress response in flowering plants.
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Affiliation(s)
- Minoru Ueda
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Plant Epigenome Regulation Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa 244-0813, Japan
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26
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Ru B, Sun J, Tong Y, Wong CN, Chandra A, Tang ATS, Chow LKY, Wun WL, Levitskaya Z, Zhang J. CR2Cancer: a database for chromatin regulators in human cancer. Nucleic Acids Res 2019; 46:D918-D924. [PMID: 29036683 PMCID: PMC5753221 DOI: 10.1093/nar/gkx877] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 09/28/2017] [Indexed: 12/19/2022] Open
Abstract
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining. We collected and integrated genomic, transcriptomic, proteomic, clinical and functional information for over 400 CRs across multiple cancer types. We also built diverse types of CR-associated relations, including cancer type dependent (CR-target and miRNA-CR) and independent (protein-protein interaction and drug-target) ones. Furthermore, we manually curated around 6000 items of aberrant molecular alterations and interactions of CRs in cancer development from 5007 publications. CR2Cancer provides a user-friendly web interface to conveniently browse, search and download data of interest. We believe that this database would become a valuable resource for cancer epigenetics investigation and potential clinical application. CR2Cancer is freely available at http://cis.hku.hk/CR2Cancer.
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Affiliation(s)
- Beibei Ru
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Jianlong Sun
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Yin Tong
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Ching Ngar Wong
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Aditi Chandra
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Acacia Tsz So Tang
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Larry Ka Yue Chow
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Wai Lam Wun
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Zarina Levitskaya
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
| | - Jiangwen Zhang
- School of Biological Sciences, The University of Hong Kong, Hong Kong 999077, China
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27
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Abstract
Epigenetics is the study of heritable mechanisms that can modify gene activity and phenotype without modifying the genetic code. The basis for the concept of epigenetics originated more than 2,000 yr ago as a theory to explain organismal development. However, the definition of epigenetics continues to evolve as we identify more of the components that make up the epigenome and dissect the complex manner by which they regulate and are regulated by cellular functions. A substantial and growing body of research shows that nutrition plays a significant role in regulating the epigenome. Here, we critically assess this diverse body of evidence elucidating the role of nutrition in modulating the epigenome and summarize the impact such changes have on molecular and physiological outcomes with regards to human health.
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Affiliation(s)
- Folami Y Ideraabdullah
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
| | - Steven H Zeisel
- Departments of Genetics and Nutrition, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina; and Departments of Nutrition and Pediatrics, Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, North Carolina
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28
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van der Heijden CDCC, Noz MP, Joosten LAB, Netea MG, Riksen NP, Keating ST. Epigenetics and Trained Immunity. Antioxid Redox Signal 2018; 29:1023-1040. [PMID: 28978221 PMCID: PMC6121175 DOI: 10.1089/ars.2017.7310] [Citation(s) in RCA: 152] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
SIGNIFICANCE A growing body of clinical and experimental evidence has challenged the traditional understanding that only the adaptive immune system can mount immunological memory. Recent findings describe the adaptive characteristics of the innate immune system, underscored by its ability to remember antecedent foreign encounters and respond in a nonspecific sensitized manner to reinfection. This has been termed trained innate immunity. Although beneficial in the context of recurrent infections, this might actually contribute to chronic immune-mediated diseases, such as atherosclerosis. Recent Advances: In line with its proposed role in sustaining cellular memories, epigenetic reprogramming has emerged as a critical determinant of trained immunity. Recent technological and computational advances that improve unbiased acquisition of epigenomic profiles have significantly enhanced our appreciation for the complexities of chromatin architecture in the contexts of diverse immunological challenges. CRITICAL ISSUES Key to resolving the distinct chromatin signatures of innate immune memory is a comprehensive understanding of the precise physiological targets of regulatory proteins that recognize, deposit, and remove chemical modifications from chromatin as well as other gene-regulating factors. Drawing from a rapidly expanding compendium of experimental and clinical studies, this review details a current perspective of the epigenetic pathways that support the adapted phenotypes of monocytes and macrophages. FUTURE DIRECTIONS We explore future strategies that are aimed at exploiting the mechanism of trained immunity to improve the prevention and treatment of infections and immune-mediated chronic disorders.
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Affiliation(s)
| | - Marlies P Noz
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Leo A B Joosten
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Mihai G Netea
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands .,2 Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn , Bonn, Germany
| | - Niels P Riksen
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
| | - Samuel T Keating
- 1 Department of Internal Medicine, Radboud University Medical Center , Nijmegen, The Netherlands
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29
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Lavender P, Kelly A, Hendy E, McErlean P. CRISPR-based reagents to study the influence of the epigenome on gene expression. Clin Exp Immunol 2018; 194:9-16. [PMID: 30030848 PMCID: PMC6156815 DOI: 10.1111/cei.13190] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2018] [Indexed: 12/22/2022] Open
Abstract
The use of epigenome editing is set to expand our knowledge of how epigenetic landscapes facilitate gene expression capacity within a given cell. As epigenetic landscape profiling in health and disease becomes more commonplace, so does the requirement to assess the functional impact that particular regulatory domains and DNA methylation profiles have upon gene expression capacity. That functional assessment is particularly pertinent when analysing epigenomes in disease states where the reversible nature of histone and DNA modification might yield plausible therapeutic targets. In this review we discuss first the nature of the epigenetic landscape, secondly the types of factors that deposit and erase the various modifications, consider how modifications transduce their signals, and lastly address current tools for experimental epigenome editing with particular emphasis on the immune system.
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Affiliation(s)
- P. Lavender
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial ScienceMRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College LondonLondonUK
| | - A. Kelly
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial ScienceMRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College LondonLondonUK
| | - E. Hendy
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial ScienceMRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College LondonLondonUK
| | - P. McErlean
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial ScienceMRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King’s College LondonLondonUK
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30
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Zhai G, Dong H, Guo Z, Feng W, Jin J, Zhang T, Chen C, Chen P, Tian S, Bai X, Shi L, Fan E, Zhang Y, Zhang K. An Efficient Approach for Selective Enrichment of Histone Modification Readers Using Self-Assembled Multivalent Photoaffinity Peptide Probes. Anal Chem 2018; 90:11385-11392. [PMID: 30188686 DOI: 10.1021/acs.analchem.8b02342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Histone post-translational modifications (HPTMs) provide signaling platforms to recruit proteins or protein complexes (e.g., transcription factors, the so-called "readers" of the histone code), changing DNA accessibility in the regulation of gene expression. Thus, it is an essential task to identify HPTM readers for understanding of epigenetic regulation. Herein we designed and prepared a novel HPTM probe based on self-assembled multivalent photo-cross-linking technique for selective enrichment and identification of HPTM readers. By use of trimethylation of histone H3 lysine 4, we showcased that the functionalized HPTM probe was able to capture its reader with high enrichment efficiency and remarkable specificity even in a complex environment. Notably, this approach was readily applicable for exploring crosstalk among multiple HPTMs. Combining the probes with a mass spectrometry-based proteomic approach, our approach reached a fairly high coverage of known H3K4me3 readers. We further demonstrated that the HPTM probes can enrich a new type of HPTM readers and uncovered several novel putative binders of crotonylation of histone H3 lysine 9, expanding the repertoire of readers for this epigenetic mark. More broadly, our work provides a general strategy for rapid and robust interrogating HPTM readers and will be of great importance to elucidate epigenetic mechanism in regulating gene activity.
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Affiliation(s)
- Guijin Zhai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Hanyang Dong
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Zhenchang Guo
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Wei Feng
- School of Biomedical Engineering , Tianjin Medical University , Tianjin 300070 , China
| | - Jin Jin
- College of Pharmacy , Nankai University , Tianjin 300071 , China
| | - Tao Zhang
- School of Biomedical Engineering , Tianjin Medical University , Tianjin 300070 , China
| | - Cong Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Pu Chen
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Shanshan Tian
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Xue Bai
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Lei Shi
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
| | - Enguo Fan
- Institut für Biochemie und Molekularbiologie , Universität Freiburg , Stefan-Meier-Straße 17 , Freiburg 79104 , Germany
| | - Yukui Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences , 457 Zhongshan Road , Dalian 116023 , China
| | - Kai Zhang
- 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Department of Biochemistry and Molecular Biology, Key Laboratory of Breast Cancer Prevention and Treatment (Ministry of Education), Cancer Institute and Hospital , Tianjin Medical University , Tianjin 300070 , China
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31
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Bacci M, Langini C, Vymětal J, Caflisch A, Vitalis A. Focused conformational sampling in proteins. J Chem Phys 2018; 147:195102. [PMID: 29166086 DOI: 10.1063/1.4996879] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A detailed understanding of the conformational dynamics of biological molecules is difficult to obtain by experimental techniques due to resolution limitations in both time and space. Computer simulations avoid these in theory but are often too short to sample rare events reliably. Here we show that the progress index-guided sampling (PIGS) protocol can be used to enhance the sampling of rare events in selected parts of biomolecules without perturbing the remainder of the system. The method is very easy to use as it only requires as essential input a set of several features representing the parts of interest sufficiently. In this feature space, new states are discovered by spontaneous fluctuations alone and in unsupervised fashion. Because there are no energetic biases acting on phase space variables or projections thereof, the trajectories PIGS generates can be analyzed directly in the framework of transition networks. We demonstrate the possibility and usefulness of such focused explorations of biomolecules with two loops that are part of the binding sites of bromodomains, a family of epigenetic "reader" modules. This real-life application uncovers states that are structurally and kinetically far away from the initial crystallographic structures and are also metastable. Representative conformations are intended to be used in future high-throughput virtual screening campaigns.
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Affiliation(s)
- Marco Bacci
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Cassiano Langini
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jiří Vymětal
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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32
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Alam H, Li N, Dhar SS, Wu SJ, Lv J, Chen K, Flores ER, Baseler L, Lee MG. HP1γ Promotes Lung Adenocarcinoma by Downregulating the Transcription-Repressive Regulators NCOR2 and ZBTB7A. Cancer Res 2018; 78:3834-3848. [PMID: 29764865 DOI: 10.1158/0008-5472.can-17-3571] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 03/09/2018] [Accepted: 05/11/2018] [Indexed: 12/16/2022]
Abstract
Lung adenocarcinoma is a major form of lung cancer, which is the leading cause of cancer death. Histone methylation reader proteins mediate the effect of histone methylation, a hallmark of epigenetic and transcriptional regulation of gene expression. However, their roles in lung adenocarcinoma are poorly understood. Here, our bioinformatic screening and analysis in search of a lung adenocarcinoma-promoting histone methylation reader protein show that heterochromatin protein 1γ (HP1γ; also called CBX3) is among the most frequently overexpressed and amplified histone reader proteins in human lung adenocarcinoma, and that high HP1γ mRNA levels are associated with poor prognosis in patients with lung adenocarcinoma. In vivo depletion of HP1γ reduced K-RasG12D-driven lung adenocarcinoma and lengthened survival of mice bearing K-RasG12D-induced lung adenocarcinoma. HP1γ and its binding activity to methylated histone H3 lysine 9 were required for the proliferation, colony formation, and migration of lung adenocarcinoma cells. HP1γ directly repressed expression of the transcription-repressive regulators NCOR2 and ZBTB7A. Knockdown of NCOR2 or ZBTB7A significantly restored defects in proliferation, colony formation, and migration in HP1γ-depleted lung adenocarcinoma cells. Low NCOR2 or ZBTB7A mRNA levels were associated with poor prognosis in patients with lung adenocarcinoma and correlated with high HP1γ mRNA levels in lung adenocarcinoma samples. NCOR2 and ZBTB7A downregulated expression of tumor-promoting factors such as ELK1 and AXL, respectively. These findings highlight the importance of HP1γ and its reader activity in lung adenocarcinoma tumorigenesis and reveal a unique lung adenocarcinoma-promoting mechanism in which HP1γ downregulates NCOR2 and ZBTB7A to enhance expression of protumorigenic genes.Significance: Direct epigenetic repression of the transcription-repressive regulators NCOR2 and ZBTB7A by the histone reader protein HP1γ leads to activation of protumorigenic genes in lung adenocarcinoma. Cancer Res; 78(14); 3834-48. ©2018 AACR.
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Affiliation(s)
- Hunain Alam
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Na Li
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shilpa S Dhar
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sarah J Wu
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
| | - Jie Lv
- Institute for Academic Medicine, the Methodist Hospital Research Institute, Houston, Texas.,Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, the Methodist Hospital Research Institute, Houston, Texas.,Weill Cornell Medical College, Cornell University, New York, New York
| | - Kaifu Chen
- Institute for Academic Medicine, the Methodist Hospital Research Institute, Houston, Texas.,Center for Cardiovascular Regeneration, Department of Cardiovascular Sciences, the Methodist Hospital Research Institute, Houston, Texas.,Weill Cornell Medical College, Cornell University, New York, New York
| | - Elsa R Flores
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, Florida
| | - Laura Baseler
- Department of Veterinary Medicine and Surgery, the University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Min Gyu Lee
- Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, Texas. .,The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, Texas
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33
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Langini C, Caflisch A, Vitalis A. The ATAD2 bromodomain binds different acetylation marks on the histone H4 in similar fuzzy complexes. J Biol Chem 2017; 292:16734-16745. [PMID: 28798233 DOI: 10.1074/jbc.m117.786350] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/21/2017] [Indexed: 12/22/2022] Open
Abstract
Bromodomains are protein modules adopting conserved helix bundle folds. Some bromodomain-containing proteins, such as ATPase family AAA domain-containing protein 2 (ATAD2), isoform A, have attracted much interest because they are overexpressed in many types of cancer. Bromodomains bind to acetylated lysine residues on histone tails and thereby facilitate the reading of the histone code. Epigenetic regulators in general have been implicated as indicators, mediators, or causes of a large number of diseases and disorders. To interfere with or modulate these processes, it is therefore of fundamental interest to understand the molecular mechanisms by which epigenetic regulation occurs. Here, we present results from molecular dynamics simulations of a doubly acetylated histone H4 peptide bound to the bromodomain of ATAD2 (hereafter referred to as ATAD2A). These simulations revealed how the flexibility of ATAD2A's major loop, the so-called ZA loop, creates an adaptable interface that preserves the disorder of both peptide and loop in the bound state. We further demonstrate that the binding involves an almost identical average pattern of interactions irrespective of which acetyl mark is inserted into the pocket. In conjunction with a likely mechanism of electrostatically driven recruitment, our simulation results highlight how the bromodomain is built toward promiscuous binding with low specificity. In conclusion, the simulations indicate that disorder and electrostatic steering function jointly to recruit ATAD2A to the histone core and that these fuzzy interactions may promote cooperativity between nearby epigenetic marks.
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Affiliation(s)
- Cassiano Langini
- From the Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Amedeo Caflisch
- From the Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Andreas Vitalis
- From the Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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34
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Podobinska M, Szablowska-Gadomska I, Augustyniak J, Sandvig I, Sandvig A, Buzanska L. Epigenetic Modulation of Stem Cells in Neurodevelopment: The Role of Methylation and Acetylation. Front Cell Neurosci 2017; 11:23. [PMID: 28223921 PMCID: PMC5293809 DOI: 10.3389/fncel.2017.00023] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022] Open
Abstract
The coordinated development of the nervous system requires fidelity in the expression of specific genes determining the different neural cell phenotypes. Stem cell fate decisions during neurodevelopment are strictly correlated with their epigenetic status. The epigenetic regulatory processes, such as DNA methylation and histone modifications discussed in this review article, may impact both neural stem cell (NSC) self-renewal and differentiation and thus play an important role in neurodevelopment. At the same time, stem cell decisions regarding fate commitment and differentiation are highly dependent on the temporospatial expression of specific genes contingent on the developmental stage of the nervous system. An interplay between the above, as well as basic cell processes, such as transcription regulation, DNA replication, cell cycle regulation and DNA repair therefore determine the accuracy and function of neuronal connections. This may significantly impact embryonic health and development as well as cognitive processes such as neuroplasticity and memory formation later in the adult.
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Affiliation(s)
- Martyna Podobinska
- Stem Cell Bioengineering Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences Warsaw, Poland
| | | | - Justyna Augustyniak
- Stem Cell Bioengineering Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences Warsaw, Poland
| | - Ioanna Sandvig
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU) Trondheim, Norway
| | - Axel Sandvig
- Department of Neuromedicine and Movement Science, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology (NTNU) Trondheim, Norway
| | - Leonora Buzanska
- Stem Cell Bioengineering Unit, Mossakowski Medical Research Centre, Polish Academy of Sciences Warsaw, Poland
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