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Cao S, Chen ZJ. Transgenerational epigenetic inheritance during plant evolution and breeding. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00112-2. [PMID: 38806375 DOI: 10.1016/j.tplants.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/12/2024] [Accepted: 04/25/2024] [Indexed: 05/30/2024]
Abstract
Plants can program and reprogram their genomes to create genetic variation and epigenetic modifications, leading to phenotypic plasticity. Although consequences of genetic changes are comprehensible, the basis for transgenerational inheritance of epigenetic variation is elusive. This review addresses contributions of external (environmental) and internal (genomic) factors to the establishment and maintenance of epigenetic memory during plant evolution, crop domestication, and modern breeding. Dynamic and pervasive changes in DNA methylation and chromatin modifications provide a diverse repertoire of epigenetic variation potentially for transgenerational inheritance. Elucidating and harnessing epigenetic inheritance will help us develop innovative breeding strategies and biotechnological tools to improve crop yield and resilience in the face of environmental challenges. Beyond plants, epigenetic principles are shared across sexually reproducing organisms including humans with relevance to medicine and public health.
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Affiliation(s)
- Shuai Cao
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA.
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2
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Xia YQ, Yang Y, Liu YY, Cheng JX, Liu Y, Li CH, Liu PF. DNA Methylation Analysis Reveals Potential Mechanism in Takifugu rubripes Against Cryptocaryon irritans Infection. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:288-305. [PMID: 38446292 DOI: 10.1007/s10126-024-10296-x] [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: 12/17/2023] [Accepted: 02/02/2024] [Indexed: 03/07/2024]
Abstract
Takifugu rubripes (T. rubripes) is a valuable commercial fish, and Cryptocaryon irritans (C. irritans) has a significant impact on its aquaculture productivity. DNA methylation is one of the earliest discovered ways of gene epigenetic modification and also an important form of modification, as well as an essential type of alteration that regulates gene expression, including immune response. To further explore the anti-infection mechanism of T. rubripes in inhibiting this disease, we determined genome-wide DNA methylation profiles in the gill of T. rubripes using whole-genome bisulfite sequencing (WGBS) and combined with RNA sequence (RNA-seq). A total of 4659 differentially methylated genes (DMGs) in the gene body and 1546 DMGs in the promoter between the infection and control group were identified. And we identified 2501 differentially expressed genes (DEGs), including 1100 upregulated and 1401 downregulated genes. After enrichment analysis, we identified DMGs and DEGs of immune-related pathways including MAPK, Wnt, ErbB, and VEGF signaling pathways, as well as node genes prkcb, myca, tp53, and map2k2a. Based on the RNA-Seq results, we plotted a network graph to demonstrate the relationship between immune pathways and functional related genes, in addition to gene methylation and expression levels. At the same time, we predicted the CpG island and transcription factor of four immune-related key genes prkcb and mapped the gene structure. These unique discoveries could be helpful in the understanding of C. irritans pathogenesis, and the candidate genes screened may serve as optimum methylation-based biomarkers that can be utilized for the correct diagnosis and therapy T. rubripes in the development of the ability to resist C. irritans infection.
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Affiliation(s)
- Yu-Qing Xia
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Yi Yang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Yan-Yun Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
| | - Jian-Xin Cheng
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Life Science, Liaoning Normal University, Dalian, 116081, People's Republic of China
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, People's Republic of China
| | - Cheng-Hua Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, People's Republic of China.
| | - Peng-Fei Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian, 116023, People's Republic of China.
- College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, People's Republic of China.
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de Almeida BC, dos Anjos LG, Dobroff AS, Baracat EC, Yang Q, Al-Hendy A, Carvalho KC. Epigenetic Features in Uterine Leiomyosarcoma and Endometrial Stromal Sarcomas: An Overview of the Literature. Biomedicines 2022; 10:2567. [PMID: 36289829 PMCID: PMC9599831 DOI: 10.3390/biomedicines10102567] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/04/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
There is a consensus that epigenetic alterations play a key role in cancer initiation and its biology. Studies evaluating the modification in the DNA methylation and chromatin remodeling patterns, as well as gene regulation profile by non-coding RNAs (ncRNAs) have led to the development of novel therapeutic approaches to treat several tumor types. Indeed, despite clinical and translational challenges, combinatorial therapies employing agents targeting epigenetic modifications with conventional approaches have shown encouraging results. However, for rare neoplasia such as uterine leiomyosarcomas (LMS) and endometrial stromal sarcomas (ESS), treatment options are still limited. LMS has high chromosomal instability and molecular derangements, while ESS can present a specific gene fusion signature. Although they are the most frequent types of "pure" uterine sarcomas, these tumors are difficult to diagnose, have high rates of recurrence, and frequently develop resistance to current treatment options. The challenges involving the management of these tumors arise from the fact that the molecular mechanisms governing their progression have not been entirely elucidated. Hence, to fill this gap and highlight the importance of ongoing and future studies, we have cross-referenced the literature on uterine LMS and ESS and compiled the most relevant epigenetic studies, published between 2009 and 2022.
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Affiliation(s)
- Bruna Cristine de Almeida
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento de Obstetricia e Ginecologia, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 05403-010, Brazil
| | - Laura Gonzalez dos Anjos
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento de Obstetricia e Ginecologia, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 05403-010, Brazil
| | - Andrey Senos Dobroff
- UNM Comprehensive Cancer Center (UNMCCC), University of New Mexico, Albuquerque, NM 87131, USA
- Division of Molecular Medicine, Department of Internal Medicine, (UNM) School of Medicine, UNM Health Sciences Center, 1 University of New Mexico, Albuquerque, NM 87131, USA
| | - Edmund Chada Baracat
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento de Obstetricia e Ginecologia, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 05403-010, Brazil
| | - Qiwei Yang
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
| | - Ayman Al-Hendy
- Department of Obstetrics and Gynecology, University of Chicago, Chicago, IL 60637, USA
| | - Katia Candido Carvalho
- Laboratório de Ginecologia Estrutural e Molecular (LIM 58), Disciplina de Ginecologia, Departamento de Obstetricia e Ginecologia, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), São Paulo 05403-010, Brazil
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DNA-nanopore technology: a human perspective. Emerg Top Life Sci 2021; 5:455-463. [PMID: 34282838 DOI: 10.1042/etls20200282] [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: 02/05/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/17/2022]
Abstract
The purpose of this article is to give a brief overview of the current state of nanopore sequencing in relation to forensic science with a brief outline of where it stands in relation to current methods, its potential uses in forensic science and factors which may influence acceptance of this technology by forensic practitioners, the judiciary and law enforcement. Perhaps most importantly consideration is also given to concerns which may influence the acceptance of the technology by the general public.
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Sagonas K, Meyer BS, Kaufmann J, Lenz TL, Häsler R, Eizaguirre C. Experimental Parasite Infection Causes Genome-Wide Changes in DNA Methylation. Mol Biol Evol 2020; 37:2287-2299. [PMID: 32227215 PMCID: PMC7531312 DOI: 10.1093/molbev/msaa084] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Parasites are arguably among the strongest drivers of natural selection, constraining hosts to evolve resistance and tolerance mechanisms. Although, the genetic basis of adaptation to parasite infection has been widely studied, little is known about how epigenetic changes contribute to parasite resistance and eventually, adaptation. Here, we investigated the role of host DNA methylation modifications to respond to parasite infections. In a controlled infection experiment, we used the three-spined stickleback fish, a model species for host-parasite studies, and their nematode parasite Camallanus lacustris. We showed that the levels of DNA methylation are higher in infected fish. Results furthermore suggest correlations between DNA methylation and shifts in key fitness and immune traits between infected and control fish, including respiratory burst and functional trans-generational traits such as the concentration of motile sperm. We revealed that genes associated with metabolic, developmental, and regulatory processes (cell death and apoptosis) were differentially methylated between infected and control fish. Interestingly, genes such as the neuropeptide FF receptor 2 and the integrin alpha 1 as well as molecular pathways including the Th1 and Th2 cell differentiation were hypermethylated in infected fish, suggesting parasite-mediated repression mechanisms of immune responses. Altogether, we demonstrate that parasite infection contributes to genome-wide DNA methylation modifications. Our study brings novel insights into the evolution of vertebrate immunity and suggests that epigenetic mechanisms are complementary to genetic responses against parasite-mediated selection.
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Affiliation(s)
- Kostas Sagonas
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Britta S Meyer
- Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | - Joshka Kaufmann
- School of Biological, Earth & Environmental Sciences, University College Cork, Cork, Republic of Ireland
- Department for Evolutionary Ecology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Christophe Eizaguirre
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Gu Y, Ci C, Zhang X, Su M, Lv W, Chen C, Liu H, Zhang D, Zhang S, Zhang Y. Prediction of circRNAs Based on the DNA Methylation-Mediated Feature Sponge Function in Breast Cancer. Front Bioeng Biotechnol 2019; 7:365. [PMID: 32039169 PMCID: PMC6988805 DOI: 10.3389/fbioe.2019.00365] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 11/12/2019] [Indexed: 11/22/2022] Open
Abstract
Several studies have found that DNA methylation is associated with transcriptional regulation and affect sponge regulation of non-coding RNAs in cancer. The integration of circRNA, miRNA, DNA methylation and gene expression data to identify sponge circRNAs is important for revealing the role of DNA methylation-mediated regulation of sponge circRNAs in cancer progression. We established a DNA methylation-mediated circRNA crosstalk network by integrating gene expression, DNA methylation and non-coding RNA data of breast cancer in TCGA. Four modules (26 candidate circRNAs) were mined. Next, 10 DNA methylation-mediated sponge circRNAs (sp_circRNAs) and five sponge driver genes (sp_driver genes) in breast cancer were identified in the CMD network using a computational process. Among the identified genes, ERBB2 was associated with six sponge circRNAs, which illustrates its better sponge regulatory function. Survival analysis showed that DNA methylations of 10 sponge circRNA host genes are potential prognostic biomarkers in the TCGA dataset (p = 0.0239) and GSE78754 dataset (p = 0.0377). In addition, the DNA methylation of two sponge circRNA host genes showed a significant negative correlation with their driver gene expressions. We developed a strategy to predict sponge circRNAs by DNA methylation mediated with playing the role of regulating breast cancer sponge driver genes.
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Affiliation(s)
- Yue Gu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ce Ci
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xingda Zhang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Mu Su
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Wenhua Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chuangeng Chen
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Hui Liu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Dongwei Zhang
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shumei Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- College of Information and Computer Engineering, Northeast Forestry University, Harbin, China
| | - Yan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
- State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, China
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Functional Prediction of Candidate MicroRNAs for CRC Management Using in Silico Approach. Int J Mol Sci 2019; 20:ijms20205190. [PMID: 31635135 PMCID: PMC6834124 DOI: 10.3390/ijms20205190] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/13/2019] [Accepted: 09/14/2019] [Indexed: 02/07/2023] Open
Abstract
Approximately 30–50% of malignant growths can be prevented by avoiding risk factors and implementing evidence-based strategies. Colorectal cancer (CRC) accounted for the second most common cancer and the third most common cause of cancer death worldwide. This cancer subtype can be reduced by early detection and patients’ management. In this study, the functional roles of the identified microRNAs were determined using an in silico pipeline. Five microRNAs identified using an in silico approach alongside their seven target genes from our previous study were used as datasets in this study. Furthermore, the secondary structure and the thermodynamic energies of the microRNAs were revealed by Mfold algorithm. The triplex binding ability of the oligonucleotide with the target promoters were analyzed by Trident. Finally, evolutionary stage-specific somatic events and co-expression analysis of the target genes in CRC were analyzed by SEECancer and GeneMANIA plugin in Cytoscape. Four of the five microRNAs have the potential to form more than one secondary structure. The ranges of the observed/expected ratio of CpG dinucleotides of these genes range from 0.60 to 1.22. Three of the candidate microRNA were capable of forming multiple triplexes along with three of the target mRNAs. Four of the total targets were involved in either early or metastatic stage-specific events while three other genes were either a product of antecedent or subsequent events of the four genes implicated in CRC. The secondary structure of the candidate microRNAs can be used to explain the different degrees of genetic regulation in CRC due to their conformational role to modulate target interaction. Furthermore, due to the regulation of important genes in the CRC pathway and the enrichment of the microRNA with triplex binding sites, they may be a useful diagnostic biomarker for the disease subtype.
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Kagohara LT, Stein-O’Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Brief Funct Genomics 2019; 17:49-63. [PMID: 28968850 PMCID: PMC5860551 DOI: 10.1093/bfgp/elx018] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding RNAs, posttranslational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations were once thought to be crucial only for the malignant phenotype maintenance. Now, epigenetic alterations are also recognized as critical for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. The precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review also describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems and bioinformatics algorithms for their analysis. Advances in bioinformatics data that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer. These integrative algorithms are also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations during tumor initiation and progression. This deeper understanding is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Daria A Gaykalova
- Corresponding authors: Daria A. Gaykalova, Otolaryngology - Head and Neck Surgery, The Johns Hopkins University School of Medicine, 1550 Orleans Street, Rm 574, CRBII Baltimore, MD 21231, USA. Tel.: +1 410 614 2745; Fax: +1 410 614 1411; E-mail: ; Elana J. Fertig, Assistant Professor of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University, 550 N Broadway, 1101 E Baltimore, MD 21205, USA. Tel.: +1 410 955 4268; Fax: +1 410 955 0859; E-mail:
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Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Wick HC, Danilova LV, Easwaran H, Favorov AV, Qian J, Gaykalova DA, Fertig EJ. Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. Brief Funct Genomics 2018. [PMID: 28968850 DOI: 10.1101/114025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in even individual malignant cells. Epigenetic changes are critical mediators of these functional changes that drive and maintain the malignant phenotype. Changes in DNA methylation, histone acetylation and methylation, noncoding RNAs, posttranslational modifications are all epigenetic drivers in cancer, independent of changes in the DNA sequence. These epigenetic alterations were once thought to be crucial only for the malignant phenotype maintenance. Now, epigenetic alterations are also recognized as critical for disrupting essential pathways that protect the cells from uncontrolled growth, longer survival and establishment in distant sites from the original tissue. In this review, we focus on DNA methylation and chromatin structure in cancer. The precise functional role of these alterations is an area of active research using emerging high-throughput approaches and bioinformatics analysis tools. Therefore, this review also describes these high-throughput measurement technologies, public domain databases for high-throughput epigenetic data in tumors and model systems and bioinformatics algorithms for their analysis. Advances in bioinformatics data that combine these epigenetic data with genomics data are essential to infer the function of specific epigenetic alterations in cancer. These integrative algorithms are also a focus of this review. Future studies using these emerging technologies will elucidate how alterations in the cancer epigenome cooperate with genetic aberrations during tumor initiation and progression. This deeper understanding is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies.
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10
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Sheinkopf SJ, Righi G, Marsit CJ, Lester BM. Methylation of the Glucocorticoid Receptor (NR3C1) in Placenta Is Associated with Infant Cry Acoustics. Front Behav Neurosci 2016; 10:100. [PMID: 27313516 PMCID: PMC4889592 DOI: 10.3389/fnbeh.2016.00100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/11/2016] [Indexed: 11/13/2022] Open
Abstract
Epigenetic mechanisms regulating expression of the glucocorticoid receptor gene (NR3C1) promoter may influence behavioral and biological aspects of stress response in human infants. Acoustic features of infant crying are an indicator of neurobehavioral and neurological status not yet investigated in relation to epigenetic mechanisms. We examined NR3C1 methylation in placental tissue from a series of 120 healthy newborn infants in relation to a detailed set of acoustic features extracted from newborn infant cries. We identified significant associations of NR3C1 methylation with energy variation in infants' cries as well as with the presence of very high fundamental frequency in cry utterances. The presence of high fundamental frequency in cry (above 1 kHz) has been linked to poor vocal tract control, poor regulation of stress response, and may be an indicator or poor neurobehavioral integrity. Thus, these results add to evidence linking epigenetic alteration of the NR3C1 gene in the placenta to neurodevelopmental features in infants.
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Affiliation(s)
- Stephen J Sheinkopf
- The Brown Center for the Study of Children at Risk, Women and Infants HospitalProvidence, RI, USA; Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown UniversityProvidence, RI, USA; Department of Pediatrics, Warren Alpert Medical School of Brown UniversityProvidence, RI, USA
| | - Giulia Righi
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University Providence, RI, USA
| | - Carmen J Marsit
- Section of Biostatistics and Epidemiology, Department of Pharmacology and Toxicology and of Community and Family Medicine, Geisel School of Medicine at Dartmouth Hanover, NH, USA
| | - Barry M Lester
- The Brown Center for the Study of Children at Risk, Women and Infants HospitalProvidence, RI, USA; Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown UniversityProvidence, RI, USA; Department of Pediatrics, Warren Alpert Medical School of Brown UniversityProvidence, RI, USA
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Jacobs DI, Mao Y, Fu A, Kelly WK, Zhu Y. Dysregulated methylation at imprinted genes in prostate tumor tissue detected by methylation microarray. BMC Urol 2013; 13:37. [PMID: 23890537 PMCID: PMC3751920 DOI: 10.1186/1471-2490-13-37] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 07/15/2013] [Indexed: 11/18/2022] Open
Abstract
Background Imprinting is an important epigenetic regulator of gene expression that is often disrupted in cancer. While loss of imprinting (LOI) has been reported for two genes in prostate cancer (IGF2 and TFPI2), disease-related changes in methylation across all imprinted gene regions has not been investigated. Methods Using an Illumina Infinium Methylation Assay, we analyzed methylation of 396 CpG sites in the promoter regions of 56 genes in a pooled sample of 12 pairs of prostate tumor and adjacent normal tissue. Selected LOI identified from the array was validated using the Sequenom EpiTYPER assay for individual samples and further confirmed by expression data from publicly available datasets. Results Methylation significantly increased in 52 sites and significantly decreased in 17 sites across 28 unique genes (P < 0.05), and the strongest evidence for loss of imprinting was demonstrated in tumor suppressor genes DLK1, PLAGL1, SLC22A18, TP73, and WT1. Differential expression of these five genes in prostate tumor versus normal tissue using array data from a publicly available database were consistent with the observed LOI patterns, and WT1 hypermethylation was confirmed using quantitative DNA methylation analysis. Conclusions Together, these findings suggest a more widespread dysregulation of genetic imprinting in prostate cancer than previously reported and warrant further investigation.
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Affiliation(s)
- Daniel I Jacobs
- Yale School of Public Health, Yale University School of Medicine, New Haven, CT, USA
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12
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Majumdar S, Buckles E, Estrada J, Koochekpour S. Aberrant DNA methylation and prostate cancer. Curr Genomics 2012; 12:486-505. [PMID: 22547956 PMCID: PMC3219844 DOI: 10.2174/138920211797904061] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2011] [Revised: 08/15/2011] [Accepted: 09/05/2011] [Indexed: 12/28/2022] Open
Abstract
Prostate cancer (PCa) is the most prevalent cancer, a significant contributor to morbidity and a leading cause of cancer-related death in men in Western industrialized countries. In contrast to genetic changes that vary among individual cases, somatic epigenetic alterations are early and highly consistent events. Epigenetics encompasses several different phenomena, such as DNA methylation, histone modifications, RNA interference, and genomic imprinting. Epigenetic processes regulate gene expression and can change malignancy-associated phenotypes such as growth, migration, invasion, or angiogenesis. Methylations of certain genes are associated with PCa progression. Compared to normal prostate tissues, several hypermethylated genes have also been identified in benign prostate hyperplasia, which suggests a role for aberrant methylation in this growth dysfunction. Global and gene-specific DNA methylation could be affected by environmental and dietary factors. Among other epigenetic changes, aberrant DNA methylation might have a great potential as diagnostic or prognostic marker for PCa and could be tested in tumor tissues and various body fluids (e.g., serum, urine). The DNA methylation markers are simple in nature, have high sensitivity, and could be detected either quantitatively or qualitatively. Availability of genome-wide screening methodologies also allows the identification of epigenetic signatures in high throughput population studies. Unlike irreversible genetic changes, epigenetic alterations are reversible and could be used for PCa targeted therapies.
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Affiliation(s)
- Sunipa Majumdar
- Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70122, USA
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13
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Feng Z, Xu Q, Chen W. Epigenetic and genetic alterations-based molecular classification of head and neck cancer. Expert Rev Mol Diagn 2012; 12:279-90. [PMID: 22468818 DOI: 10.1586/erm.12.19] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The long-term survival rates for patients diagnosed with advanced head and neck cancer (HNC) remain poor. Many perplexing factors, including etiology and comorbidity, lead to different molecular malfunctions of HNC cells and determine the prognosis of the disease. Traditional diagnostic methods are limited in that they fail to provide an effective classification diagnosis, such as a more precise prediction of prognosis and decisions for personalized treatment regimens. Recently, molecular biology techniques, especially epigenetic and genetic techniques, have been developed that have enabled us to gain a greater insight into the molecular pathways underlying the cancers. Translating the research into a format that will facilitate effective molecular classification, support personalized treatment and determine prognosis remains a challenge. In this review, the authors provide an overview of cancer epigenetic and genetic alterations, tissue banks, and several promising biomarkers or candidates that may ultimately prove to be beneficial in a clinical setting for patients with HNC.
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Affiliation(s)
- Zhien Feng
- Department of Oral and Maxillofacial Surgery, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhizaoju Road, Shanghai 200011, China
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Oxidative stress and DNA methylation in prostate cancer. Obstet Gynecol Int 2010; 2010:302051. [PMID: 20671914 PMCID: PMC2910495 DOI: 10.1155/2010/302051] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2009] [Accepted: 05/12/2010] [Indexed: 12/20/2022] Open
Abstract
The protective effects of fruits, vegetables, and other foods on prostate cancer may be due to their antioxidant properties. An imbalance in the oxidative stress/antioxidant status is observed in prostate cancer patients. Genome oxidative damage in prostate cancer patients is associated with higher lipid peroxidation and lower antioxidant levels. Oxygen radicals are associated with different steps of carcinogenesis, including structural DNA damage, epigenetic changes, and protein and lipid alterations. Epigenetics affects genetic regulation, cellular differentiation, embryology, aging, cancer, and other diseases. DNA methylation is perhaps the most extensively studied epigenetic modification, which plays an important role in the regulation of gene expression and chromatin architecture, in association with histone modification and other chromatin-associated proteins. This review will provide a broad overview of the interplay of oxidative stress and DNA methylation, DNA methylation changes in regulation of gene expression, lifestyle changes for prostate cancer prevention, DNA methylation as biomarkers for prostate cancer, methods for detection of methylation, and clinical application of DNA methylation inhibitors for epigenetic therapy.
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15
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Mydlarz WK, Hennessey PT, Califano JA. Advances and Perspectives in the Molecular Diagnosis of Head and Neck Cancer. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2010; 4:53-65. [PMID: 20161611 PMCID: PMC2811380 DOI: 10.1517/17530050903338068] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
BACKGROUND: Head and neck squamous cell carcinoma (HNSCC) is a debilitating and lethal disease. Despite significant advances in radiotherapy and surgical management, the 5-year survival rate for head and neck cancer has remained a dismal 50%. Advances in early detection have been made, but to improve patient outcomes better biomarkers and targeted therapeutic agents are needed. Novel biomarkers can improve early detection and provide data to optimize therapeutic strategy and patient survival, and could lead to potentially effective targeted therapies. OBJECTIVE: Report the advances in the discovery of novel biomarkers for HNSCC, and review the potential utility of biomarkers in the molecular diagnosis of HNSCC. METHODS: A review of the English literature (PubMed) from 1980 to 2009. RESULTS/CONCLUSION: Currently the most widely accepted biomarker for HNSCC is high risk HPV status. EGFR is another promising biomarker, however, further research is necessary to determine its prognostic benefit. A large number of promising biomarker candidates are currently being evaluated including epigenetic, expression, and genomic based markers. Studies to validate the sensitivity and specificity of these biomarkers in clinical samples from adequately powered prospective cohorts are needed for successful translation of these findings into potential molecular diagnostic, prognostic, and therapeutic biomarkers for HNSCC.
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Affiliation(s)
- Wojciech K. Mydlarz
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21231 United States
| | - Patrick T. Hennessey
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21231 United States
| | - Joseph A. Califano
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21231 United States
- Milton J Dance Head and Neck Center, Greater Baltimore Medical Center, Baltimore, MD 21204, United States
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16
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Estécio MR, Issa JPJ. Tackling the methylome: recent methodological advances in genome-wide methylation profiling. Genome Med 2009; 1:106. [PMID: 19930617 PMCID: PMC2808741 DOI: 10.1186/gm106] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
DNA methylation of promoter CpG islands is strongly associated with gene silencing and is known as a frequent cause of loss of expression of tumor suppressor genes, as well as other genes involved in tumor formation. DNA methylation of driver genes is very likely outnumbered by the number of methylated passenger genes, though these can be useful as tumor markers. Much of what is known about the importance of DNA methylation in cancer was gained through small- and moderate-scale analysis of gene promoters and tumor samples. A much better understanding of the role of DNA methylation in cancer, either as a marker of disease or as an active driver of tumorigenesis, will likely be gained from genome-wide studies of this modification in normal and malignant cells. This goal has become more attainable with the recent introduction of large-scale genome analysis methodologies and these have been modified to allow for investigation of DNA methylation. Several research groups have been formed to coordinate efforts and apply these methodologies to decipher the methylome of healthy and diseased tissues. In this article we review technological advances in genome-wide methylation profiling.
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Affiliation(s)
- Marcos Rh Estécio
- Department of Leukemia, UT MD Anderson Cancer Center, Houston, TX 77030, USA
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17
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Abstract
Alteration in epigenetic regulation of gene expression is a frequent event in human cancer. CpG island hypermethylation and downregulation is observed for many genes involved in a diverse range of functions and pathways that become deregulated in cancer. Paradoxically, global hypomethylation is a hallmark of almost all human cancers. Methylation profiles can be used as molecular markers to distinguish subtypes of cancers and potentially as predictors of disease outcome and treatment response. The role of epigenetics in diagnosis and treatment is likely to increase as mechanisms leading to the transcriptional silencing of genes involved in human cancers are revealed. Drugs that inhibit methylation are used both as a research tool to assess reactivation of genes silenced in cancer by hypermethylation and in the treatment of some hematological malignancies. Multidimensional analysis, evaluating genetic and epigenetic alterations on a global and locus-specific scale in human cancer, is imperative to understand mechanisms driving changes in gene dosage, and as a means towards identifying pathways driving cancer initiation and progression.
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Affiliation(s)
- Emily A Vucic
- British Columbia Cancer Research Centre, Department of Cancer Genetics and Developmental Biology, 675 West 10th Avenue, V5Z 1L3, Vancouver, BC, Canada.
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18
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Baek D, Davis C, Ewing B, Gordon D, Green P. Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res 2007; 17:145-55. [PMID: 17210929 PMCID: PMC1781346 DOI: 10.1101/gr.5872707] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Recent studies suggest that surprisingly many mammalian genes have alternative promoters (APs); however, their biological roles, and the characteristics that distinguish them from single promoters (SPs), remain poorly understood. We constructed a large data set of evolutionarily conserved promoters, and used it to identify sequence features, functional associations, and expression patterns that differ by promoter type. The four promoter categories CpG-rich APs, CpG-poor APs, CpG-rich SPs, and CpG-poor SPs each show characteristic strengths and patterns of sequence conservation, frequencies of putative transcription-related motifs, and tissue and developmental stage expression preferences. APs display substantially higher sequence conservation than SPs and CpG-poor promoters than CpG-rich promoters. Among CpG-poor promoters, APs and SPs show sharply contrasting developmental stage preferences and TATA box frequencies. We developed a discriminator to computationally predict promoter type, verified its accuracy through experimental tests that incorporate a novel method for deconvolving mixed sequence traces, and used it to find several new APs. The discriminator predicts that almost half of all mammalian genes have evolutionarily conserved APs. This high frequency of APs, together with the strong purifying selection maintaining them, implies a crucial role in expanding the expression diversity of the mammalian genome.
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Affiliation(s)
- Daehyun Baek
- Department of Bioengineering, University of Washington, Seattle, Washington 98195, USA
- Corresponding authors.E-mail ; fax (206) 685-9720.E-mail ; fax (206) 685-9720
| | - Colleen Davis
- Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Brent Ewing
- Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - David Gordon
- Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Phil Green
- Howard Hughes Medical Institute and Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
- Corresponding authors.E-mail ; fax (206) 685-9720.E-mail ; fax (206) 685-9720
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19
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Ehrlich M. Cancer-linked DNA hypomethylation and its relationship to hypermethylation. Curr Top Microbiol Immunol 2006; 310:251-74. [PMID: 16909914 DOI: 10.1007/3-540-31181-5_12] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
It is not surprising that cancer, a kind of derangement of development, hijacks DNA methylation, which is necessary for normal mammalian embryogenesis. Both decreases and increases in DNA methylation are a frequent characteristic of a wide variety of cancers. There is often more hypomethylation than hypermethylation of DNA during carcinogenesis, leading to a net decrease in the genomic 5-methylcytosine content. Although the exact methylation changes between different cancers of the same type are not the same, there are cancer type-specific differences in the frequency of hypermethylation or hypomethylation of certain genomic sequences. These opposite types of DNA methylation changes appear to be mostly independent of one another, although they may arise because of a similar abnormality leading to long-lasting epigenetic instability in cancers. Both tandem and interspersed DNA repeats often exhibit cancer-associated hypomethylation. However, one of these repeated sequences (NBL2) displayed predominant increases in methylation in some ovarian carcinomas and Wilms tumors and decreases in others. Furthermore, decreases and increases in CpG methylation can be interspersed within a small subregion of the 1.4-kb repeat unit of these tandem arrays. While the transcription-silencing role of DNA hypermethylation at promoters of many tumor-suppressor genes is clear, the biological effects of cancer-linked hypomethylation of genomic DNA are less well understood. Evidence suggests that DNA hypomethylation functions in direct or indirect control of transcription and in destabilizing chromosomal integrity. Recent studies of cancer-linked DNA hypomethylation indicate that changes to DNA methylation during tumorigenesis and tumor progression have a previously underestimated plasticity and dynamic nature.
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Affiliation(s)
- M Ehrlich
- Human Genetics Program, Department of Biochemistry, and Tulane Cancer Center, Tulane Medical School, New Orleans, LA 70112, USA.
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20
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Ehrlich M. The controversial denouement of vertebrate DNA methylation research. BIOCHEMISTRY (MOSCOW) 2005; 70:568-75. [PMID: 15948710 DOI: 10.1007/s10541-005-0150-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The study of the biological role of DNA methylation in vertebrates has involved considerable controversy. Research in this area has proceeded well despite the complexity of the subject and the difficulties in establishing biological roles, some of which are summarized in this review. Now there is justifiably much more interest in DNA methylation than previously, and many more laboratories are engaged in this research. The results of numerous studies indicate that some tissue-specific differences in vertebrate DNA methylation help maintain patterns of gene expression or are involved in fine-tuning or establishing expression patterns. Therefore, vertebrate DNA methylation cannot just be assigned a role in silencing transposable elements and foreign DNA sequences, as has been suggested. DNA methylation is clearly implicated in modulating X chromosome inactivation and in establishing genetic imprinting. Also, hypermethylation of CpG-rich promoters of tumor suppressor genes in cancer has a critical role in downregulating expression of these genes and thus participating in carcinogenesis. The complex nature of DNA methylation patterns extends to carcinogenesis because global DNA hypomethylation is found in the same cancers displaying hypermethylation elsewhere in the genome. A wide variety of cancers display both DNA hypomethylation and hypermethylation, and either of these types of changes can be significantly associated with tumor progression. These findings and the independence of cancer-linked DNA hypomethylation from cancer-linked hypermethylation strongly implicate DNA hypomethylation, as well as hypermethylation, in promoting carcinogenesis. Furthermore, various DNA demethylation methodologies have been shown to increase the formation of certain types of cancers in animals, and paradoxically, DNA hypermethylation can cause carcinogenesis in other model systems. Therefore, there is a need for caution in the current use of demethylating agents as anti-cancer drugs. Nonetheless, DNA demethylation therapy clearly may be very useful in cases where better alternatives do not exist.
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Affiliation(s)
- M Ehrlich
- Human Genetics Program SL31, Tulane Medical School, New Orleans, LA 70112, USA.
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21
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Schug J, Schuller WP, Kappen C, Salbaum JM, Bucan M, Stoeckert CJ. Promoter features related to tissue specificity as measured by Shannon entropy. Genome Biol 2005; 6:R33. [PMID: 15833120 PMCID: PMC1088961 DOI: 10.1186/gb-2005-6-4-r33] [Citation(s) in RCA: 330] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2004] [Revised: 01/27/2005] [Accepted: 02/16/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The regulatory mechanisms underlying tissue specificity are a crucial part of the development and maintenance of multicellular organisms. A genome-wide analysis of promoters in the context of gene-expression patterns in tissue surveys provides a means of identifying the general principles for these mechanisms. RESULTS We introduce a definition of tissue specificity based on Shannon entropy to rank human genes according to their overall tissue specificity and by their specificity to particular tissues. We apply our definition to microarray-based and expressed sequence tag (EST)-based expression data for human genes and use similar data for mouse genes to validate our results. We show that most genes show statistically significant tissue-dependent variations in expression level. We find that the most tissue-specific genes typically have a TATA box, no CpG island, and often code for extracellular proteins. As expected, CpG islands are found in most of the least tissue-specific genes, which often code for proteins located in the nucleus or mitochondrion. The class of genes with no CpG island or TATA box are the most common mid-specificity genes and commonly code for proteins located in a membrane. Sp1 was found to be a weak indicator of less-specific expression. YY1 binding sites, either as initiators or as downstream sites, were strongly associated with the least-specific genes. CONCLUSIONS We have begun to understand the components of promoters that distinguish tissue-specific from ubiquitous genes, to identify associations that can predict the broad class of gene expression from sequence data alone.
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Affiliation(s)
- Jonathan Schug
- Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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22
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Walter RB, Li HY, Intano GW, Kazianis S, Walter CA. Absence of global genomic cytosine methylation pattern erasure during medaka (Oryzias latipes) early embryo development. Comp Biochem Physiol B Biochem Mol Biol 2002; 133:597-607. [PMID: 12470822 DOI: 10.1016/s1096-4959(02)00144-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Two techniques were used to analyze global genomic 5-methyl cytosine methylation at CCGG sites of medaka embryo DNA. DNA was labeled by incorporation of microinjected radiolabeled deoxynucleotide into one-cell embryos. After Hpa II or Msp I digestion the radiolabeled DNA was fractionated in agarose gels and the distribution of label quantified throughout each sample lane to detect differences in fragment distribution. Alternately isolated DNA was digested with Hpa II or Msp I and the resulting generated termini end-labeled. The end-labeled digestion products were then analyzed for fragment distribution after gel fractionation. These techniques proved to be extremely sensitive, allowing comparison of genomic DNA methylation values from as few as 640 fish cells. The data suggest that in medaka embryos the vast majority (>90%) of genomic DNA is methylated at CCGG sites. Furthermore, these data support the conclusion that the extent of methylation at these sites does not change or changes very little during embryogenesis (from 16 cells to the hatchling). These data argue against active demethylation, or loss of methylation patterns by dilution, during the developmental stages between the one cell zygote and gastrulation. From a comparative viewpoint, these data may indicate that mammals and fishes methylate and demethylate their genomes in very different manners during development.
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Affiliation(s)
- Ronald B Walter
- Department of Chemistry and Biochemistry, Southwest Texas State University, 419 Centennial Hall, 601 University Drive, San Marcos, TX 78666-4616, USA.
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23
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Kiyomasu T, Katamura K, Ueno H, Iio J, Ohmura K, Heike T, Furusho K. Hypomethylation of the proximal and intronic regulatory regions of the IFN-gamma gene is not essential for its transcription by naive CD4+ T cells cultured with IL-4. Immunol Lett 1999; 69:239-45. [PMID: 10482358 DOI: 10.1016/s0165-2478(99)00078-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Recently, long-term preculture with IL-4 or IL-7 has been reported to induce IFN-gamma-producing ability in naive CD4+ T cells without stimulation via TCR. The mechanism of IFN-gamma-transcription in naive CD4+ T cells precultured with IL-4 was analyzed and compared with that in typical Th1 cells by focusing on the TATA proximal and first intronic regulatory regions of the IFN-gamma gene. Both regulatory regions in these IL-4-primed naive CD4+ T cells, which produce a large amount of IFN-gamma upon stimulation with PMA and ionomycin, were completely methylated in contrast to the same hypomethylated regions in Th1 cells. DNase I hypersensitive site analysis suggested that both regulatory regions in IL-4-primed naive CD4+ T cells were not active for IFN-gamma-expression. Moreover, we demonstrated that the composition of transcriptional factors that can bind to the proximal regulatory region is different between IL-4-primed naive CD4+ T cells and Th1 cells. These results indicated that the transcriptional machinery involved in the expression of the IFN-gamma gene by CD4+ T cells varied depending on their modes of differentiation in both the responsive regulatory regions and the specific nuclear factors.
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Affiliation(s)
- T Kiyomasu
- Department of Pediatrics, Graduate School of Medicine, Kyoto University, Japan
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24
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Fairbrother KS, Hopwood AJ, Lockley AK, Bardsley RG. Meat speciation by restriction fragment length polymorphism analysis using an α-actin cDNA probe. Meat Sci 1998; 50:105-14. [DOI: 10.1016/s0309-1740(98)00020-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/1997] [Revised: 02/23/1998] [Accepted: 02/27/1998] [Indexed: 11/16/2022]
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25
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Lund A, Duch M, Pedersen F. Transcriptional Silencing of Retroviral Vectors. J Biomed Sci 1996; 3:365-378. [PMID: 11725119 DOI: 10.1007/bf02258042] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Although retroviral vector systems have been found to efficiently transduce a variety of cell types in vitro, the use of vectors based on murine leukemia virus in preclinical models of somatic gene therapy has led to the identification of transcriptional silencing in vivo as an important problem. Extinction of long-term vector expression has been observed after implantation of transduced hematopoietic cells as well as fibroblasts, myoblasts and hepatocytes. Here we review the influence of vector structure, integration site and cell type on transcriptional silencing. While down-regulation of proviral transcription is known from a number of cellular and animal models, major insight has been gained from studies in the germ line and embryonal cells of the mouse. Key elements for the transfer and expression of retroviral vectors, such as the viral transcriptional enhancer and the binding site for the tRNA primer for reverse transcription may have a major influence on transcriptional silencing. Alterations of these elements of the vector backbone as well as the use of internal promoter elements from housekeeping genes may contribute to reduce transcriptional silencing. The use of cell culture and animal models in the testing and improvement of vector design is discussed. Copyright 1996 S. Karger AG, Basel
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Affiliation(s)
- A.H. Lund
- Department of Molecular and Structural Biology, University of Aarhus, Denmark
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26
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Kuwabara N, Kondo N, Fukutomi O, Fujii H, Orii T. Methylation patterns of I epsilon region in B cells stimulated with interleukin 4 and Epstein-Barr virus in patients with a high level of serum IgE. EUROPEAN JOURNAL OF IMMUNOGENETICS : OFFICIAL JOURNAL OF THE BRITISH SOCIETY FOR HISTOCOMPATIBILITY AND IMMUNOGENETICS 1995; 22:265-75. [PMID: 8547233 DOI: 10.1111/j.1744-313x.1995.tb00241.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Human IgE synthesis requires the presence of both interleukin 4 (IL-4) and T-cells. However, it is not clear what role IL-4 and T-cells play in the induction of IgE synthesis at the level of gene regulation. B cells that were obtained from patients with a high level of serum IgE and from healthy donors were immortalized by Epstein-Barr virus. We examined IgE production of these B cells stimulated with IL-4. Supernatant IgE levels of patient's B cells cultured with or without IL-4 were higher than those of healthy donor's B cells. Our results indicated that B cells stimulated with IL-4 from patients produced IgE, germline C epsilon transcript, and S mu S epsilon recombination. The germline C epsilon transcript was dose-dependently induced in the presence of IL-4 and related to the supernatant IgE level. In B cell stimulated with IL-4 that were obtained from patients, (some of the) DNA near or within the I epsilon region was (already partly) unmethylated, unlike those from healthy donors, and there was a loss of methyl groups of the DNA upon the addition of IL-4 in B cells from both patients and normal donors. IgE synthesis of B cells stimulated with IL-4 in patients with a high level of serum IgE is due to an accessibility in the immunoglobulin heavy-chain isotype switch, and this may reflect the accessibility in synthesis of germline C epsilon transcript, which may be caused by the increase of opening chromatin structures because of their unmethylation in the I epsilon region.
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Affiliation(s)
- N Kuwabara
- Department of Pediatrics, Gifu University School of Medicine, Japan
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27
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Kondo N, Inoue R, Kasahara K, Kaneko H, Kameyama T, Orii T. Failure of IgG production due to a defect in the opening of the chromatin structure of I gamma 1 region in a patient with IgG and IgA deficiency. Clin Exp Immunol 1995; 99:21-8. [PMID: 7813107 PMCID: PMC1534132 DOI: 10.1111/j.1365-2249.1995.tb03467.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Patients with common variable immunodeficiency (CVID) display reduced levels of two or all three of the major immunoglobulin isotypes, and the deficiency is characterized by failure of B cells to differentiate into plasma cells in many cases. A patient (14 years old, female) showed normal serum IgM levels and low serum IgG and IgA levels, including low levels of all IgG subclasses. Northern blot analysis suggested that the patient's B cells may be defective at the immunoglobulin heavy chain isotype switch. The germ-line C gamma 1 transcript was amplified from cDNA of healthy controls by the addition of recombinant IL-2 (rIL-2) to pokeweed mitogen-stimulated peripheral mononuclear cells or Staphylococcus aureus Cowan I (SAC)-stimulated IgM-producing lymphoblastoid cell lines (LCL) transformed by Epstein-Barr virus, while it was not amplified from cDNA of the patient. In the I gamma 1 region of LCL cultured with SAC plus rIL-2, the inner cytosine in the 5' C-C-G-G 3' sequence nearest the 3' site of the I gamma 1 region, at least, was not completely unmethylated in the patient. Moreover, the DNase I hypersensitive site was not induced in the patient's LCL by SAC plus rIL-2. These results indicate that the defects of the immunoglobulin heavy chain isotype switch in the patient's B cells are due to failure in the synthesis of germ-line C gamma transcripts, and this may be caused by defects in opening of the chromatin structures of specific switch regions.
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Affiliation(s)
- N Kondo
- Department of Paediatrics, Gifu University School of Medicine, Japan
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28
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Chigira M, Watanabe H. Is 'senescence' of diploid cells an ad hoc mechanism suppressing 'replicon' or not? Med Hypotheses 1993; 41:384-9. [PMID: 8289710 DOI: 10.1016/0306-9877(93)90090-d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
So-called 'limited life span' of diploid cells does not depend on their unresponsiveness to growth factors from the data obtained by complete protein-free culture of tumor cells. Limited proliferation (called limited life span) of diploid cells is one of the 'ad-hoc' negative regulatory mechanisms in animals, and can not be differentiated from other inhibitory mechanisms called 'tumor suppression' and 'terminal differentiation'. Metabolic imbalance induced by proliferation-dependent time-bomb mechanisms including infidelity of DNA repair is suggested to explain limited proliferation of cells. After maturation, autonomic progression of negative regulators in cells is induced by no prohibition of terminal differentiation, since organisms prepare no programs to stop development and differentiation. It is an attractive hypothesis that a proliferation-dependent time-bomb has been developed to control organogenesis for maturation and to determine body size. It is true that limited proliferation of cells can not explain longevity of individuals, although the so-called longevity genes play roles in ageing. Teleologically, longevity of individuals has been developed to produce genetic heterogeneity according to the selfish gene theory. This inter- and intra-species genetic heterogeneity increases the probability of selfish gene replication in germ cell line. After maturation and reproduction of DNA in germ cell line, individuals as vehicles for the DNA can be discarded by the 'selfish' genes.
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Affiliation(s)
- M Chigira
- Department of Orthopedic Surgery, Gunma University School of Medicine, Japan
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29
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Abstract
The development of double-minute chromosomes (DMs) and subsequent gene amplification are important genomic alterations resulting in increased oncogene expression in a variety of tumors. The molecular mechanisms mediating the development of these acentric extrachromosomal elements have not been completely defined. To elucidate the mechanisms involved in DM formation, we have developed strategies to map amplified circular DM DNA. In this study, we present a long-range restriction map of a 980-kb DM. A cell line cloned from mouse EMT-6 cells was developed by stepwise selection for resistance to methotrexate. This cloned cell line contains multiple copies of the 980-kb DM carrying the dihydrofolate reductase (DHFR) gene. A long-range restriction map was developed in which a hypomethylated CpG-rich region near the DHFR gene served as a landmark. This strategy was combined with plasmid-like analysis of ethidium bromide-stained pulsed-field gels and indicated that a single copy of the DHFR gene was located near a hypomethylated region containing SsII and NotI sites. At least 490 kb of this DM appears to be composed of unrearranged chromosomal DNA.
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30
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Abstract
The development of double-minute chromosomes (DMs) and subsequent gene amplification are important genomic alterations resulting in increased oncogene expression in a variety of tumors. The molecular mechanisms mediating the development of these acentric extrachromosomal elements have not been completely defined. To elucidate the mechanisms involved in DM formation, we have developed strategies to map amplified circular DM DNA. In this study, we present a long-range restriction map of a 980-kb DM. A cell line cloned from mouse EMT-6 cells was developed by stepwise selection for resistance to methotrexate. This cloned cell line contains multiple copies of the 980-kb DM carrying the dihydrofolate reductase (DHFR) gene. A long-range restriction map was developed in which a hypomethylated CpG-rich region near the DHFR gene served as a landmark. This strategy was combined with plasmid-like analysis of ethidium bromide-stained pulsed-field gels and indicated that a single copy of the DHFR gene was located near a hypomethylated region containing SsII and NotI sites. At least 490 kb of this DM appears to be composed of unrearranged chromosomal DNA.
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Affiliation(s)
- J L Beland
- Department of Radiology, State University of New York, Syracuse 13210
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31
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Samadder P, Evans JA, Chudley AE. Segregation analysis of rare autosomal folate sensitive fragile sites. AMERICAN JOURNAL OF MEDICAL GENETICS 1993; 46:165-71. [PMID: 8484403 DOI: 10.1002/ajmg.1320460213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have studied 12 families with rare autosomal folate sensitive fragile sites (RAFSFS). Of these, 9 were informative for segregation analysis of fragile sites in order to assess differences in parental transmission. We identified 20 families with RAFSFS from the literature from 1985 to 1989; thirteen of these were informative for segregation analysis. Segregation analysis confirmed that paternal fragile site transmission rates deviated significantly from the expected 50% for a Mendelian co-dominant trait. Sex ratio comparisons showed a significant excess of transmitting females and a significant excess of males among fragile site non-carriers from the literature families. Comparison of the fragile site carriers with non-carriers in the combined data showed a non-significant excess of non-carriers. We confirmed a deficiency of offspring expressing fragile sites when transmission was through fathers, suggesting gametic selection or the phenomenon of parental genomic imprinting.
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Affiliation(s)
- P Samadder
- Department of Human Genetics, University of Manitoba, Winnipeg, Canada
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32
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Espinás ML, Carballo M. Pulsed-field gel electrophoresis analysis of higher-order chromatin structures of Zea mays. Highly methylated DNA in the 50 kb chromatin structure. PLANT MOLECULAR BIOLOGY 1993; 21:847-57. [PMID: 8385508 DOI: 10.1007/bf00027116] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
We have investigated the presence of higher-order chromatin structures in different maize tissues. Taking advantage of the pulsed-field gel electrophoresis technique to analyse large DNA fragments from intact nuclei and cells, we have determined the size distribution of the high-molecular-weight DNA fragments obtained from chromatin degradation by endogenous nucleases in isolated nuclei. Chromatin digestion leads to the appearance of stable DNA fragments of about 50 kb in all the tissues examined, suggesting the folding of DNA in higher-order chromatin domain structures. It has been reported that such chromatin domains are formed by loops of the 30 nm fibers anchored to the nuclear matrix by a complex set of proteins, including DNA topoisomerase II. Treatment of maize protoplasts with the calcium ionophore A23187 and the antitumour drug VM-26, which specifically inhibit the religation of the cleaved DNA in the topoisomerase II reaction, also produces the 50 kb structure. Analysis of the DNA contained in the 50 kb chromatin structure shows a higher degree of methylation than in bulk maize chromosomal DNA. The role of methylated DNA in the chromatin folding is discussed.
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Affiliation(s)
- M L Espinás
- Departamento de Génetica Molecular, Centro de Investigación y Desarrollo (CSIC), Barcelona, Spain
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33
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Chu C, Shen CK. DNA methylation: its possible functional roles in developmental regulation of human globin gene families. EXS 1993; 64:385-403. [PMID: 7678204 DOI: 10.1007/978-3-0348-9118-9_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- C Chu
- Department of Genetics, University of California, Davis 95616
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34
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35
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Affiliation(s)
- C H Spruck
- Urologic Cancer Research Laboratory, Kenneth Norris Jr. Comprehensive Cancer Center, University of Southern California, Los Angeles 90033
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36
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Loennechen T, Nilsen IW, Moens U, Andersen A, Aarbakke J. Is there an association between an increase in c-myc RNA steady state levels and c-myc methylation in HL-60 cells treated with 3-deaza-(+/-)-aristeromycin, an indirect inhibitor of methylation? Biochem Pharmacol 1992; 44:1283-9. [PMID: 1417952 DOI: 10.1016/0006-2952(92)90527-p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Alteration in gene expression of the proto-oncogene c-myc in HL-60 cells is associated with differentiation of these cells. We have studied the steady state levels of c-myc transcripts, the levels of transmethylation metabolites S-adenosylmethionine and S-adenosyl-homocysteine and the methylation pattern of the c-myc gene after treatment of HL-60 cells with the transmethylation inhibitor and granulocytic inducer, 3-deaza-(+/-)-aristeromycin. A transient increase in c-myc RNA levels after 45 min of drug exposure was observed which was accompanied by changes in the ratio of transmethylation metabolites in both whole cells and nuclei. The changes in transmethylation metabolites in whole cells, although compatible with levels frequently associated with hypomethylation of cellular components, caused no changes in methylation of c-myc DNA sequences of the HL-60 cells as detected by HpaII or MspI digestion and Southern blotting.
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Affiliation(s)
- T Loennechen
- Department of Pharmacology, University of Tromsø, Norway
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37
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Günzburg WH, Salmons B. Factors controlling the expression of mouse mammary tumour virus. Biochem J 1992; 283 ( Pt 3):625-32. [PMID: 1317161 PMCID: PMC1130929 DOI: 10.1042/bj2830625] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- W H Günzburg
- GSF-Forschungszentrum für Umwelt und Gesundheit GmbH, Institut für Molekulare Virologie, Neuherberg, Germany
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38
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Mares A, Towbin J, Bies RD, Roberts R. Molecular biology for the cardiologist. Curr Probl Cardiol 1992; 17:1-72. [PMID: 1563272 DOI: 10.1016/0146-2806(92)90010-l] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- A Mares
- Section of Cardiology, Baylor College of Medicine
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39
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Konstantinov Y, Rivkin M, Deineko E. Possible Free-Radical Mechanism of Somaclonal Variations Appearance in Plants. BIOTECHNOL BIOTEC EQ 1992. [DOI: 10.1080/13102818.1992.10818664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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40
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de Capoa A, Aleixandre C, Felli MP, Ravenna L, Costantino MA, Giancotti P, Vicenti O, Poggesi I, Grappelli C, Miller DA. Inheritance of ribosomal gene activity and level of DNA methylation of individual gene clusters in a three generation family. Hum Genet 1991; 88:146-52. [PMID: 1721893 DOI: 10.1007/bf00206062] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Ribosomal gene activity and levels of DNA methylation were investigated by cytochemical and immunological methods in the nucleolar organizer regions (NORs) of individually recognised acrocentric chromosomes. Mendelian inheritance of ribosomal gene activity in a three generation family was demonstrated, together with consistent behaviour of individual gene clusters in different carriers, even when environmental conditions were changed. For most chromosomes, an inverse relationship between gene activity and the level of DNA methylation was observed. Exceptions were the two chromosomes 15 and chromosomes 13cp and 22p, all being strongly chromomycin-A3-positive in their short arms. These chromosomes bound to anti-5-MeC antibodies with differential frequencies in the different carriers. The possibility of involvement of repetitive GC-rich DNA in this behaviour is discussed.
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Affiliation(s)
- A de Capoa
- Department of Genetics and Molecular Biology, University of Rome La Sapienza, Italy
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41
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Gray MD, Jesch SA, Stein GH. 5-Azacytidine-induced demethylation of DNA to senescent level does not block proliferation of human fibroblasts. J Cell Physiol 1991; 149:477-84. [PMID: 1720786 DOI: 10.1002/jcp.1041490317] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
IMR-90 human diploid fibroblasts (HDF) lose from 30-50% of their genomic 5-methyldeoxycytidine (5mdC) during the cellular aging process. In contrast, immortal SV40-transformed IMR-90 maintain a constant level of 5mdC in culture. Precrisis SV40-transformed HDF (AG3204) represent a stage in between normal cell aging and immortalization because these cells still have a finite proliferative lifespan, but it is longer than that of normal HDF and ends in cell death rather than in G1-arrest. We find that AG3204 cells continue to lose from 12-33% of their 5mdC after a population has become 99% positive for SV40 T-antigen. Both IMR-90 cells and AG3204 cells have similar levels of 5mdC (average of 2.25%) at the end of lifespan. We investigated whether this level of 5mdC is an absolute block to further proliferation by treating IMR-90 and AG3204 cells with 5-azacytidine (5azaC) to reduce their 5mdC levels below the terminal level normally achieved at end of lifespan. We find that both IMR-90 and AG3204 cells undergo extensive proliferation with subterminal levels of 5mdC and that the lifespans of both cell types are shortened by 5azaC treatment. These studies indicate that random genomic DNA demethylation to a specific level of 5mdC is not a direct cause of finite proliferative lifespan. However, the correlation between accelerated DNA demethylation and accelerated aging still suggests that these two phenomena are related. Two ways to explain this relationship are: (1) DNA demethylation during aging is not random, and/or (2) both DNA demethylation and other independent aging processes cooperate to produce finite lifespan. In both cases, accelerated random DNA demethylation could accelerate aging, but not necessarily in direct relationship to the final genomic level of 5mdC achieved during the normal aging process.
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Affiliation(s)
- M D Gray
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347
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42
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Abstract
A large body of evidence demonstrates that DNA methylation plays a role in gene regulation in animal cells. Not only is there a correlation between gene transcription and undermethylation, but also transfection experiments clearly show that the presence of methyl moieties inhibits gene expression in vivo. Furthermore, gene activation can be induced by treatment of cells with 5-azacytidine, a potent demethylating agent. Methylation appears to influence gene expression by affecting the interactions with DNA of both chromatin proteins and specific transcription factors. Although methylation patterns are very stable in somatic cells, the early embryo is characterized by large alterations in DNA modification. New methodologies are now becoming available for studying methylation at this stage and in the germ line. During development, tissue-specific genes undergo demethylation in their tissue of expression. In tissue culture cells this process is highly specific and appears to involve an active mechanism which takes place in the absence of DNA replication. The X chromosome undergoes inactivation during development; this is accompanied by de novo methylation, which appears necessary to stably maintain its silent state. As opposed to the programmed changes in DNA methylation which occur in vivo, immortalized tissue culture cells demonstrate alterations in DNA modification which take place over a long time scale and which appear to be the result of selective pressures present during the growth of these cells in culture.
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Affiliation(s)
- A Razin
- Department of Cellular Biochemistry, Hebrew University Medical School, Jerusalem, Israel
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43
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Arnholdt-Schmitt B, Holzapfel B, Schillinger A, Neumann KH. Variable methylation and differential replication of genomic DNA in cultured carrot root expiants during growth induction as influenced by hormonal treatments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 1991; 82:283-288. [PMID: 24213171 DOI: 10.1007/bf02190613] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/1991] [Accepted: 01/23/1991] [Indexed: 06/02/2023]
Abstract
The methylation and amplification pattern of genomic DNA of carrot root expiants (Daucus carota L.) undergoes transitory changes during the cultural cycle. A high degree of variation was observed as early as 36 h after the incubation of fresh expiants in the nutrient medium and, depending on the hormonal treatment significant modifications occurred during 14 days of culture. Proliferative tissue conditioned by kinetin showed an extensive reduction in DNA methylation. Changes in the DNA amplification pattern were not necessarily linked to methylation.
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Affiliation(s)
- B Arnholdt-Schmitt
- Institut für Pflanzenernährung, Abteilung Gewebekultur, Justus-Liebig-Universität Giessen, Südanlage 6, W-6300, Giessen, FRG
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44
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Ichinose M, Miki K, Wong RN, Tatematsu M, Furihata C, Konishi T, Matsushima M, Tanji M, Sano J, Kurokawa K. Methylation and expression of human pepsinogen genes in normal tissues and their alteration in stomach cancer. Jpn J Cancer Res 1991; 82:686-92. [PMID: 1906854 PMCID: PMC5918501 DOI: 10.1111/j.1349-7006.1991.tb01904.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In normal human tissues, pepsinogen A mRNA was expressed only in the fundic mucosa of the stomach, whereas pepsinogen C mRNA was expressed in all regions of the stomach mucosa and also in the proximal duodenal mucosa. The distributions of these mRNAs were consistent with those of pepsinogens A and C in the gastroduodenal mucosa. Methylation analysis of DNAs from normal tissues with methylation-sensitive restriction enzymes, HpaII and HhaI, revealed that pepsinogen A and C genes are hypomethylated in tissues producing pepsinogens A and C, suggesting a role of DNA methylation in the regulation of the differential expression of the genes for the two human pepsinogens during normal differentiation. In stomach cancer tissues and cancer cell lines, the expressions of the pepsinogen genes were decreased or lost, in good accordance with their pepsinogen productions. No gross structural changes of the pepsinogen genes were observed in these cancers, but the methylation patterns of the pepsinogen genes were found to be altered in different ways in different cancers. The functional significance of the altered methylation is unknown; however, these results suggest that considerable heterogeneity of the methylation patterns occurs in human stomach cancers.
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Affiliation(s)
- M Ichinose
- First Department of Internal Medicine, Faculty of Medicine, University of Tokyo
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45
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Hepburn P, Margison G, Tisdale M. Enzymatic methylation of cytosine in DNA is prevented by adjacent O6-methylguanine residues. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)92928-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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46
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Hepburn PA, Tisdale MJ. Importance of the O6 position of guanine residues in the binding of DNA methylase to DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1088:341-4. [PMID: 2015298 DOI: 10.1016/0167-4781(91)90123-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Methylation of Micrococcus lysodeikticus DNA by purified DNA methylase isolated from L1210 leukaemia cells is potently and specifically inhibited by both hetero and homoribo and deoxyribopolynucleotides containing guanine residues. The inhibitory effect is unaffected by chain length, but is abolished when the O6 residue of guanine is substituted as in poly[d(O6MeG)]20. Potent inhibition is also shown by polyinosinic and polyxanthylic acids, but not by polyadenylic acid or by heteropolymers containing adenine and thymine. These results suggest that the 6-position of the purine nucleus is important in binding of the DNA methylase to a particular region of the DNA duplex and that the hydrogen bonding properties of this group are important in enzyme recognition.
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Affiliation(s)
- P A Hepburn
- CRC Experimental Chemotherapy Group, Aston University, Birmingham, U.K
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47
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Götz F, Schulze-Forster K, Wagner H, Kröger H, Simon D. Transcription inhibition of SV40 by in vitro DNA methylation. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1087:323-9. [PMID: 2174269 DOI: 10.1016/0167-4781(90)90006-n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
SV40 DNA was methylated in vitro with prokaryotic or eukaryotic DNA cytosine-5-methyltransferases and the inhibition of transcription by methylation was studied in Xenopus oocytes. Methylation with the prokaryotic HhaI or HpaII methyltransferases did essentially not inhibit transcription of SV40. Methylation with a rat liver methyltransferase led only to minor inhibition of the SV40 early genes, but to a complete shut shut off of the SV40 late genes. Partial methylation showed that methylation of both, the regulatory region and the 5' end of the SV40 late genes, was necessary for the effect on transcription. The TK gene could be inactivated by eukaryotic methylation of either the promoter and the first 50 nucleotides of the gene or the 3' rest of the gene. Insertion of the SV40 enhancer, not containing methylatable CpGs, into the TK upstream region, had no influence on the inhibition of TK gene transcription by methylation.
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Affiliation(s)
- F Götz
- Robert Koch-Institut, Berlin, F.R.G
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48
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Antequera F, Boyes J, Bird A. High levels of de novo methylation and altered chromatin structure at CpG islands in cell lines. Cell 1990; 62:503-14. [PMID: 1974172 DOI: 10.1016/0092-8674(90)90015-7] [Citation(s) in RCA: 531] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
CpG islands are normally methylation free in cells of the animal, even when the associated gene is transcriptionally silent. In mouse NIH 3T3 and L cells, however, over half of the islands are heavily methylated. Near identity of the methylated subset in the two cell lines suggested that methylation is confined to genes that are nonessential in culture. In agreement with this, islands at several tissue-specific genes, but not at housekeeping genes, have become methylated in many human and mouse cell lines. At the chromatin level, methylated islands are Mspl resistant compared with their nonmethylated counterparts. We suggest that mutation-like gene inactivation due to CpG island methylation is widespread in many cell lines and could explain the loss of cell type-specific functions in culture.
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Affiliation(s)
- F Antequera
- Research Institute of Molecular Pathology, Vienna, Austria
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49
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Slagboom PE, de Leeuw WJ, Vijg J. Messenger RNA levels and methylation patterns of GAPDH and beta-actin genes in rat liver, spleen and brain in relation to aging. Mech Ageing Dev 1990; 53:243-57. [PMID: 2376984 DOI: 10.1016/0047-6374(90)90042-e] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Messenger RNA levels and methylation patterns of the glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and beta-actin genes were studied in spleen, liver and brain of 6-, 24- and 36-month old female inbred rats. In the spleen, the mRNA levels of both housekeeping genes significantly increased between 24 and 36 months. No age-related alterations in the expression of GAPDH or beta-actin mRNA were observed in brain or liver. A considerable intertissue and interindividual variation was observed in the mRNA levels of these genes in all age-groups as compared to the level of 28 S rRNA, which was used as an internal control. In this respect the interindividual variation in the level of GAPDH mRNA paralleled the variation observed in the beta-actin mRNA level in the three tissues studied. The methylation pattern of beta-actin was found to be tissue-specific in contrast to that of GAPDH, which was identical in all three tissues. No significant age-related alterations were observed in the GAPDH methylation pattern, whereas beta-actin appeared to become slightly demethylated with age in the spleen at the CpG site for which tissue-specificity was observed.
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Affiliation(s)
- P E Slagboom
- Department of Molecular Biology, TNO Institute for Experimental Gerontology, Rijswijk, The Netherlands
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50
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Schulze-Forster K, Götz F, Wagner H, Kröger H, Simon D. Transcription of HIV1 is inhibited by DNA methylation. Biochem Biophys Res Commun 1990; 168:141-7. [PMID: 2327994 DOI: 10.1016/0006-291x(90)91685-l] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A possible role of DNA methylation as a factor in HIV latency was studied by methylating a HIV1-LTR-CAT plasmid in vitro and measuring its expression after transfection on Vero cells. Methylation with a eukaryotic DNA methylase resulted in a 70% inhibition of chloramphenicol acetyltransferase expression, in the absence as well as in the presence of the HIV1 trans-activator protein TAT in the cell. A similar degree of transcription inhibition was obtained by methylation of the only Hpa II site at position-143 in the HIV1-LTR with the bacterial Hpa II methylase. In contrast to the effect by eukaryotic methylation, the inhibition by Hpa II methylation could be partially reversed by cotransfection of the TAT gene. The reason may lie in an about 40% demethylation at the Hpa II site which was concomitantly observed.
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