1 Epigenetic Modulation of Nrf2 and Ogg1 Gene Expression in Testicular
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DNA Methylation Analysis: Choosing the Right Method
biology Review DNA Methylation Analysis: Choosing the Right Method Sergey Kurdyukov 1,* and Martyn Bullock 2 Received: 8 July 2015; Accepted: 22 December 2015; Published: 6 January 2016 Academic Editor: Melanie Ehrlich 1 Genomics Core facility, Kolling Institute of Medical Research, University of Sydney, Sydney 2065, Australia 2 Cancer Genetics Laboratory, Kolling Institute of Medical Research, University of Sydney, Sydney 2065, Australia; [email protected] * Correspondence: [email protected]; Tel.: +61-299-264-756 Abstract: In the burgeoning field of epigenetics, there are several methods available to determine the methylation status of DNA samples. However, choosing the method that is best suited to answering a particular biological question still proves to be a difficult task. This review aims to provide biologists, particularly those new to the field of epigenetics, with a simple algorithm to help guide them in the selection of the most appropriate assay to meet their research needs. First of all, we have separated all methods into two categories: those that are used for: (1) the discovery of unknown epigenetic changes; and (2) the assessment of DNA methylation within particular regulatory regions/genes of interest. The techniques are then scrutinized and ranked according to their robustness, high throughput capabilities and cost. This review includes the majority of methods available to date, but with a particular focus on commercially available kits or other simple and straightforward solutions that have proven to be useful. Keywords: DNA methylation; 5-methylcytosine; CpG islands; epigenetics; next generation sequencing 1. Introduction DNA methylation in vertebrates is characterized by the addition of a methyl or hydroxymethyl group to the C5 position of cytosine, which occurs mainly in the context of CG dinucleotides. -
Epigenetic Regulation of DNA Repair Genes and Implications for Tumor Therapy ⁎ ⁎ Markus Christmann , Bernd Kaina
Mutation Research-Reviews in Mutation Research xxx (xxxx) xxx–xxx Contents lists available at ScienceDirect Mutation Research-Reviews in Mutation Research journal homepage: www.elsevier.com/locate/mutrev Review Epigenetic regulation of DNA repair genes and implications for tumor therapy ⁎ ⁎ Markus Christmann , Bernd Kaina Department of Toxicology, University of Mainz, Obere Zahlbacher Str. 67, D-55131 Mainz, Germany ARTICLE INFO ABSTRACT Keywords: DNA repair represents the first barrier against genotoxic stress causing metabolic changes, inflammation and DNA repair cancer. Besides its role in preventing cancer, DNA repair needs also to be considered during cancer treatment Genotoxic stress with radiation and DNA damaging drugs as it impacts therapy outcome. The DNA repair capacity is mainly Epigenetic silencing governed by the expression level of repair genes. Alterations in the expression of repair genes can occur due to tumor formation mutations in their coding or promoter region, changes in the expression of transcription factors activating or Cancer therapy repressing these genes, and/or epigenetic factors changing histone modifications and CpG promoter methylation MGMT Promoter methylation or demethylation levels. In this review we provide an overview on the epigenetic regulation of DNA repair genes. GADD45 We summarize the mechanisms underlying CpG methylation and demethylation, with de novo methyl- TET transferases and DNA repair involved in gain and loss of CpG methylation, respectively. We discuss the role of p53 components of the DNA damage response, p53, PARP-1 and GADD45a on the regulation of the DNA (cytosine-5)- methyltransferase DNMT1, the key enzyme responsible for gene silencing. We stress the relevance of epigenetic silencing of DNA repair genes for tumor formation and tumor therapy. -
Environmental Epigenetics
Powerful ideas for a healthier world Andrea Baccarelli, MD, PhD, MPH Laboratory of Environmental Epigenetics Environmental Epigenetics Methods and Tools for Human Environmental Health Studies Objective of my presentation • To review (all) the steps for designing and carrying out an epigenetic study – Focus on environmental exposure – Applications to human studies Step by step Step 1 Step 4 Step 7 Intro to epigenetics Starting a Study Wrap up Step 2 Step 5 Epigenetics & Environment Lab Analysis Step 3 Step 6 Study Design Data Analysis Step by step Step 1 Intro to epigenetics A Symphonic Example DNA Phenotype Epigenetics Epigenetics & Music Use the Same Markings pencil markings (can be erased) markings in ink (permanent) Epigenetics & Music Use the & Music Epigenetics Same Markings Epigenetic markings DNA methylation Methyl marks added to certain DNA bases repress gene transcription Histone modifications A combination of different molecules can attach to the ‘tails’ of proteins called histones. These alter the activity of the DNA wrapped around them Within- vs. between-individual variability (Day 1 and 4) 12.00 IFNγ RASSF1A 10.00 8.00 ET-1 6.00 individual individual variability - 4.00 within IL6 p53 CDH13 iNOS 2.00 APC TNFα hTERT eNOS LINE-1 p16 0.00 Alu 0 5 10 15 20 25 between-individual variability (σID) Byun HM et al, Plos One 2012 Predicting variability Byun et al, PLoS ONE Step by step Step 1 Intro to epigenetics Step 2 Epigenetics & Environment Why Epigenetics in Environmental Health? • The epigenome is environmentally sensitive – -
Methylation in the P53 Promoter Is a Supplementary Route To
0023-6837/01/8104-573$03.00/0 LABORATORY INVESTIGATION Vol. 81, No. 4, p. 573, 2001 Copyright © 2001 by The United States and Canadian Academy of Pathology, Inc. Printed in U.S.A. Methylation in the p53 Promoter Is a Supplementary Route to Breast Carcinogenesis: Correlation between CpG Methylation in the p53 Promoter and the Mutation of the p53 Gene in the Progression from Ductal Carcinoma In Situ to Invasive Ductal Carcinoma Joo Hyun Kang, Sun Jung Kim, Dong-Young Noh, In Ae Park, Kuk Jin Choe, Ook Joon Yoo, and Han-Sung Kang Department of Biological Science (JHK, OJY), Biomedical Research Center, Korean Advanced Institute of Science and Technology, Taejon; Department of Biology (SJK), Dongguk University, and Departments of Surgery (D-YN, KJC) and Pathology (IAP), College of Medicine, Seoul National University, Seoul; and Department of Surgery (H-SK), National Cancer Center, Kyungki do, Korea SUMMARY: Aberrant methylation in the CpG sites located in the promoter region of several tumor suppressor genes has been reported in various types of cancers. However, the methylation status of the p53 promoter has not been clearly determined and no information is available on its role in breast cancer. The aim of the study was to determine the presence and timing of the methylation of CpG sites in the p53 promoter, in the progression from ductal carcinoma in situ to invasive cancer. We also explored the correlation between the CpG methylation of the p53 promoter and p53 mutation during the progression of breast cancer. The corresponding lesions of both the invasive and noninvasive types were microdissected in paraffin-embedded tissue of 26 breast carcinomas. -
The Two Faces of the Guanyl Radical: Molecular Context and Behavior
molecules Review The Two Faces of the Guanyl Radical: Molecular Context and Behavior Chryssostomos Chatgilialoglu 1,2 1 ISOF, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy; [email protected]; Tel.: +39-051-6398309 2 Center of Advanced Technologies, Adam Mickiewicz University, 61-712 Pozna´n,Poland Abstract: The guanyl radical or neutral guanine radical G(-H)• results from the loss of a hydrogen atom (H•) or an electron/proton (e–/H+) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC•+ pair. The role of the two G(-H)• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed. Keywords: guanine; guanyl radical; tautomerism; guanine radical cation; oligonucleotides; DNA; G-quadruplex; time-resolved spectroscopies; reactive oxygen species (ROS); oxidation 1. The Guanine Sink Citation: Chatgilialoglu, C. The Two The free radical chemistry associated with guanine (Gua) and its derivatives, guano- Faces of the Guanyl Radical: sine (Guo), 2’-deoxyguanosine (dGuo), guanosine-50-monophosphate (GMP), and 20- Molecular Context and Behavior. deoxyguanosine-50-monophosphate (dGMP), is of particular interest due to its biological Molecules 2021, 26, 3511. -
DNA Excision Repair Proteins and Gadd45 As Molecular Players for Active DNA Demethylation
Cell Cycle ISSN: 1538-4101 (Print) 1551-4005 (Online) Journal homepage: http://www.tandfonline.com/loi/kccy20 DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation Dengke K. Ma, Junjie U. Guo, Guo-li Ming & Hongjun Song To cite this article: Dengke K. Ma, Junjie U. Guo, Guo-li Ming & Hongjun Song (2009) DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation, Cell Cycle, 8:10, 1526-1531, DOI: 10.4161/cc.8.10.8500 To link to this article: http://dx.doi.org/10.4161/cc.8.10.8500 Published online: 15 May 2009. Submit your article to this journal Article views: 135 View related articles Citing articles: 92 View citing articles Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=kccy20 Download by: [University of Pennsylvania] Date: 27 April 2017, At: 12:48 [Cell Cycle 8:10, 1526-1531; 15 May 2009]; ©2009 Landes Bioscience Perspective DNA excision repair proteins and Gadd45 as molecular players for active DNA demethylation Dengke K. Ma,1,2,* Junjie U. Guo,1,3 Guo-li Ming1-3 and Hongjun Song1-3 1Institute for Cell Engineering; 2Department of Neurology; and 3The Solomon Snyder Department of Neuroscience; Johns Hopkins University School of Medicine; Baltimore, MD USA Abbreviations: DNMT, DNA methyltransferases; PGCs, primordial germ cells; MBD, methyl-CpG binding protein; NER, nucleotide excision repair; BER, base excision repair; AP, apurinic/apyrimidinic; SAM, S-adenosyl methionine Key words: DNA demethylation, Gadd45, Gadd45a, Gadd45b, Gadd45g, 5-methylcytosine, deaminase, glycosylase, base excision repair, nucleotide excision repair DNA cytosine methylation represents an intrinsic modifica- silencing of gene activity or parasitic genetic elements (Fig. -
Tautomerization-Dependent Recognition and Excision of Oxidation Damage in Base-Excision DNA Repair
Tautomerization-dependent recognition and excision of oxidation damage in base-excision DNA repair Chenxu Zhua,1, Lining Lua,1, Jun Zhangb,c,1, Zongwei Yuea, Jinghui Songa, Shuai Zonga, Menghao Liua,d, Olivia Stoviceke, Yi Qin Gaob,c,2, and Chengqi Yia,d,f,2 aState Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; bInstitute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; cBiodynamic Optical Imaging Center, Peking University, Beijing 100871, China; dPeking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; eUniversity of Chicago, Chicago, IL 60637; and fSynthetic and Functional Biomolecules Center, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China Edited by Suse Broyde, New York University, New York, NY, and accepted by Editorial Board Member Dinshaw J. Patel June 1, 2016 (received for review March 29, 2016) NEIL1 (Nei-like 1) is a DNA repair glycosylase guarding the mamma- (FapyA and FapyG), spiroiminodihydantoin (Sp), and guanidino- lian genome against oxidized DNA bases. As the first enzymes in hydantoin (Gh) (23–27). Among these lesions, Tg is the most the base-excision repair pathway, glycosylases must recognize common pyrimidine base modification produced under oxidative the cognate substrates and catalyze their excision. Here we stress and ionizing radiation (28)—arising from oxidation of thy- present crystal structures of human NEIL1 bound to a range of mine and 5-methylcytosine—and is also a preferred substrate of duplex DNA. Together with computational and biochemical NEIL1 (3). -
Cpg Island Clusters and Pro-Epigenetic Selection for Cpgs in Protein-Coding Exons of HOX and Other Transcription Factors
CpG island clusters and pro-epigenetic selection for CpGs in protein-coding exons of HOX and other transcription factors Sergio Branciamorea, Zhao-Xia Chenb, Arthur D. Riggsb,1, and Sergei N. Rodina,1 aDepartment of Molecular and Cellular Biology and bDivision of Biology, Beckman Research Institute, City of Hope, Duarte, CA 91010 Contributed by Arthur D. Riggs, July 27, 2010 (sent for review May 26, 2010) CpG dinucleotides contribute to epigenetic mechanisms by being system seems to be at work. Although on average 5-fold depleted in the only site for DNA methylation in mammalian somatic cells. frequency, those CpGs within genes tend to be highly methylated They are also mutation hotspots and ∼5-fold depleted genome- (15), and it is now clear that such methylation not only is compatible wide. We report here a study focused on CpG sites in the coding with transcription but also may be positively correlated with tran- regions of Hox and other transcription factor genes, comparing scription level (10, 14, 15). The biological significance of intragenic methylated genomes of Homo sapiens, Mus musculus, and Danio CpG methylation is only beginning to be appreciated and its impact rerio with nonmethylated genomes of Drosophila melanogaster on gene expression and development is still poorly understood. and Caenorhabditis elegans. We analyzed 4-fold degenerate, syn- Furthermore, it remains unclear in general whether there is (and, if onymous codons with the potential for CpG. That is, we studied so, how strong) a link between epigenetic marking via methylation “ ” silent changes that do not affect protein products but could of CpGs in genes coding regions and major factors of evolution, fi damage epigenetic marking. -
Cpg-Creating Mutations Are Costly in Many Human Viruses
Evolutionary Ecology (2020) 34:339–359 https://doi.org/10.1007/s10682-020-10039-z ORIGINAL PAPER CpG‑creating mutations are costly in many human viruses Victoria R. Caudill1,2 · Sarina Qin1,3 · Ryan Winstead1 · Jasmeen Kaur1 · Kaho Tisthammer1 · E. Geo Pineda1 · Caroline Solis1 · Sarah Cobey16 · Trevor Bedford4 · Oana Carja5 · Rosalind M. Eggo6 · Katia Koelle7 · Katrina Lythgoe8 · Roland Regoes17 · Scott Roy1 · Nicole Allen1 · Milo Aviles1 · Brittany A. Baker1 · William Bauer1 · Shannel Bermudez1 · Corey Carlson1 · Edgar Castellanos1 · Francisca L. Catalan1,9 · Angeline Katia Chemel1 · Jacob Elliot1 · Dwayne Evans1,10 · Natalie Fiutek1 · Emily Fryer1,11 · Samuel Melvin Goodfellow1,12 · Mordecai Hecht1 · Kellen Hopp1 · E. Deshawn Hopson Jr.1 · Amirhossein Jaberi1 · Christen Kinney1 · Derek Lao1 · Adrienne Le1 · Jacky Lo1 · Alejandro G. Lopez1 · Andrea López1 · Fernando G. Lorenzo1 · Gordon T. Luu1 · Andrew R. Mahoney1 · Rebecca L. Melton1,13 · Gabriela Do Nascimento1 · Anjani Pradhananga1 · Nicole S. Rodrigues1,14 · Annie Shieh1 · Jasmine Sims1,15 · Rima Singh1 · Hasan Sulaeman1 · Ricky Thu1 · Krystal Tran1 · Livia Tran1 · Elizabeth J. Winters1 · Albert Wong1 · Pleuni S. Pennings1 Received: 5 July 2019 / Accepted: 11 March 2020 / Published online: 24 April 2020 © The Author(s) 2020 Abstract Mutations can occur throughout the virus genome and may be benefcial, neutral or delete- rious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transi- tion mutations are more costly than similar non-CpG-creating mutations. -
PREDICTING DNA METHYLATION SUSCEPTIBILITY USING Cpg FLANKING SEQUENCES
Pacific Symposium on Biocomputing 13:315-326(2008) September 25, 2007 10:50 Proceedings Trim Size: 9in x 6in dna-methylation-kim-final PREDICTING DNA METHYLATION SUSCEPTIBILITY USING CpG FLANKING SEQUENCES S. KIM1,2, M. LI3, H. PAIK3, AND K. NEPHEW3 1School of Informatics, 2Center for Genomics and Bioinformatics, 3Medical Sciences, Indiana University, Bloomington, IN 47408, USA E-mail: {sunkim2,menli,hyupaikknephew}@indiana.edu H. SHI4, R. KRAMER5 AND D. XU5,6 4Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, 5Department of Computer Sciences and 6Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65212, USA E-mail: {ShiHu@health.,kramer@,xudong@}missouri.edu T-H. HUANG7 7Human Cancer Genetics, The Ohio State University, Columbus, OH 43210, USA; E-mail: [email protected] DNA methylation is a type of chemical modification of DNA that adds a methyl group to DNA at the fifth carbon of the cytosine pyrimidine ring. In normal cells, methylation of CpG dinucleotides is extensively found across the genome. How- ever, specific DNA regions known as the CpG islands, short CpG dinucleotide-rich stretches (500bp - 2000bp), are commonly unmethylated. During tumorigenesis, on the other hand, global de-methylation and CpG island hypermethylation are widely observed. De novo hypermethylation at CpG dinucleotides is typically associated with loss of expression of flanking genes, thus it is believed to be an alternative to mutation and deletion in the inactivation of tumor suppressor genes. In this paper, we report that sequences flanking CpG sites can be used for predict- ing DNA methylation levels. DNA methylation levels were measured by utilizing a new high throughput sequencing technology (454) to sequence bisulfite treated DNA from four types of primary leukemia and lymphoma cells and normal periph- eral blood lymphocytes. -
The Role of Oxidative Stress in Alzheimer's Disease Robin Petroze University of Kentucky
Kaleidoscope Volume 2 Article 15 2003 The Role of Oxidative Stress in Alzheimer's Disease Robin Petroze University of Kentucky Follow this and additional works at: https://uknowledge.uky.edu/kaleidoscope Part of the Medical Biochemistry Commons Right click to open a feedback form in a new tab to let us know how this document benefits you. Recommended Citation Petroze, Robin (2003) "The Role of Oxidative Stress in Alzheimer's Disease," Kaleidoscope: Vol. 2, Article 15. Available at: https://uknowledge.uky.edu/kaleidoscope/vol2/iss1/15 This Beckman Scholars Program is brought to you for free and open access by the The Office of Undergraduate Research at UKnowledge. It has been accepted for inclusion in Kaleidoscope by an authorized editor of UKnowledge. For more information, please contact [email protected]. BECKMAN ScHOLARS PROGRAM Abstract Over four million individuals in the United States currently suffer from Alzheimer's disease (AD), a devastating disorder of progressive dementia. Within the next several decades, AD is expected to affect over 22 million people globally. AD can only be definitively diagnosed by postmortem exami nation. Thus, investigation into the specific patho genesis of neuronal degeneration and death in AD on a biochemical level is essential for both earlier diagnosis and potential treatment and prevention options. Overproduction of amyloid [3-peptide (A[3) in the brain leads to both free radical oxidative stress and toxicity to neurons in AD. My under graduate biochemical studies with regard to AD explore the various ways in which free radical oxi dative stress might contribute to the pathology of AD. -
Infinium Humanmethylation450 Beadchip
Data Sheet: Epigenetics Infinium® HumanMethylation450 BeadChip The ideal solution for affordable, large sample–size genome-wide DNA methylation studies. HumanMethylation450 BeadChip Highlights Figure 1: Infinium HumanMethylation450 BeadChip • Unique Combination of Genome-Wide Coverage, High-Throughput, and Low Cost Over 450,000 methylation sites per sample at single- nucleotide resolution • Unrivaled Assay Reproducibility > 98% reproducibility for technical replicates • Simple Workflow PCR-free protocol with the powerful Infinium HD Assay • Compatibile with FFPE Samples Protocol available for methylation studies on FFPE samples Introduction ® DNA methylation plays an important and dynamic role in regulating 4305493023 gene expression. It allows cells to become specialized and stably maintain those unique characteristics throughout the life of the The Infinium HumanMethylation450 BeadChip features more than 450,000 organism, suppresses the deleterious expression of viral genes methylation sites, within and outside of CpG islands. and other non-host DNA elements, and provides a mechanism for response to environmental stimuli. Aberrant DNA methylation (hyper- or hypomethylation) and its impact on gene expression have been Importantly, coverage was targeted across gene regions with sites in implicated in many disease processes, including cancer1. the promoter region, 5'UTR, first exon, gene body, and 3'UTR in order to provide the broadest, most comprehensive view of methylation To enable cost-effective DNA methylation analysis for a variety of applica- state possible (Figure 2). This multiple-site approach was extended tions, Illumina offers a robust methylation profiling platform consisting of to CpG islands/CpG island regions for which 96% of islands were ® proven chemistries and the iScan and HiScan SQ systems. The Human- covered overall, with multiple sites within islands and island shores, as Methylation450 BeadChip (Figure 1) offers a unique combination of well as those regions flanking island shores (island shelves).