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Viswanathan R, Cheruba E, Wong PM, Yi Y, Ngang S, Chong DQ, Loh YH, Tan IB, Cheow LF. DARESOME enables concurrent profiling of multiple DNA modifications with restriction enzymes in single cells and cell-free DNA. SCIENCE ADVANCES 2023; 9:eadi0197. [PMID: 37713482 PMCID: PMC10881072 DOI: 10.1126/sciadv.adi0197] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/15/2023] [Indexed: 09/17/2023]
Abstract
5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are the most abundant DNA modifications that have important roles in gene regulation. Detailed studies of these different epigenetic marks aimed at understanding their combined effects and dynamic interconversion are, however, hampered by the inability of current methods to simultaneously measure both modifications, particularly in samples with limited quantities. We present DNA analysis by restriction enzyme for simultaneous detection of multiple epigenomic states (DARESOME), an assay based on modification-sensitive restriction digest and sequential tag ligation that can concurrently perform quantitative profiling of unmodified cytosine, 5mC, and 5hmC in CCGG sites genome-wide. DARESOME reveals the opposing roles of 5mC and 5hmC in gene expression regulation as well as their interconversion during aging in mouse brain. Implementation of DARESOME in single cells demonstrates pronounced 5hmC strand bias that reflects the semiconservative replication of DNA. Last, we showed that DARESOME enables integrative genomic, 5mC, and 5hmC profiling of cell-free DNA that uncovered multiomics cancer signatures in liquid biopsy.
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Affiliation(s)
- Ramya Viswanathan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Pui-Mun Wong
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
| | - Yao Yi
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
| | - Shaun Ngang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Dawn Qingqing Chong
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Yuin-Han Loh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Iain Beehuat Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672, Singapore
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
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2
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Sui Z, Zhang Z, Zhang Y, Zhang J, Li Q, Xing F. Analysis of Methylation and mRNA Expression of Lin28B Gene Promoter Region in the Hypothalamus of Dolang Sheep During Pubertal Initiation. DNA Cell Biol 2023; 42:130-139. [PMID: 36809059 DOI: 10.1089/dna.2022.0281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Lin28B plays an important role in puberty initiation in sheep. This study aimed to discuss the correlation between different growth periods and the methylation status of cytosine-guanine dinucleotide (CpG) islands in the promoter region of the Lin28B gene in the Dolang sheep's hypothalamus. In this study, the sequence of the Lin28B gene promoter region in Dolang sheep was obtained by cloning and sequencing, and methyl groups of the CpG island of the Lin28B gene promoter in the hypothalamus were detected by bisulfite sequencing PCR during the three periods of prepuberty, adolescence, and postpuberty in Dolang sheep. Lin28B expression in the Dolang sheep's hypothalamus was detected by fluorescence quantitative PCR at three stages: prepuberty, puberty, and postpuberty. In this experiment, the 2993-bp Lin28B promoter region was obtained, and it was predicted that there was a CpG island containing 15 transcription factor binding sites and 12 CpG sites, which may play a role in gene expression regulation. Overall, methylation levels increased from prepuberty to postpuberty, while Lin28B expression levels decreased, indicating that Lin28B expression was negatively correlated with promoter methylation levels. Variance analysis showed significant differences in the methylation status of CpG5, CpG7, and CpG9 between pre- and postpuberty (p < 0.05). Our data show that Lin28B expression is increased by demethylation of promoter CpG islands, with CpG5, CpG7, and CpG9 implicated as critical regulatory sites.
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Affiliation(s)
- Zhiyuan Sui
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Zhishuai Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Yongjie Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Jihu Zhang
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Qingjin Li
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
| | - Feng Xing
- Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production and Construction Group, College of Animal Science, Tarim University, Alaer, China
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Ahmar S, Gruszka D. In-Silico Study of Brassinosteroid Signaling Genes in Rice Provides Insight Into Mechanisms Which Regulate Their Expression. Front Genet 2022; 13:953458. [PMID: 35873468 PMCID: PMC9299959 DOI: 10.3389/fgene.2022.953458] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 06/14/2022] [Indexed: 12/14/2022] Open
Abstract
Brassinosteroids (BRs) regulate a diverse spectrum of processes during plant growth and development and modulate plant physiology in response to environmental fluctuations and stress factors. Thus, the BR signaling regulators have the potential to be targeted for gene editing to optimize the architecture of plants and make them more resilient to environmental stress. Our understanding of the BR signaling mechanism in monocot crop species is limited compared to our knowledge of this process accumulated in the model dicot species - Arabidopsis thaliana. A deeper understanding of the BR signaling and response during plant growth and adaptation to continually changing environmental conditions will provide insight into mechanisms that govern the coordinated expression of the BR signaling genes in rice (Oryza sativa) which is a model for cereal crops. Therefore, in this study a comprehensive and detailed in silico analysis of promoter sequences of rice BR signaling genes was performed. Moreover, expression profiles of these genes during various developmental stages and reactions to several stress conditions were analyzed. Additionally, a model of interactions between the encoded proteins was also established. The obtained results revealed that promoters of the 39 BR signaling genes are involved in various regulatory mechanisms and interdependent processes that influence growth, development, and stress response in rice. Different transcription factor-binding sites and cis-regulatory elements in the gene promoters were identified which are involved in regulation of the genes’ expression during plant development and reactions to stress conditions. The in-silico analysis of BR signaling genes in O. sativa provides information about mechanisms which regulate the coordinated expression of these genes during rice development and in response to other phytohormones and environmental factors. Since rice is both an important crop and the model species for other cereals, this information may be important for understanding the regulatory mechanisms that modulate the BR signaling in monocot species. It can also provide new ways for the plant genetic engineering technology by providing novel potential targets, either cis-elements or transcriptional factors, to create elite genotypes with desirable traits.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
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Vaillancourt K, Chen GG, Fiori L, Maussion G, Yerko V, Théroux JF, Ernst C, Labonté B, Calipari E, Nestler EJ, Nagy C, Mechawar N, Mash DC, Turecki G. Methylation of the tyrosine hydroxylase gene is dysregulated by cocaine dependence in the human striatum. iScience 2021; 24:103169. [PMID: 34693223 PMCID: PMC8517202 DOI: 10.1016/j.isci.2021.103169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/15/2021] [Accepted: 09/21/2021] [Indexed: 02/01/2023] Open
Abstract
Cocaine dependence is a chronic, relapsing disorder caused by lasting changes in the brain. Animal studies have identified cocaine-related alterations in striatal DNA methylation; however, it is unclear how methylation is related to cocaine dependence in humans. We generated methylomic profiles of the nucleus accumbens using human postmortem brains from a cohort of individuals with cocaine dependence and healthy controls (n = 25 per group). We found hypermethylation in a cluster of CpGs within the gene body of tyrosine hydroxylase (TH), containing a putative binding site for the early growth response 1 (EGR1) transcription factor, which is hypermethylated in the caudate nucleus of cocaine-dependent individuals. We replicated this finding and found it to be specific to striatal neuronal nuclei. Furthermore, this locus demonstrates enhancer activity which is attenuated by methylation and enhanced by EGR1 overexpression. These results suggest that cocaine dependence alters the epigenetic regulation of dopaminergic signaling genes.
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Affiliation(s)
- Kathryn Vaillancourt
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Verdun, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Gang G. Chen
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Verdun, QC, Canada
| | - Laura Fiori
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Verdun, QC, Canada
| | - Gilles Maussion
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, Montreal, QC, Canada
| | - Volodymyr Yerko
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Verdun, QC, Canada
| | - Jean-François Théroux
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Verdun, QC, Canada
| | - Carl Ernst
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Benoit Labonté
- Centre de Recherche Cervo, Université Laval, Québec, QC, Canada
| | - Erin Calipari
- Departments of Pharmacology, Molecular Physiology and Biophysics, Psychiatry and Behavioral Sciences; Vanderbilt Center for Addiction Research; Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN, USA
| | - Eric J. Nestler
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Corina Nagy
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Verdun, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Naguib Mechawar
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Verdun, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Deborah C. Mash
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Verdun, QC, Canada
- Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
- Department of Psychiatry, McGill University, Montreal, QC, Canada
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5
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Xu Y, Chen X, Yu L, Wang Y, Wang H, Wu Z, Wu S, Bao W. SLC4A11 and MFSD3 Gene Expression Changes in Deoxynivalenol Treated IPEC-J2 Cells. Front Genet 2021; 12:697883. [PMID: 34367255 PMCID: PMC8335166 DOI: 10.3389/fgene.2021.697883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/21/2021] [Indexed: 12/22/2022] Open
Abstract
Deoxynivalenol (DON) caused serious cytotoxicity for animal cells. However, genes involved in regulating DON toxicity and the underlying molecular mechanisms remain largely unknown. This study explored the role of SLC4A11 and MFSD3 in alleviating DON toxicity and analyzed the DNA methylation changes of these two genes. Viability and cell cycle analysis showed that DON exposure decreased the IPEC-J2 viability (P < 0.01), blocked the cell cycle in the G2/M phase (P < 0.01), and increased the rate of apoptosis (P < 0.05). Expression of the SLC4A11 and MFSD3 genes was significantly downregulated upon DON exposure (P < 0.01). Overexpression of SLC4A11 and MFSD3 can enhance the cell viability (P < 0.01). DNA methylation assays indicated that promoter methylation of SLC4A11 (mC-1 and mC-23) and MFSD3 (mC-1 and mC-12) were significantly higher compared with those in the controls and correlated negatively with mRNA expression (P < 0.05). Further analysis showed that mC-1 of SLC4A11 and MFSD3 was located in transcription factor binding sites for NF-1 and Sp1. Our findings revealed the novel biological functions of porcine SLC4A11 and MFSD3 genes in regulating the cytotoxic effects induced by DON, and may contribute to the detection of biomarkers and drug targets for predicting and eliminating the potential toxicity of DON.
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Affiliation(s)
- Yafei Xu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiaolei Chen
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Luchen Yu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yi Wang
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Haifei Wang
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhengchang Wu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shenglong Wu
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Wenbin Bao
- Key Laboratory for Animal Genetic, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
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6
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Martín B, Pappa S, Díez-Villanueva A, Mallona I, Custodio J, Barrero MJ, Peinado MA, Jordà M. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics 2020; 15:765-779. [PMID: 32041475 DOI: 10.1080/15592294.2020.1722398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Alu repeats constitute a major fraction of human genome and for a small subset of them a role in gene regulation has been described. The number of studies focused on the functional characterization of particular Alu elements is very limited. Most Alu elements are DNA methylated and then assumed to lie in repressed chromatin domains. We hypothesize that Alu elements with low or variable DNA methylation are candidates for a functional role. In a genome-wide study in normal and cancer tissues, we pinpointed an Alu repeat (AluSq2) with differential methylation located upstream of the promoter region of the DIEXF gene. DIEXF encodes a highly conserved factor essential for the development of zebrafish digestive tract. To characterize the contribution of the Alu element to the regulation of DIEXF we analysed the epigenetic landscapes of the gene promoter and flanking regions in different cell types and cancers. Alternate epigenetic profiles (DNA methylation and histone modifications) of the AluSq2 element were associated with DIEXF transcript diversity as well as protein levels, while the epigenetic profile of the CpG island associated with the DIEXF promoter remained unchanged. These results suggest that AluSq2 might directly contribute to the regulation of DIEXF transcription and protein expression. Moreover, AluSq2 was DNA hypomethylated in different cancer types, pointing out its putative contribution to DIEXF alteration in cancer and its potential as tumoural biomarker.
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Affiliation(s)
- Berta Martín
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Stella Pappa
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Anna Díez-Villanueva
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Izaskun Mallona
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Joaquín Custodio
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - María José Barrero
- Center for Regenerative Medicine in Barcelona (CMRB), Avinguda de la Granvia de l'Hospitalet , Barcelona, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
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7
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Viswanathan R, Cheruba E, Cheow LF. DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells. Nucleic Acids Res 2019; 47:e122. [PMID: 31418018 PMCID: PMC6821369 DOI: 10.1093/nar/gkz717] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/21/2019] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of complex cell populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single-cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.
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Affiliation(s)
- Ramya Viswanathan
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
| | - Elsie Cheruba
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
| | - Lih Feng Cheow
- Department of Biomedical Engineering, National University of Singapore, Singapore 117583, Singapore.,Institute for Health Innovation and Technology (iHealthtech), National University of Singapore, Singapore 117583, Singapore
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Sun L, Namboodiri S, Chen E, Sun S. Preliminary Analysis of Within-Sample Co-methylation Patterns in Normal and Cancerous Breast Samples. Cancer Inform 2019; 18:1176935119880516. [PMID: 31631960 PMCID: PMC6778999 DOI: 10.1177/1176935119880516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 09/14/2019] [Indexed: 12/29/2022] Open
Abstract
DNA methylation plays a significant role in regulating the expression of certain genes in both cancerous and normal breast tissues. It is therefore important to study within-sample co-methylation, ie, methylation patterns between consecutive sites in a chromosome. In this article, we develop 2 new methods to compare co-methylation patterns between normal and cancerous breast samples. In particular, we investigate the co-methylation patterns of 4 different methylation states/levels separately. Using these 2 methods, we focus on addressing the following questions: How often does 1 methylation state change to other methylation states and how is this change dependent on chromosome distance? What co-methylation patterns do normal and cancerous breast samples have? Do genomic sites with different methylation states/levels have different co-methylation patterns? Our results show that cancerous and normal co-methylation patterns are significantly different. We find that this difference exists even when the physical distance of 2 sites are less than 50 bases. Breast cancer cell lines tend to remain in the same methylation state more often than normal samples, especially for the no/low or high/full methylation states. We also find that the co-methylation region lengths for various methylation states (no/low, partial, and high/full methylation states) are very different. For example, the co-methylation region lengths for partial methylation regions are shorter than the unmethylated or fully methylated regions. Our research may provide a deep understanding of co-methylation patterns. These co-methylation patterns will aid in discovering and understanding new methylation events that may be related to novel biomarkers.
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Affiliation(s)
| | | | | | - Shuying Sun
- Department of Mathematics, Texas State University, San Marcos, TX, USA
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9
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Wu Z, Feng H, Cao Y, Huang Y, Dai C, Wu S, Bao W. New Insight into the Molecular Mechanism of the FUT2 Regulating Escherichia coli F18 Resistance in Weaned Piglets. Int J Mol Sci 2018; 19:E3301. [PMID: 30352970 PMCID: PMC6275016 DOI: 10.3390/ijms19113301] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Accepted: 10/10/2018] [Indexed: 11/23/2022] Open
Abstract
Escherichia coli (E. coli) F18 is the main pathogen responsible for post-weaning diarrhea (PWD) in piglets. Resistance to E. coli F18 depends on the expression of the cognate receptors in the intestinal epithelial cells. However, the molecular mechanism of E. coli F18 resistance in weaned piglets remains unclear. Here, we performed a comparative transcriptome study of the duodenal tissue from Sutai E. coli F18 sensitive and resistant pigs by RNA-seq, and pig α(1,2) fucosyltransferase 2 (FUT2) was identified as a host differentially expressed gene controlling the E. coli F18 infection. Function analysis showed that the FUT2 expression was high in the duodenum and jejunum, with higher levels detected in sensitive individuals than in resistant individuals (p < 0.01). Expression levels of FUT2 were upregulated in IPEC-J2 cells after lipopolysaccharide (LPS)-induction or E. coli stimulation. FUT2 knockdown decreased the adhesion of E. coli F18 to IPEC-J2 cells (p < 0.05). FUT2 overexpression markedly increased the adhesion of E. coli F18 to IPEC-J2 cells (p < 0.05 or p < 0.01). Furthermore, the FUT2 mRNA levels correlated with methylation levels of the mC-22 site in the specificity protein 1 (Sp1) transcription factor (p < 0.05). Electrophoretic mobility shift assays (EMSA) showed that Sp1 interacts with the wild-type FUT2 promoter DNA, but not with methylated DNA. Our data suggested that FUT2 methylation at the mC-22 site inhibits Sp1 binding to the FUT2 promoter, thereby reducing FUT2 expression and enhancing E. coli F18 resistance in weaned piglets. These observations highlight FUT2 as a promising new target for combating E. coli F18 susceptibility in weaned piglets.
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Affiliation(s)
- Zhengchang Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Haiyue Feng
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Yue Cao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Yanjie Huang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Chaohui Dai
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
- Joint International Research Laboratory of Agriculture & Agri-Product Safety, Yangzhou University, Yangzhou 225009, China.
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10
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Kaur A, Pati PK, Pati AM, Nagpal AK. In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PLoS One 2017; 12:e0184523. [PMID: 28910327 PMCID: PMC5598985 DOI: 10.1371/journal.pone.0184523] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/27/2017] [Indexed: 01/24/2023] Open
Abstract
Pathogenesis related (PR) proteins are low molecular weight family of proteins induced in plants under various biotic and abiotic stresses. They play an important role in plant-defense mechanism. PRs have wide range of functions, acting as hydrolases, peroxidases, chitinases, anti-fungal, protease inhibitors etc. In the present study, an attempt has been made to analyze promoter regions of PR1, PR2, PR5, PR9, PR10 and PR12 of Arabidopsis thaliana and Oryza sativa. Analysis of cis-element distribution revealed the functional multiplicity of PRs and provides insight into the gene regulation. CpG islands are observed only in rice PRs, which indicates that monocot genome contains more GC rich motifs than dicots. Tandem repeats were also observed in 5' UTR of PR genes. Thus, the present study provides an understanding of regulation of PR genes and their versatile roles in plants.
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Affiliation(s)
- Amritpreet Kaur
- Department of Botanical and Environmental sciences, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Pratap Kumar Pati
- Department of Biotechnology, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Aparna Maitra Pati
- Planning Project Monitoring and Evaluation Cell, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Avinash Kaur Nagpal
- Department of Botanical and Environmental sciences, Guru Nanak Dev University, Amritsar, Punjab, India
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11
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Han L, Wu HJ, Zhu H, Kim KY, Marjani SL, Riester M, Euskirchen G, Zi X, Yang J, Han J, Snyder M, Park IH, Irizarry R, Weissman SM, Michor F, Fan R, Pan X. Bisulfite-independent analysis of CpG island methylation enables genome-scale stratification of single cells. Nucleic Acids Res 2017; 45:e77. [PMID: 28126923 PMCID: PMC5605247 DOI: 10.1093/nar/gkx026] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 01/20/2017] [Indexed: 01/03/2023] Open
Abstract
Conventional DNA bisulfite sequencing has been extended to single cell level, but the coverage consistency is insufficient for parallel comparison. Here we report a novel method for genome-wide CpG island (CGI) methylation sequencing for single cells (scCGI-seq), combining methylation-sensitive restriction enzyme digestion and multiple displacement amplification for selective detection of methylated CGIs. We applied this method to analyzing single cells from two types of hematopoietic cells, K562 and GM12878 and small populations of fibroblasts and induced pluripotent stem cells. The method detected 21 798 CGIs (76% of all CGIs) per cell, and the number of CGIs consistently detected from all 16 profiled single cells was 20 864 (72.7%), with 12 961 promoters covered. This coverage represents a substantial improvement over results obtained using single cell reduced representation bisulfite sequencing, with a 66-fold increase in the fraction of consistently profiled CGIs across individual cells. Single cells of the same type were more similar to each other than to other types, but also displayed epigenetic heterogeneity. The method was further validated by comparing the CpG methylation pattern, methylation profile of CGIs/promoters and repeat regions and 41 classes of known regulatory markers to the ENCODE data. Although not every minor methylation differences between cells are detectable, scCGI-seq provides a solid tool for unsupervised stratification of a heterogeneous cell population.
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Affiliation(s)
- Lin Han
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Hua-Jun Wu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Haiying Zhu
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.,Department of Cell Biology, Second Military Medical University, Shanghai 200433, China
| | - Kun-Yong Kim
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Sadie L Marjani
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Markus Riester
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Ghia Euskirchen
- Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Xiaoyuan Zi
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.,Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA.,Department of Cell Biology, Second Military Medical University, Shanghai 200433, China
| | - Jennifer Yang
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jasper Han
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Michael Snyder
- Department of Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - In-Hyun Park
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, 10 Amistad, 201B, New Haven, CT 06520, USA
| | - Rafael Irizarry
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Sherman M Weissman
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Franziska Michor
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02215, USA
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT 06520, USA
| | - Xinghua Pan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, Guangzhou, China.,Guangdong Key Laboratory of Biochip Technology, Southern Medical University, Guangzhou 510515, Guangdong, China
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12
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Goel N, Karir P, Garg VK. Role of DNA methylation in human age prediction. Mech Ageing Dev 2017; 166:33-41. [DOI: 10.1016/j.mad.2017.08.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/24/2017] [Accepted: 08/20/2017] [Indexed: 12/19/2022]
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13
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Ling KY, Cheow LF, Quake SR, Burkholder WF, Messerschmidt DM. Single Cell Restriction Enzyme-Based Analysis of Methylation at Genomic Imprinted Regions in Preimplantation Mouse Embryos. Methods Mol Biol 2017; 1605:171-189. [PMID: 28456965 DOI: 10.1007/978-1-4939-6988-3_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The methylation of cytosines in DNA is a fundamental epigenetic regulatory mechanism. During preimplantation development, mammalian embryos undergo extensive epigenetic reprogramming, including the global erasure of germ cell-specific DNA methylation marks, to allow for the establishment of the pluripotent state of the epiblast. However, DNA methylation marks at specific regions, such as imprinted gene regions, escape this reprogramming process, as their inheritance from germline to soma is paramount for proper development. To study the dynamics of DNA methylation marks in single blastomeres of mouse preimplantation embryos, we devised a new approach-single cell restriction enzyme analysis of methylation (SCRAM). SCRAM allows for reliable, fast, and high-throughput analysis of DNA methylation states of multiple regions of interest from single cells. In the method described below, SCRAM is specifically used to address loss of DNA methylation at genomic imprints or other highly methylated regions of interest.
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Affiliation(s)
- Ka Yi Ling
- Developmental Epigenetics and Disease Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lih Feng Cheow
- Microfluidics Systems Biology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Stephen R Quake
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - William F Burkholder
- Microfluidics Systems Biology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daniel M Messerschmidt
- Developmental Epigenetics and Disease Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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14
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Buj R, Mallona I, Díez-Villanueva A, Barrera V, Mauricio D, Puig-Domingo M, Reverter JL, Matias-Guiu X, Azuara D, Ramírez JL, Alonso S, Rosell R, Capellà G, Perucho M, Robledo M, Peinado MA, Jordà M. Quantification of unmethylated Alu (QUAlu): a tool to assess global hypomethylation in routine clinical samples. Oncotarget 2016; 7:10536-46. [PMID: 26859682 PMCID: PMC4891138 DOI: 10.18632/oncotarget.7233] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/25/2016] [Indexed: 01/05/2023] Open
Abstract
Hypomethylation of DNA is a hallmark of cancer and its analysis as tumor biomarker has been proposed, but its determination in clinical settings is hampered by lack of standardized methodologies. Here, we present QUAlu (Quantification of Unmethylated Alu), a new technique to estimate the Percentage of UnMethylated Alu (PUMA) as a surrogate for global hypomethylation. QUAlu consists in the measurement by qPCR of Alu repeats after digestion of genomic DNA with isoschizomers with differential sensitivity to DNA methylation. QUAlu performance has been evaluated for reproducibility, trueness and specificity, and validated by deep sequencing. As a proof of use, QUAlu has been applied to a broad variety of pathological examination specimens covering five cancer types. Major findings of the preliminary application of QUAlu to clinical samples include: (1) all normal tissues displayed similar PUMA; (2) tumors showed variable PUMA with the highest levels in lung and colon and the lowest in thyroid cancer; (3) stools from colon cancer patients presented higher PUMA than those from control individuals; (4) lung squamous cell carcinomas showed higher PUMA than lung adenocarcinomas, and an increasing hypomethylation trend associated with smoking habits. In conclusion, QUAlu is a simple and robust method to determine Alu hypomethylation in human biospecimens and may be easily implemented in research and clinical settings.
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Affiliation(s)
- Raquel Buj
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain
| | - Izaskun Mallona
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain
| | - Anna Díez-Villanueva
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain
| | - Víctor Barrera
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain
| | - Dídac Mauricio
- Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.,Department of Endocrinology and Nutrition, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.,ISCIII Center for Biomedical Research on Diabetes and Metabolic Associated Diseases (CIBERDEM), Madrid, Spain
| | - Manel Puig-Domingo
- Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.,Department of Endocrinology and Nutrition, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain.,ISCIII Center for Biomedical Research on Diabetes and Metabolic Associated Diseases (CIBERDEM), Madrid, Spain
| | - Jordi L Reverter
- Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.,Department of Endocrinology and Nutrition, University Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Xavier Matias-Guiu
- Department of Pathology and Molecular Genetics, University Hospital Arnau de Vilanova and University of Lleida, Biomedical Research Institute of Lleida (IRBLLEIDA), Lleida, Spain
| | - Daniel Azuara
- Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jose L Ramírez
- Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.,Catalan Institute of Oncology (ICO), Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Sergio Alonso
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain
| | - Rafael Rosell
- Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.,Catalan Institute of Oncology (ICO), Hospital Germans Trias i Pujol, Badalona, Barcelona, Spain
| | - Gabriel Capellà
- Catalan Institute of Oncology (ICO-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Manuel Perucho
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Mercedes Robledo
- Hereditary Endocrine Cancer Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain.,ISCIII Center for Biomedical Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Miguel A Peinado
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain
| | - Mireia Jordà
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona, Barcelona, Spain.,Germans Trias i Pujol Health Sciences Research Institute (IGTP), Badalona, Barcelona, Spain
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15
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Jordà M, Díez-Villanueva A, Mallona I, Martín B, Lois S, Barrera V, Esteller M, Vavouri T, Peinado MA. The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells. Genome Res 2016; 27:118-132. [PMID: 27999094 PMCID: PMC5204336 DOI: 10.1101/gr.207522.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 11/10/2016] [Indexed: 12/16/2022]
Abstract
Cancer cells exhibit multiple epigenetic changes with prominent local DNA hypermethylation and widespread hypomethylation affecting large chromosomal domains. Epigenome studies often disregard the study of repeat elements owing to technical complexity and their undefined role in genome regulation. We have developed NSUMA (Next-generation Sequencing of UnMethylated Alu), a cost-effective approach allowing the unambiguous interrogation of DNA methylation in more than 130,000 individual Alu elements, the most abundant retrotransposon in the human genome. DNA methylation profiles of Alu repeats have been analyzed in colon cancers and normal tissues using NSUMA and whole-genome bisulfite sequencing. Normal cells show a low proportion of unmethylated Alu (1%–4%) that may increase up to 10-fold in cancer cells. In normal cells, unmethylated Alu elements tend to locate in the vicinity of functionally rich regions and display epigenetic features consistent with a direct impact on genome regulation. In cancer cells, Alu repeats are more resistant to hypomethylation than other retroelements. Genome segmentation based on high/low rates of Alu hypomethylation allows the identification of genomic compartments with differential genetic, epigenetic, and transcriptomic features. Alu hypomethylated regions show low transcriptional activity, late DNA replication, and its extent is associated with higher chromosomal instability. Our analysis demonstrates that Alu retroelements contribute to define the epigenetic landscape of normal and cancer cells and provides a unique resource on the epigenetic dynamics of a principal, but largely unexplored, component of the primate genome.
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Affiliation(s)
- Mireia Jordà
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Anna Díez-Villanueva
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Izaskun Mallona
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Berta Martín
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Sergi Lois
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Víctor Barrera
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08908, Catalonia, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona 08907, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Catalonia, Spain
| | - Tanya Vavouri
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Catalonia, Spain
| | - Miguel A Peinado
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
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16
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Kitchen MO, Bryan RT, Emes RD, Glossop JR, Luscombe C, Cheng KK, Zeegers MP, James ND, Devall AJ, Mein CA, Gommersall L, Fryer AA, Farrell WE. Quantitative genome-wide methylation analysis of high-grade non-muscle invasive bladder cancer. Epigenetics 2016; 11:237-46. [PMID: 26929985 DOI: 10.1080/15592294.2016.1154246] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
High-grade non-muscle invasive bladder cancer (HG-NMIBC) is a clinically unpredictable disease with greater risks of recurrence and progression relative to their low-intermediate-grade counterparts. The molecular events, including those affecting the epigenome, that characterize this disease entity in the context of tumor development, recurrence, and progression, are incompletely understood. We therefore interrogated genome-wide DNA methylation using HumanMethylation450 BeadChip arrays in 21 primary HG-NMIBC tumors relative to normal bladder controls. Using strict inclusion-exclusion criteria we identified 1,057 hypermethylated CpGs within gene promoter-associated CpG islands, representing 256 genes. We validated the array data by bisulphite pyrosequencing and examined 25 array-identified candidate genes in an independent cohort of 30 HG-NMIBC and 18 low-intermediate-grade NMIBC. These analyses revealed significantly higher methylation frequencies in high-grade tumors relative to low-intermediate-grade tumors for the ATP5G2, IRX1 and VAX2 genes (P<0.05), and similarly significant increases in mean levels of methylation in high-grade tumors for the ATP5G2, VAX2, INSRR, PRDM14, VSX1, TFAP2b, PRRX1, and HIST1H4F genes (P<0.05). Although inappropriate promoter methylation was not invariantly associated with reduced transcript expression, a significant association was apparent for the ARHGEF4, PON3, STAT5a, and VAX2 gene transcripts (P<0.05). Herein, we present the first genome-wide DNA methylation analysis in a unique HG-NMIBC cohort, showing extensive and discrete methylation changes relative to normal bladder and low-intermediate-grade tumors. The genes we identified hold significant potential as targets for novel therapeutic intervention either alone, or in combination, with more conventional therapeutic options in the treatment of this clinically unpredictable disease.
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Affiliation(s)
- Mark O Kitchen
- a Institute for Science and Technology in Medicine, Keele University , UK.,b Urology Department , University Hospitals of North Midlands NHS Trust , UK
| | - Richard T Bryan
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Richard D Emes
- d Advanced Data Analysis Center, University of Nottingham , UK
| | - John R Glossop
- a Institute for Science and Technology in Medicine, Keele University , UK
| | | | - K K Cheng
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Maurice P Zeegers
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK.,e Department of Complex Genetics , Maastricht University Medical Center , The Netherlands.,f NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University Medical Center , The Netherlands.,g CAPHRI School for Public Health and Primary Care, Maastricht University Medical Center , The Netherlands
| | | | - Adam J Devall
- c Institute of Cancer and Genomic Sciences, University of Birmingham , UK
| | - Charles A Mein
- i The Genome Center, Barts and the London School of Medicine and Dentistry , London , UK
| | - Lyndon Gommersall
- b Urology Department , University Hospitals of North Midlands NHS Trust , UK
| | - Anthony A Fryer
- a Institute for Science and Technology in Medicine, Keele University , UK
| | - William E Farrell
- a Institute for Science and Technology in Medicine, Keele University , UK
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17
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Simultaneous Analysis of SEPT9 Promoter Methylation Status, Micronuclei Frequency, and Folate-Related Gene Polymorphisms: The Potential for a Novel Blood-Based Colorectal Cancer Biomarker. Int J Mol Sci 2015; 16:28486-97. [PMID: 26633373 PMCID: PMC4691060 DOI: 10.3390/ijms161226113] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/09/2015] [Accepted: 11/17/2015] [Indexed: 12/11/2022] Open
Abstract
One challenge in colorectal cancer (CRC) is identifying novel biomarkers to be introduced in screening programs. The present study investigated the promoter methylation status of the SEPT9 gene in peripheral blood samples of subjects' positive fecal occult blood test (FOBT). In order to add new insights, we investigated the association between SEPT9 promoter methylation and micronuclei frequency, and polymorphisms in the folate-related pathway genes. SEPT9 promoter methylation, micronuclei frequency, and genotypes were evaluated on 74 individuals' FOBT positive. Individuals were subjected to a colonoscopy that provided written informed consent for study participation. SEPT9 promoter methylation status was significantly lower in the CRC group than controls (p = 0.0006). In contrast, the CaCo2 cell-line, analyzed as a tissue specific model of colon adenocarcinoma, showed a significantly higher percentage of SEPT9 promoter methylation compared to the CRC group (p < 0.0001). Linear regression analysis showed an inverse correlation between micronuclei frequency and the decrease in the methylation levels of SEPT9 promoter region among CRC patients (β = -0.926, p = 0.0001). With regard to genotype analysis, we showed the involvement of the DHFR polymorphism (rs70991108) in SEPT9 promoter methylation level in CRC patients only. In particular, the presence of at least one 19 bp del allele significantly correlates with decreased SEPT9 promoter methylation, compared to the 19 bp ins/ins genotype (p = 0.007). While remaining aware of the strengths and limitations of the study, this represents the first evidence of a novel approach for the early detection of CRC, using SEPT9 promoter methylation, micronuclei frequency and genotypes, with the potential to improve CRC risk assessment.
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18
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Dong W, Yin X, Sun L, Wang J, Sun S, Zhu G, Wu S, Bao W. Age-associated methylation change of TAP1 promoter in piglet. Gene 2015; 573:70-4. [PMID: 26169022 DOI: 10.1016/j.gene.2015.07.026] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/29/2015] [Accepted: 07/09/2015] [Indexed: 01/01/2023]
Abstract
Diarrhea and edematous disease are two major causes of mortality in postweaning piglets. These conditions lead to huge economic losses in the swine industry. Escherichia coli F18 is the primary causative agent of these two diseases. Transported associated with antigen processing (TAP) plays an important role in the immune response and the TAP1 gene could be an effective anti-E. coli F18 molecular marker in pigs. The aim of this study was to determine the correlation between TAP1 gene promoter CpG island methylation status and mRNA expression in piglets. In this study, bisulfite sequencing PCR (BSP) was used to detect the methylation status of the TAP1 gene promoter CpG islands and fluorescence quantitative PCR was used to detect TAP1 expression in the jejunum of Sutai piglets from birth to weaning age. The fragment of the TAP1 gene promoter region under investigation has no mutation, has 13 putative transcription factor binding sites containing 19 CpG sites, and may be important for regulation of gene expression. With increasing age, the overall methylation levels decreased, while the TAP1 expression levels increased, indicating a negative correlation between TAP1 expression and promoter methylation levels. Variance analysis showed significant differences in the methylation status of CpG_4, CpG_13 and CpG_15 among the different age groups (P<0.05). Our data indicate that TAP1 expression is increased by demethylation of promoter CpG islands, with CpG_4, CpG_13 and CpG_15 implicated as the critical regulatory sites.
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Affiliation(s)
- Wenhua Dong
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Xuemei Yin
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Li Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Jing Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Shouyong Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, PR China.
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19
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Casco-Robles MM, Miura T, Chiba C. The newt (Cynops pyrrhogaster) RPE65 promoter: molecular cloning, characterization and functional analysis. Transgenic Res 2015; 24:463-73. [PMID: 25490979 PMCID: PMC4436847 DOI: 10.1007/s11248-014-9857-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/29/2014] [Indexed: 12/20/2022]
Abstract
The adult newt has the ability to regenerate the neural retina following injury, a process achieved primarily by the retinal pigment epithelium (RPE). To deliver exogenous genes to the RPE for genetic manipulation of regenerative events, we isolated the newt RPE65 promoter region by genome walking. First, we cloned the 2.8 kb RPE65 promoter from the newt, Cynops pyrrhogaster. Sequence analysis revealed several conserved regulatory elements described previously in mouse and human RPE65 promoters. Second, having previously established an I-SceI-mediated transgenic protocol for the newt, we used it here to examine the -657 bp proximal promoter of RPE65. The promoter assay used with F0 transgenic newts confirmed transgene expression of mCherry fluorescent protein in the RPE. Using bioinformatic tools and the TRANSFAC database, we identified a 340 bp CpG island located between -635 and -296 bp in the promoter; this region contains response elements for the microphthalmia-associated transcription factor known as MITF (CACGTG, CATGTG), and E-boxes (CANNTG). Sex-determining region box 9 (or SOX9) response element previously reported in the regulation of RPE genes (including RPE65) was also identified in the newt RPE65 promoter. Third, we identified DNA motif boxes in the newt RPE65 promoter that are conserved among other vertebrates. The newt RPE65 promoter is an invaluable tool for site-specific delivery of exogenous genes or genetic manipulation systems for the study of retinal regeneration in this animal.
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Affiliation(s)
- Martin Miguel Casco-Robles
- Department of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8572 Japan
| | - Tomoya Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8572 Japan
| | - Chikafumi Chiba
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennoudai 1-1-1, Tsukuba, Ibaraki 305-8572 Japan
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20
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Forn M, Díez-Villanueva A, Merlos-Suárez A, Muñoz M, Lois S, Carriò E, Jordà M, Bigas A, Batlle E, Peinado MA. Overlapping DNA methylation dynamics in mouse intestinal cell differentiation and early stages of malignant progression. PLoS One 2015; 10:e0123263. [PMID: 25933092 PMCID: PMC4416816 DOI: 10.1371/journal.pone.0123263] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/17/2015] [Indexed: 12/20/2022] Open
Abstract
Mouse models of intestinal crypt cell differentiation and tumorigenesis have been used to characterize the molecular mechanisms underlying both processes. DNA methylation is a key epigenetic mark and plays an important role in cell identity and differentiation programs and cancer. To get insights into the dynamics of cell differentiation and malignant transformation we have compared the DNA methylation profiles along the mouse small intestine crypt and early stages of tumorigenesis. Genome-scale analysis of DNA methylation together with microarray gene expression have been applied to compare intestinal crypt stem cells (EphB2high), differentiated cells (EphB2negative), ApcMin/+ adenomas and the corresponding non-tumor adjacent tissue, together with small and large intestine samples and the colon cancer cell line CT26. Compared with late stages, small intestine crypt differentiation and early stages of tumorigenesis display few and relatively small changes in DNA methylation. Hypermethylated loci are largely shared by the two processes and affect the proximities of promoter and enhancer regions, with enrichment in genes associated with the intestinal stem cell signature and the PRC2 complex. The hypermethylation is progressive, with minute levels in differentiated cells, as compared with intestinal stem cells, and reaching full methylation in advanced stages. Hypomethylation shows different signatures in differentiation and cancer and is already present in the non-tumor tissue adjacent to the adenomas in ApcMin/+ mice, but at lower levels than advanced cancers. This study provides a reference framework to decipher the mechanisms driving mouse intestinal tumorigenesis and also the human counterpart.
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Affiliation(s)
- Marta Forn
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Díez-Villanueva
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Merlos-Suárez
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
| | - Mar Muñoz
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Sergi Lois
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Elvira Carriò
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Mireia Jordà
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
| | - Anna Bigas
- Institut Hospital del Mar d’Investigació Mèdica (IMIM) 08003 Barcelona, Spain
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona) 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miguel A. Peinado
- Institute of Predictive and Personalized Medicine of Cancer (IMPPC) 08916 Badalona, Barcelona, Spain
- * E-mail:
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21
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Carrió E, Díez-Villanueva A, Lois S, Mallona I, Cases I, Forn M, Peinado MA, Suelves M. Deconstruction of DNA methylation patterns during myogenesis reveals specific epigenetic events in the establishment of the skeletal muscle lineage. Stem Cells 2015; 33:2025-36. [PMID: 25801824 DOI: 10.1002/stem.1998] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/06/2015] [Indexed: 12/17/2022]
Abstract
The progressive restriction of differentiation potential from pluripotent embryonic stem cells (ESCs) to tissue-specific stem cells involves widespread epigenetic reprogramming, including modulation of DNA methylation patterns. Skeletal muscle stem cells are required for the growth, maintenance, and regeneration of skeletal muscle. To investigate the contribution of DNA methylation to the establishment of the myogenic program, we analyzed ESCs, skeletal muscle stem cells in proliferating (myoblasts) and differentiating conditions (myotubes), and mature myofibers. About 1.000 differentially methylated regions were identified during muscle-lineage determination and terminal differentiation, mainly located in gene bodies and intergenic regions. As a whole, myogenic stem cells showed a gain of DNA methylation, while muscle differentiation was accompanied by loss of DNA methylation in CpG-poor regions. Notably, the hypomethylated regions in myogenic stem cells were neighbored by enhancer-type chromatin, suggesting the involvement of DNA methylation in the regulation of cell-type specific enhancers. Interestingly, we demonstrated the hypomethylation of the muscle cell-identity Myf5 super-enhancer only in muscle cells. Furthermore, we observed that upstream stimulatory factor 1 binding to Myf5 super-enhancer occurs upon DNA demethylation in myogenic stem cells. Taken altogether, we characterized the unique DNA methylation signature of skeletal muscle stem cells and highlighted the importance of DNA methylation-mediated regulation of cell identity Myf5 super-enhancer during cellular differentiation.
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Affiliation(s)
- Elvira Carrió
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Anna Díez-Villanueva
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Sergi Lois
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Izaskun Mallona
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Ildefonso Cases
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Marta Forn
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC)
| | - Miguel A Peinado
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
| | - Mònica Suelves
- Institut de Medicina Predictiva i Personalitzada del Càncer (IMPPC).,Institut Germans Trias i Pujol (IGTP), Campus Can Ruti, 08916, Badalona, Spain
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22
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Abstract
This protocol details a method for measuring the DNA methylation state of multiple target sites in single cells, otherwise known as single-cell restriction analysis of methylation (SCRAM). The basic steps include isolating and lysing single cells, digesting genomic DNA with a methylation-sensitive restriction endonuclease (MSRE) and amplification of multiple targets by two rounds of PCR to determine the methylation status of target sites. The method can reliably and accurately detect the methylation status of multiple target sites in each single cell, and it can be completed in a relatively short time (<2 d) at low cost. Consequently, the method may be preferable over whole-genome methods in applications requiring highly reliable and cost-effective coverage of specific target sites in all cells from a sample and in cases when the DNA methylation states of single CpG sites are representative of the methylation status of corresponding regions of interest.
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23
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Stenz L, Zewdie S, Laforge-Escarra T, Prados J, La Harpe R, Dayer A, Paoloni-Giacobino A, Perroud N, Aubry JM. BDNF promoter I methylation correlates between post-mortem human peripheral and brain tissues. Neurosci Res 2014; 91:1-7. [PMID: 25450314 DOI: 10.1016/j.neures.2014.10.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/25/2014] [Accepted: 10/06/2014] [Indexed: 10/25/2022]
Abstract
Several psychiatric disorders have been associated with CpG methylation changes in CG rich promoters of the brain-derived neurotrophic factor (BDNF) mainly by extracting DNA from peripheral blood cells. Whether changes in peripheral DNA methylation can be used as a proxy for brain-specific alterations remains an open question. In this study we aimed to compare DNA methylation levels in BDNF promoter regions in human blood cells, muscle and brain regions using bisulfite-pyrosequencing. We found a significant correlation between the levels of BDNF promoter I methylation measured in quadriceps and vPFC tissues extracted from the same individuals (n = 98, Pearson, r = 0.48, p = 4.5 × 10(-7)). In the hippocampus, BDNF promoter I and IV methylation levels were strongly correlated (Pearson, n = 37, r = 0.74, p = 1.4 × 10(-7)). We found evidence for sex-dependent effect on BDNF promoter methylation levels in the various tissues and blood samples. Taken together, these data indicate a strong intra-individual correlation between peripheral and brain tissue. They also suggest that sex determines methylation patterns in BDNF promoter region across different types of tissue, including muscle, brain, and blood.
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Affiliation(s)
- Ludwig Stenz
- Department of Psychiatry, University of Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland.
| | - Seblewongel Zewdie
- Department of Psychiatry, University of Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland
| | - Térèse Laforge-Escarra
- Department of Genetic and Laboratory Medicine, Geneva University Hospital, 1211 Geneva 14, Switzerland
| | - Julien Prados
- Department of Psychiatry, University of Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland
| | - Romano La Harpe
- Institute of Forensic Medicine, University of Geneva, Switzerland
| | - Alexandre Dayer
- Department of Mental Health and Psychiatry, University Hospital of Geneva, Geneva, Switzerland; Department of Basic Neurosciences, University of Geneva Medical School, Geneva, Switzerland
| | - Ariane Paoloni-Giacobino
- Department of Genetic and Laboratory Medicine, Geneva University Hospital, 1211 Geneva 14, Switzerland
| | - Nader Perroud
- Department of Psychiatry, University of Geneva, Switzerland; Department of Mental Health and Psychiatry, University Hospital of Geneva, Geneva, Switzerland
| | - Jean-Michel Aubry
- Department of Psychiatry, University of Geneva, Switzerland; Department of Mental Health and Psychiatry, University Hospital of Geneva, Geneva, Switzerland
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Wang J, Yin X, Sun L, Sun S, Zi C, Zhu G, Wu S, Bao W. Correlation between BPI gene upstream CpG island methylation and mRNA expression in piglets. Int J Mol Sci 2014; 15:10989-98. [PMID: 24945309 PMCID: PMC4100193 DOI: 10.3390/ijms150610989] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 05/28/2014] [Accepted: 06/09/2014] [Indexed: 01/15/2023] Open
Abstract
Diarrhea and edematous disease are two major causes of mortality in postweaning piglets, and these conditions lead to huge economic losses in the swine industry. E. coli F18 is the primary causative agent of these two diseases. Bactericidal/permeability-increasing protein (BPI) plays an important role in the natural defense of the host. The aim of this study was to determine the correlation between BPI gene upstream CpG island methylation and mRNA expression. In this study, bisulfite sequencing PCR (BSP) was used to detect the methylation status of the BPI gene upstream CpG island and fluorescence quantitative PCR was used to detect BPI expression in the duodenum of piglets from birth to weaning age. BPI upstream CpG islands were shown to have many putative transcription factor binding sites, 10 CpG sites and every CpG site was methylated. The CpG island methylation level was lowest in 30-day piglets and was significantly lower than levels in 8-day piglets (p < 0.05). BPI mRNA expression was significantly higher in 30-day piglets than at any other age (p < 0.05). Pearson’s correlation analysis showed that the methylation status of the CpG island was negatively correlated with BPI mRNA expression. Statistical significances were found in CpG_1, CpG_3, CpG_4, CpG_7 and CpG_10 (p < 0.05). The data indicate that BPI expression is improved by demethylation of the BPI gene upstream CpG island. Furthermore, CpG_1, CpG_3, CpG_4, CpG_7 and CpG_10 may be critical sites in the regulation of BPI gene expression.
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Affiliation(s)
- Jing Wang
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Xuemei Yin
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Li Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Shouyong Sun
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Chen Zi
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China.
| | - Shenglong Wu
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
| | - Wenbin Bao
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China.
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25
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Medvedeva YA, Khamis AM, Kulakovskiy IV, Ba-Alawi W, Bhuyan MSI, Kawaji H, Lassmann T, Harbers M, Forrest ARR, Bajic VB. Effects of cytosine methylation on transcription factor binding sites. BMC Genomics 2014; 15:119. [PMID: 24669864 PMCID: PMC3986887 DOI: 10.1186/1471-2164-15-119] [Citation(s) in RCA: 164] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 08/16/2013] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND DNA methylation in promoters is closely linked to downstream gene repression. However, whether DNA methylation is a cause or a consequence of gene repression remains an open question. If it is a cause, then DNA methylation may affect the affinity of transcription factors (TFs) for their binding sites (TFBSs). If it is a consequence, then gene repression caused by chromatin modification may be stabilized by DNA methylation. Until now, these two possibilities have been supported only by non-systematic evidence and they have not been tested on a wide range of TFs. An average promoter methylation is usually used in studies, whereas recent results suggested that methylation of individual cytosines can also be important. RESULTS We found that the methylation profiles of 16.6% of cytosines and the expression profiles of neighboring transcriptional start sites (TSSs) were significantly negatively correlated. We called the CpGs corresponding to such cytosines "traffic lights". We observed a strong selection against CpG "traffic lights" within TFBSs. The negative selection was stronger for transcriptional repressors as compared with transcriptional activators or multifunctional TFs as well as for core TFBS positions as compared with flanking TFBS positions. CONCLUSIONS Our results indicate that direct and selective methylation of certain TFBS that prevents TF binding is restricted to special cases and cannot be considered as a general regulatory mechanism of transcription.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Vladimir B Bajic
- Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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26
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An integrated epigenetic and transcriptomic analysis reveals distinct tissue-specific patterns of DNA methylation associated with atopic dermatitis. J Invest Dermatol 2014; 134:1873-1883. [PMID: 24739813 DOI: 10.1038/jid.2014.87] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 01/29/2014] [Accepted: 01/29/2014] [Indexed: 12/22/2022]
Abstract
Epigenetic alterations are increasingly recognized as mechanisms for disease-associated changes in genome function and important risk factors for complex diseases. The epigenome differs between cell types and so far has been characterized in few human tissues only. In order to identify disease-associated DNA methylation differences for atopic dermatitis (AD), we investigated DNA from whole blood, T cells, B cells, as well as lesional and non-lesional epidermis from AD patients and healthy controls. To elicit functional links, we examined epidermal mRNA expression profiles. No genome-wide significant DNA methylation differences between AD cases and controls were observed in whole blood, T cells, and B cells, and, in general, intra-individual differences in DNA methylation were larger than interindividual differences. However, striking methylation differences were observed between lesional epidermis from patients and healthy control epidermis for various CpG sites, which partly correlated with altered transcript levels of genes predominantly relevant for epidermal differentiation and innate immune response. Significant DNA methylation differences were discordant in skin and blood samples, suggesting that blood is not an ideal surrogate for skin tissue. Our pilot study provides preliminary evidence for functionally relevant DNA methylation differences associated with AD, particularly in the epidermis, and represents a starting point for future investigations of epigenetic mechanisms in AD.
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27
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Ibragimova I, Dulaimi E, Slifker MJ, Chen DY, Uzzo RG, Cairns P. A global profile of gene promoter methylation in treatment-naïve urothelial cancer. Epigenetics 2014; 9:760-73. [PMID: 24521710 PMCID: PMC4063835 DOI: 10.4161/epi.28078] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The epigenetic alteration of aberrant hypermethylation in the promoter CpG island of a gene is associated with repression of transcription. In neoplastic cells, aberrant hypermethylation is well described as a mechanism of allele inactivation of particular genes with a tumor suppressor function. To investigate the role of aberrant hypermethylation in the biology and progression of urothelial cancer, we examined 101 urothelial (transitional cell) carcinomas (UC), broadly representative of the disease at presentation, with no prior immunotherapy, chemotherapy or radiotherapy, by Infinium HM27 containing 14,495 genes. The genome-wide signature of aberrant promoter hypermethylation in UC consisted of 729 genes significant by a Wilcoxon test, hypermethylated in a CpG island within 1 kb of the transcriptional start site and unmethylated in normal urothelium from aged individuals. We examined differences in gene methylation between the two main groups of UC: the 75% that are superficial, which often recur but rarely progress, and the 25% with muscle invasion and poor prognosis. We further examined pairwise comparisons of the pathologic subgroups of high or low grade, invasive or non-invasive (pTa), and high grade superficial or low grade superficial UC. Pathways analysis indicated over-representation of genes involved in cell adhesion or metabolism in muscle-invasive UC. Notably, the TET2 epigenetic regulator was one of only two genes more frequently methylated in superficial tumors and the sole gene in low grade UC. Other chromatin remodeling genes, MLL3 and ACTL6B, also showed aberrant hypermethylation. The Infinium methylation value for representative genes was verified by pyrosequencing. An available mRNA expression data set indicated many of the hypermethylated genes of interest to be downregulated in UC. Unsupervised clustering of the most differentially methylated genes distinguished muscle invasive from superficial UC. After filtering, cluster analysis showed a CpG Island Methylator Phenotype (CIMP)-like pattern of widespread methylation in 11 (11%) tumors. Nine of these 11 tumors had hypermethylation of TET2. Our analysis provides a basis for further studies of hypermethylation in the development and progression of UC.
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Affiliation(s)
- Ilsiya Ibragimova
- Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia PA, USA
| | - Essel Dulaimi
- Department of Pathology; Fox Chase Cancer Center; Philadelphia PA, USA
| | - Michael J Slifker
- Department of Biostatistics and Bioinformatics; Fox Chase Cancer Center; Philadelphia PA, USA
| | - David Y Chen
- Department of Urology; Fox Chase Cancer Center; Philadelphia PA, USA
| | - Robert G Uzzo
- Department of Urology; Fox Chase Cancer Center; Philadelphia PA, USA
| | - Paul Cairns
- Cancer Epigenetics Program; Fox Chase Cancer Center; Philadelphia PA, USA
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28
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Song N, Endo D, Koji T. Roles of epigenome in mammalian spermatogenesis. Reprod Med Biol 2013; 13:59-69. [PMID: 29699150 DOI: 10.1007/s12522-013-0167-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Accepted: 08/07/2013] [Indexed: 10/26/2022] Open
Abstract
Mammalian spermatogenesis is a successive process consisting of spermatogonial proliferation, spermatocytic meiosis, and spermiogenesis, representing the maturation of haploid spermatids. During the process, 25-75 % of the expected sperm yield is thought to be lost through apoptosis. In addition, spermatogenesis is considered to be a process undergoing successive heterochromatinization, finally reaching a complete condensed form in the sperm head. Thus, cell proliferation, differentiation and death may be strictly regulated by epigenetic factors in this process. This review describes the current understanding of the role of epigenome in spermatogenesis, especially focusing on the following aspects; DNA methylation, modification of histones, and small RNA function. These epigenetic factors affect each other and play a central role in events essential for spermatogenesis, fertilization and embryogenesis, through the regulation of gene expression, transposon activities, meiotic sex chromosome inactivation, histone remodeling and genome imprinting. Finally, a brief discussion of future avenues of study is highlighted.
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Affiliation(s)
- Ning Song
- Department of Histology and Cell Biology Nagasaki University Graduate School of Biomedical Sciences 1-12-4 Sakamoto 852-8523 Nagasaki Japan
| | - Daisuke Endo
- Department of Histology and Cell Biology Nagasaki University Graduate School of Biomedical Sciences 1-12-4 Sakamoto 852-8523 Nagasaki Japan
| | - Takehiko Koji
- Department of Histology and Cell Biology Nagasaki University Graduate School of Biomedical Sciences 1-12-4 Sakamoto 852-8523 Nagasaki Japan
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29
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Zeilinger S, Kühnel B, Klopp N, Baurecht H, Kleinschmidt A, Gieger C, Weidinger S, Lattka E, Adamski J, Peters A, Strauch K, Waldenberger M, Illig T. Tobacco smoking leads to extensive genome-wide changes in DNA methylation. PLoS One 2013; 8:e63812. [PMID: 23691101 PMCID: PMC3656907 DOI: 10.1371/journal.pone.0063812] [Citation(s) in RCA: 574] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/05/2013] [Indexed: 11/19/2022] Open
Abstract
Environmental factors such as tobacco smoking may have long-lasting effects on DNA methylation patterns, which might lead to changes in gene expression and in a broader context to the development or progression of various diseases. We conducted an epigenome-wide association study (EWAs) comparing current, former and never smokers from 1793 participants of the population-based KORA F4 panel, with replication in 479 participants from the KORA F3 panel, carried out by the 450K BeadChip with genomic DNA obtained from whole blood. We observed wide-spread differences in the degree of site-specific methylation (with p-values ranging from 9.31E-08 to 2.54E-182) as a function of tobacco smoking in each of the 22 autosomes, with the percent of variance explained by smoking ranging from 1.31 to 41.02. Depending on cessation time and pack-years, methylation levels in former smokers were found to be close to the ones seen in never smokers. In addition, methylation-specific protein binding patterns were observed for cg05575921 within AHRR, which had the highest level of detectable changes in DNA methylation associated with tobacco smoking (–24.40% methylation; p = 2.54E-182), suggesting a regulatory role for gene expression. The results of our study confirm the broad effect of tobacco smoking on the human organism, but also show that quitting tobacco smoking presumably allows regaining the DNA methylation state of never smokers.
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Affiliation(s)
- Sonja Zeilinger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Brigitte Kühnel
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Norman Klopp
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Hansjörg Baurecht
- Department of Dermatology, Allergology, and Venerology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
- Graduate School of Information Science in Health (GSISH), Technische Universität München, Munich, Germany
| | - Anja Kleinschmidt
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Stephan Weidinger
- Department of Dermatology, Allergology, and Venerology, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Eva Lattka
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Jerzy Adamski
- Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, Neuherberg, Germany
- Chair of Experimental Genetics, Technische Universität München, Munich, Germany
| | - Annette Peters
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Informatics, Biometry and Epidemiology, Chair of Genetic Epidemiology, Ludwig-Maximilians-Universität, Munich, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- * E-mail:
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
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Ibragimova I, Maradeo ME, Dulaimi E, Cairns P. Aberrant promoter hypermethylation of PBRM1, BAP1, SETD2, KDM6A and other chromatin-modifying genes is absent or rare in clear cell RCC. Epigenetics 2013; 8:486-93. [PMID: 23644518 PMCID: PMC3741218 DOI: 10.4161/epi.24552] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Recent sequencing studies of clear cell (conventional) renal cell carcinoma (ccRCC) have identified inactivating point mutations in the chromatin-modifying genes PBRM1, KDM6A/UTX, KDM5C/JARID1C, SETD2, MLL2 and BAP1. To investigate whether aberrant hypermethylation is a mechanism of inactivation of these tumor suppressor genes in ccRCC, we sequenced the promoter region within a bona fide CpG island of PBRM1, KDM6A, SETD2 and BAP1 in bisulfite-modified DNA of a representative series of 50 primary ccRCC, 4 normal renal parenchyma specimens and 5 RCC cell lines. We also interrogated the promoter methylation status of KDM5C and ARID1A in the Cancer Genome Atlas (TCGA) ccRCC Infinium data set. PBRM1, KDM6A, SETD2 and BAP1 were unmethylated in all tumor and normal specimens. KDM5C and ARID1A were unmethylated in the TCGA 219 ccRCC and 119 adjacent normal specimens. Aberrant promoter hypermethylation of PBRM1, BAP1 and the other chromatin-modifying genes examined here is therefore absent or rare in ccRCC.
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Affiliation(s)
- Ilsiya Ibragimova
- Cancer Epigenetics Program and Kidney Keystone Program, Fox Chase Cancer Center, Philadelphia, PA, USA
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31
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Warden CD, Lee H, Tompkins JD, Li X, Wang C, Riggs AD, Yu H, Jove R, Yuan YC. COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis. Nucleic Acids Res 2013; 41:e117. [PMID: 23598999 PMCID: PMC3675470 DOI: 10.1093/nar/gkt242] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
COHCAP (City of Hope CpG Island Analysis Pipeline) is an algorithm to analyze single-nucleotide resolution DNA methylation data produced by either an Illumina methylation array or targeted bisulfite sequencing. The goal of the COHCAP algorithm is to identify CpG islands that show a consistent pattern of methylation among CpG sites. COHCAP is currently the only DNA methylation package that provides integration with gene expression data to identify a subset of CpG islands that are most likely to regulate downstream gene expression, and it can generate lists of differentially methylated CpG islands with ∼50% concordance with gene expression from both cell line data and heterogeneous patient data. For example, this article describes known breast cancer biomarkers (such as estrogen receptor) with a negative correlation between DNA methylation and gene expression. COHCAP also provides visualization for quality control metrics, regions of differential methylation and correlation between methylation and gene expression. This software is freely available at https://sourceforge.net/projects/cohcap/.
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Affiliation(s)
- Charles D Warden
- Bioinformatics Core, City of Hope National Medical Center, Duarte, CA 91010, USA.
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