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      Integrative epigenome-wide analysis demonstrates that DNA methylation may mediate genetic risk in inflammatory bowel disease

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          Abstract

          Epigenetic alterations may provide important insights into gene-environment interaction in inflammatory bowel disease (IBD). Here we observe epigenome-wide DNA methylation differences in 240 newly-diagnosed IBD cases and 190 controls. These include 439 differentially methylated positions (DMPs) and 5 differentially methylated regions (DMRs), which we study in detail using whole genome bisulphite sequencing. We replicate the top DMP ( RPS6KA2) and DMRs ( VMP1, ITGB2 and TXK) in an independent cohort. Using paired genetic and epigenetic data, we delineate methylation quantitative trait loci; VMP1/microRNA-21 methylation associates with two polymorphisms in linkage disequilibrium with a known IBD susceptibility variant. Separated cell data shows that IBD-associated hypermethylation within the TXK promoter region negatively correlates with gene expression in whole-blood and CD8 + T cells, but not other cell types. Thus, site-specific DNA methylation changes in IBD relate to underlying genotype and associate with cell-specific alteration in gene expression.

          Abstract

          Epigenetic perturbations may be an important factor in diseases where both genes and environment play a role. Here, Ventham and colleagues show that DNA methylation changes in inflammatory bowel disease are related to the underlying genotype, and are associated with cell-specific changes to gene expression.

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          Most cited references35

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          High density DNA methylation array with single CpG site resolution.

          We have developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of the human genome. The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel. The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts. The well-characterized Infinium® Assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA. We applied this technology to analyze DNA methylation in normal and tumor DNA samples and compared results with whole-genome bisulfite sequencing (WGBS) data obtained for the same samples. Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95). The ability to determine genome-wide methylation patterns will rapidly advance methylation research. Copyright © 2011 Elsevier Inc. All rights reserved.
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            Repurposing the CRISPR-Cas9 system for targeted DNA methylation

            Epigenetic studies relied so far on correlations between epigenetic marks and gene expression pattern. Technologies developed for epigenome editing now enable direct study of functional relevance of precise epigenetic modifications and gene regulation. The reversible nature of epigenetic modifications, including DNA methylation, has been already exploited in cancer therapy for remodeling the aberrant epigenetic landscape. However, this was achieved non-selectively using epigenetic inhibitors. Epigenetic editing at specific loci represents a novel approach that might selectively and heritably alter gene expression. Here, we developed a CRISPR-Cas9-based tool for specific DNA methylation consisting of deactivated Cas9 (dCas9) nuclease and catalytic domain of the DNA methyltransferase DNMT3A targeted by co–expression of a guide RNA to any 20 bp DNA sequence followed by the NGG trinucleotide. We demonstrated targeted CpG methylation in a ∼35 bp wide region by the fusion protein. We also showed that multiple guide RNAs could target the dCas9-DNMT3A construct to multiple adjacent sites, which enabled methylation of a larger part of the promoter. DNA methylation activity was specific for the targeted region and heritable across mitotic divisions. Finally, we demonstrated that directed DNA methylation of a wider promoter region of the target loci IL6ST and BACH2 decreased their expression.
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              L1-regularization path algorithm for generalized linear models

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                Author and article information

                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group
                2041-1723
                25 November 2016
                2016
                : 7
                : 13507
                Affiliations
                [1 ]Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, University of Edinburgh , Edinburgh EH4 6XU, UK
                [2 ]CNAG-CRG, Centro Nacional de Análisis Genómico, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST) , Baldiri i Reixac 4, Barcelona 08028, Spain
                [3 ]Universitat Pompeu Fabra (UPF) , Barcelona 08002, Spain
                [4 ]Department of Child Life and Health, University of Edinburgh , Edinburgh EH9 1UW, UK
                [5 ]Genos Glycoscience Research Laboratory , Hondlova 2/11, Zagreb 10000, Croatia
                [6 ]Centre for Population Health Sciences, University of Edinburgh , Edinburgh EH8 9AG, UK
                [7 ]F.Widjaja Family Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center , Los Angeles, California 90048, USA
                [8 ]Department of Medical and Surgical Sciences, Division of Gastroenterology University Hospital Careggi , Largo Brambilla 3, Florence 50141, Italy
                [9 ]Department of Biochemistry and Molecular Biology, University of Zagreb Faculty of Pharmacy and Biochemistry , A. Kovačića 1, Zagreb HR-10000, Croatia
                [10 ]IP Research Consulting SAS , 34 rue Carnot 93160 Noisy-le-grand, Paris, France
                [11 ]Center for Proteomics and Metabolomics, Leiden University Medical Center , Zone S3 Albinusdreef 2, Leiden 2333 ZA, The Netherlands
                [12 ]Division of BioAnalytical Chemistry, VU University Amsterdam , De Boelelaan 1083, room M-352, Amsterdam 1081 HV, The Netherlands
                [13 ]Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces , Potsdam-Golm Science Park, Potsdam D-14424, Germany
                [14 ]Ludger Ltd, Culham Science Centre , Oxford OX14 3EB, UK
                [15 ]Paediatric Gastroenterology Unit, AOU Meyer, Viale Pieraccini , Viale Pieraccini 24, Florence 50139, Italy
                [16 ]Department of Medical Sciences, Division of Gastroenterology, IRCCS-CSS Hospital , Viale Cappuccini, 1, S. Giovanni Rotondo, Rotondo, Italy
                [17 ]Division of Gastroenterology, S. Camillo Hospital , Via Portuense 332, Rome I-00149, Italy
                [18 ]Gastrointestinal Unit, University of Padua , Hospital Via Giustiniani 2, Padua 35128, Italy
                [19 ]IBD Unit, Humanitas Research Institute, Rozzano , Via Manzoni 56, Milan 20089, Italy
                [20 ]Department of Gastroenterology, Western General Hospital , Edinburgh EH4 6XU, UK
                [21 ]Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and Medical Research Council Human Genetics Unit , Edinburgh EH4 6XU, UK
                [22 ]Wellcome Trust Clinical Research Facility, University of Edinburgh, Western General Hospital , Edinburgh EH4 6XU, UK
                [23 ]Institute of Cytology and Genetics SB RAS , Novosibirsk 630090, Russia
                [24 ]Novosibirsk State University , Novosibirsk 630090, Russia
                [25 ]Maastricht University Medical Centre (MUMC) , P. Debyelaan 25, Maastricht 6229 HX, The Netherlands
                [26 ]Akershus University Hospital, Department of Gastroenterology , Sykehusveien 25, Lørenskog 1478, Akershus, Norway
                [27 ]Oslo University Hospital, Department of Gastroenterology , Bygg 6, 3 etg. Kirkeveien 166, Oslo N-0424, Norway
                [28 ]Linköping University Hospital, Department of Surgery , Linköping 581 83, Sweden
                [29 ]Department of Gastroenterology and Hepatology, UHL, County Council of Östergötland , Linköping 581 85, Sweden
                [30 ]Örebro University, Department of Gastroenterology, Faculty of Medicine and Health, Långhuset , Fakultetsgatan 1, Örebro 702 81, Sweden
                [31 ]University of Zaragoza, Gastroenterology , Calle de Pedro Cerbuna, 12, Zaragoza 50009, Spain
                [32 ]BioCruces Health Research Institute, Cruces Plaza , Barakaldo, Bilbao 48903, Spain
                [33 ]Department of Biosciences and Nutrition, Karolinska Institutet , Stockholm SE-171 77, Sweden
                [34 ]Olink Proteomics, Uppsala Science Park , Hammarskjölds väg 52A, Uppsala 752 37, Sweden
                [35 ]Diagenode, Liege Science Park , Rue du Bois Saint-Jean 3, Liège 4102, Belgium
                [36 ]Genetic Analysis, Storo , Nycoveien 2, Oslo 0485, Norway
                Author notes
                Author information
                http://orcid.org/0000-0002-9550-0897
                Article
                ncomms13507
                10.1038/ncomms13507
                5133631
                27886173
                7e4de8de-579b-4dd2-9392-de59f0c3a66d
                Copyright © 2016, The Author(s)

                This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/

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                : 23 March 2016
                : 11 October 2016
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