Literature DB >> 32238907

CpG-SNP site methylation regulates allele-specific expression of MTHFD1 gene in type 2 diabetes.

Manik Vohra1, Prabha Adhikari2, Sydney C D' Souza3, Shivashankar K Nagri4, Shashikiran Umakanth5, Kapaettu Satyamoorthy6, Padmalatha S Rai7.   

Abstract

The interaction of genetic and epigenetic mechanisms is one of the underlying causes of phenotypic variability in complex diseases such as type 2 diabetes (T2D). To explore the influence of genetic and epigenetic changes in T2D, we examined the effect of methylation of CpG-SNP sites on allele-specific expression (ASE) in one-carbon metabolism pathway genes in T2D. Case-control study was conducted on 860 individuals (430 T2D and 430 controls). CpG-SNPs shortlisted through in silico analysis were genotyped using tetra ARMS PCR and validated using Sanger DNA sequencing. Global DNA methylation was carried out using RP-HPLC. Promoter DNA methylation and CpG site-specific methylation were carried out using bisulfite sequencing. mRNA expression and ASE were examined by SYBR green and TaqMan assay, respectively. Four exonic CpG-SNPs of MTHFD1, MTRR, and GGH genes were identified in folate pathway genes. Among these, MTHFD1 rs2236225 showed significant association with T2D independent of obesity, displayed ASE, and correlated with CpG-SNP site-specific methylation when compared with controls. Our results demonstrate that SNP rs2236225 in the CpG site of MTHFD1, which regulates allele-specific gene expression in PBMCs is methylation dependent and may perturb one-carbon metabolism pathway in T2D subjects.

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Year:  2020        PMID： 32238907     DOI： 10.1038/s41374-020-0422-7

Source DB:  PubMed          Journal:  Lab Invest        ISSN： 0023-6837            Impact factor:   5.662


  43 in total

1.  Identification of low-frequency and rare sequence variants associated with elevated or reduced risk of type 2 diabetes.

Authors:  Valgerdur Steinthorsdottir; Gudmar Thorleifsson; Patrick Sulem; Hannes Helgason; Niels Grarup; Asgeir Sigurdsson; Hafdis T Helgadottir; Hrefna Johannsdottir; Olafur T Magnusson; Sigurjon A Gudjonsson; Johanne M Justesen; Marie N Harder; Marit E Jørgensen; Cramer Christensen; Ivan Brandslund; Annelli Sandbæk; Torsten Lauritzen; Henrik Vestergaard; Allan Linneberg; Torben Jørgensen; Torben Hansen; Maryam S Daneshpour; Mohammad-Sadegh Fallah; Astradur B Hreidarsson; Gunnar Sigurdsson; Fereidoun Azizi; Rafn Benediktsson; Gisli Masson; Agnar Helgason; Augustine Kong; Daniel F Gudbjartsson; Oluf Pedersen; Unnur Thorsteinsdottir; Kari Stefansson
Journal:  Nat Genet       Date:  2014-01-26       Impact factor: 38.330

Review 2.  Genetic and environmental factors associated with type 2 diabetes and diabetic vascular complications.

Authors:  Mariana Murea; Lijun Ma; Barry I Freedman
Journal:  Rev Diabet Stud       Date:  2012-05-10

3.  Twelve type 2 diabetes susceptibility loci identified through large-scale association analysis.

Authors:  Benjamin F Voight; Laura J Scott; Valgerdur Steinthorsdottir; Andrew P Morris; Christian Dina; Ryan P Welch; Eleftheria Zeggini; Cornelia Huth; Yurii S Aulchenko; Gudmar Thorleifsson; Laura J McCulloch; Teresa Ferreira; Harald Grallert; Najaf Amin; Guanming Wu; Cristen J Willer; Soumya Raychaudhuri; Steve A McCarroll; Claudia Langenberg; Oliver M Hofmann; Josée Dupuis; Lu Qi; Ayellet V Segrè; Mandy van Hoek; Pau Navarro; Kristin Ardlie; Beverley Balkau; Rafn Benediktsson; Amanda J Bennett; Roza Blagieva; Eric Boerwinkle; Lori L Bonnycastle; Kristina Bengtsson Boström; Bert Bravenboer; Suzannah Bumpstead; Noisël P Burtt; Guillaume Charpentier; Peter S Chines; Marilyn Cornelis; David J Couper; Gabe Crawford; Alex S F Doney; Katherine S Elliott; Amanda L Elliott; Michael R Erdos; Caroline S Fox; Christopher S Franklin; Martha Ganser; Christian Gieger; Niels Grarup; Todd Green; Simon Griffin; Christopher J Groves; Candace Guiducci; Samy Hadjadj; Neelam Hassanali; Christian Herder; Bo Isomaa; Anne U Jackson; Paul R V Johnson; Torben Jørgensen; Wen H L Kao; Norman Klopp; Augustine Kong; Peter Kraft; Johanna Kuusisto; Torsten Lauritzen; Man Li; Aloysius Lieverse; Cecilia M Lindgren; Valeriya Lyssenko; Michel Marre; Thomas Meitinger; Kristian Midthjell; Mario A Morken; Narisu Narisu; Peter Nilsson; Katharine R Owen; Felicity Payne; John R B Perry; Ann-Kristin Petersen; Carl Platou; Christine Proença; Inga Prokopenko; Wolfgang Rathmann; N William Rayner; Neil R Robertson; Ghislain Rocheleau; Michael Roden; Michael J Sampson; Richa Saxena; Beverley M Shields; Peter Shrader; Gunnar Sigurdsson; Thomas Sparsø; Klaus Strassburger; Heather M Stringham; Qi Sun; Amy J Swift; Barbara Thorand; Jean Tichet; Tiinamaija Tuomi; Rob M van Dam; Timon W van Haeften; Thijs van Herpt; Jana V van Vliet-Ostaptchouk; G Bragi Walters; Michael N Weedon; Cisca Wijmenga; Jacqueline Witteman; Richard N Bergman; Stephane Cauchi; Francis S Collins; Anna L Gloyn; Ulf Gyllensten; Torben Hansen; Winston A Hide; Graham A Hitman; Albert Hofman; David J Hunter; Kristian Hveem; Markku Laakso; Karen L Mohlke; Andrew D Morris; Colin N A Palmer; Peter P Pramstaller; Igor Rudan; Eric Sijbrands; Lincoln D Stein; Jaakko Tuomilehto; Andre Uitterlinden; Mark Walker; Nicholas J Wareham; Richard M Watanabe; Gonçalo R Abecasis; Bernhard O Boehm; Harry Campbell; Mark J Daly; Andrew T Hattersley; Frank B Hu; James B Meigs; James S Pankow; Oluf Pedersen; H-Erich Wichmann; Inês Barroso; Jose C Florez; Timothy M Frayling; Leif Groop; Rob Sladek; Unnur Thorsteinsdottir; James F Wilson; Thomas Illig; Philippe Froguel; Cornelia M van Duijn; Kari Stefansson; David Altshuler; Michael Boehnke; Mark I McCarthy
Journal:  Nat Genet       Date:  2010-07       Impact factor: 38.330

4.  Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.

Authors:  Jaspal S Kooner; Danish Saleheen; Xueling Sim; Joban Sehmi; Weihua Zhang; Philippe Frossard; Latonya F Been; Kee-Seng Chia; Antigone S Dimas; Neelam Hassanali; Tazeen Jafar; Jeremy B M Jowett; Xinzhong Li; Venkatesan Radha; Simon D Rees; Fumihiko Takeuchi; Robin Young; Tin Aung; Abdul Basit; Manickam Chidambaram; Debashish Das; Elin Grundberg; Asa K Hedman; Zafar I Hydrie; Muhammed Islam; Chiea-Chuen Khor; Sudhir Kowlessur; Malene M Kristensen; Samuel Liju; Wei-Yen Lim; David R Matthews; Jianjun Liu; Andrew P Morris; Alexandra C Nica; Janani M Pinidiyapathirage; Inga Prokopenko; Asif Rasheed; Maria Samuel; Nabi Shah; A Samad Shera; Kerrin S Small; Chen Suo; Ananda R Wickremasinghe; Tien Yin Wong; Mingyu Yang; Fan Zhang; Goncalo R Abecasis; Anthony H Barnett; Mark Caulfield; Panos Deloukas; Timothy M Frayling; Philippe Froguel; Norihiro Kato; Prasad Katulanda; M Ann Kelly; Junbin Liang; Viswanathan Mohan; Dharambir K Sanghera; James Scott; Mark Seielstad; Paul Z Zimmet; Paul Elliott; Yik Ying Teo; Mark I McCarthy; John Danesh; E Shyong Tai; John C Chambers
Journal:  Nat Genet       Date:  2011-08-28       Impact factor: 38.330

5.  Meta-analysis of genome-wide association studies identifies eight new loci for type 2 diabetes in east Asians.

Authors:  Yoon Shin Cho; Chien-Hsiun Chen; Cheng Hu; Jirong Long; Rick Twee Hee Ong; Xueling Sim; Fumihiko Takeuchi; Ying Wu; Min Jin Go; Toshimasa Yamauchi; Yi-Cheng Chang; Soo Heon Kwak; Ronald C W Ma; Ken Yamamoto; Linda S Adair; Tin Aung; Qiuyin Cai; Li-Ching Chang; Yuan-Tsong Chen; Yutang Gao; Frank B Hu; Hyung-Lae Kim; Sangsoo Kim; Young Jin Kim; Jeannette Jen-Mai Lee; Nanette R Lee; Yun Li; Jian Jun Liu; Wei Lu; Jiro Nakamura; Eitaro Nakashima; Daniel Peng-Keat Ng; Wan Ting Tay; Fuu-Jen Tsai; Tien Yin Wong; Mitsuhiro Yokota; Wei Zheng; Rong Zhang; Congrong Wang; Wing Yee So; Keizo Ohnaka; Hiroshi Ikegami; Kazuo Hara; Young Min Cho; Nam H Cho; Tien-Jyun Chang; Yuqian Bao; Åsa K Hedman; Andrew P Morris; Mark I McCarthy; Ryoichi Takayanagi; Kyong Soo Park; Weiping Jia; Lee-Ming Chuang; Juliana C N Chan; Shiro Maeda; Takashi Kadowaki; Jong-Young Lee; Jer-Yuarn Wu; Yik Ying Teo; E Shyong Tai; Xiao Ou Shu; Karen L Mohlke; Norihiro Kato; Bok-Ghee Han; Mark Seielstad
Journal:  Nat Genet       Date:  2011-12-11       Impact factor: 38.330

Review 6.  Genetics of type 2 diabetes-pitfalls and possibilities.

Authors:  Rashmi B Prasad; Leif Groop
Journal:  Genes (Basel)       Date:  2015-03-12       Impact factor: 4.096

Review 7.  Recent progress in genetic and epigenetic research on type 2 diabetes.

Authors:  Soo Heon Kwak; Kyong Soo Park
Journal:  Exp Mol Med       Date:  2016-03-11       Impact factor: 8.718

8.  Allele-specific expression reveals interactions between genetic variation and environment.

Authors:  David A Knowles; Joe R Davis; Hilary Edgington; Anil Raj; Marie-Julie Favé; Xiaowei Zhu; James B Potash; Myrna M Weissman; Jianxin Shi; Douglas F Levinson; Philip Awadalla; Sara Mostafavi; Stephen B Montgomery; Alexis Battle
Journal:  Nat Methods       Date:  2017-05-22       Impact factor: 28.547

9.  Genome-wide association study in a Chinese population identifies a susceptibility locus for type 2 diabetes at 7q32 near PAX4.

Authors:  R C W Ma; C Hu; C H Tam; R Zhang; P Kwan; T F Leung; G N Thomas; M J Go; K Hara; X Sim; J S K Ho; C Wang; H Li; L Lu; Y Wang; J W Li; Y Wang; V K L Lam; J Wang; W Yu; Y J Kim; D P Ng; H Fujita; K Panoutsopoulou; A G Day-Williams; H M Lee; A C W Ng; Y-J Fang; A P S Kong; F Jiang; X Ma; X Hou; S Tang; J Lu; T Yamauchi; S K W Tsui; J Woo; P C Leung; X Zhang; N L S Tang; H Y Sy; J Liu; T Y Wong; J Y Lee; S Maeda; G Xu; S S Cherny; T F Chan; M C Y Ng; K Xiang; A P Morris; S Keildson; R Hu; L Ji; X Lin; Y S Cho; T Kadowaki; E S Tai; E Zeggini; M I McCarthy; K L Hon; L Baum; B Tomlinson; W Y So; Y Bao; J C N Chan; W Jia
Journal:  Diabetologia       Date:  2013-03-27       Impact factor: 10.122

10.  Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.

Authors:  Andrew P Morris; Benjamin F Voight; Tanya M Teslovich; Teresa Ferreira; Ayellet V Segrè; Valgerdur Steinthorsdottir; Rona J Strawbridge; Hassan Khan; Harald Grallert; Anubha Mahajan; Inga Prokopenko; Hyun Min Kang; Christian Dina; Tonu Esko; Ross M Fraser; Stavroula Kanoni; Ashish Kumar; Vasiliki Lagou; Claudia Langenberg; Jian'an Luan; Cecilia M Lindgren; Martina Müller-Nurasyid; Sonali Pechlivanis; N William Rayner; Laura J Scott; Steven Wiltshire; Loic Yengo; Leena Kinnunen; Elizabeth J Rossin; Soumya Raychaudhuri; Andrew D Johnson; Antigone S Dimas; Ruth J F Loos; Sailaja Vedantam; Han Chen; Jose C Florez; Caroline Fox; Ching-Ti Liu; Denis Rybin; David J Couper; Wen Hong L Kao; Man Li; Marilyn C Cornelis; Peter Kraft; Qi Sun; Rob M van Dam; Heather M Stringham; Peter S Chines; Krista Fischer; Pierre Fontanillas; Oddgeir L Holmen; Sarah E Hunt; Anne U Jackson; Augustine Kong; Robert Lawrence; Julia Meyer; John R B Perry; Carl G P Platou; Simon Potter; Emil Rehnberg; Neil Robertson; Suthesh Sivapalaratnam; Alena Stančáková; Kathleen Stirrups; Gudmar Thorleifsson; Emmi Tikkanen; Andrew R Wood; Peter Almgren; Mustafa Atalay; Rafn Benediktsson; Lori L Bonnycastle; Noël Burtt; Jason Carey; Guillaume Charpentier; Andrew T Crenshaw; Alex S F Doney; Mozhgan Dorkhan; Sarah Edkins; Valur Emilsson; Elodie Eury; Tom Forsen; Karl Gertow; Bruna Gigante; George B Grant; Christopher J Groves; Candace Guiducci; Christian Herder; Astradur B Hreidarsson; Jennie Hui; Alan James; Anna Jonsson; Wolfgang Rathmann; Norman Klopp; Jasmina Kravic; Kaarel Krjutškov; Cordelia Langford; Karin Leander; Eero Lindholm; Stéphane Lobbens; Satu Männistö; Ghazala Mirza; Thomas W Mühleisen; Bill Musk; Melissa Parkin; Loukianos Rallidis; Jouko Saramies; Bengt Sennblad; Sonia Shah; Gunnar Sigurðsson; Angela Silveira; Gerald Steinbach; Barbara Thorand; Joseph Trakalo; Fabrizio Veglia; Roman Wennauer; Wendy Winckler; Delilah Zabaneh; Harry Campbell; Cornelia van Duijn; Andre G Uitterlinden; Albert Hofman; Eric Sijbrands; Goncalo R Abecasis; Katharine R Owen; Eleftheria Zeggini; Mieke D Trip; Nita G Forouhi; Ann-Christine Syvänen; Johan G Eriksson; Leena Peltonen; Markus M Nöthen; Beverley Balkau; Colin N A Palmer; Valeriya Lyssenko; Tiinamaija Tuomi; Bo Isomaa; David J Hunter; Lu Qi; Alan R Shuldiner; Michael Roden; Ines Barroso; Tom Wilsgaard; John Beilby; Kees Hovingh; Jackie F Price; James F Wilson; Rainer Rauramaa; Timo A Lakka; Lars Lind; George Dedoussis; Inger Njølstad; Nancy L Pedersen; Kay-Tee Khaw; Nicholas J Wareham; Sirkka M Keinanen-Kiukaanniemi; Timo E Saaristo; Eeva Korpi-Hyövälti; Juha Saltevo; Markku Laakso; Johanna Kuusisto; Andres Metspalu; Francis S Collins; Karen L Mohlke; Richard N Bergman; Jaakko Tuomilehto; Bernhard O Boehm; Christian Gieger; Kristian Hveem; Stephane Cauchi; Philippe Froguel; Damiano Baldassarre; Elena Tremoli; Steve E Humphries; Danish Saleheen; John Danesh; Erik Ingelsson; Samuli Ripatti; Veikko Salomaa; Raimund Erbel; Karl-Heinz Jöckel; Susanne Moebus; Annette Peters; Thomas Illig; Ulf de Faire; Anders Hamsten; Andrew D Morris; Peter J Donnelly; Timothy M Frayling; Andrew T Hattersley; Eric Boerwinkle; Olle Melander; Sekar Kathiresan; Peter M Nilsson; Panos Deloukas; Unnur Thorsteinsdottir; Leif C Groop; Kari Stefansson; Frank Hu; James S Pankow; Josée Dupuis; James B Meigs; David Altshuler; Michael Boehnke; Mark I McCarthy
Journal:  Nat Genet       Date:  2012-08-12       Impact factor: 38.330
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Authors:  Congrong Wang; Rossella Alfano; Brigitte Reimann; Janneke Hogervorst; Mariona Bustamante; Immaculata De Vivo; Michelle Plusquin; Tim S Nawrot; Dries S Martens
Journal:  Front Genet       Date:  2022-10-04       Impact factor: 4.772

2.  CpG site hypomethylation at ETS1‑binding region regulates DLK1 expression in Chinese patients with Tetralogy of Fallot.

Authors:  Guixiang Tian; Lili He; Ruoyi Gu; Jingwei Sun; Weicheng Chen; Yanyan Qian; Xiaojing Ma; Weili Yan; Zhenshan Zhao; Ziqing Xu; Meijiao Suo; Wei Sheng; Guoying Huang
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