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Methylation QTL

Rainer Malik, Martin Dichgans
Stroke, ischemic stroke and subtypes of ischemic stroke display substantial heritability. Compared to related vascular conditions, the number of established risk loci reaching genome-wide significance for association with stroke is still in the lower range, particularly for etiological stroke subtypes such as large artery atherosclerotic stroke or small vessel stroke. Nevertheless, for individual loci substantial progress has been made in determining the specific mechanisms mediating stroke risk. In this review, we present a roadmap for functional follow-up of common risk variants associated with stroke...
March 15, 2018: Cardiovascular Research
F Nicole Dijk, Chengjian Xu, Erik Melén, Anne-Elie Carsin, Asish Kumar, Ilja M Nolte, Olena Gruzieva, Goran Pershagen, Neomi S Grotenboer, Olga E M Savenije, Josep Maria Antó, Iris Lavi, Carlota Dobaño, Jean Bousquet, Pieter van der Vlies, Ralf J P van der Valk, Johan C de Jongste, Martijn C Nawijn, Stefano Guerra, Dirkje S Postma, Gerard H Koppelman
Interleukin-1 receptor-like 1 ( IL1RL1 ) is an important asthma gene. (Epi)genetic regulation of IL1RL1 protein expression has not been established. We assessed the association between IL1RL1 single nucleotide polymorphisms (SNPs), IL1RL1 methylation and serum IL1RL1-a protein levels, and aimed to identify causal pathways in asthma.Associations of IL1RL1 SNPs with asthma were determined in the Dutch Asthma Genome-wide Association Study cohort and three European birth cohorts, BAMSE (Children/Barn, Allergy, Milieu, Stockholm, an Epidemiological survey), INMA (Infancia y Medio Ambiente) and PIAMA (Prevention and Incidence of Asthma and Mite Allergy), participating in the Mechanisms of the Development of Allergy study...
March 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
Brandon L Pierce, Lin Tong, Maria Argos, Kathryn Demanelis, Farzana Jasmine, Muhammad Rakibuz-Zaman, Golam Sarwar, Md Tariqul Islam, Hasan Shahriar, Tariqul Islam, Mahfuzar Rahman, Md Yunus, Muhammad G Kibriya, Lin S Chen, Habibul Ahsan
Inherited genetic variation affects local gene expression and DNA methylation in humans. Most expression quantitative trait loci (cis-eQTLs) occur at the same genomic location as a methylation QTL (cis-meQTL), suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, here we use co-localization methods to identify eQTL-meQTL pairs likely to share a causal variant. We use partial correlation and mediation analyses to identify >400 of these pairs showing evidence of a causal relationship between expression and methylation (i...
February 23, 2018: Nature Communications
Navot Galpaz, Itay Gonda, Doron Shem-Tov, Omer Barad, Galil Tzuri, Shery Lev, Zhangjun Fei, Yimin Xu, Nadia Lombardi, Linyong Mao, Chen Jiao, Rotem Harel-Beja, Adi Doron-Faigenboim, Oren Tzfadia, Einat Bar, Ayala Meir, Uzi Sa'ar, Aaron Fait, Eran Halperin, Merav Kenigswald, Elazar Fallik, Guy Kol, Gil Ronen, Yosef Burger, Amit Gur, Ya'akov Tadmor, Vitaly Portnoy, Arthur A Schaffer, Efraim Lewinsohn, James J Giovannoni, Nurit Katzir
Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic and transcriptomic data from a melon recombinant inbred line (RIL) population. RNA sequencing (RNA-Seq) of fruit from 96 RILs yielded a highly saturated collection of >58,000 single-nucleotide polymorphisms, identifying 6,636 recombination events that separated the genome into 3,663 genomic bins. Bin-based QTL analysis of 79 RILs and 129 fruit-quality traits affecting taste, aroma and color resulted in the mapping of 241 QTL...
January 31, 2018: Plant Journal: for Cell and Molecular Biology
Chandra Bhan Yadav, Garima Pandey, Mehanathan Muthamilarasan, Manoj Prasad
The genetic material DNA in association with histone proteins forms the complex structure called chromatin, which is prone to undergo modification through certain epigenetic mechanisms including cytosine DNA methylation, histone modifications, and small RNA-mediated methylation. Alterations in chromatin structure lead to inaccessibility of genomic DNA to various regulatory proteins such as transcription factors, which eventually modulates gene expression. Advancements in high-throughput sequencing technologies have provided the opportunity to study the epigenetic mechanisms at genome-wide levels...
January 23, 2018: Advances in Biochemical Engineering/biotechnology
Jarrett D Morrow, Kimberly Glass, Michael H Cho, Craig P Hersh, Victor Pinto-Plata, Bartolome Celli, Nathaniel Marchetti, Gerard Criner, Raphael Bueno, George Washko, Augustine M K Choi, John Quackenbush, Edwin K Silverman, Dawn L DeMeo
RATIONALE: As the third leading cause of death in the United States, the impact of chronic obstructive pulmonary disease (COPD) makes identification of its molecular mechanisms of great importance. Genome-wide association studies have identified multiple genomic regions associated with COPD. However, genetic variation only explains a small fraction of the susceptibility to COPD and sub-genome-wide significant loci may play a role in pathogenesis. OBJECTIVES: Regulatory annotation with epigenetic evidence may give priority for further investigation, particularly for GWAS associations in non-coding regions...
January 9, 2018: American Journal of Respiratory and Critical Care Medicine
Riccardo E Marioni, Allan F McRae, Jan Bressler, Elena Colicino, Eilis Hannon, Shuo Li, Diddier Prada, Jennifer A Smith, Letizia Trevisi, Pei-Chien Tsai, Dina Vojinovic, Jeannette Simino, Daniel Levy, Chunyu Liu, Michael Mendelson, Claudia L Satizabal, Qiong Yang, Min A Jhun, Sharon L R Kardia, Wei Zhao, Stefania Bandinelli, Luigi Ferrucci, Dena G Hernandez, Andrew B Singleton, Sarah E Harris, John M Starr, Douglas P Kiel, Robert R McLean, Allan C Just, Joel Schwartz, Avron Spiro, Pantel Vokonas, Najaf Amin, M Arfan Ikram, Andre G Uitterlinden, Joyce B J van Meurs, Tim D Spector, Claire Steves, Andrea A Baccarelli, Jordana T Bell, Cornelia M van Duijn, Myriam Fornage, Yi-Hsiang Hsu, Jonathan Mill, Thomas H Mosley, Sudha Seshadri, Ian J Deary
Cognitive functions are important correlates of health outcomes across the life-course. Individual differences in cognitive functions are partly heritable. Epigenetic modifications, such as DNA methylation, are susceptible to both genetic and environmental factors and may provide insights into individual differences in cognitive functions. Epigenome-wide meta-analyses for blood-based DNA methylation levels at ~420,000 CpG sites were performed for seven measures of cognitive functioning using data from 11 cohorts...
January 8, 2018: Molecular Psychiatry
Rosana A Estévez, Miriam G Contreras Mostazo, Eduardo Rodriguez, Juan Carlos Espinoza, Juan Kuznar, Zophonías O Jónsson, Guðmundur H Guðmundsson, Valerie H Maier
Maintaining fish health is one of the most important aims in aquaculture. Prevention of fish diseases therefore is crucial and can be achieved by various different strategies, including most often a combination of different methods such as optimal feed and fish density, as well as strengthening the immune system. Understanding the fish innate immune system and developing methods to activate it, in an effort to prevent infections in the first place, has been a goal in recent years. In this study we choose different inducers of the innate immune system and examined their effects in vitro on the salmon cell line CHSE-214...
January 2018: Fish & Shellfish Immunology
D B Hancock, Y Guo, G W Reginsson, N C Gaddis, S M Lutz, R Sherva, A Loukola, C C Minica, C A Markunas, Y Han, K A Young, D F Gudbjartsson, F Gu, D W McNeil, B Qaiser, C Glasheen, S Olson, M T Landi, P A F Madden, L A Farrer, J Vink, N L Saccone, M C Neale, H R Kranzler, J McKay, R J Hung, C I Amos, M L Marazita, D I Boomsma, T B Baker, J Gelernter, J Kaprio, N E Caporaso, T E Thorgeirsson, J E Hokanson, L J Bierut, K Stefansson, E O Johnson
Cigarette smoking is a leading cause of preventable mortality worldwide. Nicotine dependence, which reduces the likelihood of quitting smoking, is a heritable trait with firmly established associations with sequence variants in nicotine acetylcholine receptor genes and at other loci. To search for additional loci, we conducted a genome-wide association study (GWAS) meta-analysis of nicotine dependence, totaling 38,602 smokers (28,677 Europeans/European Americans and 9925 African Americans) across 15 studies...
October 3, 2017: Molecular Psychiatry
Venea Dara Daygon, Mariafe Calingacion, Louise C Forster, James J De Voss, Brett D Schwartz, Ben Ovenden, David E Alonso, Susan R McCouch, Mary J Garson, Melissa A Fitzgerald
Since it was first characterised in 1983, 2-acetyl-1-pyrroline (2AP) has been considered to be the most important aroma compound in rice. In this study, we show four other amine heterocycles: 6-methyl, 5-oxo-2,3,4,5-tetrahydropyridine (6M5OTP), 2-acetylpyrrole, pyrrole and 1-pyrroline, that correlate strongly with the production of 2AP, and are present in consistent proportions in a set of elite aromatic rice varieties from South East Asia and Australia as well as in a collection of recombinant inbred lines (RILs) derived from indica Jasmine-type varieties, Australian long grain varieties (temperate japonica) and Basmati-type rice (Grp V)...
August 18, 2017: Scientific Reports
Eilis Hannon, Mike Weedon, Nicholas Bray, Michael O'Donovan, Jonathan Mill
Most genetic variants identified in genome-wide association studies (GWASs) of complex traits are thought to act by affecting gene regulation rather than directly altering the protein product. As a consequence, the actual genes involved in disease are not necessarily the most proximal to the associated variants. By integrating data from GWAS analyses with those from genetic studies of regulatory variation, it is possible to identify variants pleiotropically associated with both a complex trait and measures of gene regulation...
June 1, 2017: American Journal of Human Genetics
Lin Zhang, Hong Yu, Bin Ma, Guifu Liu, Jianjun Wang, Junmin Wang, Rongcun Gao, Jinjun Li, Jiyun Liu, Jing Xu, Yingying Zhang, Qun Li, Xuehui Huang, Jianlong Xu, Jianming Li, Qian Qian, Bin Han, Zuhua He, Jiayang Li
Super hybrid rice varieties with ideal plant architecture (IPA) have been critical in enhancing food security worldwide. However, the molecular mechanisms underlying their improved yield remain unclear. Here, we report the identification of a QTL, qWS8/ipa1-2D, in the super rice Yongyou12 (YY12) and related varieties. In-depth genetic molecular characterization of qWS8/ipa1-2D reveals that this newly identified QTL results from three distal naturally occurring tandem repeats upstream of IPA1, a key gene/locus previously shown to shape rice ideal plant architecture and greatly enhance grain yield...
March 20, 2017: Nature Communications
Meiling Zou, Cheng Lu, Shengkui Zhang, Qing Chen, Xianglai Sun, Pingan Ma, Meizhen Hu, Ming Peng, Zilong Ma, Xin Chen, Xincheng Zhou, Haiyan Wang, Subin Feng, Kaixin Fang, Hairong Xie, Zaiyun Li, Kede Liu, Qiongyao Qin, Jinli Pei, Shujuan Wang, Kun Pan, Wenbin Hu, Binxiao Feng, Dayong Fan, Bin Zhou, Chunling Wu, Ming Su, Zhiqiang Xia, Kaimian Li, Wenquan Wang
Cassava (Manihot esculenta Crantz) is an important tropical starchy root crop that is adapted to drought but extremely cold sensitive. A cold-tolerant, high-quality, and robust supply of cassava is urgently needed. Here, we clarify genome-wide distribution and classification of CCGG hemi-methylation and full-methylation, and detected 77 much candidate QTLs(epi) for cold stress and 103 much candidate QTLs(epi) for storage root quality and yield in 186 cassava population, generated by crossing two non-inbred lines with female parent KU50 and male parent SC124 (KS population)...
January 25, 2017: Scientific Reports
Monica Sharma, Rajat Sandhir, Anuradha Singh, Pankaj Kumar, Ankita Mishra, Sanjay Jachak, Sukhvinder P Singh, Jagdeep Singh, Joy Roy
Phenolic compounds (PCs) affect the bread quality and can also affect the other types of end-use food products such as chapatti (unleavened flat bread), now globally recognized wheat-based food product. The detailed analysis of PCs and their biosynthesis genes in diverse bread wheat (Triticum aestivum) varieties differing for chapatti quality have not been studied. In this study, the identification and quantification of PCs using UPLC-QTOF-MS and/or MS/MS and functional genomics techniques such as microarrays and qRT-PCR of their biosynthesis genes have been studied in a good chapatti variety, "C 306" and a poor chapatti variety, "Sonalika...
2016: Frontiers in Plant Science
Xuewen Xu, Jing Ji, Qiang Xu, Xiaohua Qi, Xuehao Chen
The hypocotyl-derived adventitious root (AR) is an important morphological acclimation to waterlogging stress; however, its genetic basis has not been adequately understood. In the present study, a mixed major gene plus polygene inheritance model was used to analyze AR numbers (ARN) 7 days after waterlogging treatment in six generations (P1, P2, F1, B1, B2, and F2), using cucumber waterlogging tolerant line Zaoer-N and sensitive Pepino as parents. The results showed that the genetic model D-4, mixed one negative dominance major gene and additive-dominance polygenes, is the best-fitting genetic model for waterlogging-triggered ARN phenotype...
April 2017: Molecular Genetics and Genomics: MGG
Åsa K Hedman, Mihkel Zilmer, Johan Sundström, Lars Lind, Erik Ingelsson
BACKGROUND: Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits and disease may be partly mediated through changes in epigenetic marks (e.g. DNA methylation). Studies relating differential methylation with intermediate phenotypes and disease endpoints may be useful in identifying additional candidate genes and mechanisms involved in disease...
November 25, 2016: BMC Medical Genomics
Lu Chen, Bing Ge, Francesco Paolo Casale, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yan, Kousik Kundu, Simone Ecker, Avik Datta, David Richardson, Frances Burden, Daniel Mead, Alice L Mann, Jose Maria Fernandez, Sophia Rowlston, Steven P Wilder, Samantha Farrow, Xiaojian Shao, John J Lambourne, Adriana Redensek, Cornelis A Albers, Vyacheslav Amstislavskiy, Sofie Ashford, Kim Berentsen, Lorenzo Bomba, Guillaume Bourque, David Bujold, Stephan Busche, Maxime Caron, Shu-Huang Chen, Warren Cheung, Oliver Delaneau, Emmanouil T Dermitzakis, Heather Elding, Irina Colgiu, Frederik O Bagger, Paul Flicek, Ehsan Habibi, Valentina Iotchkova, Eva Janssen-Megens, Bowon Kim, Hans Lehrach, Ernesto Lowy, Amit Mandoli, Filomena Matarese, Matthew T Maurano, John A Morris, Vera Pancaldi, Farzin Pourfarzad, Karola Rehnstrom, Augusto Rendon, Thomas Risch, Nilofar Sharifi, Marie-Michelle Simon, Marc Sultan, Alfonso Valencia, Klaudia Walter, Shuang-Yin Wang, Mattia Frontini, Stylianos E Antonarakis, Laura Clarke, Marie-Laure Yaspo, Stephan Beck, Roderic Guigo, Daniel Rico, Joost H A Martens, Willem H Ouwehand, Taco W Kuijpers, Dirk S Paul, Hendrik G Stunnenberg, Oliver Stegle, Kate Downes, Tomi Pastinen, Nicole Soranzo
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14(+) monocytes, CD16(+) neutrophils, and naive CD4(+) T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies...
November 17, 2016: Cell
Sandeep K Singh, Philip J Lupo, Michael E Scheurer, Anshul Saxena, Amy E Kennedy, Boubakari Ibrahimou, Manuel Alejandro Barbieri, Ken I Mills, Jacob L McCauley, Mehmet Fatih Okcu, Mehmet Tevfik Dorak
Childhood acute lymphoblastic leukemia (ALL) occurs more frequently in males. Reasons behind sex differences in childhood ALL risk are unknown. In the present genome-wide association study (GWAS), we explored the genetic basis of sex differences by comparing genotype frequencies between male and female cases in a case-only study to assess effect-modification by sex.The case-only design included 236 incident cases of childhood ALL consecutively recruited at the Texas Children's Cancer Center in Houston, Texas from 2007 to 2012...
November 2016: Medicine (Baltimore)
Yoo-Jeong Han, Jing Zhang, Yonglan Zheng, Dezheng Huo, Olufunmilayo I Olopade
Genome wide association studies (GWAS) have identified low penetrance and high frequency single nucleotide polymorphisms (SNPs) that contribute to genetic susceptibility of breast cancer. The SNPs at 16q12, close to the TOX3 and CASC16 genes, represent one of the susceptibility loci identified by GWAS, showing strong evidence for breast cancer association across various populations. To examine molecular mechanisms of TOX3 regulation in breast cancer, we investigated both genetic and epigenetic factors using cell lines and datasets derived from primary breast tumors available through The Cancer Genome Atlas (TCGA)...
2016: PloS One
Peilin Jia, Guangchun Han, Junfei Zhao, Pinyi Lu, Zhongming Zhao
SZGR 2.0 is a comprehensive resource of candidate variants and genes for schizophrenia, covering genetic, epigenetic, transcriptomic, translational and many other types of evidence. By systematic review and curation of multiple lines of evidence, we included almost all variants and genes that have ever been reported to be associated with schizophrenia. In particular, we collected ∼4200 common variants reported in genome-wide association studies, ∼1000 de novo mutations discovered by large-scale sequencing of family samples, 215 genes spanning rare and replication copy number variations, 99 genes overlapping with linkage regions, 240 differentially expressed genes, 4651 differentially methylated genes and 49 genes as antipsychotic drug targets...
January 4, 2017: Nucleic Acids Research
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