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https://www.readbyqxmd.com/read/29149290/discovering-the-3-utr-mediated-regulation-of-alpha-synuclein
#1
Domenica Marchese, Teresa Botta-Orfila, Davide Cirillo, Juan Antonio Rodriguez, Carmen Maria Livi, Rubén Fernández-Santiago, Mario Ezquerra, Maria J Martí, Elias Bechara, Gian Gaetano Tartaglia
Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro/in silico screening we identified RNA-binding proteins (RBPs) that interact with SNCA 3' UTRs. We identified two RBPs, ELAVL1 and TIAR, that bind with high affinity to the most abundant and translationally active 3' UTR isoform (575 nt)...
November 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29142228/genome-wide-mapping-of-genetic-determinants-influencing-dna-methylation-and-gene-expression-in-human-hippocampus
#2
Herbert Schulz, Ann-Kathrin Ruppert, Stefan Herms, Christiane Wolf, Nazanin Mirza-Schreiber, Oliver Stegle, Darina Czamara, Andreas J Forstner, Sugirthan Sivalingam, Susanne Schoch, Susanne Moebus, Benno Pütz, Axel Hillmer, Nadine Fricker, Hartmut Vatter, Bertram Müller-Myhsok, Markus M Nöthen, Albert J Becker, Per Hoffmann, Thomas Sander, Sven Cichon
Emerging evidence emphasizes the strong impact of regulatory genomic elements in neurodevelopmental processes and the complex pathways of brain disorders. The present genome-wide quantitative trait loci analyses explore the cis-regulatory effects of single-nucleotide polymorphisms (SNPs) on DNA methylation (meQTL) and gene expression (eQTL) in 110 human hippocampal biopsies. We identify cis-meQTLs at 14,118 CpG methylation sites and cis-eQTLs for 302 3'-mRNA transcripts of 288 genes. Hippocampal cis-meQTL-CpGs are enriched in flanking regions of active promoters, CpG island shores, binding sites of the transcription factor CTCF and brain eQTLs...
November 15, 2017: Nature Communications
https://www.readbyqxmd.com/read/29138229/genomic-structural-variations-lead-to-dysregulation-of-important-coding-and-non-coding-rna-species-in-dilated-cardiomyopathy
#3
Jan Haas, Stefan Mester, Alan Lai, Karen S Frese, Farbod Sedaghat-Hamedani, Elham Kayvanpour, Tobias Rausch, Rouven Nietsch, Jes-Niels Boeckel, Avisha Carstensen, Mirko Völkers, Carsten Dietrich, Dietmar Pils, Ali Amr, Daniel B Holzer, Diana Martins Bordalo, Daniel Oehler, Tanja Weis, Derliz Mereles, Sebastian Buss, Eva Riechert, Emil Wirsz, Maximilian Wuerstle, Jan O Korbel, Andreas Keller, Hugo A Katus, Andreas E Posch, Benjamin Meder
The transcriptome needs to be tightly regulated by mechanisms that include transcription factors, enhancers, and repressors as well as non-coding RNAs. Besides this dynamic regulation, a large part of phenotypic variability of eukaryotes is expressed through changes in gene transcription caused by genetic variation. In this study, we evaluate genome-wide structural genomic variants (SVs) and their association with gene expression in the human heart. We detected 3,898 individual SVs affecting all classes of gene transcripts (e...
November 14, 2017: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/29114259/identification-of-splicing-quantitative-trait-loci-sqtl-in-drosophila-melanogaster-with-developmental-lead-pb-2-exposure
#4
Wen Qu, Katherine Gurdziel, Roger Pique-Regi, Douglas M Ruden
Lead (Pb) poisoning has been a major public health issue globally and the recent Flint water crisis has drawn nation-wide attention to its effects. To better understand how lead plays a role as a neurotoxin, we utilized the Drosophila melanogaster model to study the genetic effects of lead exposure during development and identified lead-responsive genes. In our previous studies, we have successfully identified hundreds of lead-responsive expression QTLs (eQTLs) by using RNA-seq analysis on heads collected from the Drosophila Synthetic Population Resource...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/29074555/efficient-prioritization-of-multiple-causal-eqtl-variants-via-sparse-polygenic-modeling
#5
Naoki Nariai, William W Greenwald, Christopher DeBoever, He Li, Kelly A Frazer
Expression quantitative trait loci (eQTL) studies have typically used single-variant association analysis to identify genetic variants correlated with gene expression. However, this approach has several drawbacks: causal variants cannot be distinguished from non-functional variants in strong linkage disequilibrium, combined effects from multiple causal variants cannot be captured, and low-frequency (<5% MAF) eQTL variants are difficult to identify. While these issues possibly could be overcome by using sparse polygenic models which associate multiple genetic variants with gene expression simultaneously, the predictive performance of these models for eQTL studies has not been evaluated...
October 26, 2017: Genetics
https://www.readbyqxmd.com/read/29059182/profiling-rna-seq-at-multiple-resolutions-markedly-increases-the-number-of-causal-eqtls-in-autoimmune-disease
#6
Christopher A Odhams, Deborah S Cunninghame Graham, Timothy J Vyse
Genome-wide association studies have identified hundreds of risk loci for autoimmune disease, yet only a minority (~25%) share genetic effects with changes to gene expression (eQTLs) in immune cells. RNA-Seq based quantification at whole-gene resolution, where abundance is estimated by culminating expression of all transcripts or exons of the same gene, is likely to account for this observed lack of colocalisation as subtle isoform switches and expression variation in independent exons can be concealed. We performed integrative cis-eQTL analysis using association statistics from twenty autoimmune diseases (560 independent loci) and RNA-Seq data from 373 individuals of the Geuvadis cohort profiled at gene-, isoform-, exon-, junction-, and intron-level resolution in lymphoblastoid cell lines...
October 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29058714/predicting-causal-variants-affecting-expression-by-using-whole-genome-sequencing-and-rna-seq-from-multiple-human-tissues
#7
Andrew Anand Brown, Ana Viñuela, Olivier Delaneau, Tim D Spector, Kerrin S Small, Emmanouil T Dermitzakis
Genetic association mapping produces statistical links between phenotypes and genomic regions, but identifying causal variants remains difficult. Whole-genome sequencing (WGS) can help by providing complete knowledge of all genetic variants, but it is financially prohibitive for well-powered GWAS studies. We performed mapping of expression quantitative trait loci (eQTLs) with WGS and RNA-seq, and found that lead eQTL variants called with WGS were more likely to be causal. Through simulations, we derived properties of causal variants and used them to develop a method for identifying likely causal SNPs...
October 23, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29053642/allelic-expression-imbalance-in-the-human-retinal-transcriptome-and-potential-impact-on-inherited-retinal-diseases
#8
Pablo Llavona, Michele Pinelli, Margherita Mutarelli, Veer Singh Marwah, Simone Schimpf-Linzenbold, Sebastian Thaler, Efdal Yoeruek, Jan Vetter, Susanne Kohl, Bernd Wissinger
Inherited retinal diseases (IRDs) are often associated with variable clinical expressivity (VE) and incomplete penetrance (IP). Underlying mechanisms may include environmental, epigenetic, and genetic factors. Cis-acting expression quantitative trait loci (cis-eQTLs) can be implicated in the regulation of genes by favoring or hampering the expression of one allele over the other. Thus, the presence of such loci elicits allelic expression imbalance (AEI) that can be traced by massive parallel sequencing techniques...
October 20, 2017: Genes
https://www.readbyqxmd.com/read/29025893/disease-specific-biases-in-alternative-splicing-and-tissue-specific-dysregulation-revealed-by-multitissue-profiling-of-lymphocyte-gene-expression-in-type-1-diabetes
#9
Jeremy R B Newman, Ana Conesa, Matthew Mika, Felicia N New, Suna Onengut-Gumuscu, Mark A Atkinson, Stephen S Rich, Lauren M McIntyre, Patrick Concannon
Genome-wide association studies (GWAS) have identified multiple, shared allelic associations with many autoimmune diseases. However, the pathogenic contributions of variants residing in risk loci remain unresolved. The location of the majority of shared disease-associated variants in noncoding regions suggests they contribute to risk of autoimmunity through effects on gene expression in the immune system. In the current study, we test this hypothesis by applying RNA sequencing to CD4(+), CD8(+), and CD19(+) lymphocyte populations isolated from 81 subjects with type 1 diabetes (T1D)...
November 2017: Genome Research
https://www.readbyqxmd.com/read/28957414/red-blood-cell-distribution-width-genetic-evidence-for-aging-pathways-in-116-666-volunteers
#10
Luke C Pilling, Janice L Atkins, Michael O Duff, Robin N Beaumont, Samuel E Jones, Jessica Tyrrell, Chia-Ling Kuo, Katherine S Ruth, Marcus A Tuke, Hanieh Yaghootkar, Andrew R Wood, Anna Murray, Michael N Weedon, Lorna W Harries, George A Kuchel, Luigi Ferrucci, Timothy M Frayling, David Melzer
INTRODUCTION: Variability in red blood cell volumes (distribution width, RDW) increases with age and is strongly predictive of mortality, incident coronary heart disease and cancer. We investigated inherited genetic variation associated with RDW in 116,666 UK Biobank human volunteers. RESULTS: A large proportion RDW is explained by genetic variants (29%), especially in the older group (60+ year olds, 33.8%, <50 year olds, 28.4%). RDW was associated with 194 independent genetic signals; 71 are known for conditions including autoimmune disease, certain cancers, BMI, Alzheimer's disease, longevity, age at menopause, bone density, myositis, Parkinson's disease, and age-related macular degeneration...
2017: PloS One
https://www.readbyqxmd.com/read/28903782/natural-genetic-variation-of-the-cardiac-transcriptome-in-non-diseased-donors-and-patients-with-dilated-cardiomyopathy
#11
Matthias Heinig, Michiel E Adriaens, Sebastian Schafer, Hanneke W M van Deutekom, Elisabeth M Lodder, James S Ware, Valentin Schneider, Leanne E Felkin, Esther E Creemers, Benjamin Meder, Hugo A Katus, Frank Rühle, Monika Stoll, François Cambien, Eric Villard, Philippe Charron, Andras Varro, Nanette H Bishopric, Alfred L George, Cristobal Dos Remedios, Aida Moreno-Moral, Francesco Pesce, Anja Bauerfeind, Franz Rüschendorf, Carola Rintisch, Enrico Petretto, Paul J Barton, Stuart A Cook, Yigal M Pinto, Connie R Bezzina, Norbert Hubner
BACKGROUND: Genetic variation is an important determinant of RNA transcription and splicing, which in turn contributes to variation in human traits, including cardiovascular diseases. RESULTS: Here we report the first in-depth survey of heart transcriptome variation using RNA-sequencing in 97 patients with dilated cardiomyopathy and 108 non-diseased controls. We reveal extensive differences of gene expression and splicing between dilated cardiomyopathy patients and controls, affecting known as well as novel dilated cardiomyopathy genes...
September 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28879530/correlation-analyses-revealed-global-microrna-mrna-expression-associations-in-human-peripheral-blood-mononuclear-cells
#12
Lan Wang, Jiang Zhu, Fei-Yan Deng, Long-Fei Wu, Xing-Bo Mo, Xiao-Wei Zhu, Wei Xia, Fang-Fei Xie, Pei He, Peng-Fei Bing, Ying-Hua Qiu, Xiang Lin, Xin Lu, Lei Zhang, Neng-Jun Yi, Yong-Hong Zhang, Shu-Feng Lei
MicroRNAs (miRNAs) can regulate gene expression through binding to complementary sites in the 3'-untranslated regions of target mRNAs, which will lead to existence of correlation in expression between miRNA and mRNA. However, the miRNA-mRNA correlation patterns are complex and remain largely unclear yet. To establish the global correlation patterns in human peripheral blood mononuclear cells (PBMCs), multiple miRNA-mRNA correlation analyses and expression quantitative trait locus (eQTL) analysis were conducted in this study...
September 6, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28877428/what-has-gwas-done-for-hla-and-disease-associations
#13
REVIEW
A E Kennedy, U Ozbek, M T Dorak
The major histocompatibility complex (MHC) is located in chromosome 6p21 and contains crucial regulators of immune response, including human leucocyte antigen (HLA) genes, alongside other genes with nonimmunological roles. More recently, a repertoire of noncoding RNA genes, including expressed pseudogenes, has also been identified. The MHC is the most gene dense and most polymorphic part of the human genome. The region exhibits haplotype-specific linkage disequilibrium patterns, contains the strongest cis- and trans-eQTLs/meQTLs in the genome and is known as a hot spot for disease associations...
October 2017: International Journal of Immunogenetics
https://www.readbyqxmd.com/read/28869584/an-xqtl-map-integrates-the-genetic-architecture-of-the-human-brain-s-transcriptome-and-epigenome
#14
Bernard Ng, Charles C White, Hans-Ulrich Klein, Solveig K Sieberts, Cristin McCabe, Ellis Patrick, Jishu Xu, Lei Yu, Chris Gaiteri, David A Bennett, Sara Mostafavi, Philip L De Jager
We report a multi-omic resource generated by applying quantitative trait locus (xQTL) analyses to RNA sequence, DNA methylation and histone acetylation data from the dorsolateral prefrontal cortex of 411 older adults who have all three data types. We identify SNPs significantly associated with gene expression, DNA methylation and histone modification levels. Many of these SNPs influence multiple molecular features, and we demonstrate that SNP effects on RNA expression are fully mediated by epigenetic features in 9% of these loci...
October 2017: Nature Neuroscience
https://www.readbyqxmd.com/read/28854703/expression-quantitative-trait-loci-eqtls-in-human-placentas-suggest-developmental-origins-of-complex-diseases
#15
Shouneng Peng, Maya A Deyssenroth, Antonio F Di Narzo, Luca Lambertini, Carmen J Marsit, Jia Chen, Ke Hao
Epidemiologic studies support that at least part of the risk of chronic diseases in childhood and even adulthood may have an in utero origin, and the placenta is a key organ that plays a pivotal role in fetal growth and development. The transcriptomes of 159 human placenta tissues were profiled by genome-wide RNA sequencing (Illumina High-Seq 2500), and linked to fetal genotypes assessed by a high density single nucleotide polymorphism (SNP) genotyping array (Illumina MegaEx). Expression quantitative trait loci (eQTLs) across all annotated transcripts were mapped and examined for enrichment for disease susceptibility loci annotated in the genome-wide association studies (GWAS) catalog...
September 1, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28805827/transcriptional-risk-scores-link-gwas-to-eqtls-and-predict-complications-in-crohn-s-disease
#16
COMPARATIVE STUDY
Urko M Marigorta, Lee A Denson, Jeffrey S Hyams, Kajari Mondal, Jarod Prince, Thomas D Walters, Anne Griffiths, Joshua D Noe, Wallace V Crandall, Joel R Rosh, David R Mack, Richard Kellermayer, Melvin B Heyman, Susan S Baker, Michael C Stephens, Robert N Baldassano, James F Markowitz, Mi-Ok Kim, Marla C Dubinsky, Judy Cho, Bruce J Aronow, Subra Kugathasan, Greg Gibson
Gene expression profiling can be used to uncover the mechanisms by which loci identified through genome-wide association studies (GWAS) contribute to pathology. Given that most GWAS hits are in putative regulatory regions and transcript abundance is physiologically closer to the phenotype of interest, we hypothesized that summation of risk-allele-associated gene expression, namely a transcriptional risk score (TRS), should provide accurate estimates of disease risk. We integrate summary-level GWAS and expression quantitative trait locus (eQTL) data with RNA-seq data from the RISK study, an inception cohort of pediatric Crohn's disease...
October 2017: Nature Genetics
https://www.readbyqxmd.com/read/28792098/identification-of-expression-quantitative-trait-loci-eqtls-in-human-peripheral-blood-mononuclear-cells-pbmcs-and-shared-with-liver-and-brain
#17
Pei He, Wei Xia, Lan Wang, Jian Wu, Yu-Fan Guo, Ke-Qin Zeng, Ming-Jun Wang, Peng-Fei Bing, Fang-Fei Xie, Xin Lu, Yong-Hong Zhang, Shu-Feng Lei, Fei-Yan Deng
PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified...
August 9, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28634199/characterising-cis-regulatory-variation-in-the-transcriptome-of-histologically-normal-and-tumour-derived-pancreatic-tissues
#18
Mingfeng Zhang, Soren Lykke-Andersen, Bin Zhu, Wenming Xiao, Jason W Hoskins, Xijun Zhang, Lauren M Rost, Irene Collins, Martijn van de Bunt, Jinping Jia, Hemang Parikh, Tongwu Zhang, Lei Song, Ashley Jermusyk, Charles C Chung, Bin Zhu, Weiyin Zhou, Gail L Matters, Robert C Kurtz, Meredith Yeager, Torben Heick Jensen, Kevin M Brown, Halit Ongen, William R Bamlet, Bradley A Murray, Mark I McCarthy, Stephen J Chanock, Nilanjan Chatterjee, Brian M Wolpin, Jill P Smith, Sara H Olson, Gloria M Petersen, Jianxin Shi, Laufey Amundadottir
OBJECTIVE: To elucidate the genetic architecture of gene expression in pancreatic tissues. DESIGN: We performed expression quantitative trait locus (eQTL) analysis in histologically normal pancreatic tissue samples (n=95) using RNA sequencing and the corresponding 1000 genomes imputed germline genotypes. Data from pancreatic tumour-derived tissue samples (n=115) from The Cancer Genome Atlas were included for comparison. RESULTS: We identified 38 615 cis-eQTLs (in 484 genes) in histologically normal tissues and 39 713 cis-eQTL (in 237 genes) in tumour-derived tissues (false discovery rate <0...
June 20, 2017: Gut
https://www.readbyqxmd.com/read/28627442/the-association-of-rs710886-in-lncrna-pcat1-with-bladder-cancer-risk-in-a-chinese-population
#19
Yadi Lin, Yuqiu Ge, Yunyan Wang, Gaoxiang Ma, Xiaowei Wang, Hanting Liu, Meilin Wang, Zhengdong Zhang, Haiyan Chu
OBJECTIVE: The long noncoding RNA PCAT1 is an important gene involved in urinary tumors. In this study, we aimed to explore the association between polymorphisms in PCAT1 and bladder cancer susceptibility. METHODS: A two-stage case-control study was conducted to assess the association between four tagging SNPs (i.e., rs4871771, rs1902432, rs16901904 and rs710886) and bladder cancer risk. Odds ratios (ORs) and their 95% confidence intervals (CIs) were calculated with unconditional univariate and multivariate logistic regression...
September 5, 2017: Gene
https://www.readbyqxmd.com/read/28575649/genetic-variation-driven-gene-expression-changes-highlight-genes-with-important-functions-for-kidney-disease
#20
Yi-An Ko, Huiguang Yi, Chengxiang Qiu, Shizheng Huang, Jihwan Park, Nora Ledo, Anna Köttgen, Hongzhe Li, Daniel J Rader, Michael A Pack, Christopher D Brown, Katalin Susztak
Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question. Expression quantitative trait loci (eQTL) analysis is a method to identify genetic variation associated with gene expression changes in specific tissue types...
June 1, 2017: American Journal of Human Genetics
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