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SNP genome editing

Aine C O'Brien, Michelle M Judge, Sean Fair, Donagh P Berry
The objective of the present study was to quantify the accuracy of imputing medium-density single nucleotide polymorphism (SNP) genotypes from lower-density panels (384 to 12,000 SNPs) derived using alternative selection methods to select the most informative SNPs. Four different selection methods were used to select SNPs based on genomic characteristics (i.e. minor allele frequency (MAF) and linkage disequilibrium (LD)) within five sheep breeds (642 Belclare; 645 Charollais; 715 Suffolk; 440 Texel; and 620 Vendeen) separately...
February 5, 2019: Journal of Animal Science
Emily A Pinheiro, K Ashley Fetterman, Paul W Burridge
The genomic predisposition to oncology-drug-induced cardiovascular toxicity has been postulated for many decades. Only recently has it become possible to experimentally validate this hypothesis via the use of patient-specific human induced pluripotent stem cells (hiPSCs) and suitably powered genome-wide association studies (GWAS). Identifying the individual single nucleotide polymorphisms (SNPs) responsible for the susceptibility to toxicity from a specific drug is a daunting task as this precludes the use of one of the most powerful tools in genomics: comparing phenotypes to close relatives, as these are highly unlikely to have been treated with the same drug...
January 24, 2019: Cardiovascular Research
Wenxiang Hu, Chunjie Jiang, Dongyin Guan, Pieterjan Dierickx, Rong Zhang, Arden Moscati, Girish N Nadkarni, David J Steger, Ruth J F Loos, Cheng Hu, Weiping Jia, Raymond E Soccio, Mitchell A Lazar
Thiazolidinedione drugs (TZDs) target the transcriptional activity of peroxisome proliferator activated receptor γ (PPARγ) to reverse insulin resistance in type 2 diabetes, but side effects limit their clinical use. Here, using human adipose stem cell-derived adipocytes, we demonstrate that SNPs were enriched at sites of patient-specific PPARγ binding, which correlated with the individual-specific effects of the TZD rosiglitazone (rosi) on gene expression. Rosi induction of ABCA1, which regulates cholesterol metabolism, was dependent upon SNP rs4743771, which modulated PPARγ binding by influencing the genomic occupancy of its cooperating factor, NFIA...
December 23, 2018: Cell Stem Cell
Leif Karlsson, Michela Barbaro, Ewoud Ewing, David Gomez-Cabrero, Svetlana Lajic
Prenatal treatment with dexamethasone (DEX) reduces virilization in girls with congenital adrenal hyperplasia (CAH). It has potential short- and long-term risks and has been shown to affect cognitive functions. Here, we investigate whether epigenetic modification of DNA during early developmental stages may be a key mediating mechanism by which prenatal DEX treatment could result in poor outcomes in the offspring. We analyzed genome-wide CD4+ T cell DNA methylation, assessed using the Infinium HumanMethylation450 BeadChip array in 29 individuals (mean age = 16...
January 1, 2019: Journal of the Endocrine Society
Wolfram Georg Brenner, Malte Mader, Niels Andreas Müller, Hans Hoenicka, Hilke Schroeder, Ingo Zorn, Matthias Fladung, Birgit Kersten
RNA editing occurs in the endosymbiont organelles of higher plants as C-to-U conversions of defined nucleotides. The availability of large quantities of RNA sequencing data makes it possible to identify RNA editing sites and to quantify their editing extent. We have investigated RNA editing in 34 protein-coding mitochondrial transcripts of four Populus species, a genus noteworthy for its remarkably small number of RNA editing sites compared to other angiosperms. 27 of these transcripts were subject to RNA editing in at least one species...
January 7, 2019: G3: Genes—Genomes—Genetics
Ming Huang, Mikeal L Roose, Qibin Yu, Dongliang Du, Yuan Yu, Yi Zhang, Zhanao Deng, Ed Stover, Frederick G Gmitter
Huanglongbing (HLB), or citrus greening, is the most devastating disease in citrus worldwide. Commercial citrus varieties including sweet orange ( Citrus sinensis ) are highly susceptible to HLB, and trifoliate orange ( Poncirus trifoliata , a close Citrus relative) is widely considered resistant or highly tolerant to HLB. In this study, an intergeneric F1 population of sweet orange and trifoliate orange was genotyped by Genotyping-by-Sequencing, and high-density SNP-based genetic maps were constructed separately for trifoliate orange and sweet orange...
2018: Frontiers in Plant Science
Yuki Hitomi, Ken Nakatani, Kaname Kojima, Nao Nishida, Yosuke Kawai, Minae Kawashima, Yoshihiro Aiba, Masao Nagasaki, Minoru Nakamura, Katsushi Tokunaga
BACKGROUND & AIMS: Primary biliary cholangitis (PBC) is a chronic and cholestatic liver disease that eventually leads to liver cirrhosis and hepatic failure. We recently identified several susceptibility genes included the nuclear factor kappa B subunit 1 (NFKB1) and mannosidase beta (MANBA) for PBC in the Japanese population by genome-wide association study (GWAS). However, the primary functional variants in the NFKB1/MANBA region and the molecular mechanism for conferring disease susceptibility to PBC have not yet been clarified...
December 4, 2018: Cellular and Molecular Gastroenterology and Hepatology
Matthew D Krause, Ru-Ting Huang, David Wu, Tzu-Pin Shentu, Devin L Harrison, Michael B Whalen, Lindsey K Stolze, Anna Di Rienzo, Ivan P Moskowitz, Mete Civelek, Casey E Romanoski, Yun Fang
Biomechanical cues dynamically control major cellular processes, but whether genetic variants actively participate in mechanosensing mechanisms remains unexplored. Vascular homeostasis is tightly regulated by hemodynamics. Exposure to disturbed blood flow at arterial sites of branching and bifurcation causes constitutive activation of vascular endothelium contributing to atherosclerosis, the major cause of coronary artery disease (CAD) and ischemic stroke (IS). Conversely, unidirectional flow promotes quiescent endothelium...
November 27, 2018: Proceedings of the National Academy of Sciences of the United States of America
Danxin Wang, Katherine Hartmann, Michal Seweryn, Wolfgang Sadee
BACKGROUND: CYP7A1 (cholesterol 7α-hydroxylase) catalyzes the rate-limiting step in bile acid biosynthesis from cholesterol-a main pathway for cholesterol removal from the body. CYP7A1 single-nucleotide polymorphisms (SNPs) are associated with total cholesterol and LDL (low-density lipoprotein) levels, risk of cardiovascular diseases, and other phenotypes; however, results are inconsistent, and causative variants remain uncertain, except for a frequent promoter SNP (rs3808607). METHODS: We used chromatin conformation capture (4C assay), chromatin immunoprecipitation qPCR assay in hepatocytes, and CRISPR (clustered regularly interspaced short palindromic repeats)-mediated genome editing in hepatocellular carcinoma cell line cells to identify regulatory regions for CYP7A1...
October 2018: Circulation. Genomic and precision medicine
Lucas B Harrington, David Burstein, Janice S Chen, David Paez-Espino, Enbo Ma, Isaac P Witte, Joshua C Cofsky, Nikos C Kyrpides, Jillian F Banfield, Jennifer A Doudna
CRISPR-Cas systems provide microbes with adaptive immunity to infectious nucleic acids and are widely employed as genome editing tools. These tools use RNA-guided Cas proteins whose large size (950 to 1400 amino acids) has been considered essential to their specific DNA- or RNA-targeting activities. Here we present a set of CRISPR-Cas systems from uncultivated archaea that contain Cas14, a family of exceptionally compact RNA-guided nucleases (400 to 700 amino acids). Despite their small size, Cas14 proteins are capable of targeted single-stranded DNA (ssDNA) cleavage without restrictive sequence requirements...
November 16, 2018: Science
Engin Deniz, Emily K Mis, Maura Lane, Mustafa K Khokha
In the US and Europe, birth defects are the leading cause of infant mortality. Among birth defects, Congenital Heart Disease (CHD) occurs in approximately 8 out of 1000 live births, affects 1.3 million newborns per year worldwide, and has the highest mortality rate. While there is evidence to indicate that CHD does have a genetic basis, most of the CHD burden remains unexplained genetically. Fortunately, new genomics technologies are enabling genetic analyses of CHD patients. Whole exome sequencing of trios as well as copy number variations assayed by high-density SNP arrays can now be obtained at high efficiency and relatively low cost...
2018: Methods in Molecular Biology
Stephane E Castel, Alejandra Cervera, Pejman Mohammadi, François Aguet, Ferran Reverter, Aaron Wolman, Roderic Guigo, Ivan Iossifov, Ana Vasileva, Tuuli Lappalainen
Coding variants represent many of the strongest associations between genotype and phenotype; however, they exhibit inter-individual differences in effect, termed 'variable penetrance'. Here, we study how cis-regulatory variation modifies the penetrance of coding variants. Using functional genomic and genetic data from the Genotype-Tissue Expression Project (GTEx), we observed that in the general population, purifying selection has depleted haplotype combinations predicted to increase pathogenic coding variant penetrance...
September 2018: Nature Genetics
Zhong-Yin Zhou, Yue Hu, Aimin Li, Ying-Ju Li, Hui Zhao, Si-Qi Wang, Newton O Otecko, Dejiu Zhang, Jin-Huan Wang, Yajun Liu, David M Irwin, Yan Qin, Ya-Ping Zhang
RNA editing is one of the most common RNA level modifications that potentially generate amino acid changes similar to those resulting from genomic nonsynonymous mutations. However, unlike DNA level allele-specific modifications such as DNA methylation, it is currently unknown whether RNA editing displays allele-specificity across tissues and species. Here, we analyzed allele-specific RNA editing in human tissues and from brain tissues of heterozygous mice generated by crosses between divergent mouse strains and found a high proportion of overlap of allele-specific RNA editing sites between different samples...
September 28, 2018: Nucleic Acids Research
M Y Nawaz, F Jimenez-Krassel, J P Steibel, Y Lu, A Baktula, N Vukasinovic, L Neuder, J L H Ireland, J J Ireland, R J Tempelman
Anti-Müllerian hormone (AMH) is an ovarian growth factor that plays an important role in regulation of ovarian follicle growth. The objectives of this study were to estimate the genomic heritability of AMH and identify genomic regions associated with AMH production in a genome-wide association (GWA) analysis. Concentrations of AMH were determined in 2,905 dairy Holstein heifers genotyped using the Zoetis medium density panel (Zoetis Inclusions, Kalamazoo, MI) with 54,519 single nucleotide polymorphism (SNP) markers remaining after standard genotype quality control edits...
September 2018: Journal of Dairy Science
Sandosh Padmanabhan, Alisha Aman, Anna F Dominiczak
PURPOSE OF REVIEW: Hypertension is recognised as the biggest contributor to the global burden of disease, but it is controlled in less than a fifth of patients worldwide, despite being relatively easy to detect and the availability of inexpensive safe generic drugs. Blood pressure is regulated by a complex network of physiologic pathways with currently available drugs targeting key receptors or enzymes in the top pathways. Major advances in the dissection of both monogenic and polygenic determinants of blood pressure regulation and variation have not resulted in rapid translation of these discoveries into clinical applications or precision medicine...
June 7, 2018: Current Hypertension Reports
Thirunavukkarsau Nepolean, Jyoti Kaul, Ganapati Mukri, Shikha Mittal
Breeding science has immensely contributed to the global food security. Several varieties and hybrids in different food crops including maize have been released through conventional breeding. The ever growing population, decreasing agricultural land, lowering water table, changing climate, and other variables pose tremendous challenge to the researchers to improve the production and productivity of food crops. Drought is one of the major problems to sustain and improve the productivity of food crops including maize in tropical and subtropical production systems...
2018: Frontiers in Plant Science
Maitri Y Shah, Manuela Ferracin, Valentina Pileczki, Baoqing Chen, Roxana Redis, Linda Fabris, Xinna Zhang, Cristina Ivan, Masayoshi Shimizu, Cristian Rodriguez-Aguayo, Mihnea Dragomir, Katrien Van Roosbroeck, Maria Ines Almeida, Maria Ciccone, Daniela Nedelcu, Maria Angelica Cortez, Taghi Manshouri, Steliana Calin, Muharrem Muftuoglu, Pinaki P Banerjee, Mustafa H Badiwi, Jan Parker-Thornburg, Asha Multani, James William Welsh, Marcos Roberto Estecio, Hui Ling, Ciprian Tomuleasa, Delia Dima, Hui Yang, Hector Alvarez, M James You, Milan Radovich, Elizabeth Shpall, Muller Fabbri, Katy Rezvani, Leonard Girnita, Ioana Berindan-Neagoe, Anirban Maitra, Srdan Verstovsek, Riccardo Fodde, Carlos Bueso-Ramos, Mihai Gagea, Guillermo Garcia Manero, George A Calin
The cancer-risk-associated rs6983267 single nucleotide polymorphism (SNP) and the accompanying long noncoding RNA CCAT2 in the highly amplified 8q24.21 region have been implicated in cancer predisposition, although causality has not been established. Here, using allele-specific CCAT2 transgenic mice, we demonstrate that CCAT2 overexpression leads to spontaneous myeloid malignancies. We further identified that CCAT2 is overexpressed in bone marrow and peripheral blood of myelodysplastic/myeloproliferative neoplasms (MDS/MPN) patients...
April 2018: Genome Research
Dong-Li Zhu, Xiao-Feng Chen, Wei-Xin Hu, Shan-Shan Dong, Bing-Jie Lu, Yu Rong, Yi-Xiao Chen, Hao Chen, Hlaing Nwe Thynn, Nai-Ning Wang, Yan Guo, Tie-Lin Yang
RANKL is a key regulator involved in bone metabolism, and a drug target for osteoporosis. The clinical diagnosis and assessment of osteoporosis are mainly based on bone mineral density (BMD). Previous powerful genomewide association studies (GWASs) have identified multiple intergenic single-nucleotide polymorphisms (SNPs) located over 100 kb upstream of RANKL and 65 kb downstream of AKAP11 at 13q14.11 for osteoporosis. Whether these SNPs exert their roles on osteoporosis through RANKL is unknown. In this study, we conducted integrative analyses combining expression quantitative trait locus (eQTL), genomic chromatin interaction (high-throughput chromosome conformation capture [Hi-C]), epigenetic annotation, and a series of functional assays...
July 2018: Journal of Bone and Mineral Research: the Official Journal of the American Society for Bone and Mineral Research
Kalevi Trontti, Juho Väänänen, Tessa Sipilä, Dario Greco, Iiris Hovatta
Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by (i) identifying miRNA SNPs in whole-genome sequence data from 36 strains, and (ii) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of six strains, to facilitate the study of miRNAs in neurobehavioral phenotypes...
May 2018: RNA
Ting Zou, Qiao Xiao, Wenjie Li, Tao Luo, Guoqiang Yuan, Zhiyuan He, Mingxing Liu, Qiao Li, Peizhou Xu, Jun Zhu, Yueyang Liang, Qiming Deng, Shiquan Wang, Aiping Zheng, Lingxia Wang, Ping Li, Shuangcheng Li
BACKGROUND: Male fertility is crucial for rice yield, and the improvement of rice yield requires hybrid production that depends on male sterile lines. Although recent studies have revealed several important genes in male reproductive development, our understanding of the mechanisms of rice pollen development remains unclear. RESULTS: We identified a rice mutant oslap6 with complete male sterile phenotype caused by defects in pollen exine formation. By using the MutMap method, we found that a single nucleotide polymorphism (SNP) variation located in the second exon of OsLAP6/OsPKS1 was responsible for the mutant phenotype...
December 28, 2017: Rice
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