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SNP genome editing

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https://www.readbyqxmd.com/read/30010932/genome-wide-analyses-uncover-allele-specific-rna-editing-in-human-and-mouse
#1
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...
July 12, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/30007805/genomic-heritability-and-genome-wide-association-analysis-of-anti-m%C3%A3-llerian-hormone-in-holstein-dairy-heifers
#2
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...
July 12, 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29881931/recent-findings-in-the-genetics-of-blood-pressure-how-to-apply-in-practice-or-is-a-moonshot-required
#3
REVIEW
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
https://www.readbyqxmd.com/read/29696027/genomics-enabled-next-generation-breeding-approaches-for-developing-system-specific-drought-tolerant-hybrids-in-maize
#4
REVIEW
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
https://www.readbyqxmd.com/read/29567676/cancer-associated-rs6983267-snp-and-its-accompanying-long-noncoding-rna-ccat2-induce-myeloid-malignancies-via-unique-snp-specific-rna-mutations
#5
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
https://www.readbyqxmd.com/read/29528523/multiple-functional-variants-at-13q14-risk-locus-for-osteoporosis-regulate-rankl-expression-through-long-range-super-enhancer
#6
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
https://www.readbyqxmd.com/read/29445025/strong-conservation-of-inbred-mouse-strain-microrna-loci-but-broad-variation-in-brain-micrornas-due-to-rna-editing-and-isomir-expression
#7
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
https://www.readbyqxmd.com/read/29282604/oslap6-ospks1-an-orthologue-of-arabidopsis-pksa-lap6-is-critical-for-proper-pollen-exine-formation
#8
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
https://www.readbyqxmd.com/read/29128227/genome-wide-association-study-for-ketosis-in-us-jerseys-using-producer-recorded-data
#9
K L Parker Gaddis, J H Megonigal, J S Clay, C W Wolfe
Ketosis is one of the most frequently reported metabolic health events in dairy herds. Several genetic analyses of ketosis in dairy cattle have been conducted; however, few have focused specifically on Jersey cattle. The objectives of this research included estimating variance components for susceptibility to ketosis and identification of genomic regions associated with ketosis in Jersey cattle. Voluntary producer-recorded health event data related to ketosis were available from Dairy Records Management Systems (Raleigh, NC)...
January 2018: Journal of Dairy Science
https://www.readbyqxmd.com/read/29123154/modification-of-single-nucleotide-polymorphism-in-a-fully-humanized-cyp3a-mouse-by-genome-editing-technology
#10
Satoshi Abe, Kaoru Kobayashi, Asami Oji, Tetsushi Sakuma, Kanako Kazuki, Shoko Takehara, Kazuomi Nakamura, Azusa Okada, Yasuko Tsukazaki, Naoto Senda, Kazuhisa Honma, Takashi Yamamoto, Masahito Ikawa, Kan Chiba, Mitsuo Oshimura, Yasuhiro Kazuki
Cytochrome P450, family 3, subfamily A (CYP3A) enzymes metabolize approximately 50% of commercially available drugs. Recently, we developed fully humanized transchromosomic (Tc) CYP3A mice with the CYP3A cluster including CYP3A4, CYP3A5, CYP3A7, and CYP3A43. Our humanized CYP3A mice have the CYP3A5*3 (g.6986G) allele, resulting in the almost absence of CYP3A5 protein expression in the liver and intestine. To produce model mice for predicting CYP3A5's contribution to pharmacokinetics, we performed a single-nucleotide polymorphism (SNP) modification of CYP3A5 (g...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29118424/methods-for-scarless-selection-free-generation-of-human-cells-and-allele-specific-functional-analysis-of-disease-associated-snps-and-variants-of-uncertain-significance
#11
Nicole B Coggins, Jacob Stultz, Henriette O'Geen, Luis G Carvajal-Carmona, David J Segal
With the continued emergence of risk loci from Genome-Wide Association studies and variants of uncertain significance identified from patient sequencing, better methods are required to translate these human genetic findings into improvements in public health. Here we combine CRISPR/Cas9 gene editing with an innovative high-throughput genotyping pipeline utilizing KASP (Kompetitive Allele-Specific PCR) genotyping technology to create scarless isogenic cell models of cancer variants in ~1 month. We successfully modeled two novel variants previously identified by our lab in the PALB2 gene in HEK239 cells, resulting in isogenic cells representing all three genotypes for both variants...
November 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29047335/candidate-lethal-haplotypes-and-causal-mutations-in-angus-cattle
#12
Jesse L Hoff, Jared E Decker, Robert D Schnabel, Jeremy F Taylor
BACKGROUND: If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized...
October 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29036410/sprint-an-snp-free-toolkit-for-identifying-rna-editing-sites
#13
Feng Zhang, Yulan Lu, Sijia Yan, Qinghe Xing, Weidong Tian
Motivation: RNA editing generates post-transcriptional sequence alterations. Detection of RNA editing sites (RESs) typically requires the filtering of SNVs called from RNA-seq data using an SNP database, an obstacle that is difficult to overcome for most organisms. Results: Here, we present a novel method named SPRINT that identifies RESs without the need to filter out SNPs. SPRINT also integrates the detection of hyper RESs from remapped reads, and has been fully automated to any RNA-seq data with reference genome sequence available...
November 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29033962/unveiling-chloroplast-rna-editing-events-using-next-generation-small-rna-sequencing-data
#14
Nureyev F Rodrigues, Ana P Christoff, Guilherme C da Fonseca, Franceli R Kulcheski, Rogerio Margis
Organellar RNA editing involves the modification of nucleotide sequences to maintain conserved protein functions, mainly by reverting non-neutral codon mutations. The loss of plastid editing events, resulting from mutations in RNA editing factors or through stress interference, leads to developmental, physiological and photosynthetic alterations. Recently, next generation sequencing technology has generated the massive discovery of sRNA sequences and expanded the number of sRNA data. Here, we present a method to screen chloroplast RNA editing using public sRNA libraries from Arabidopsis, soybean and rice...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28979294/interpreting-gene-expression-effects-of-disease-associated-variants-a-lesson-from-snca-rs356168
#15
Omolara-Chinue Glenn, Lidia Tagliafierro, Thomas G Beach, Randy L Woltjer, Ornit Chiba-Falek
The SNCA intronic single nucleotide polymorphism (SNP), rs356168, has been associated with Parkinson's disease (PD) in large genome wide association studies (GWAS). Recently, the PD-risk allele, rs356168-G was shown to increase SNCA-mRNA expression using genome edited human induced pluripotent stem cells (iPSC)-derived neurons. In this study, as means of validation, we tested the effect of rs356168 on total SNCA-mRNA levels using brain tissues, temporal and frontal cortex, from healthy control donors. Carriers of the rs356168-G allele demonstrated a borderline significant decrease of SNCA-mRNA levels in temporal brain tissues (p = 0...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28973302/pseudoexfoliation-and-alzheimer-s-associated-clu-risk-variant-rs2279590-lies-within-an-enhancer-element-and-regulates-clu-ephx2-and-ptk2b-gene-expression
#16
Biswajit Padhy, Bushra Hayat, Gargi Gouranga Nanda, Pranjya Paramita Mohanty, Debasmita Pankaj Alone
Genetic variants at PTK2B-CLU locus pose as high-risk factors for many age-related disorders. However, the role of these variants in disease progression is less characterized. In this study, we aimed to investigate the functional significance of a clusterin intronic SNP, rs2279590, that has been associated with pseudoexfoliation, Alzheimer's disease (AD) and diabetes. We have previously shown that the alleles at rs2279590 differentially regulate clusterin (CLU) gene expression in lens capsule tissues. This polymorphism resides in an active regulatory region marked by H3K27Ac and DNase I hypersensitive site and is an eQTL for CLU expression...
November 15, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28835080/-high-throughput-targeted-sequencing-panel-for-exploring-radiosensitivity-associated-genes-in-esophageal-squamous-cell-carcinoma
#17
Y Qiao, C X Hu, D A Song, S Q Li, L H Zhou, X D Jiang
Objective: To explore radiosensitivity-associated genes in esophageal squamous cell carcinoma by targeted sequencing panel. Methods: The peripheral blood from 22 esophageal squamous cell carcinoma (ESCC) patients received radiotherapy alone were collected, respectively. The genomic DNA (gDNA) of peripheral blood was extracted and used to create a library of gDNA restriction fragments. The gDNA restriction fragments were hybridized to the HaloPlex probe capture library, which comprises 356 cancer genes selected from the Catalogue of Somatic Mutations in Cancer (Cosmic) database of 2011 updated edition...
August 23, 2017: Zhonghua Zhong Liu za Zhi [Chinese Journal of Oncology]
https://www.readbyqxmd.com/read/28821270/calmodulin-like-protein-3-is-an-estrogen-receptor-alpha-coregulator-for-gene-expression-and-drug-response-in-a-snp-estrogen-and-serm-dependent-fashion
#18
Sisi Qin, James N Ingle, Mohan Liu, Jia Yu, D Lawrence Wickerham, Michiaki Kubo, Richard M Weinshilboum, Liewei Wang
BACKGROUND: We previously performed a case-control genome-wide association study in women treated with selective estrogen receptor modulators (SERMs) for breast cancer prevention and identified single nucleotide polymorphisms (SNPs) in ZNF423 as potential biomarkers for response to SERM therapy. The ZNF423rs9940645 SNP, which is approximately 200 bp away from the estrogen response elements, resulted in the SNP, estrogen, and SERM-dependent regulation of ZNF423 expression and, "downstream", that of BRCA1...
August 18, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28753427/a-genetic-variant-associated-with-five-vascular-diseases-is-a-distal-regulator-of-endothelin-1-gene-expression
#19
Rajat M Gupta, Joseph Hadaya, Aditi Trehan, Seyedeh M Zekavat, Carolina Roselli, Derek Klarin, Connor A Emdin, Catharina R E Hilvering, Valerio Bianchi, Christian Mueller, Amit V Khera, Russell J H Ryan, Jesse M Engreitz, Robbyn Issner, Noam Shoresh, Charles B Epstein, Wouter de Laat, Jonathan D Brown, Renate B Schnabel, Bradley E Bernstein, Sekar Kathiresan
Genome-wide association studies (GWASs) implicate the PHACTR1 locus (6p24) in risk for five vascular diseases, including coronary artery disease, migraine headache, cervical artery dissection, fibromuscular dysplasia, and hypertension. Through genetic fine mapping, we prioritized rs9349379, a common SNP in the third intron of the PHACTR1 gene, as the putative causal variant. Epigenomic data from human tissue revealed an enhancer signature at rs9349379 exclusively in aorta, suggesting a regulatory function for this SNP in the vasculature...
July 27, 2017: Cell
https://www.readbyqxmd.com/read/28388432/large-diverse-population-cohorts-of-hipscs-and-derived-hepatocyte-like-cells-reveal-functional-genetic-variation-at-blood-lipid-associated-loci
#20
Evanthia E Pashos, YoSon Park, Xiao Wang, Avanthi Raghavan, Wenli Yang, Deepti Abbey, Derek T Peters, Juan Arbelaez, Mayda Hernandez, Nicolas Kuperwasser, Wenjun Li, Zhaorui Lian, Ying Liu, Wenjian Lv, Stacey L Lytle-Gabbin, Dawn H Marchadier, Peter Rogov, Jianting Shi, Katherine J Slovik, Ioannis M Stylianou, Li Wang, Ruilan Yan, Xiaolan Zhang, Sekar Kathiresan, Stephen A Duncan, Tarjei S Mikkelsen, Edward E Morrisey, Daniel J Rader, Christopher D Brown, Kiran Musunuru
Genome-wide association studies have struggled to identify functional genes and variants underlying complex phenotypes. We recruited a multi-ethnic cohort of healthy volunteers (n = 91) and used their tissue to generate induced pluripotent stem cells (iPSCs) and hepatocyte-like cells (HLCs) for genome-wide mapping of expression quantitative trait loci (eQTLs) and allele-specific expression (ASE). We identified many eQTL genes (eGenes) not observed in the comparably sized Genotype-Tissue Expression project's human liver cohort (n = 96)...
April 6, 2017: Cell Stem Cell
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