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https://www.readbyqxmd.com/read/29031633/translation-of-noncoding-rnas-focus-on-lncrnas-pri-mirnas-and-circrnas
#1
REVIEW
Lian-Ju Li, Rui-Xue Leng, Yin-Guang Fan, Hai-Feng Pan, Dong-Qing Ye
Mammalian genome is pervasively transcribed, producing large number of noncoding RNAs (ncRNAs), including long noncoding RNAs (lncRNAs), primary miRNAs (pri-miRNA), and circular RNAs (circRNAs). The translation of these ncRNAs has long been overlooked. Increasing studies, however, based on ribosome profiling in various organisms provide important clues to unanticipated translation potential of lncRNAs. Moreover, a few functional peptides encoded by lncRNAs and pri-miRNAs underline the significance of their translation...
October 11, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/29030403/new-blood-pressure-associated-loci-identified-in-meta-analyses-of-475%C3%A2-000-individuals
#2
Aldi T Kraja, James P Cook, Helen R Warren, Praveen Surendran, Chunyu Liu, Evangelos Evangelou, Alisa K Manning, Niels Grarup, Fotios Drenos, Xueling Sim, Albert Vernon Smith, Najaf Amin, Alexandra I F Blakemore, Jette Bork-Jensen, Ivan Brandslund, Aliki-Eleni Farmaki, Cristiano Fava, Teresa Ferreira, Karl-Heinz Herzig, Ayush Giri, Franco Giulianini, Megan L Grove, Xiuqing Guo, Sarah E Harris, Christian T Have, Aki S Havulinna, He Zhang, Marit E Jørgensen, AnneMari Käräjämäki, Charles Kooperberg, Allan Linneberg, Louis Little, Yongmei Liu, Lori L Bonnycastle, Yingchang Lu, Reedik Mägi, Anubha Mahajan, Giovanni Malerba, Riccardo E Marioni, Hao Mei, Cristina Menni, Alanna C Morrison, Sandosh Padmanabhan, Walter Palmas, Alaitz Poveda, Rainer Rauramaa, Nigel William Rayner, Muhammad Riaz, Ken Rice, Melissa A Richard, Jennifer A Smith, Lorraine Southam, Alena Stančáková, Kathleen E Stirrups, Vinicius Tragante, Tiinamaija Tuomi, Ioanna Tzoulaki, Tibor V Varga, Stefan Weiss, Andrianos M Yiorkas, Robin Young, Weihua Zhang, Michael R Barnes, Claudia P Cabrera, He Gao, Michael Boehnke, Eric Boerwinkle, John C Chambers, John M Connell, Cramer K Christensen, Rudolf A de Boer, Ian J Deary, George Dedoussis, Panos Deloukas, Anna F Dominiczak, Marcus Dörr, Roby Joehanes, Todd L Edwards, Tõnu Esko, Myriam Fornage, Nora Franceschini, Paul W Franks, Giovanni Gambaro, Leif Groop, Göran Hallmans, Torben Hansen, Caroline Hayward, Oksa Heikki, Erik Ingelsson, Jaakko Tuomilehto, Marjo-Riitta Jarvelin, Sharon L R Kardia, Fredrik Karpe, Jaspal S Kooner, Timo A Lakka, Claudia Langenberg, Lars Lind, Ruth J F Loos, Markku Laakso, Mark I McCarthy, Olle Melander, Karen L Mohlke, Andrew P Morris, Colin N A Palmer, Oluf Pedersen, Ozren Polasek, Neil R Poulter, Michael A Province, Bruce M Psaty, Paul M Ridker, Jerome I Rotter, Igor Rudan, Veikko Salomaa, Nilesh J Samani, Peter J Sever, Tea Skaaby, Jeanette M Stafford, John M Starr, Pim van der Harst, Peter van der Meer, Cornelia M van Duijn, Anne-Claire Vergnaud, Vilmundur Gudnason, Nicholas J Wareham, James G Wilson, Cristen J Willer, Daniel R Witte, Eleftheria Zeggini, Danish Saleheen, Adam S Butterworth, John Danesh, Folkert W Asselbergs, Louise V Wain, Georg B Ehret, Daniel I Chasman, Mark J Caulfield, Paul Elliott, Cecilia M Lindgren, Daniel Levy, Christopher Newton-Cheh, Patricia B Munroe, Joanna M M Howson
BACKGROUND: Genome-wide association studies have recently identified >400 loci that harbor DNA sequence variants that influence blood pressure (BP). Our earlier studies identified and validated 56 single nucleotide variants (SNVs) associated with BP from meta-analyses of exome chip genotype data. An additional 100 variants yielded suggestive evidence of association. METHODS AND RESULTS: Here, we augment the sample with 140 886 European individuals from the UK Biobank, in whom 77 of the 100 suggestive SNVs were available for association analysis with systolic BP or diastolic BP or pulse pressure...
October 2017: Circulation. Cardiovascular Genetics
https://www.readbyqxmd.com/read/29029458/lmo1-polymorphisms-reduce-neuroblastoma-risk-in-chinese-children-a-two-center-case-control-study
#3
Jiao Zhang, Huiran Lin, Jiaxiang Wang, Jing He, Da Zhang, Pan Qin, Lin Yang, Lizhao Yan
Previous genome-wide association and validation studies suggest that LIM domain only 1 (LMO1) gene polymorphisms affect neuroblastoma susceptibility. In this work, we used Taqman methodology to genotype four LMO1 polymorphisms (rs110419 A > G, rs4758051 G > A, rs10840002 A > G and rs204938 A > G) in 118 neuroblastoma cases and 281 controls from Northern China. Odds ratios (ORs) and 95% confidence intervals (CIs) were used to evaluate the association. We found that rs4758051 G > A was associated with a decreased neuroblastoma risk (AA vs...
September 12, 2017: Oncotarget
https://www.readbyqxmd.com/read/29029269/an-overlooked-paleo-tetraploidization-in-cucurbitaceae
#4
Jinpeng Wang, Pengchuan Sun, Yuxian Li, Yinzhe Liu, Nanshan Yang, Jigao Yu, Xuelian Ma, Sangrong Sun, Ruiyan Xia, Xiaojian Liu, Dongcen Ge, Sainan Luo, Yinmeng Liu, Youting Kong, Xiaobo Cui, Tianyu Lei, Li Wang, Zhenyi Wang, Weina Ge, Lan Zhang, Xiaoming Song, Min Yuan, Di Guo, Dianchuan Jin, Wei Chen, Yuxin Pan, Tao Liu, Guixian Yang, Yue Xiao, Jinshuai Sun, Cong Zhang, Zhibo Li, Haiqing Xu, Xueqian Duan, Shaoqi Shen, Zhonghua Zhang, Sanwen Huang, Xiyin Wang
Cucurbitaceae plants are of considerable biological and economic importance, and genomes of cucumber, watermelon, and melon have been sequenced. However, a comparative genomics exploration of their genome structures and evolution has not been available. Here, we aimed at performing a hierarchical inference of genomic homology resulted from recursive paleo-polyploidizations. Unexpectedly, we found that, shortly after a core-eudicot-common hexaploidy (ECH), a cucurbit-common tetraploidization (CCT) occurred, overlooked by previous reports...
September 28, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29028907/oncomir-an-online-resource-for-exploring-pan-cancer-microrna-dysregulation
#5
Nathan W Wong, Yuhao Chen, Shuai Chen, Xiaowei Wang
Summary: Dysregulation of microRNAs (miRNAs) is extensively associated with cancer development and progression. miRNAs have been shown to be biomarkers for predicting tumor formation and outcome. However, identification of the relationships between miRNA expression and tumor characteristics can be difficult and time-consuming without appropriate bioinformatics expertise. To address this issue, we present OncomiR, an online resource for exploring miRNA dysregulation in cancer. Using combined miRNA-seq, RNA-seq, and clinical data from The Cancer Genome Atlas, we systematically performed statistical analyses to identify dysregulated miRNAs that are associated with tumor development and progression in most major cancer types...
October 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028415/crispr-cas9-mediated-noncoding-rna-editing-in-human-cancers
#6
Jie Yang, Xiaodan Meng, Jinchang Pan, Nan Jiang, Chengwei Zhou, Zhenhua Wu, Zhaohui Gong
Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system...
October 13, 2017: RNA Biology
https://www.readbyqxmd.com/read/29027393/down-regulated-serum-microrna-101-is-associated-with-aggressive-progression-and-poor-prognosis-of-cervical-cancer
#7
Wei Jiang, Jia Jia Pan, Ying Hui Deng, Mei Rong Liang, Li Hua Yao
OBJECTIVE: MicroRNAs (miRNAs) play a vital role in pathogenesis and progression of many cancers, including cervical cancer. However, importance of serum level of miR-101 in cervical cancer has rarely been studied. In the present study, clinical significance and prognostic value of serum miR-101 for cervical cancer was investigated. METHODS: Association between miR-101 level in cervical cancer tissues and prognosis of patients was analyzed by using data retrieved from The Cancer Genome Atlas (TCGA) database, which was followed with our clinical study in which miR-101 serum level comparison between cervical cancer patients and healthy controls was conducted by real-time quantitative polymerase chain reaction (PCR)...
November 2017: Journal of Gynecologic Oncology
https://www.readbyqxmd.com/read/29023197/mutational-landscape-of-rna-binding-proteins-in-human-cancers
#8
Yaseswini Neelamraju, Abel Gonzalez-Perez, Poornima Bhat-Nakshatri, Harikrishna Nakshatri, Sarath Chandra Janga
RNA Binding Proteins (RBPs) are a class of post-transcriptional regulatory molecules which are increasingly documented to be dysfunctional in cancer genomes. However, our current understanding of these alterations is limited. Here, we delineate the mutational landscape of ∼1300 RBPs in ∼6000 cancer genomes. Our analysis revealed that RBPs have an average of ∼3 mutations per Mb across 26 cancer types. We identified 281 RBPs to be enriched for mutations (GEMs) in at least one cancer type. GEM RBPs were found to undergo frequent frameshift and inframe deletions as well as missense, nonsense and silent mutations when compared to those that are not enriched for mutations...
October 12, 2017: RNA Biology
https://www.readbyqxmd.com/read/29021619/pan-cancer-analysis-of-bi-allelic-alterations-in-homologous-recombination-dna-repair-genes
#9
Nadeem Riaz, Pedro Blecua, Raymond S Lim, Ronglai Shen, Daniel S Higginson, Nils Weinhold, Larry Norton, Britta Weigelt, Simon N Powell, Jorge S Reis-Filho
BRCA1 and BRCA2 are involved in homologous recombination (HR) DNA repair and are germ-line cancer pre-disposition genes that result in a syndrome of hereditary breast and ovarian cancer (HBOC). Whether germ-line or somatic alterations in these genes or other members of the HR pathway and if mono- or bi-allelic alterations of HR-related genes have a phenotypic impact on other cancers remains to be fully elucidated. Here, we perform a pan-cancer analysis of The Cancer Genome Atlas (TCGA) data set and observe that bi-allelic pathogenic alterations in homologous recombination (HR) DNA repair-related genes are prevalent across many malignancies...
October 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/29021567/classical-swine-fever-virus-nonstructural-protein-p7-modulates-infectious-virus-production
#10
Cheng Zhao, Xiaofang Shen, Rui Wu, Ling Li, Zishu Pan
The classical swine fever virus (CSFV) nonstructural protein p7 is crucial for virus production, yet precisely how the p7 modulates this process is unclear. In this study, we first identified the interactions of p7 with E2 and NS2. The key binding regions of both p7 and NS2 mapped to the first transmembrane (TM1) domain of two proteins. Three amino acid substitutions in the TM1 region of p7 (p7(TDI18/19/20AAA), p7(EVV21/22/23AAA) and p7(YFY25/26/30AAA)) impaired infectious virus production and reduced the interaction of p7 with the NS2 protein...
October 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29020009/genome-sequences-of-lower-great-lakes-microcystis-sp-reveal-strain-specific-genes-that-are-present-and-expressed-in-western-lake-erie-blooms
#11
Kevin Anthony Meyer, Timothy W Davis, Susan B Watson, Vincent J Denef, Michelle A Berry, Gregory J Dick
Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of "omics" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M...
2017: PloS One
https://www.readbyqxmd.com/read/29017889/complete-genome-sequence-of-acinetobacter-baumannii-a1296-st1469-with-a-small-plasmid-harboring-the-tet39-tetracycline-resistance-gene
#12
Xiaoting Hua, Chao Pan, Li Zhu, Zhicheng Liu, Qingye Xu, Hengliang Wang, Yunsong Yu
OBJECTIVES: Acinetobacter baumannii is considered an important nosocomial pathogen worldwide due to its increasing antibiotic resistance. This study aimed to determine the complete genome sequence of A. baumannii strain A1296 and comparative analysis among A. baumannii. METHODS: The complete genome sequence of A. baumannii A1296 was sequenced on two SMRT cells using P6C4 chemistry on a Pacific Biosciences Single Molecule, Real-Time RS II instrument. The A1296 genome sequence was annotated via NCBI, and its MLST and resistance genes were analyzed...
October 7, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/29017450/complete-genome-sequence-of-citrobacter-werkmanii-strain-bf-6-isolated-from-industrial-putrefaction
#13
Gang Zhou, Hong Peng, Ying-Si Wang, Xiao-Mo Huang, Xiao-Bao Xie, Qing-Shan Shi
BACKGROUND: In our previous study, Citrobacter werkmanii BF-6 was isolated from an industrial spoilage sample and demonstrated an excellent ability to form biofilms, which could be affected by various environmental factors. However, the genome sequence of this organism has not been reported so far. RESULTS: We report the complete genome sequence of C. werkmanii BF-6 together with the description of the genome features and its annotation. The size of the complete chromosome is 4,929,789 bp with an average coverage of 137×...
October 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28992048/comparative-whole-genome-analysis-reveals-artificial-selection-effects-on-ustilago-esculenta-genome
#14
Zihong Ye, Yao Pan, Yafen Zhang, Haifeng Cui, Gulei Jin, Alice C McHardy, Longjiang Fan, Xiaoping Yu
Ustilago esculenta, infects Zizania latifolia, and induced host stem swollen to be a popular vegetable called Jiaobai in China. It is the long-standing artificial selection that maximizes the occurrence of favourable Jiaobai, and thus maintaining the plant-fungi interaction and modulating the fungus evolving from plant pathogen to entophyte. In this study, whole genome of U. esculenta was sequenced and transcriptomes of the fungi and its host were analysed. The 20.2 Mb U. esculenta draft genome of 6,654 predicted genes including mating, primary metabolism, secreted proteins, shared a high similarity to related Smut fungi...
July 19, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28991750/kmerind-a-flexible-parallel-library-for-k-mer-indexing-of-biological-sequences-on-distributed-memory-systems
#15
Tony Pan, Patrick Flick, Chirag Jain, Yongchao Liu, Srinivas Aluru
Counting and indexing fixed length substrings, or k-mers, in biological sequences is a key step in many bioinformatics tasks including genome alignment and mapping, genome assembly, and error correction. While advances in next generation sequencing technologies have dramatically reduced the cost and improved latency and throughput, few bioinformatics tools can efficiently process the datasets at the current generation rate of 1.8 terabases every 3 days. We present Kmerind, a high performance parallel k-mer indexing library for distributed memory environments...
October 9, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28991226/lsd1-promotes-s-phase-entry-and-tumorigenesis-via-chromatin-co-occupation-with-e2f1-and-selective-h3k9-demethylation
#16
Y He, Y Zhao, L Wang, L R Bohrer, Y Pan, L Wang, H Huang
Histone H3 lysine-9 (H3K9) methylation is essential for retinoblastoma protein (RB)-mediated heterochromatin formation, epigenetic silencing of S-phase genes and permanent cell cycle arrest or cellular senescence. Besides as an H3K4 demethylase, lysine-specific demethylase-1 (LSD1) has been shown to promote H3K9 demethylation. However, it is unexplored whether LSD1 has a causal role in regulating cell cycle entry and senescence. Here we demonstrate that genetic depletion or pharmacological inhibition of LSD1 triggers G1 arrest and cellular senescence...
October 9, 2017: Oncogene
https://www.readbyqxmd.com/read/28984208/unique-protein-expression-signatures-of-survival-time-in-kidney-renal-clear-cell-carcinoma-through-a-pan-cancer-screening
#17
Guangchun Han, Wei Zhao, Xiaofeng Song, Patrick Kwok-Shing Ng, Jose A Karam, Eric Jonasch, Gordon B Mills, Zhongming Zhao, Zhiyong Ding, Peilin Jia
BACKGROUND: In 2016, it is estimated that there will be 62,700 new cases of kidney cancer in the United States, and 14,240 patients will die from the disease. Because the incidence of kidney renal clear cell carcinoma (KIRC), the most common type of kidney cancer, is expected to continue to increase in the US, there is an urgent need to find effective diagnostic biomarkers for KIRC that could help earlier detection of and customized treatment strategies for the disease. Accordingly, in this study we systematically investigated KIRC's prognostic biomarkers for survival using the reverse phase protein array (RPPA) data and the high throughput sequencing data from The Cancer Genome Atlas (TCGA)...
October 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28981937/-application-of-chromosomal-microarray-analysis-for-fetuses-with-ventricular-septal-defects
#18
Qiong Deng, Fang Fu, Ru Li, Xiangyi Jing, Tingying Lei, Xin Yang, Min Pan, Li Zhen, Jin Han, Can Liao
OBJECTIVE: To explore the genetic etiology of fetuses with ventricular septal defects (VSD) using chromosomal microarray analysis (CMA). METHODS: A total of 248 fetuses were divided into isolated VSD group, VSD with other cardiac and/or great vessels malformation group, VSD with extra-cardiac anomalies group (including malformation and sonographic soft markers), and VSD with both cardiac and extra-cardiac anomalies group. Standard karyotyping was carried out for all fetuses, and CMA was performed for 6 fetuses with an abnormal karyotype and a proportion of fetuses with a normal karyotype...
October 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28981788/empty-pericarp11-serves-as-a-factor-for-splicing-of-mitochondrial-nad1-intron-and-is-required-to-ensure-proper-seed-development-in-maize
#19
Xuemei Ren, Zhenyuan Pan, Hailiang Zhao, Junli Zhao, Manjun Cai, Jiang Li, Zuxin Zhang, Fazhan Qiu, Gerhard Leubner
Group II introns are common in the mitochondrial genome of higher plant species. The splicing of these introns is a complex process involving the synergistic action of multiple factors. However, few of these factors have been characterized in maize. In this study, we found that the Empty pericarp11 (Emp11) gene, which encodes a P-type pentatricopeptide repeat (PPR) protein, is required for the development of maize seeds. The loss of Emp11 function seriously impairs embryo and endosperm development, resulting in empty pericarp seeds in maize, and alteration in Emp11 expression leads to quantitative variation in kernel size and weight...
July 20, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28981191/retinoic-acid-receptor-%C3%AE-regulates-synthetic-events-in-human-platelets
#20
Hansjörg Schwertz, Jesse W Rowley, Guy A Zimmerman, Andrew S Weyrich, Matthew T Rondina
BACKGROUND: Translational control mechanisms in platelets are incompletely defined. Here, we determined whether the nuclear transcription factor RARα controls protein translational events in human platelets. METHODS: Isolated human platelets were treated with the pan-RAR agonist all-trans-retinoic acid (atRA). Global and targeted translational events were examined. RESULTS: Stimulation of platelets with (atRA) significantly increased global protein expression...
October 5, 2017: Journal of Thrombosis and Haemostasis: JTH
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