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Results: 50
Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.
Lisa M Maier, Deborah J Smyth, Adrian Vella, Felicity Payne, Jason D Cooper, Rebecca Pask, Christopher Lowe, John Hulme, Luc J Smink, Heather Fraser, Carolyn Moule, Kara M Hunter, Giselle Chamberlain, Neil Walker, Sarah Nutland, Dag E Undlien, Kjersti S Rønningen, Cristian Guja, Constantin Ionescu-Tîrgoviste, David A Savage, David P Strachan, Laurence B Peterson, John A Todd, Linda S Wicker, Rebecca C Twells
Jun 14, 2011
Sex differences in oncogenic mutational processes.
Constance H Li, Stephenie D Prokopec, Ren X Sun, Fouad Yousif, Nathaniel Schmitz, PCAWG Tumour Subtypes and Clinical Translation, Paul C Boutros, PCAWG Consortium
Sep 11, 2020
Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have...
Evolutionarily conserved inhibitory uORFs sensitize Hox mRNA translation to start codon selection stringency.
Ivaylo P Ivanov, James A Saba, Chen-Ming Fan, Ji Wang, Andrew E Firth, Chune Cao, Rachel Green, Thomas E Dever
Mar 29, 2022
Translation start site selection in eukaryotes is influenced by context nucleotides flanking the AUG codon and by levels of the eukaryotic translation initiation factors eIF1 and eIF5. In a search of mammalian genes, we...
RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs.
Pierre Murat, Giovanni Marsico, Barbara Herdy, Avazeh T Ghanbarian, Guillem Portella, Shankar Balasubramanian
Jan 07, 2019
Low-Frequency and Rare-Coding Variation Contributes to Multiple Sclerosis Risk.
International Multiple Sclerosis Genetics Consortium. Electronic address: chris.cotsapas@yale.edu, International Multiple Sclerosis Genetics Consortium
Sep 21, 2018
Multiple sclerosis is a complex neurological disease, with ∼20% of risk heritability attributable to common genetic variants, including >230 identified by genome-wide association studies. Multiple strands of evidence suggest...
Complex Coding and Regulatory Polymorphisms in a Restriction Factor Determine the Susceptibility of Drosophila to Viral Infection.
It is common to find that major-effect genes are an important cause of variation in susceptibility to infection. Here we have characterized natural variation in a gene called pastrel that explains over half of the genetic...
DCV Drosophila Genetics of immunity natural variation pastrel viral infection Animals Disease Resistance Drosophila Proteins Drosophila melanogaster Genetic Heterogeneity Genomic Structural Variation Insect Viruses Mutation Open Reading Frames Polymorphism Single Nucleotide Regulatory Sequences Nucleic Acid
The crystal structure of Trz1, the long form RNase Z from yeast.
Miao Ma, Ines Li de la Sierra-Gallay, Noureddine Lazar, Olivier Pellegrini, Dominique Durand, Anita Marchfelder, Ciarán Condon, Herman van Tilbeurgh
Aug 20, 2021
tRNAs are synthesized as precursor RNAs that have to undergo processing steps to become functional. Yeast Trz1 is a key endoribonuclease involved in the 3΄ maturation of tRNAs in all domains of life. It is a member of the...
Amino Acid Sequence Catalytic Domain Conserved Sequence Crystallography X-Ray Endoribonucleases evolution Molecular Models Molecular Open Reading Frames Protein Conformation Protein Domains RNA Transfer Recombinant Fusion Proteins Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins Sequence Alignment Sequence Homology Amino Acid
A +1 ribosomal frameshifting motif prevalent among plant amalgaviruses.
Transcript specific regulation of expression influences susceptibility to multiple sclerosis.
Maria Ban, Wenjia Liao, Amie Baker, Alastair Compston, John Thorpe, Paul Molyneux, Mary Fraser, Jyoti Khadake, Joanne Jones, Alasdair Coles, Stephen Sawcer
Dec 19, 2019
Genome-wide association studies (GWAS) have identified over 100 loci containing single nucleotide variants (SNVs) that influence the risk of developing multiple sclerosis (MS). Most of these loci lie in non-coding regulatory...
Identification, variation and transcription of pneumococcal repeat sequences.
BACKGROUND: Small interspersed repeats are commonly found in many bacterial chromosomes. Two families of repeats (BOX and RUP) have previously been identified in the genome of Streptococcus pneumoniae, a nasopharyngeal commensal...
Exome-chip meta-analysis identifies novel loci associated with cardiac conduction, including ADAMTS6.
Bram P Prins, Timothy J Mead, Jennifer A Brody, Gardar Sveinbjornsson, Ioanna Ntalla, Nathan A Bihlmeyer, Marten van den Berg, Jette Bork-Jensen, Stefania Cappellani, Stefan Van Duijvenboden, Nikolai T Klena, George C Gabriel, Xiaoqin Liu, Cagri Gulec, Niels Grarup, Jeffrey Haessler, Leanne M Hall, Annamaria Iorio, Aaron Isaacs, Ruifang Li-Gao, Honghuang Lin, Ching-Ti Liu, Leo-Pekka Lyytikäinen, Jonathan Marten, Hao Mei, Martina Müller-Nurasyid, Michele Orini, Sandosh Padmanabhan, Farid Radmanesh, Julia Ramirez, Antonietta Robino, Molly Schwartz, Jessica van Setten, Albert V Smith, Niek Verweij, Helen R Warren, Stefan Weiss, Alvaro Alonso, David O Arnar, Michiel L Bots, Rudolf A de Boer, Anna F Dominiczak, Mark Eijgelsheim, Patrick T Ellinor, Xiuqing Guo, Stephan B Felix, Tamara B Harris, Caroline Hayward, Susan R Heckbert, Paul L Huang, JW Jukema, Mika Kähönen, Jan A Kors, Pier D Lambiase, Lenore J Launer, Man Li, Allan Linneberg, Christopher P Nelson, Oluf Pedersen, Marco Perez, Annette Peters, Ozren Polasek, Bruce M Psaty, Olli T Raitakari, Kenneth M Rice, Jerome I Rotter, Moritz F Sinner, Elsayed Z Soliman, Tim D Spector, Konstantin Strauch, Unnur Thorsteinsdottir, Andrew Tinker, Stella Trompet, André Uitterlinden, Ilonca Vaartjes, Peter van der Meer, Uwe Völker, Henry Völzke, Melanie Waldenberger, James G Wilson, Zhijun Xie, Folkert W Asselbergs, Marcus Dörr, Cornelia M van Duijn, Paolo Gasparini, Daniel F Gudbjartsson, Vilmundur Gudnason, Torben Hansen, Stefan Kääb, Jørgen K Kanters, Charles Kooperberg, Terho Lehtimäki, Henry J Lin, Steven A Lubitz, Dennis O Mook-Kanamori, Francesco J Conti, Christopher H Newton-Cheh, Jonathan Rosand, Igor Rudan, Nilesh J Samani, Gianfranco Sinagra, Blair H Smith, Hilma Holm, Bruno H Stricker, Sheila Ulivi, Nona Sotoodehnia, Suneel S Apte, Pim van der Harst, Kari Stefansson, Patricia B Munroe, Dan E Arking, Cecilia W Lo, Yalda Jamshidi
Sep 17, 2018
ADAMTS6 Conduction exome chip Meta-Analysis ADAMTS Proteins Animals Black People Connexin 43 Electrocardiography Exome Female Gene Expression Gene Expression Profiling Genetic Loci Genome-Wide Association Study Heart Conduction System Humans Male Mice Middle Aged Myocardium Open Reading Frames Polymorphism Single Nucleotide White People Exome Sequencing
The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.
Betty Y Chung, Thomas J Hardcastle, Joshua D Jones, Nerea Irigoyen, Andrew E Firth, David C Baulcombe, Ian Brierley
Jan 22, 2016
Ribosomal frameshifting and transcriptional slippage
Animals carbon cycle Chromosomes Codon DNA-Directed DNA Polymerase DNA-Directed RNA Polymerases Frameshifting Ribosomal Humans Mitochondria Nucleic Acid Conformation Open Reading Frames Polyamines RNA Messenger RNA Ribosomal RNA-Directed DNA Polymerase Retroelements Saccharomyces cerevisiae Telomerase Transcription Genetic viruses
Isolation and characterization of Nylanderia fulva virus 1, a positive-sense, single-stranded RNA virus infecting the tawny crazy ant, Nylanderia fulva.
Steven M Valles, David H Oi, James J Becnel, James K Wetterer, John S LaPolla, Andrew E Firth
Jul 13, 2016
Transposon-driven transcription is a conserved feature of vertebrate spermatogenesis and transcript evolution.
Matthew P Davis, Claudia Carrieri, Harpreet K Saini, Stijn van Dongen, Tommaso Leonardi, Giovanni Bussotti, Jack M Monahan, Tania Auchynnikava, Angelo Bitetti, Juri Rappsilber, Robin C Allshire, Alena Shkumatava, Dónal O'Carroll, Anton J Enright
Nov 23, 2017
Spermatogenesis is associated with major and unique changes to chromosomes and chromatin. Here, we sought to understand the impact of these changes on spermatogenic transcriptomes. We show that long terminal repeats (LTRs) of...
endogenous retroviruses genome evolution lncRNA Spermatogenesis Transcriptome Animals DNA Transposable Elements Endogenous Retroviruses evolution Molecular Genomics Male Mice Open Reading Frames Promoter Regions Genetic RNA Long Noncoding Spermatocytes Spermatogenesis Terminal Repeat Sequences Transcription Genetic Transcriptome
In silico identification of novel open reading frames in Plasmodium falciparum oocyte and salivary gland sporozoites using proteogenomics framework.
BACKGROUND: Plasmodium falciparum causes the deadliest form of malaria, which remains one of the most prevalent infectious diseases. Unfortunately, the only licensed vaccine showed limited protection and resistance to...
The Neighborhood of the Spike Gene Is a Hotspot for Modular Intertypic Homologous and Nonhomologous Recombination in Coronavirus Genomes.
Marios Nikolaidis, Panayotis Markoulatos, Yves Van de Peer, Stephen G Oliver, Grigorios D Amoutzias
Oct 26, 2021
Coronaviruses (CoVs) have very large RNA viral genomes with a distinct genomic architecture of core and accessory open reading frames (ORFs). It is of utmost importance to understand their patterns and limits of homologous and...
Discovery of a novel Tymoviridae-like virus in mosquitoes from Mexico.
Jermilia Charles, Chandra S Tangudu, Stefanie L Hurt, Charlotte Tumescheit, Andrew E Firth, Julian E Garcia-Rejon, Carlos Machain-Williams, Bradley J Blitvich
Dec 07, 2018
A novel Tymoviridae-like virus, designated Ek Balam virus, was isolated from male Culex quinquefasciatus mosquitoes collected in Yucatan, Mexico. The genome was fully sequenced and shown to have no more than 69% nt sequence...
A PiggyBac-based recessive screening method to identify pluripotency regulators.
Phenotype driven genetic screens allow unbiased exploration of the genome to discover new biological regulators. Bloom syndrome gene (Blm) deficient embryonic stem (ES) cells provide an opportunity for recessive screening due to...
Protein-directed ribosomal frameshifting temporally regulates gene expression
A novel sweet potato potyvirus open reading frame (ORF) is expressed via polymerase slippage and suppresses RNA silencing.
Milton Untiveros, Allan Olspert, Katrin Artola, Andrew E Firth, Jan F Kreuze, Jari PT Valkonen
Dec 22, 2015
RNA silencing suppression RNA virus frameshift Gene Expression overlapping gene transcriptional slippage Amino Acid Motifs Amino Acid Sequence Base Sequence DNA-Directed RNA Polymerases Genes Suppressor Genetic Vectors Genome Viral Genomics High-Throughput Nucleotide Sequencing Ipomoea batatas Mutation Open Reading Frames Peptides Phenotype Polymorphism Single Nucleotide Potyvirus RNA Interference RNA Viral Structure-Activity Relationship SUPPRESSION Genetic Transcription Genetic Viral Proteins
Functional screening of willow alleles in Arabidopsis combined with QTL mapping in willow (Salix) identifies SxMAX4 as a coppicing response gene.
Willows (Salix spp.) are important biomass crops due to their ability to grow rapidly with low fertilizer inputs and ease of cultivation in short-rotation coppice cycles. They are relatively undomesticated and highly diverse...
Arabidopsis QTL Salix allelic diversity mutant rescue Strigolactone Alleles Amino Acid Sequence Arabidopsis Base Sequence Chromosome Mapping Genes Plant Genetic Testing genetic variation Molecular Sequence Data Open Reading Frames Plant Proteins Plant Shoots Quantitative Trait Loci Salix Sequence Alignment Transformation Genetic
Codon choice directs constitutive mRNA levels in trypanosomes.
Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs...
ASXL gain-of-function truncation mutants
Background: Programmed ribosomal frameshifting (PRF) is a gene expression mechanism which enables the translation of two N-terminally coincident, C-terminally distinct protein products from a single mRNA. Many viruses utilize...
Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection.
Jessica Sook Yuin Ho, Matthew Angel, Yixuan Ma, Elizabeth Sloan, Guojun Wang, Carles Martinez-Romero, Marta Alenquer, Vladimir Roudko, Liliane Chung, Simin Zheng, Max Chang, Yesai Fstkchyan, Sara Clohisey, Adam M Dinan, James Gibbs, Robert Gifford, Rong Shen, Quan Gu, Nerea Irigoyen, Laura Campisi, Cheng Huang, Nan Zhao, Joshua D Jones, Ingeborg van Knippenberg, Zeyu Zhu, Natasha Moshkina, Léa Meyer, Justine Noel, Zuleyma Peralta, Veronica Rezelj, Robyn Kaake, Brad Rosenberg, Bo Wang, Jiajie Wei, Slobodan Paessler, Helen M Wise, Jeffrey Johnson, Alessandro Vannini, Maria João Amorim, J Kenneth Baillie, Emily R Miraldi, Christopher Benner, Ian Brierley, Paul Digard, Marta Łuksza, Andrew E Firth, Nevan Krogan, Benjamin D Greenbaum, Megan K MacLeod, Harm van Bakel, Adolfo Garcìa-Sastre, Jonathan W Yewdell, Edward Hutchinson, Ivan Marazzi
Jul 06, 2020
RNA viruses are a major human health threat. The life cycles of many highly pathogenic RNA viruses like influenza A virus (IAV) and Lassa virus depends on host mRNA, because viral polymerases cleave 5'-m7G-capped host...
RNA hybrid cap-snatching chimeric proteins gene origination Influenza segmented negative-strand RNA viruses uORFs upstream AUG viral RNA Viral evolution 5' Untranslated Regions Animals Cattle Cell Line Cricetinae Dogs Humans Influenza A virus Mice Mutant Chimeric Proteins Open Reading Frames RNA Caps RNA Virus Infections RNA Viruses RNA Messenger RNA Viral RNA-Dependent RNA Polymerase Recombinant Fusion Proteins Transcription Genetic Viral Proteins Virus Replication
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