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https://www.readbyqxmd.com/read/28334749/ctg-repeat-targeting-oligonucleotides-for-down-regulating-huntingtin-expression
#1
Eman M Zaghloul, Olof Gissberg, Pedro M D Moreno, Lee Siggens, Mattias Hällbrink, Anna S Jørgensen, Karl Ekwall, Rula Zain, Jesper Wengel, Karin E Lundin, C I Edvard Smith
Huntington's disease (HD) is a fatal, neurodegenerative disorder in which patients suffer from mobility, psychological and cognitive impairments. Existing therapeutics are only symptomatic and do not significantly alter the disease progression or increase life expectancy. HD is caused by expansion of the CAG trinucleotide repeat region in exon 1 of the Huntingtin gene (HTT), leading to the formation of mutant HTT transcripts (muHTT). The toxic gain-of-function of muHTT protein is a major cause of the disease...
February 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28297718/dnd1-maintains-germline-stem-cells-via-recruitment-of-the-ccr4-not-complex-to-target-mrnas
#2
Masashi Yamaji, Miki Jishage, Cindy Meyer, Hemant Suryawanshi, Evan Der, Misaki Yamaji, Aitor Garzia, Pavel Morozov, Sudhir Manickavel, Hannah L McFarland, Robert G Roeder, Markus Hafner, Thomas Tuschl
The vertebrate-conserved RNA-binding protein DND1 is required for the survival of primordial germ cells (PGCs), as well as the suppression of germ cell tumours in mice. Here we show that in mice DND1 binds a UU(A/U) trinucleotide motif predominantly in the 3' untranslated regions of mRNA, and destabilizes target mRNAs through direct recruitment of the CCR4-NOT deadenylase complex. Transcriptomic analysis reveals that the extent of suppression is dependent on the number of DND1-binding sites. This DND1-dependent mRNA destabilization is required for the survival of mouse PGCs and spermatogonial stem cells by suppressing apoptosis...
March 15, 2017: Nature
https://www.readbyqxmd.com/read/28292918/non-homologous-end-joining-with-minimal-sequence-loss-is-promoted-by-the-mre11-rad50-nbs1-ctp1-complex-in-schizosaccharomyces-pombe
#3
Yanhui Li, Jinyu Wang, Gang Zhou, Michael Lajeunesse, Nga Le, Brittany N Stawicki, Yalitza Lopez Corcino, Kathleen L Berkner, Kurt W Runge
While the Mre11-Rad50-Nbs1 (MRN) complex has known roles in repair processes like homologous recombination and microhomology-mediated end-joining, its role in non-homologous end-joining (NHEJ) is unclear as Saccharomyces cerevisiae, Schizosaccharomyces pombe and mammals have different requirements for repairing cut DNA ends. Most double-strand breaks (DSBs) require nucleolytic processing prior to DNA ligation. We therefore studied repair using the Hermes transposon, whose excision leaves a DSB capped by hairpin ends similar to structures generated by palindromes and trinucleotide repeats...
March 14, 2017: Genetics
https://www.readbyqxmd.com/read/28289517/retroviral-integrase-protein-and-intasome-nucleoprotein-complex-structures
#4
REVIEW
Julia Grawenhoff, Alan N Engelman
Retroviral replication proceeds through the integration of a DNA copy of the viral RNA genome into the host cellular genome, a process that is mediated by the viral integrase (IN) protein. IN catalyzes two distinct chemical reactions: 3'-processing, whereby the viral DNA is recessed by a di- or trinucleotide at its 3'-ends, and strand transfer, in which the processed viral DNA ends are inserted into host chromosomal DNA. Although IN has been studied as a recombinant protein since the 1980s, detailed structural understanding of its catalytic functions awaited high resolution structures of functional IN-DNA complexes or intasomes, initially obtained in 2010 for the spumavirus prototype foamy virus (PFV)...
February 26, 2017: World Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28282950/development%C3%A2-of%C3%A2-gene-based%C3%A2-ssr%C3%A2-markers%C3%A2-in%C3%A2-winged%C3%A2-bean%C3%A2-psophocarpus%C3%A2-tetragonolobus%C3%A2-l-%C3%A2-dc-%C3%A2-for%C3%A2-diversity%C3%A2-assessment
#5
Quin Nee Wong, Alberto Stefano Tanzi, Wai Kuan Ho, Sunir Malla, Martin Blythe, Asha Karunaratne, Festo Massawe, Sean Mayes
Winged bean (Psophocarpus tetragonolobus) is an herbaceous multipurpose legume grown in hot and humid countries as a pulse, vegetable (leaves and pods), or root tuber crop depending on local consumption preferences. In addition to its different nutrient-rich edible parts which could contribute to food and nutritional security, it is an efficient nitrogen fixer as a component of sustainable agricultural systems. Generating genetic resources and improved lines would help to accelerate the breeding improvement of this crop, as the lack of improved cultivars adapted to specific environments has been one of the limitations preventing wider use...
March 9, 2017: Genes
https://www.readbyqxmd.com/read/28282710/early-onset-friedreich-s-ataxia-with-oculomotor-apraxia
#6
Amene Saghazadeh, Sina Hafizi, Firouzeh Hosseini, Mahmoud Reza Ashrafi, Nima Rezaei
Friedreich's ataxia (FRDA) is a rare autosomal recessive spinocerebellar ataxia which in the majority of cases is associated with a GAA-trinucleotide repeat expansion in the first intron of Frataxin gene located on chromosome 9. The clinical features include progressive gait and limb ataxia, cerebellar dysarthria, neuropathy, optic atrophy, and loss of vibration and proprioception. Ataxia with ocular motor apraxia type 1 (AOA1) is another autosomal recessive cerebellar ataxia which is associated with oculomotor apraxia, hypoalbuminaemia, and hypercholesterolemia...
February 2017: Acta Medica Iranica
https://www.readbyqxmd.com/read/28278294/validation-of-a-commercially-available-test-that-enables-the-quantification-of-the-numbers-of-cgg-trinucleotide-repeat-expansion-in-fmr1-gene
#7
Grace X Y Lim, Minli Yeo, Yvonne Y Koh, Tri Indah Winarni, Indhu-Shree Rajan-Babu, Samuel S Chong, Sultana M H Faradz, Ming Guan
In the present study, we evaluated a commercially available TP-PCR-based assay, the FastFraXTM FMR1 Sizing kit, as a test in quantifying the number of CGG repeats in the FMR1 gene. Based on testing with well characterized DNA samples from Coriell, the kit yielded size results within 3 repeats of those obtained by common consensus (n = 14), with the exception of one allele. Furthermore, based on data obtained using all Coriell samples with or without common consensus (n = 29), the Sizing kit was 97.5% in agreement with existing approaches...
2017: PloS One
https://www.readbyqxmd.com/read/28278169/molecular-cytogenetic-fish-and-genome-analysis-of-diploid-wheatgrasses-and-their-phylogenetic-relationship
#8
Gabriella Linc, Eszter Gaál, István Molnár, Diana Icsó, Ekaterina Badaeva, Márta Molnár-Láng
This paper reports detailed FISH-based karyotypes for three diploid wheatgrass species Agropyron cristatum (L.) Beauv., Thinopyrum bessarabicum (Savul.&Rayss) A. Löve, Pseudoroegneria spicata (Pursh) A. Löve, the supposed ancestors of hexaploid Thinopyrum intermedium (Host) Barkworth & D.R.Dewey, compiled using DNA repeats and comparative genome analysis based on COS markers. Fluorescence in situ hybridization (FISH) with repetitive DNA probes proved suitable for the identification of individual chromosomes in the diploid JJ, StSt and PP genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28270748/huntingtin-is-required-for-neural-but-not-cardiac-pancreatic-progenitor-differentiation-of-mouse-embryonic-stem-cells-in-vitro
#9
Man Shan Yu, Naoko Tanese
Mutation in the huntingtin (HTT) gene causes Huntington's disease (HD). It is an autosomal dominant trinucleotide-repeat expansion disease in which CAG repeat sequence expands to >35. This results in the production of mutant HTT protein with an increased stretch of glutamines near the N-terminus. The wild type HTT gene encodes a 350 kD protein whose function remains elusive. Mutant HTT protein has been implicated in transcription, axonal transport, cytoskeletal structure/function, signal transduction, and autophagy...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28265888/huntington-disease-linking-pathogenesis-to-the-development-of-experimental-therapeutics
#10
REVIEW
Tiago A Mestre, Cristina Sampaio
Huntington disease (HD) is an autosomal dominant neurodegenerative condition caused by a CAG trinucleotide expansion in the huntingtin gene. At present, the HD field is experiencing exciting times with the assessment for the first time in human subjects of interventions aimed at core disease mechanisms. Out of a portfolio of interventions that claim a potential disease-modifying effect in HD, the target huntingtin has more robust validation. In this review, we discuss the spectrum of huntingtin-lowering therapies that are currently being considered...
February 2017: Current Neurology and Neuroscience Reports
https://www.readbyqxmd.com/read/28243313/utilizing-selected-di-and-trinucleotides-of-sirna-to-predict-rnai-activity
#11
Ye Han, Yuanning Liu, Hao Zhang, Fei He, Chonghe Shu, Liyan Dong
Small interfering RNAs (siRNAs) induce posttranscriptional gene silencing in various organisms. siRNAs targeted to different positions of the same gene show different effectiveness; hence, predicting siRNA activity is a crucial step. In this paper, we developed and evaluated a powerful tool named "siRNApred" with a new mixed feature set to predict siRNA activity. To improve the prediction accuracy, we proposed 2-3NTs as our new features. A Random Forest siRNA activity prediction model was constructed using the feature set selected by our proposed Binary Search Feature Selection (BSFS) algorithm...
2017: Computational and Mathematical Methods in Medicine
https://www.readbyqxmd.com/read/28239713/enhancerpred2-0-predicting-enhancers-and-their-strength-based-on-position-specific-trinucleotide-propensity-and-electron-ion-interaction-potential-feature-selection
#12
Wenying He, Cangzhi Jia
Enhancers are cis-acting elements that play major roles in upregulating eukaryotic gene expression by providing binding sites for transcription factors and their complexes. Because enhancers are highly cell/tissue specific, lack common motifs, and are far from the target gene, the systematic and precise identification of enhancer regions in DNA sequences is a big challenge. In this study, we developed an enhancer prediction method called EnhancerPred2.0 by combining position-specific trinucleotide propensity (PSTNP) information with the electron-ion interaction potential (EIIP) values for trinucleotides, to predict enhancers and their subgroups...
February 27, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28238939/temporary-removal-unitary-circular-code-motifs-in-genomes-of-eukaryotes
#13
Karim El Soufi, Christian J Michel
The publisher regrets that this article has been temporarily removed. A replacement will appear as soon as possible in which the reason for the removal of the article will be specified, or the article will be reinstated. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy.
February 24, 2017: Bio Systems
https://www.readbyqxmd.com/read/28212312/genome-wide-prediction-of-dna-methylation-using-dna-composition-and-sequence-complexity-in-human
#14
Chengchao Wu, Shixin Yao, Xinghao Li, Chujia Chen, Xuehai Hu
DNA methylation plays a significant role in transcriptional regulation by repressing activity. Change of the DNA methylation level is an important factor affecting the expression of target genes and downstream phenotypes. Because current experimental technologies can only assay a small proportion of CpG sites in the human genome, it is urgent to develop reliable computational models for predicting genome-wide DNA methylation. Here, we proposed a novel algorithm that accurately extracted sequence complexity features (seven features) and developed a support-vector-machine-based prediction model with integration of the reported DNA composition features (trinucleotide frequency and GC content, 65 features) by utilizing the methylation profiles of embryonic stem cells in human...
February 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28205498/cognitive-control-learning-and-clinical-motor-ratings-are-most-highly-associated-with-basal-ganglia-brain-volumes-in-the-premanifest-huntington-s-disease-phenotype
#15
Maria B Misiura, Spencer Lourens, Vince D Calhoun, Jeffrey Long, Jeremy Bockholt, Hans Johnson, Ying Zhang, Jane S Paulsen, Jessica A Turner, Jingyu Liu, Betul Kara, Elizabeth Fall
OBJECTIVES: Huntington's disease (HD) is a debilitating genetic disorder characterized by motor, cognitive and psychiatric abnormalities associated with neuropathological decline. HD pathology is the result of an extended chain of CAG (cytosine, adenine, guanine) trinucleotide repetitions in the HTT gene. Clinical diagnosis of HD requires the presence of an otherwise unexplained extrapyramidal movement disorder in a participant at risk for HD. Over the past 15 years, evidence has shown that cognitive, psychiatric, and subtle motor dysfunction is evident decades before traditional motor diagnosis...
February 2017: Journal of the International Neuropsychological Society: JINS
https://www.readbyqxmd.com/read/28202696/low-cancer-prevalence-in-polyglutamine-expansion-diseases
#16
Giulia Coarelli, Alhassane Diallo, Morgane Sonia Thion, Daisy Rinaldi, Fabienne Calvas, Ouahid Lagha Boukbiza, Alina Tataru, Perrine Charles, Christine Tranchant, Cecilia Marelli, Claire Ewenczyk, Maya Tchikviladzé, Marie-Lorraine Monin, Bertrand Carlander, Mathieu Anheim, Alexis Brice, Fanny Mochel, Sophie Tezenas du Montcel, Sandrine Humbert, Alexandra Durr
OBJECTIVE: Polyglutamine (PolyQ) diseases are dominantly transmitted neurologic disorders, caused by coding and expanded CAG trinucleotide repeats. Cancer was reported retrospectively to be rare in patients with PolyQ diseases and we aimed to investigate its prevalence in France. METHODS: Consecutive patients with Huntington disease (HD) and spinocerebellar ataxia (SCA) were questioned about cancer, cardiovascular diseases, and related risk factors in 4 university hospitals in Paris, Toulouse, Strasbourg, and Montpellier...
March 21, 2017: Neurology
https://www.readbyqxmd.com/read/28187704/the-nucleotide-composition-of-microbial-genomes-indicates-differential-patterns-of-selection-on-core-and-accessory-genomes
#17
Jon Bohlin, Vegard Eldholm, John H O Pettersson, Ola Brynildsrud, Lars Snipen
BACKGROUND: The core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the genome, also known as the accessory genome. Here we examine intragenic base composition differences in core genomes and corresponding accessory genomes in 36 species, represented by the genomes of 731 bacterial strains, to assess the impact of selective forces on base composition in microbes...
February 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28170216/proteins-containing-expanded-polyglutamine-tracts-and-neurodegenerative-disease
#18
Adewale Adegbuyiro, Faezeh Sedighi, Albert W Pilkington, Sharon Groover, Justin Legleiter
Several hereditary neurological and neuromuscular diseases are caused by an abnormal expansion of trinucleotide repeats. To date, there have been 10 of these trinucleotide repeat disorders associated with an expansion of the codon CAG encoding glutamine (Q). For these polyglutamine (polyQ) diseases, there is a critical threshold length of the CAG repeat required for disease, and further expansion beyond this threshold is correlated with age of onset and symptom severity. PolyQ expansion in the translated proteins promotes their self-assembly into a variety of oligomeric and fibrillar aggregate species that accumulate into the hallmark proteinaceous inclusion bodies associated with each disease...
February 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28129118/crispr-cas9-induced-ctg%C3%A2-cag-n-repeat-instability-in-the-myotonic-dystrophy-type-1-locus-implications-for-therapeutic-genome-editing
#19
Ellen L van Agtmaal, Laurène M André, Marieke Willemse, Sarah A Cumming, Ingeborg D G van Kessel, Walther J A A van den Broek, Geneviève Gourdon, Denis Furling, Vincent Mouly, Darren G Monckton, Derick G Wansink, Bé Wieringa
Myotonic dystrophy type 1 (DM1) is caused by (CTG⋅CAG)n-repeat expansion within the DMPK gene and thought to be mediated by a toxic RNA gain of function. Current attempts to develop therapy for this disease mainly aim at destroying or blocking abnormal properties of mutant DMPK (CUG)n RNA. Here, we explored a DNA-directed strategy and demonstrate that single clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-cleavage in either its 5' or 3' unique flank promotes uncontrollable deletion of large segments from the expanded trinucleotide repeat, rather than formation of short indels usually seen after double-strand break repair...
January 4, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28128360/discovery-of-cancer-driver-long-noncoding-rnas-across-1112-tumour-genomes-new-candidates-and-distinguishing-features
#20
Andrés Lanzós, Joana Carlevaro-Fita, Loris Mularoni, Ferran Reverter, Emilio Palumbo, Roderic Guigó, Rory Johnson
Long noncoding RNAs (lncRNAs) represent a vast unexplored genetic space that may hold missing drivers of tumourigenesis, but few such "driver lncRNAs" are known. Until now, they have been discovered through changes in expression, leading to problems in distinguishing between causative roles and passenger effects. We here present a different approach for driver lncRNA discovery using mutational patterns in tumour DNA. Our pipeline, ExInAtor, identifies genes with excess load of somatic single nucleotide variants (SNVs) across panels of tumour genomes...
January 27, 2017: Scientific Reports
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