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https://www.readbyqxmd.com/read/28212312/genome-wide-prediction-of-dna-methylation-using-dna-composition-and-sequence-complexity-in-human
#1
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
#2
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
#3
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...
February 15, 2017: Neurology
https://www.readbyqxmd.com/read/28187704/the-nucleotide-composition-of-microbial-genomes-indicates-differential-patterns-of-selection-on-core-and-accessory-genomes
#4
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
#5
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 ten 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 7, 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
#6
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
#7
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
https://www.readbyqxmd.com/read/28118661/trinucleotide-repeat-expansion-in-the-transcription-factor-4-tcf4-gene-leads-to-widespread-mrna-splicing-changes-in-fuchs-endothelial-corneal-dystrophy
#8
Eric D Wieben, Ross A Aleff, Xiaojia Tang, Malinda L Butz, Krishna R Kalari, Edward W Highsmith, Jin Jen, George Vasmatzis, Sanjay V Patel, Leo J Maguire, Keith H Baratz, Michael P Fautsch
Purpose: To identify RNA missplicing events in human corneal endothelial tissue isolated from Fuchs' endothelial corneal dystrophy (FECD). Methods: Total RNA was isolated and sequenced from corneal endothelial tissue obtained during keratoplasty from 12 patients with FECD and 4 patients undergoing keratoplasty or enucleation for other indications. The length of the trinucleotide repeat (TNR) CTG in the transcription factor 4 (TCF4) gene was determined using leukocyte-derived DNA analyzed by a combination of Southern blotting and Genescan analysis...
January 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28115203/the-maximal-c-3-self-complementary-trinucleotide-circular-code-x-in-genes-of-bacteria-archaea-eukaryotes-plasmids-and-viruses
#9
Christian J Michel
In 1996, a set X of 20 trinucleotides is identified in genes of both prokaryotes and eukaryotes which has in average the highest occurrence in reading frame compared to its two shifted frames (Arquès and Michel, 1996). Furthermore, this set X has an interesting mathematical property as X is a maximal C(3) self-complementary trinucleotide circular code (Arquès and Michel, 1996). In 2015, by quantifying the inspection approach used in 1996, the circular code X is confirmed in genes of bacteria and eukaryotes and is also identified in genes of plasmids and viruses (Michel, 2015)...
January 20, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28109580/cardiac-transplantation-in-friedreich-ataxia-extended-follow-up
#10
Ashley McCormick, Julianna Shinnick, Kim Schadt, Rose Rodriguez, Linda Addonizio, Michio Hirano, Susan Perlman, Kimberly Y Lin, David R Lynch
Friedreich Ataxia (FRDA) is an autosomal recessive neurodegenerative disorder most commonly caused by guanine-adenine-adenine (GAA) trinucleotide repeat expansions in both alleles of the FXN gene. Although progressive ataxia remains the hallmark clinical feature, patients with FRDA are at high risk of developing cardiomyopathy, often resulting in premature death. There is no specific treatment for FRDA-associated cardiomyopathy; even in advanced cardiac failure cardiac transplantation is not commonly pursued...
January 10, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28102759/antisense-transcription-of-the-myotonic-dystrophy-locus-yields-low-abundant-rnas-with-and-without-cag-n-repeat
#11
Anke E E G Gudde, Simon J van Heeringen, Amanda I de Oude, Ingeborg D G van Kessel, Joseph Estabrook, Eric T Wang, Bé Wieringa, Derick G Wansink
The unstable (CTG·CAG)n trinucleotide repeat in the myotonic dystrophy type 1 (DM1) locus is bidirectionally transcribed from genes with terminal overlap. By transcription in the sense direction, the DMPK gene produces various alternatively spliced mRNAs with a (CUG)n repeat in their 3' UTR. Expression in opposite orientation reportedly yields (CAG)n-repeat containing RNA, but both structure and biological significance of this antisense gene (DM1-AS) are largely unknown. Via a combinatorial approach of computational and experimental analyses of RNA from unaffected individuals and DM1 patients we discovered that DM1-AS spans >6 kb, contains alternative transcription start sites and uses alternative polyadenylation sites up- and downstream of the (CAG)n repeat...
January 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28101439/development-of-highly-variable-microsatellite-markers-for-the-tetraploid-silene-stellata-caryophyllaceae
#12
Juannan Zhou, Michele R Dudash, Charles B Fenster, Elizabeth A Zimmer
PREMISE OF THE STUDY: We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success. METHODS AND RESULTS: A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats...
December 2016: Applications in Plant Sciences
https://www.readbyqxmd.com/read/28097058/determining-virus-host-interactions-and-glycerol-metabolism-profiles-in-geographically-diverse-solar-salterns-with-metagenomics
#13
Abraham G Moller, Chun Liang
Solar salterns are excellent model ecosystems for studying virus-microbial interactions because of their low microbial diversity, environmental stability, and high viral density. By using the power of CRISPR spacers to link viruses to their prokaryotic hosts, we explored virus-host interactions in geographically diverse salterns. Using taxonomic profiling, we identified hosts such as archaeal Haloquadratum, Halorubrum, and Haloarcula and bacterial Salinibacter, and we found that community composition related to not only salinity but also local environmental dynamics...
2017: PeerJ
https://www.readbyqxmd.com/read/28094373/conformational-dynamics-and-self-association-of-intrinsically-disordered-huntingtin-exon-1-in-cells
#14
Steffen Büning, Abhishek Sharma, Shivang Vachharajani, Estella Newcombe, Angelique Ormsby, Mimi Gao, David Gnutt, Tobias Vöpel, Danny M Hatters, Simon Ebbinghaus
Huntington's disease is caused by a CAG trinucleotide expansion mutation in the Huntingtin gene that leads to an artificially long polyglutamine sequence in the Huntingtin protein. A key feature of the disease is the intracellular aggregation of the Huntingtin exon 1 protein (Httex1) into micrometer sized inclusion bodies. The aggregation process of Httex1 has been extensively studied in vitro, however, the crucial early events of nucleation and aggregation in the cell remain elusive. Here, we studied the conformational dynamics and self-association of Httex1 by in-cell experiments using laser-induced temperature jumps and analytical ultracentrifugation...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28075481/diagnosis-of-spinocerebellar-ataxias-caused-by-trinucleotide-repeat-expansions
#15
Joanne E Martindale
Spinocerebellar ataxias (SCAs) are a group of disorders that are both clinically and genetically heterogeneous. They usually demonstrate onset in adulthood, but some forms may have juvenile or infantile onset. There are many different types of SCA, demonstrating different modes of inheritance and types of mutation. The most common forms are due to dominantly inherited expansions in trinucleotide repeat sequences located within the coding region of the relevant genes, and these are readily identifiable by molecular genetic testing...
January 11, 2017: Current Protocols in Human Genetics
https://www.readbyqxmd.com/read/28053699/identification-of-target-genes-for-spermatogenic-cell-specific-krab-transcription-factor-zfp819-in-a-male-germ-cell-line
#16
Sora Jin, Heejin Choi, Jun Tae Kwon, Jihye Kim, Juri Jeong, Jaehwan Kim, Seong Hyeon Hong, Chunghee Cho
BACKGROUND: Zfp819, a member of the Krüppel-associated box (KRAB) family, encodes a spermatogenic cell-specific transcription factor. Zfp819-overexpression induces apoptosis and inhibits proliferation in somatic cell lines. RESULTS: In the present study, we examined the cellular effects of Zfp819 in a male germ cell line (GC-2 cells). Overexpression of Zfp819 demonstrated an increase in the number of apoptotic cells, leading to inhibition of proliferation in GC-2 cells...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/28042823/identification-and-analysis-of-rna-editing-sites-in-the-chloroplast-transcripts-of-aegilops-tauschii-l
#17
Mengxing Wang, Hui Liu, Lingqiao Ge, Guangwei Xing, Meng Wang, Song Weining, Xiaojun Nie
RNA editing is an important way to convert cytidine (C) to uridine (U) at specific sites within RNA molecules at a post-transcriptional level in the chloroplasts of higher plants. Although it has been systematically studied in many plants, little is known about RNA editing in the wheat D genome donor Aegilops tauschii L. Here, we investigated the chloroplast RNA editing of Ae. tauschii and compared it with other wheat relatives to trace the evolution of wheat. Through bioinformatics prediction, a total of 34 C-to-U editing sites were identified, 17 of which were validated using RT-PCR product sequencing...
December 30, 2016: Genes
https://www.readbyqxmd.com/read/28035996/novel-nine-exon-ar-transcripts-exon-1-exon-1b-exons-2-8-in-normal-and-cancerous-breast-and-prostate-cells
#18
Dong Gui Hu, Ross A McKinnon, Julie-Ann Hulin, Peter I Mackenzie, Robyn Meech
Nearly 20 different transcripts of the human androgen receptor (AR) are reported with two currently listed as Refseq isoforms in the NCBI database. Isoform 1 encodes wild-type AR (type 1 AR) and isoform 2 encodes the variant AR45 (type 2 AR). Both variants contain eight exons: they share common exons 2-8 but differ in exon 1 with the canonical exon 1 in isoform 1 and the variant exon 1b in isoform 2. Splicing of exon 1 or exon 1b is reported to be mutually exclusive. In this study, we identified a novel exon 1b (1b/TAG) that contains an additional TAG trinucleotide upstream of exon 1b...
December 27, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28027448/induced-pluripotent-hd-monkey-stem-cells-derived-neural-cells-for-drug-discovery
#19
Tanut Kunkanjanawan, Richard Carter, Kwan-Sung Ahn, Jinjing Yang, Rangsun Parnpai, Anthony W S Chan
Huntington's disease (HD) is a neurodegenerative disease caused by an expansion of CAG trinucleotide repeat (polyglutamine [polyQ]) in the huntingtin ( HTT) gene, which leads to the formation of mutant HTT (mHTT) protein aggregates. In the nervous system, an accumulation of mHTT protein results in glutamate-mediated excitotoxicity, proteosome instability, and apoptosis. Although HD pathogenesis has been extensively studied, effective treatment of HD has yet to be developed. Therapeutic discovery research in HD has been reported using yeast, cells derived from transgenic animal models and HD patients, and induced pluripotent stem cells from patients...
December 1, 2016: Journal of Biomolecular Screening
https://www.readbyqxmd.com/read/28017481/atxn2-trinucleotide-repeat-length-correlates-with-risk-of-als
#20
William Sproviero, Aleksey Shatunov, Daniel Stahl, Maryam Shoai, Wouter van Rheenen, Ashley R Jones, Safa Al-Sarraj, Peter M Andersen, Nancy M Bonini, Francesca L Conforti, Philip Van Damme, Hussein Daoud, Maria Del Mar Amador, Isabella Fogh, Monica Forzan, Ben Gaastra, Cinzia Gellera, Aaron D Gitler, John Hardy, Pietro Fratta, Vincenzo La Bella, Isabelle Le Ber, Tim Van Langenhove, Serena Lattante, Yi-Chung Lee, Andrea Malaspina, Vincent Meininger, Stéphanie Millecamps, Richard Orrell, Rosa Rademakers, Wim Robberecht, Guy Rouleau, Owen A Ross, Francois Salachas, Katie Sidle, Bradley N Smith, Bing-Wen Soong, Gianni Sorarù, Giovanni Stevanin, Edor Kabashi, Claire Troakes, Christine van Broeckhoven, Jan H Veldink, Leonard H van den Berg, Christopher E Shaw, John F Powell, Ammar Al-Chalabi
We investigated a CAG trinucleotide repeat expansion in the ATXN2 gene in amyotrophic lateral sclerosis (ALS). Two new case-control studies, a British dataset of 1474 ALS cases and 567 controls, and a Dutch dataset of 1328 ALS cases and 691 controls were analyzed. In addition, to increase power, we systematically searched PubMed for case-control studies published after 1 August 2010 that investigated the association between ATXN2 intermediate repeats and ALS. We conducted a meta-analysis of the new and existing studies for the relative risks of ATXN2 intermediate repeat alleles of between 24 and 34 CAG trinucleotide repeats and ALS...
March 2017: Neurobiology of Aging
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