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Exon skipping

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https://www.readbyqxmd.com/read/28350844/isolation-and-characterization-of-alternatively-spliced-variants-of-the-mouse-sigma1-receptor-gene-sigmar1
#1
Ling Pan, David A Pasternak, Jin Xu, Mingming Xu, Zhigang Lu, Gavril W Pasternak, Ying-Xian Pan
The sigma1 receptor acts as a chaperone at the endoplasmic reticulum, associates with multiple proteins in various cellular systems, and involves in a number of diseases, such as addiction, pain, cancer and psychiatric disorders. The sigma1 receptor is encoded by the single copy SIGMAR1 gene. The current study identifies five alternatively spliced variants of the mouse sigma1 receptor gene using a polymerase chain reaction cloning approach. All the splice variants are generated by exon skipping or alternative 3' or 5' splicing, producing the truncated sigma1 receptor...
2017: PloS One
https://www.readbyqxmd.com/read/28339459/functional-classification-of-dna-variants-by-hybrid-minigenes-identification-of-30-spliceogenic-variants-of-brca2-exons-17-and-18
#2
Eugenia Fraile-Bethencourt, Beatriz Díez-Gómez, Valeria Velásquez-Zapata, Alberto Acedo, David J Sanz, Eladio A Velasco
Mutation screening of the breast cancer genes BRCA1 and BRCA2 identifies a large fraction of variants of uncertain clinical significance (VUS) whose functional and clinical interpretations pose a challenge for genomic medicine. Likewise, an increasing amount of evidence indicates that genetic variants can have deleterious effects on pre-mRNA splicing. Our goal was to investigate the impact on splicing of a set of reported variants of BRCA2 exons 17 and 18 to assess their role in hereditary breast cancer and to identify critical regulatory elements that may constitute hotspots for spliceogenic variants...
March 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28334849/icf-specific-dnmt3b-dysfunction-interferes-with-intragenic-regulation-of-mrna-transcription-and-alternative-splicing
#3
Sole Gatto, Miriam Gagliardi, Monica Franzese, Sylwia Leppert, Mariarosaria Papa, Marco Cammisa, Giacomo Grillo, Guillame Velasco, Claire Francastel, Shir Toubiana, Maurizio D'Esposito, Claudia Angelini, Maria R Matarazzo
Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown...
March 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334074/genome-wide-analysis-reveals-that-exon-methylation-facilitates-its-selective-usage-in-the-human-transcriptome
#4
Shengli Li, Jiwei Zhang, Shenglin Huang, Xianghuo He
DNA methylation, especially in promoter regions, is a well-characterized epigenetic marker related to gene expression regulation in eukaryotes. However, the role of intragenic DNA methylation in the usage of corresponding exons still remains elusive. In this study, we described the DNA methylome across 10 human tissues. The human genome showed both conserved and varied methylation levels among these tissues. We found that the methylation densities in promoters and first exons were negatively correlated with the corresponding gene expression level...
February 16, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28327575/analysis-of-exome-data-for-4293-trios-suggests-gpi-anchor-biogenesis-defects-are-a-rare-cause-of-developmental-disorders
#5
Alistair T Pagnamenta, Yoshiko Murakami, John M Taylor, Consuelo Anzilotti, Malcolm F Howard, Venessa Miller, Diana S Johnson, Shereen Tadros, Sahar Mansour, I Karen Temple, Rachel Firth, Elisabeth Rosser, Rachel E Harrison, Bronwen Kerr, Niko Popitsch, Taroh Kinoshita, Jenny C Taylor, Usha Kini
Over 150 different proteins attach to the plasma membrane using glycosylphosphatidylinositol (GPI) anchors. Mutations in 18 genes that encode components of GPI-anchor biogenesis result in a phenotypic spectrum that includes learning disability, epilepsy, microcephaly, congenital malformations and mild dysmorphic features. To determine the incidence of GPI-anchor defects, we analysed the exome data from 4293 parent-child trios recruited to the Deciphering Developmental Disorders (DDD) study. All probands recruited had a neurodevelopmental disorder...
March 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28327087/nt5c2-novel-splicing-variant-expands-the-phenotypic-spectrum-of-spastic-paraplegia-spg45-case-report-of-a-new-member-of-thin-corpus-callosum-spg-subgroup
#6
Mahmoud F Elsaid, Khalid Ibrahim, Nader Chalhoub, Ahmed Elsotouhy, Noora El Mudehki, Alice Abdel Aleem
BACKGROUND: Hereditary Spastic Paraplegia (HSP) is a genetically heterogeneous group of neurodegenerative diseases. Thin Corpus Callosum (TCC) associated HSP is a distinguished subgroup of complex forms. Purines and pyrimidine, the basic DNA and RNA components, are regulating the cell metabolism, having roles in signal transduction, energy preservation and cellular repair. Genetic defects in nucleotide metabolism related genes have been only recently implicated in brain and neurodegenerative diseases' pathogenesis...
March 21, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28325281/systemic-antisense-therapeutics-for-dystrophin-and-myostatin-exon-splice-modulation-improve-muscle-pathology-of-adult-mdx-mice
#7
Ngoc Lu-Nguyen, Alberto Malerba, Linda Popplewell, Fred Schnell, Gunnar Hanson, George Dickson
Antisense-mediated exon skipping is a promising approach for the treatment of Duchenne muscular dystrophy (DMD), a rare life-threatening genetic disease due to dystrophin deficiency. Such an approach can restore the disrupted reading frame of dystrophin pre-mRNA, generating a truncated form of the protein. Alternatively, antisense therapy can be used to induce destructive exon skipping of myostatin pre-mRNA, knocking down myostatin expression to enhance muscle strength and reduce fibrosis. We have reported previously that intramuscular or intraperitoneal antisense administration inducing dual exon skipping of dystrophin and myostatin pre-mRNAs was beneficial in mdx mice, a mouse model of DMD, although therapeutic effects were muscle type restricted, possibly due to the delivery routes used...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28318817/clinical-and-mutational-characteristics-of-duchenne-muscular-dystrophy-patients-based-on-a-comprehensive-database-in-south-china
#8
Dan-Ni Wang, Zhi-Qiang Wang, Lei Yan, Jin He, Min-Ting Lin, Wan-Jin Chen, Ning Wang
The development of clinical trials for Duchenne muscular dystrophy (DMD) in China faces many challenges due to limited information about epidemiological data, natural history and clinical management. To provide these detailed data, we developed a comprehensive database based on registered DMD patients from South China and analysed their clinical and mutational characteristics. The database included DMD registrants confirmed by clinical presentation, family history, genetic detection, prognostic outcome, and/or muscle biopsy...
February 21, 2017: Neuromuscular Disorders: NMD
https://www.readbyqxmd.com/read/28303491/changing-the-therapeutic-landscape-in-non-small-cell-lung-cancers-the-evolution-of-comprehensive-molecular-profiling-improves-access-to-therapy
#9
REVIEW
Joshua K Sabari, Fernando Santini, Isabella Bergagnini, W Victoria Lai, Kathryn C Arbour, Alexander Drilon
Targeting genomic alterations has led to a paradigm shift in the treatment of patients with lung cancer. In an effort to better identify potentially actionable alterations that may predict response to FDA-approved and or investigational therapies, many centers have migrated towards performing targeted exome sequencing in patients with stage IV disease. The implementation of next-generation sequencing (NGS) in the evaluation of tumor tissue from patients with NSCLC has led to the discovery of targetable alterations in tumors that previously had no known actionable targets by less comprehensive profiling...
April 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/28295493/case-of-harlequin-ichthyosis-with-a-favorable-outcome-early-treatment-and-novel-differentially-expressed-alternatively-spliced-transcripts-of-the-atp-binding-cassette-subfamily-a-member-12-gene
#10
Ken Washio, Mayuko Sumi, Kaori Nakata, Atsushi Fukunaga, Keiji Yamana, Tsubasa Koda, Ichiro Morioka, Chikako Nishigori, Kiyofumi Yamanishi
Harlequin ichthyosis (HI) is the most severe form of autosomal recessive congenital ichthyosis, with a high mortality rate. Recent advances in neonatal care and the early administration of retinoids have improved the survival rate of HI. Here, we present a case of HI who was successfully treated with early administration of etretinate and showed good prognosis. Next-generation sequencing identified novel mutations of the ATP-binding cassette subfamily A member 12 gene (ABCA12), c.5884+4_+5delAA and c.7239G>A, which caused skipping of exons 39 and 48, respectively...
March 11, 2017: Journal of Dermatology
https://www.readbyqxmd.com/read/28295039/deciphering-the-mechanism-of-q145h-sftpc-mutation-unmasks-a-splicing-defect-and-explains-the-severity-of-the-phenotype
#11
Céline Delestrain, Stéphanie Simon, Abdel Aissat, Rachel Medina, Xavier Decrouy, Elodie Nattes, Agathe Tarze, Bruno Costes, Pascale Fanen, Ralph Epaud
Mutations in the gene encoding surfactant protein C (SFTPC) have led to a broad range of phenotypes from neonatal respiratory distress syndrome to adult interstitial lung disease. We previously identified the c.435G>C variant in the SFTPC gene associated with fatal neonatal respiratory distress syndrome in an infant girl. Although this variation is predicted to change glutamine (Q) at position 145 to histidine (H), its position at the last base of exon 4 and the severity of the phenotype suggested that it might also induce a splicing defect...
March 15, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28291226/neuronal-elavl-proteins-utilize-auf-1-as-a-co-partner-to-induce-neuron-specific-alternative-splicing-of-app
#12
Apostolia Fragkouli, Pelagia Koukouraki, Ioannis S Vlachos, Maria D Paraskevopoulou, Artemis G Hatzigeorgiou, Epaminondas Doxakis
Aβ peptide that accumulates in Alzheimer's disease brain, derives from proteolytic processing of the amyloid precursor protein (APP) that exists in three main isoforms derived by alternative splicing. The isoform APP695, lacking exons 7 and 8, is predominately expressed in neurons and abnormal neuronal splicing of APP has been observed in the brain of patients with Alzheimer's disease. Herein, we demonstrate that expression of the neuronal members of the ELAVL protein family (nELAVLs) correlate with APP695 levels in vitro and in vivo...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28289848/genome-wide-associations-of-cd46-and-ifi44l-genetic-variants-with-neutralizing-antibody-response-to-measles-vaccine
#13
Iana H Haralambieva, Inna G Ovsyannikova, Richard B Kennedy, Beth R Larrabee, Michael T Zimmermann, Diane E Grill, Daniel J Schaid, Gregory A Poland
Population-based studies have revealed 2-10% measles vaccine failure rate even after two vaccine doses. While the mechanisms behind this remain unknown, we hypothesized that host genetic factors are likely to be involved. We performed a genome-wide association study of measles specific neutralizing antibody and IFNγ ELISPOT response in a combined sample of 2872 subjects. We identified two distinct chromosome 1 regions (previously associated with MMR-related febrile seizures), associated with vaccine-induced measles neutralizing antibody titers...
April 2017: Human Genetics
https://www.readbyqxmd.com/read/28289846/a-deletion-in-the-hermansky-pudlak-syndrome-4-hps4-gene-appears-to-be-responsible-for-albinism-in-channel-catfish
#14
Yueru Li, Xin Geng, Lisui Bao, Ahmed Elaswad, Kevin W Huggins, Rex Dunham, Zhanjiang Liu
Albinism is caused by a series of genetic abnormalities leading to reduction of melanin production. Albinism is quite frequent in catfish, but the causative gene and the molecular basis were unknown. In this study, we conducted a genome-wide association study (GWAS) using the 250 K SNP array. The GWAS analysis allowed mapping of the albino phenotype in the Hermansky-Pudlak syndrome 4 (Hps4) gene, which is known to be involved in melanosome biosynthesis. Sequencing analysis revealed that a 99-bp deletion was present in all analyzed albino catfish at the intron 2 and exon 3 junction...
March 13, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28285687/met-exon-14-skipping-mutation-in-triple-negative-pulmonary-adenocarcinomas-and-pleomorphic-carcinomas-an-analysis-of-intratumoral-met-status-heterogeneity-and-clinicopathological-characteristics
#15
Dohee Kwon, Jaemoon Koh, Sehui Kim, Heounjeong Go, Young A Kim, Bhumsuk Keam, Tae Min Kim, Dong-Wan Kim, Yoon Kyung Jeon, Doo Hyun Chung
OBJECTIVES: MET mutations leading to exon 14 skipping rarely occur in non-small cell lung cancer (NSCLC). Recently, small molecule inhibitors targeting MET mutations showed clinical benefit. However, the clinicopathological characteristics of NSCLC harboring MET mutations, and the correlation among mutations, protein expression, and gene copy number of MET in NSCLC remain unclear. Therefore, we address these issues. MATERIALS AND METHODS: MET exon 14 skipping mutations were evaluated using real-time quantitative reverse-transcription-PCR (qRT-PCR) in 102 triple-negative (i...
April 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28280301/eteplirsen-in-the-treatment-of-duchenne-muscular-dystrophy
#16
REVIEW
Kenji Rowel Q Lim, Rika Maruyama, Toshifumi Yokota
Duchenne muscular dystrophy is a fatal neuromuscular disorder affecting around one in 3,500-5,000 male births that is characterized by progressive muscular deterioration. It is inherited in an X-linked recessive fashion and is caused by loss-of-function mutations in the DMD gene coding for dystrophin, a cytoskeletal protein that stabilizes the plasma membrane of muscle fibers. In September 2016, the US Food and Drug Administration granted accelerated approval for eteplirsen (or Exondys 51), a drug that acts to promote dystrophin production by restoring the translational reading frame of DMD through specific skipping of exon 51 in defective gene variants...
2017: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/28280001/a-rapid-and-effective-method-for-screening-sequencing-and-reporter-verification-of-engineered-frameshift-mutations-in-zebrafish
#17
Sergey V Prykhozhij, Shelby L Steele, Babak Razaghi, Jason N Berman
Clustered Regularly Interspaced Palindromic Repeats (CRISPR)/Cas9 adaptive immunity against pathogens in bacteria has been adapted for genome editing and applied in zebrafish (Danio rerio) to generate frameshift mutations in protein-coding genes. Although there are methods to detect, quantify and sequence CRISPR/Cas9-induced mutations, identifying mutations in F1 heterozygous fish remains challenging. Additionally, sequencing a mutation and assuming that it causes a frameshift does not prove causality because of possible alternative translation start sites and potential effects of mutations on splicing...
March 9, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28276505/alternative-exon-skipping-biases-substrate-preference-of-the-deubiquitylase-usp15-for-mysterin-rnf213-the-moyamoya-disease-susceptibility-factor
#18
Yuri Kotani, Daisuke Morito, Kenshiro Sakata, Shiori Ainuki, Munechika Sugihara, Tomohisa Hatta, Shun-Ichiro Iemura, Seiji Takashima, Tohru Natsume, Kazuhiro Nagata
The deubiquitylating enzyme USP15 plays significant roles in multiple cellular pathways including TGF-β signaling, RNA splicing, and innate immunity. Evolutionarily conserved skipping of exon 7 occurs during transcription of the mRNAs encoding USP15 and its paralogue USP4, yielding two major isoforms for each gene. Exon 7 of USP15 encodes a serine-rich stretch of 29 amino acid residues located in the inter-region linker that connects the N-terminal putative regulatory region and the C-terminal enzymatic region...
March 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28270101/deciphering-alternative-splicing-and-nonsense-mediated-decay-modulate-expression-in-primary-lymphoid-tissues-of-birds-infected-with-avian-pathogenic-e-coli-apec
#19
Hongyan Sun
BACKGROUND: Avian pathogenic E. coli (APEC) can lead to a loss in millions of dollars in poultry annually because of mortality and produce contamination. Studies have verified that many immune-related genes undergo changes in alternative splicing (AS), along with nonsense mediated decay (NMD), to regulate the immune system under different conditions. Therefore, the splicing profiles of primary lymphoid tissues with systemic APEC infection need to be comprehensively examined. RESULTS: Gene expression in RNAseq data were obtained for three different immune tissues (bone marrow, thymus, and bursa) from three phenotype birds (non-challenged, resistant, and susceptible birds) at two time points...
March 7, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28258942/late-onset-of-neutral-lipid-storage-disease-due-to-novel-pnpla2-mutations-causing-total-loss-of-lipase-activity-in-a-patient-with-myopathy-and-slight-cardiac-involvement
#20
Sara Missaglia, Lorenzo Maggi, Marina Mora, Sara Gibertini, Flavia Blasevich, Piergiuseppe Agostoni, Laura Moro, Denise Cassandrini, Filippo Maria Santorelli, Simonetta Gerevini, Daniela Tavian
Neutral lipid storage disease with myopathy (NLSDM) presents with skeletal muscle myopathy and severe dilated cardiomyopathy in nearly 40% of cases. NLSDM is caused by mutations in the PNPLA2 gene, which encodes the adipose triglyceride lipase (ATGL). Here we report clinical and genetic findings of a patient carrying two novel PNPLA2 mutations (c.696+4A>G and c.553_565delGTCCCCCTTCTCG). She presented at age 39 with right upper limb abduction weakness slowly progressing over the years with asymmetric involvement of proximal upper and lower limb muscles...
January 17, 2017: Neuromuscular Disorders: NMD
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