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Exon skipping in humans

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https://www.readbyqxmd.com/read/28295039/deciphering-the-mechanism-of-q145h-sftpc-mutation-unmasks-a-splicing-defect-and-explains-the-severity-of-the-phenotype
#1
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/28178888/histone-modifications-influence-skipped-exons-inclusion
#2
Yue Hou, Huan Huang, Wenqiao Hu, Hongde Liu, Xiao Sun
Alternative splicing (AS), by which individual genes can produce multiple mRNA, associates with genomic complexity, disease, and development. Histone modifications show important roles in both transcription initiation and mRNA splicing. Here, we intended to find the link between AS and histone modifications in flanking regions through analyzing publicly available data in two human cell lines, GM12878 and K562 cell lines. According to exon inclusion levels, exons were classified into three types, included skipped exons, excluded skipped exons and expressed constitutive exons...
February 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/28100912/cryptic-splice-activation-but-not-exon-skipping-is-observed-in-minigene-assays-of-dystrophin-c-9361-1g-a-mutation-identified-by-ngs
#3
Emma Tabe Eko Niba, Atsushi Nishida, Van Khanh Tran, Dung Chi Vu, Masaaki Matsumoto, Hiroyuki Awano, Tomoko Lee, Yasuhiro Takeshima, Hisahide Nishio, Masafumi Matsuo
Next-generation sequencing (NGS) discloses nucleotide changes in the genome. Mutations at splicing regulatory elements are expected to cause splicing errors, such as exon skipping, cryptic splice site activation, partial exon loss or intron retention. In dystrophinopathy patients, prediction of splicing outcomes is essential to determine the phenotype: either severe Duchenne or mild Becker muscular dystrophy, based on the reading frame rule. In a Vietnamese patient, NGS identified a c.9361+1G>A mutation in the dystrophin gene and an additional DNA variation of A>G at +117 bases in intron 64...
January 19, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28093505/modelling-the-ferrochelatase-c-315-48c-modifier-mutation-for-erythropoietic-protoporphyria-epp-in-mice
#4
Jasmin Barman-Aksözen, Paulina Ćwiek, Vijay B Bansode, Frank Koentgen, Judith Trüb, Pawel Pelczar, Paolo Cinelli, Xiaoye Schneider-Yin, Daniel Schümperli, Elisabeth I Minder
Erythropoietic Protoporphyria (EPP) is caused by deficiency of ferrochelatase (FECH) which incorporates iron into protoporphyrin IX (PPIX) to form heme. Excitation of accumulated PPIX by light generates oxygen radicals which evoke excessive pain and, after longer light exposure, ulcerations in exposed skin areas of EPP patients. Moreover, ∼5% of the patients develop a liver dysfunction due to PPIX accumulation. Most patients (∼97%) have a severe FECH mutation (Mut) in trans to an intronic polymorphism (c...
January 12, 2017: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/28077247/mouse-dna-polymerase-%C3%AE-lacking-the-forty-two-amino-acids-encoded-by-exon-2-is-catalytically-inactive-in-vitro
#5
Ekaterina G Frank, John P McDonald, Wei Yang, Roger Woodgate
In 2003, we reported that 129-derived strains of mice carry a naturally occurring nonsense mutation at codon 27 of the Poli gene that would produce a polι peptide of just 26 amino acids, rather then the full-length 717 amino acid wild-type polymerase. In support of the genomic analysis, no polι protein was detected in testes extracts from 129X1/SvJmice, where wild-type polι is normally highly expressed. The early truncation in polι occurs before any structural domains of the polymerase are synthesized and as a consequence, we reasoned that 129-derived strains of mice should be considered as functionally defective in polι activity...
February 2017: DNA Repair
https://www.readbyqxmd.com/read/28072465/splicing-regulation-and-dysregulation-of-cholinergic-genes-expressed-at-the-neuromuscular-junction
#6
REVIEW
Kinji Ohno, Mohammad Alinoor Rahman, Mohammad Nazim, Farhana Nasrin, Yingni Lin, Jun-Ichi Takeda, Akio Masuda
We humans have evolved by acquiring diversity of alternative RNA metabolisms including alternative means of splicing and transcribing non-coding genes, and not by acquiring new coding genes. Tissue-specific and developmental stage-specific alternative RNA splicing is achieved by tightly regulated spatiotemporal regulation of expressions and activations of RNA-binding proteins that recognize their cognate splicing cis-elements on nascent RNA transcripts. Genes expressed at the neuromuscular junction (NMJ) are also alternatively spliced...
January 10, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/28049883/neuron-specific-splicing
#7
Nor Hakimah Ab Hakim, Burhanuddin Yeop Majlis, Hitoshi Suzuki, Toshifumi Tsukahara
During pre-mRNA splicing events, introns are removed from the pre-mRNA, and the remaining exons are connected together to form a single continuous molecule. Alternative splicing is a common mechanism for the regulation of gene expression in eukaryotes. More than 90% of human genes are known to undergo alternative splicing. The most common type of alternative splicing is exon skipping, which is also known as cassette exon. Other known alternative splicing events include alternative 5' splice sites, alternative 3' splice sites, intron retention, and mutually exclusive exons...
December 31, 2016: Bioscience Trends
https://www.readbyqxmd.com/read/28045018/targeted-rna-seq-profiling-of-splicing-pattern-in-the-dmd-gene-exons-are-mostly-constitutively-spliced-in-human-skeletal-muscle
#8
Anne-Laure Bougé, Eva Murauer, Emmanuelle Beyne, Julie Miro, Jessica Varilh, Magali Taulan, Michel Koenig, Mireille Claustres, Sylvie Tuffery-Giraud
We have analysed the splicing pattern of the human Duchenne Muscular Dystrophy (DMD) NB transcript in normal skeletal muscle. To achieve depth of coverage required for the analysis of this lowly expressed gene in muscle, we designed a targeted RNA-Seq procedure that combines amplification of the full-length 11.3 kb DMD cDNA sequence and 454 sequencing technology. A high and uniform coverage of the cDNA sequence was obtained that allowed to draw up a reliable inventory of the physiological alternative splicing events in the muscular DMD transcript...
January 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28013231/neurexins-1-3-each-have-a-distinct-pattern-of-expression-in-the-early-developing-human-cerebral-cortex
#9
Lauren F Harkin, Susan J Lindsay, Yaobo Xu, Ayman Alzu'bi, Alexandra Ferrara, Emily A Gullon, Owen G James, Gavin J Clowry
Neurexins (NRXNs) are presynaptic terminal proteins and candidate neurodevelopmental disorder susceptibility genes; mutations presumably upset synaptic stabilization and function. However, analysis of human cortical tissue samples by RNAseq and quantitative real-time PCR at 8-12 postconceptional weeks, prior to extensive synapse formation, showed expression of all three NRXNs as well as several potential binding partners. However, the levels of expression were not identical; NRXN1 increased with age and NRXN2 levels were consistently higher than for NRXN3 Immunohistochemistry for each NRXN also revealed different expression patterns at this stage of development...
December 23, 2016: Cerebral Cortex
https://www.readbyqxmd.com/read/27987579/response-and-acquired-resistance-to-crizotinib-in-chinese-patients-with-lung-adenocarcinomas-harboring-met-exon-14-splicing-alternations
#10
Hua-Jie Dong, Peng Li, Chang-Ling Wu, Xiao-Yue Zhou, Hong-Jun Lu, Tong Zhou
Approximately 10% of lung adenocarcinomas harbor aberrations that are targetable using the approved multitargeted TKI crizotinib. MET exon 14 skipping mutation predicts for response to crizotinib in human lung adenocarcinomas. However, a substantial part of patients still has no sufficient tissue to perform genomic analysis. As a promising noninvasive biomarker and potential surrogate for the entire tumor genome, circulating tumor DNA (ctDNA) has been applied to the detection of driver gene mutations. Here we described the MET exon 14 splicing mutations in cell-free circulating-tumor DNA by next-generation sequencing (NGS) technology...
December 2016: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/27974813/comparison-of-the-phenotypes-of-patients-harboring-in-frame-deletions-starting-at-exon-45-in-the-duchenne-muscular-dystrophy-gene-indicates-potential-for-the-development-of-exon-skipping-therapy
#11
Akinori Nakamura, Naoko Shiba, Daigo Miyazaki, Hitomi Nishizawa, Yuji Inaba, Noboru Fueki, Rika Maruyama, Yusuke Echigoya, Toshifumi Yokota
Exon skipping therapy has recently received attention for its ability to convert the phenotype of lethal Duchenne muscular dystrophy (DMD) to a more benign form, Becker muscular dystrophy (BMD), by correcting the open reading frame. This therapy has mainly focused on a hot-spot (exons 45-55) mutation in the DMD gene. Exon skipping of an entire stretch of exons 45-55 is an approach applicable to 46.9% of DMD patients. However, the resulting phenotype is not yet fully understood. Here we examined the clinical profiles of 24 patients with BMD resulting from deletions starting at exon 45...
December 15, 2016: Journal of Human Genetics
https://www.readbyqxmd.com/read/27920410/a-novel-splice-site-mutation-in-the-aspm-gene-underlies-autosomal-recessive-primary-microcephaly
#12
Jamil A Hashmi, Khalid M Al-Harbi, Khushnooda Ramzan, Alia M Albalawi, Amir Mehmood, Mohammed I Samman, Sulman Basit
BACKGROUND: Autosomal recessive primary microcephaly (MCPH) is a clinically and genetically heterogeneous disorder. Patients with MCPH exhibit reduced occipito-frontal head circumference and non-progressive intellectual disability. To date, 17 genes have been known as an underlying cause of MCPH in humans. ASPM (abnormal spindle-like, microcephaly associated) is the most commonly mutated MCPH gene. OBJECTIVE: Identify the genetic defect underlying MCPH in a Saudi family...
November 2016: Annals of Saudi Medicine
https://www.readbyqxmd.com/read/27899647/spliceosomal-protein-eftud2-mutation-leads-to-p53-dependent-apoptosis-in-zebrafish-neural-progenitors
#13
Lei Lei, Shou-Yu Yan, Ran Yang, Jia-Yu Chen, Yumei Li, Ye Bu, Nannan Chang, Qinchao Zhou, Xiaojun Zhu, Chuan-Yun Li, Jing-Wei Xiong
Haploinsufficiency of EFTUD2 (Elongation Factor Tu GTP Binding Domain Containing 2) is linked to human mandibulofacial dysostosis, Guion-Almeida type (MFDGA), but the underlying cellular and molecular mechanisms remain to be addressed. We report here the isolation, cloning and functional analysis of the mutated eftud2 (snu114) in a novel neuronal mutant fn10a in zebrafish. This mutant displayed abnormal brain development with evident neuronal apoptosis while the development of other organs appeared less affected...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27898092/transposon-mediated-generation-of-cellular-and-mouse-models-of-splicing-mutations-to-assess-the-efficacy-of-snrna-based-therapeutics
#14
Elena Barbon, Mattia Ferrarese, Laetitia van Wittenberghe, Peggy Sanatine, Giuseppe Ronzitti, Fanny Collaud, Pasqualina Colella, Mirko Pinotti, Federico Mingozzi
Disease-causing splicing mutations can be rescued by variants of the U1 small nuclear RNA (U1snRNAs). However, the evaluation of the efficacy and safety of modified U1snRNAs as therapeutic tools is limited by the availability of cellular and animal models specific for a given mutation. Hence, we exploited the hyperactive Sleeping Beauty transposon system (SB100X) to integrate human factor IX (hFIX) minigenes into genomic DNA in vitro and in vivo. We generated stable HEK293 cell lines and C57BL/6 mice harboring splicing-competent hFIX minigenes either wild type (SChFIX-wt) or mutated (SChFIXex5-2C)...
November 29, 2016: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/27885216/a-novel-heterozygous-intronic-mutation-in-pou1f1-is-associated-with-combined-pituitary-hormone-deficiency
#15
Masaki Takagi, Hotaka Kamasaki, Hiroko Yagi, Ryuji Fukuzawa, Satoshi Narumi, Tomonobu Hasegawa
POU class 1 homeobox 1 (POU1F1) regulates pituitary cell-specific gene expression of somatotropes, lactotropes, and thyrotropes. In humans, two POU1F1 isoforms (long and short isoform), which are generated by the alternative use of the splice acceptor site for exon 2, have been identified. To date, more than 30 POU1F1 mutations in patients with combined pituitary hormone deficiency (CPHD) have been described. All POU1F1 variants reported to date affect both the short and long isoforms of the POU1F1 protein; therefore, it is unclear at present whether a decrease in the function of only one of these two isoforms is sufficient for disease onset in humans...
February 27, 2017: Endocrine Journal
https://www.readbyqxmd.com/read/27854228/toxicological-characterization-of-exon-skipping-phosphorodiamidate-morpholino-oligomers-pmos-in-non-human-primates
#16
Michael P Carver, Jay S Charleston, Courtney Shanks, Jianbo Zhang, Mark Mense, Alok K Sharma, Harjeet Kaur, Peter Sazani
BACKGROUND: Phosphorodiamidate morpholino oligomers (PMOs) are a class of exon skipping drugs including eteplirsen, which has shown considerable promise for treatment of the degenerative neuromuscular disease, Duchenne musculardystrophy (DMD). OBJECTIVE: Toxicity studies in non-human primates (NHPs) of 12 weeks duration with two new PMOs for DMD, SRP-4045 and SRP-4053, along with results from a chronic study in NHPs of 39 weeks duration for eteplirsen, are described here...
August 30, 2016: Journal of Neuromuscular Diseases
https://www.readbyqxmd.com/read/27826023/allele-specific-splicing-effects-on-dkkl1-and-znf419-transcripts-in-hela-cells
#17
Grace Martin, S Duygu Selcuklu, Katherine Schouest, Victoria Nembaware, Peter C McKeown, Cathal Seoighe, Charles Spillane
Allele-specific splicing is the production of different RNA isoforms from different alleles of a gene. Altered splicing patterns such as exon skipping can have a dramatic effect on the final protein product yet have traditionally proven difficult to predict. We investigated the splicing effects of a set of nine single nucleotide polymorphisms (SNPs) which are predicted to have a direct impact on mRNA splicing, each in a different gene. Predictions were based on SNP location relative to splice junctions and intronic/exonic splicing elements, combined with an analysis of splice isoform expression data from public sources...
January 20, 2017: Gene
https://www.readbyqxmd.com/read/27820807/the-ribosome-engaged-landscape-of-alternative-splicing
#18
Robert J Weatheritt, Timothy Sterne-Weiler, Benjamin J Blencowe
High-throughput RNA sequencing (RNA-seq) has revealed an enormous complexity of alternative splicing (AS) across diverse cell and tissue types. However, it is currently unknown to what extent repertoires of splice-variant transcripts are translated into protein products. Here, we surveyed AS events engaged by the ribosome. Notably, at least 75% of human exon-skipping events detected in transcripts with medium-to-high abundance in RNA-seq data were also detected in ribosome profiling data. Furthermore, relatively small subsets of functionally related splice variants are engaged by ribosomes at levels that do not reflect their absolute abundance, thus indicating a role for AS in modulating translational output...
December 2016: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/27788395/in-silico-investigation-of-the-impact-of-synonymous-variants-in-abcb4-gene-on-mrna-stability-structure-splicing-accuracy-and-codon-usage-potential-contribution-to-pfic3-disease
#19
Boudour Khabou, Olfa Siala-Sahnoun, Lamia Gargouri, Emna Mkaouar-Rebai, Leila Keskes, Mongia Hachicha, Faiza Fakhfakh
Progressive Familial Intrahepatic Cholestasis type 3 (PFIC3) is an autosomal-recessive liver disease due to mutations in the ABCB4 gene encoding for the MDR3 protein. In the present study, we performed molecular and bioinformatic analyses in PFIC3 patients in order to understand the molecular basis of the disease. The three studied patients with PFIC3 were screened by PCR amplification followed by direct sequencing of the 27 coding exons of ABCB4. In silico analysis was performed by bioinformatic programs. We revealed three synonymous polymorphisms c...
October 22, 2016: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/27779620/double-target-antisense-u1snrnas-correct-mis-splicing-due-to-c-639-861c-t-and-c-639-919g-a-gla-deep-intronic-mutations
#20
Lorenzo Ferri, Giuseppina Covello, Anna Caciotti, Renzo Guerrini, Michela Alessandra Denti, Amelia Morrone
Fabry disease is a rare X-linked lysosomal storage disorder caused by deficiency of the α-galactosidase A (α-Gal A) enzyme, which is encoded by the GLA gene. GLA transcription in humans produces a major mRNA encoding α-Gal A and a minor mRNA of unknown function, which retains a 57-nucleotide-long cryptic exon between exons 4 and 5, bearing a premature termination codon. NM_000169.2:c.639+861C>T and NM_000169.2:c.639+919G>A GLA deep intronic mutations have been described to cause Fabry disease by inducing overexpression of the alternatively spliced mRNA, along with a dramatic decrease in the major one...
October 25, 2016: Molecular Therapy. Nucleic Acids
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