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https://www.readbyqxmd.com/read/28093505/modelling-the-ferrochelatase-c-315-48c-modifier-mutation-for-erythropoietic-protoporphyria-epp-in-mice
#1
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
#2
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...
December 21, 2016: DNA Repair
https://www.readbyqxmd.com/read/28077157/clinical-biochemical-and-molecular-characteristics-of-filipino-patients-with-mucopolysaccharidosis-type-ii-hunter-syndrome
#3
Mary Anne D Chiong, Daffodil M Canson, Mary Ann R Abacan, Melissa Mae P Baluyot, Cynthia P Cordero, Catherine Lynn T Silao
BACKGROUND: Mucopolysaccharidosis type II, an X-linked recessive disorder is the most common lysosomal storage disease detected among Filipinos. This is a case series involving 23 male Filipino patients confirmed to have Hunter syndrome. The clinical and biochemical characteristics were obtained and mutation testing of the IDS gene was done on the probands and their female relatives. RESULTS: The mean age of the patients was 11.28 (SD 4.10) years with an average symptom onset at 1...
January 11, 2017: Orphanet Journal of Rare Diseases
https://www.readbyqxmd.com/read/28076796/ribosomal-proteins-rpl22-and-rpl22l1-control-morphogenesis-by-regulating-pre-mrna-splicing
#4
Yong Zhang, Monique N O'Leary, Suraj Peri, Minshi Wang, Jikun Zha, Simon Melov, Dietmar J Kappes, Qing Feng, Jennifer Rhodes, Paul S Amieux, David R Morris, Brian K Kennedy, David L Wiest
Most ribosomal proteins (RP) are regarded as essential, static components that contribute only to ribosome biogenesis and protein synthesis. However, emerging evidence suggests that RNA-binding RP are dynamic and can influence cellular processes by performing "extraribosomal," regulatory functions involving binding to select critical target mRNAs. We report here that the RP, Rpl22, and its highly homologous paralog Rpl22-Like1 (Rpl22l1 or Like1) play critical, extraribosomal roles in embryogenesis. Indeed, they antagonistically control morphogenesis through developmentally regulated localization to the nucleus, where they modulate splicing of the pre-mRNA encoding smad2, an essential transcriptional effector of Nodal/TGF-β signaling...
January 10, 2017: Cell Reports
https://www.readbyqxmd.com/read/28072465/splicing-regulation-and-dysregulation-of-cholinergic-genes-expressed-at-the-neuromuscular-junction
#5
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
#6
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/28049741/integrating-omics-and-alternative-splicing-reveals-insights-into-grape-response-to-high-temperature
#7
Jianfu Jiang, Xinna Liu, Guotian Liu, Chonghuai Liu, Shaohua Li, Lijun Wang
Heat stress is one of the primary abiotic stresses that limit crop production. Grape is a cultivated fruit with high economic value throughout the world, with its growth and development often influenced by high temperature. Alternative splicing (AS) is a widespread phenomenon increasing transcriptome and proteome diversity. We conducted high temperature treatments (35oC, 40oC and 45oC) on grapevines (Vitis vinifera), and assessed transcriptomic (especially AS) and proteomic changes in leaves. We found that nearly 70% of the genes were alternatively spliced under high temperature...
January 3, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28049589/a-triple-exon-skipping-luciferase-reporter-assay-identifies-a-new-clk-inhibitor-pharmacophore
#8
Yihui Shi, Jaehyeon Park, Chandraiah Lagisetti, Wei Zhou, Lidia C Sambucetti, Thomas R Webb
The splicing of pre-mRNA is a critical process in normal cells and is deregulated in cancer. Compounds that modulate this process have recently been shown to target a specific vulnerability in tumors. We have developed a novel cell-based assay that specifically activates luciferase in cells exposed to SF3B1 targeted compounds, such as sudemycin D6. This assay was used to screen a combined collection of approved drugs and bioactive compounds. This screening approach identified several active hits, the most potent of which were CGP-74514A and aminopurvalanol A, both have been reported to be cyclin-dependent kinases (CDKs) inhibitors...
December 24, 2016: Bioorganic & Medicinal Chemistry Letters
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
#9
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/28031331/activation-dependent-traf3-exon-8-alternative-splicing-is-controlled-by-celf2-and-hnrnp-c-binding-to-an-upstream-intronic-element
#10
Astrid-Solveig Schultz, Marco Preußner, Mario Bunse, Rotem Karni, Florian Heyd
Cell-type specific and inducible alternative splicing has a fundamental impact on regulating gene expression and cellular function in a variety of settings including activation and differentiation. We have recently shown that activation-induced skipping of TRAF3 exon 8 activates non-canonical NFkB signaling upon T cell stimulation, but the regulatory basis for this splicing event remains unknown. Here we identify cis- and trans-regulatory elements rendering this splicing switch activation-dependent and cell-type specific...
December 28, 2016: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28031186/actg-novel-peptide-mapping-onto-gene-models
#11
Seunghyuk Choi, Hyunwoo Kim, Eunok Paek
: In many proteogenomic applications, mapping peptide sequences onto genome sequences can be very useful, because it allows us to understand origins of the gene products. Existing software tools either take the genomic position of a peptide start site as an input or assume that the peptide sequence exactly matches the coding sequence of a given gene model. In case of novel peptides resulting from genomic variations, especially structural variations such as alternative splicing, these existing tools cannot be directly applied unless users supply information about the variant, either its genomic position or its transcription model...
December 28, 2016: Bioinformatics
https://www.readbyqxmd.com/read/28025318/alternative-splicing-in-tomato-pollen-in-response-to-heat-stress
#12
Mario Keller, Yangjie Hu, Anida Mesihovic, Sotirios Fragkostefanakis, Enrico Schleiff, Stefan Simm
Alternative splicing (AS) is a key control mechanism influencing signal response cascades in different developmental stages and under stress conditions. In this study, we examined heat stress (HS)-induced AS in the heat sensitive pollen tissue of two tomato cultivars. To obtain the entire spectrum of HS-related AS, samples taken directly after HS and after recovery were combined and analysed by RNA-seq. For nearly 9,200 genes per cultivar, we observed at least one AS event under HS. In comparison to control, for one cultivar we observed 76% more genes with intron retention (IR) or exon skipping (ES) under HS...
December 26, 2016: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28024938/severe-fluoropyrimidine-toxicity-due-to-novel-and-rare-dpyd-missense-mutations-deletion-and-genomic-amplification-affecting-dpd-activity-and-mrna-splicing
#13
André B P van Kuilenburg, Judith Meijer, Dirk Maurer, Doreen Dobritzsch, Rutger Meinsma, Maartje Los, Lia C Knegt, Lida Zoetekouw, Rob L H Jansen, Vincent Dezentjé, Lieke H van Huis-Tanja, Roel J W van Kampen, Jens Michael Hertz, Raoul C M Hennekam
Dihydropyrimidine dehydrogenase (DPD) is the initial and rate-limiting enzyme in the catabolism of 5-fluorouracil (5FU). Genetic variations in DPD have emerged as predictive risk factors for severe fluoropyrimidine toxicity. Here, we report novel and rare genetic variants underlying DPD deficiency in 9 cancer patients presenting with severe fluoropyrimidine-associated toxicity. All patients possessed a strongly reduced DPD activity, ranging from 9 to 53% of controls. Analysis of the DPD gene (DPYD) showed the presence of 21 variable sites including 4 novel and 4 very rare aberrations: 3 missense mutations, 2 splice-site mutations, 1 intronic mutation, a deletion of 21 nucleotides and a genomic amplification of exons 9-12...
December 24, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28024701/a-comprehensive-analysis-of-clinical-outcomes-in-lung-cancer-patients-harboring-a-met-exon-14-skipping-mutation-compared-to-other-driver-mutations-in-an-east-asian-population
#14
Chien-Hung Gow, Min-Shu Hsieh, Shang-Gin Wu, Jin-Yuan Shih
INTRODUCTION: Recurrent somatic splice-site alterations at MET exon 14 (MET(Δ14)), which result in exon skipping and MET proto-oncogene, receptor tyrosine kinase (MET) activation, have been characterised. However, their demographic features and clinical outcomes in East Asian lung cancer patients have yet to be determined. METHODS: A one-step reverse transcription-polymerase chain reaction (RT-PCR), using RNA samples from 850 East Asian lung cancer patients, was performed in order to detect MET(Δ14) and five other major driver mutations, including those in the EGFR, KRAS, ALK, HER2, and ROS1 genes...
January 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28024693/the-race-to-target-met-exon-14-skipping-alterations-in-non-small-cell-lung-cancer-the-why-the-how-the-who-the-unknown-and-the-inevitable
#15
REVIEW
Thanyanan Reungwetwattana, Ying Liang, Viola Zhu, Sai-Hong Ignatius Ou
A number of small molecule tyrosine kinase inhibitors (TKIs) have now been approved for the treatment of non-small cell lung cancers (NSCLC), including those targeted against epidermal growth factor receptor, anaplastic lymphoma kinase, and ROS1. Despite a wealth of agents developed to target the receptor tyrosine kinase, MET, clinical outcomes have as yet been disappointing, leading to pessimism about the role of MET in the pathogenesis of NSCLC. However, in recent years, there has been a renewed interest in MET exon 14 alterations as potential drivers of lung cancer...
January 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/28013382/functional-assessment-of-a-novel-col4a5-splice-region-variant-and-immunostaining-of-plucked-hair-follicles-as-an-alternative-method-of-diagnosis-in-x-linked-alport-syndrome
#16
Andrew F Malone, Steven D Funk, Tarek Alhamad, Jeffrey H Miner
BACKGROUND: Many COL4A5 splice region variants have been described in patients with X-linked Alport syndrome, but few have been confirmed by functional analysis to actually cause defective splicing. We sought to demonstrate that a novel COL4A5 splice region variant in a family with Alport syndrome is pathogenic using functional studies. We also describe an alternative method of diagnosis. METHODS: Targeted next-generation sequencing results of an individual with Alport syndrome were analyzed and the results confirmed by Sanger sequencing in family members...
December 24, 2016: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28013231/neurexins-1-3-each-have-a-distinct-pattern-of-expression-in-the-early-developing-human-cerebral-cortex
#17
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/27997688/novel-splice-switching-oligonucleotide-promotes-brca1-aberrant-splicing-and-susceptibility-to-parp-inhibitor-action
#18
Lindsay D Smith, Flávia Leme de Calais, Michela Raponi, Massimiliano Mellone, Emanuele Buratti, Jeremy P Blaydes, Diana Baralle
Tumours carrying hereditary mutations in BRCA1, which attenuate the BRCA1 DNA damage repair pathway, are more susceptible to dual treatment with PARP inhibitors and DNA damaging therapeutics. Conversely, breast cancer tumours with non-mutated functional BRCA1 are less sensitive to PARP inhibition. We describe a method that triggers susceptibility to PARP inhibition in BRCA1-functional tumour cells. BRCA1 exon 11 is key for the function of BRCA1 in DNA damage repair. Analysis of the BRCA1 exon 11 splicing mechanism identified a key region within this exon which, when deleted, induced exon 11 skipping...
December 20, 2016: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/27988098/targeting-met-exon-14-skipping-alterations-has-lung-cancer-met-its-match
#19
EDITORIAL
Timothy A Yap, Sanjay Popat
No abstract text is available yet for this article.
January 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/27987579/response-and-acquired-resistance-to-crizotinib-in-chinese-patients-with-lung-adenocarcinomas-harboring-met-exon-14-splicing-alternations
#20
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
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