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Exon skipping in humans

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https://www.readbyqxmd.com/read/28422715/a-novel-bmx-variant-promotes-tumor-cell-growth-and-migration-in-lung-adenocarcinoma
#1
Ye Wang, Jufeng Xia, Zhaoyuan Fang, Fei Li, Duo Li, Zuoyun Wang, Yan Feng, Jian Zhang, Haiquan Chen, Hongbin Ji, Hongyan Liu
The non-receptor tyrosine kinase BMX has been reported in several solid tumors. However, the alternative splicing of BMX and its clinical relevance in lung cancer remain to be elucidated. Exon1.0 array was used to identify a novel alternative splicing of BMX, BMXΔN, which was confirmed by rapid amplification of cDNA ends and reverse transcription-polymerase chain reaction. BMXΔN, resulting from exon skipping with excluding exon 1 to exon 8 of BMX gene, was found in 12% human lung adenocarcinoma specimens...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28400409/drosha-targets-its-own-transcript-to-modulate-alternative-splicing
#2
Dooyoung Lee, Jin-Wu Nam, Chanseok Shin
The nuclear RNase III enzyme DROSHA interacts with its cofactor DGCR8 to form the Microprocessor complex, which initiates microRNA (miRNA) maturation by cleaving hairpin structures embedded in primary transcripts. Apart from its central role in the biogenesis of miRNAs, DROSHA is also known to recognize and cleave miRNA-like hairpins in a subset of transcripts without apparent small RNA production. Here, we report that the human DROSHA transcript is one such non-canonical target of DROSHA. Mammalian DROSHA genes have evolved a conserved hairpin structure spanning a specific exon-intron junction, which serves as a substrate for the Microprocessor in human cells but not in murine cells...
April 11, 2017: RNA
https://www.readbyqxmd.com/read/28398005/nanotherapy-for-duchenne-muscular-dystrophy
#3
REVIEW
Michael E Nance, Chady H Hakim, N Nora Yang, Dongsheng Duan
Duchenne muscular dystrophy (DMD) is a lethal X-linked childhood muscle wasting disease caused by mutations in the dystrophin gene. Nanobiotechnology-based therapies (such as synthetic nanoparticles and naturally existing viral and nonviral nanoparticles) hold great promise to replace and repair the mutated dystrophin gene and significantly change the disease course. While a majority of DMD nanotherapies are still in early preclinical development, several [such as adeno-associated virus (AAV)-mediated systemic micro-dystrophin gene therapy] are advancing for phase I clinical trials...
April 11, 2017: Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology
https://www.readbyqxmd.com/read/28390897/identification-and-characterization-of-two-novel-ptch1-splice-variants
#4
Pei Yu, Jinqing Yang, Yan Zhang
Patched-1 (PTCH1), one of the key molecules involved in the Hedgehog (HH) signaling pathway, acts as the receptor of the HH ligand. PTCH1 also inhibits the positive signal transducer Smoothened (SMO). Several PTCH1 splice variants have been identified and confirmed to play critical roles in HH pathway regulation. In the present study, two novel alternatively spliced variants of PTCH1 transcripts, designated PTCH1-Δ10 and PTCH1-Δ15, were found in humans, mice and zebrafish using RT-PCR, direct sequencing and ribonuclease protection assays...
April 5, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28387786/cash-a-constructing-comprehensive-splice-site-method-for-detecting-alternative-splicing-events
#5
Wenwu Wu, Jie Zong, Ning Wei, Jian Cheng, Xuexia Zhou, Yuanming Cheng, Dai Chen, Qinghua Guo, Bo Zhang, Ying Feng
RNA-sequencing (RNA-seq) can generate millions of reads to provide clues for analyzing novel or abnormal alternative splicing (AS) events in cells. However, current methods for exploring AS events are still far from being satisfactory. Here, we present Comprehensive AS Hunting (CASH), which constructs comprehensive splice sites including known and novel AS sites in cells, and identifies differentially AS events between cells. We illuminated the versatility of CASH on RNA-seq data from a wide range of species and also on simulated in silico data, validated the advantages of CASH over other AS predictors and exhibited novel differentially AS events...
April 6, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28381181/effect-of-histone-modifications-on-hmlh1-alternative-splicing-in-gastric-cancer
#6
Jin-Xuan Zhao, Xiao-Wei Li, Bing-Yu Shi, Fang Wang, Zheng-Rong Xu, Hai-Lan Meng, Yun-Yan Su, Jing-Mei Wang, Nong Xiao, Qiong He, Ya-Ping Wang, Yi-Mei Fan
hMLH1 is one of the mismatch genes closely related to the occurrence of gastric cancer. Epigenetic regulation may play more important roles than gene mutations in DNA damage repair genes to drive carcinogenesis. In this article, we discuss the role of epigenetic changes, especially histone modifications in the regulation of hMLH1 alternative splicing. Our results showed that hMLH1 delEx10, delEx11, delEx10-11, delEx16 and delEx17 transcripts were ubiquitous in sporadic Chinese gastric cancer patients and gastric cancer cell lines...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28379442/an-rrm-znf-rna-recognition-module-targets-rbm10-to-exonic-sequences-to-promote-exon-exclusion
#7
Katherine M Collins, Yaroslav A Kainov, Evangelos Christodolou, Debashish Ray, Quaid Morris, Timothy Hughes, Ian A Taylor, Eugene V Makeyev, Andres Ramos
RBM10 is an RNA-binding protein that plays an essential role in development and is frequently mutated in the context of human disease. RBM10 recognizes a diverse set of RNA motifs in introns and exons and regulates alternative splicing. However, the molecular mechanisms underlying this seemingly relaxed sequence specificity are not understood and functional studies have focused on 3΄ intronic sites only. Here, we dissect the RNA code recognized by RBM10 and relate it to the splicing regulatory function of this protein...
April 4, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28364229/invention-and-early-history-of-morpholinos-from-pipe-dream-to-practical-products
#8
James E Summerton
Beginning with my concept in 1969 to treat disease at the nucleic acid level using antisense nucleic acids, antisense has evolved to the current Morpholino oligos. Morpholinos have been the dominant gene knockdown system in developmental biology. Lack of delivery technologies has limited their use in adult animals (including humans), though alteration in muscles in Duchenne muscular dystrophy (DMD) allows delivery into adult muscle. Morpholinos are currently in Phase 3 clinical trials for DMD and a Morpholino oligo for skipping dystrophin exon 51 has been approved by the US FDA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28350844/isolation-and-characterization-of-alternatively-spliced-variants-of-the-mouse-sigma1-receptor-gene-sigmar1
#9
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/28334074/genome-wide-analysis-reveals-that-exon-methylation-facilitates-its-selective-usage-in-the-human-transcriptome
#10
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
#11
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/28295039/deciphering-the-mechanism-of-q145h-sftpc-mutation-unmasks-a-splicing-defect-and-explains-the-severity-of-the-phenotype
#12
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
#13
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
#14
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/modeling-the-ferrochelatase-c-315-48c-modifier-mutation-for-erythropoietic-protoporphyria-epp-in-mice
#15
Jasmin Barman-Aksözen, Paulina C Wiek, 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 that evoke excessive pain and, after longer light exposure, cause ulcerations in exposed skin areas of individuals with EPP. Moreover, ∼5% of the patients develop a liver dysfunction as a result of PPIX accumulation. Most patients (∼97%) have a severe FECH mutation (Mut) in trans to an intronic polymorphism (c...
March 1, 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
#16
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
#17
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
#18
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
#19
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
#20
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...
January 1, 2017: Cerebral Cortex
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