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Intronic Mutation

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https://www.readbyqxmd.com/read/28549172/orrm5-an-rna-recognition-motif-containing-protein-has-a-unique-effect-on-mitochondrial-rna-editing
#1
Xiaowen Shi, Benoit Castandet, Arnaud Germain, Maureen R Hanson, Stéphane Bentolila
Plants have an RNA editing mechanism that prevents deleterious organelle mutations from resulting in impaired proteins. A typical flowering plant modifies about 40 cytidines in chloroplast transcripts and many hundreds of cytidines in mitochondrial transcripts. The plant editosome, the molecular machinery responsible for this process, contains members of several protein families, including the organelle RNA recognition motif (ORRM)-containing family. ORRM1 and ORRM6 are chloroplast editing factors, while ORRM2, ORRM3, and ORRM4 are mitochondrial editing factors...
May 26, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28546999/a-birth-of-bipartite-exon-by-intragenic-deletion
#2
Kandai Nozu, Kazumoto Iijima, Toru Igarashi, Shiro Yamada, Jana Kralovicova, Yoshimi Nozu, Tomohiko Yamamura, Shogo Minamikawa, Ichiro Morioka, Takeshi Ninchoji, Hiroshi Kaito, Koichi Nakanishi, Igor Vorechovsky
BACKGROUND: Disease-causing mutations that activate transposon-derived exons without creating a new splice-site consensus have been reported rarely, but they provided unique insights into our understanding of structural motifs required for inclusion of intronic sequences in mature transcripts. METHODS: We employ a combination of experimental and computational techniques to characterize the first de novo bipartite exon activation in genetic disease. RESULTS: The exon originated from two separate introns as a result of an in-frame COL4A5 deletion associated with a typical Alport syndrome...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546788/dmd-transcripts-in-crl-2061-rhabdomyosarcoma-cells-show-high-levels-of-intron-retention-by-intron-specific-pcr-amplification
#3
Emma Tabe Eko Niba, Ryo Yamanaka, Abdul Qawee Mahyoob Rani, Hiroyuki Awano, Masaaki Matsumoto, Hisahide Nishio, Masafumi Matsuo
BACKGROUND: The DMD gene encoding dystrophin is mutated in Duchenne muscular dystrophy, a fatal progressive muscle wasting disease. DMD has also been shown to act as a tumor suppressor gene. Rhabdomyosarcoma (RMS) is a mesodermal sarcoma that shares characteristics of skeletal muscle precursors. Products of the DMD gene in RMS have not yet been fully clarified. Here, DMD products were analyzed in CRL-2061 cells established from alveolar RMS. METHODS: The 14-kb long DMD cDNA was PCR amplified as 20 separated fragments, as were nine short intron regions...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28542515/a-novel-frameshift-mutation-of-smpx-causes-a-rare-form-of-x-linked-nonsyndromic-hearing-loss-in-a-chinese-family
#4
Zhijie Niu, Yong Feng, Lingyun Mei, Jie Sun, Xueping Wang, Juncheng Wang, Zhengmao Hu, Yunpeng Dong, Hongsheng Chen, Chufeng He, Yalan Liu, Xinzhang Cai, Xuezhong Liu, Lu Jiang
X-linked hearing impairment is the rarest form of genetic hearing loss (HL) and represents only a minor fraction of all cases. The aim of this study was to investigate the cause of X-linked inherited sensorineural HL in a four-generation Chinese family. A novel duplication variant (c.217dupA, p.Ile73Asnfs*5) in SMPX was identified by whole-exome sequencing. The frameshift mutation predicted to result in the premature truncation of the SMPX protein was co-segregated with the HL phenotype and was absent in 295 normal controls...
2017: PloS One
https://www.readbyqxmd.com/read/28542277/first-report-of-a-japanese-family-with-spinocerebellar-ataxia-type-10-the-second-report-from-asia-after-a-report-from-china
#5
Hiroyuki Naito, Tetsuya Takahashi, Masaki Kamada, Hiroyuki Morino, Hiroyo Yoshino, Nobutaka Hattori, Hirofumi Maruyama, Hideshi Kawakami, Masayasu Matsumoto
Spinocerebellar ataxia type 10 (SCA10) is an autosomal-dominant cerebellar ataxia that is variably accompanied by epilepsy and other neurological disorders. It is caused by an expansion of the ATTCT pentanucleotide repeat in intron 9 of the ATXN10 gene. Until now, SCA10 was almost exclusively found in the American continents, while no cases had been identified in Japan. Here, we report the first case of an SCA10 family from Japan. The clinical manifestations in our cases were cerebellar ataxia accompanied by epilepsy, hyperreflexia and cognitive impairment...
2017: PloS One
https://www.readbyqxmd.com/read/28541300/splicing-modulators-act-at-the-branch-point-adenosine-binding-pocket-defined-by-the-phf5a-sf3b-complex
#6
Teng Teng, Jennifer Hc Tsai, Xiaoling Puyang, Michael Seiler, Shouyong Peng, Sudeep Prajapati, Daniel Aird, Silvia Buonamici, Benjamin Caleb, Betty Chan, Laura Corson, Jacob Feala, Peter Fekkes, Baudouin Gerard, Craig Karr, Manav Korpal, Xiang Liu, Jason T Lowe, Yoshiharu Mizui, James Palacino, Eunice Park, Peter G Smith, Vanitha Subramanian, Zhenhua Jeremy Wu, Jian Zou, Lihua Yu, Agustin Chicas, Markus Warmuth, Nicholas Larsen, Ping Zhu
Pladienolide, herboxidiene and spliceostatin have been identified as splicing modulators that target SF3B1 in the SF3b subcomplex. Here we report that PHF5A, another component of this subcomplex, is also targeted by these compounds. Mutations in PHF5A-Y36, SF3B1-K1071, SF3B1-R1074 and SF3B1-V1078 confer resistance to these modulators, suggesting a common interaction site. RNA-seq analysis reveals that PHF5A-Y36C has minimal effect on basal splicing but inhibits the global action of splicing modulators. Moreover, PHF5A-Y36C alters splicing modulator-induced intron-retention/exon-skipping profile, which correlates with the differential GC content between adjacent introns and exons...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28540003/vsx1-and-sod1-mutation-screening-in-patients-with-keratoconus-in-the-south-of-iran
#7
Mahmood Nejabat, Payam Naghash, Hassan Dastsooz, Sanaz Mohammadi, Mohsen Alipour, Majid Fardaei
PURPOSE: To investigate mutations of visual system homeobox 1 (VSX1) and superoxide dismutase 1 (SOD1) in 20 patients with keratoconus in the south of Iran. METHODS: Twenty patients with keratoconus who had a positive familial history were enrolled in this study and gave informed consent for DNA analysis. Genomic DNA was extracted from peripheral blood lymphocytes. Polymerase chain reaction (PCR) was carried out to amplify exon 2 of SOD1 and its exon-intron boundary for the detection of a seven-base deletion in intron 2 of SOD1, and also all five exons of VSX1 and their exon-intron boundaries...
April 2017: Journal of Ophthalmic & Vision Research
https://www.readbyqxmd.com/read/28533818/a-novel-bcr-abl1-fusion-gene-with-genetic-heterogeneity-indicates-a-good-prognosis-in-a-chronic-myeloid-leukemia-case
#8
Fen Zhou, Runming Jin, Yu Hu, Heng Mei
BACKGROUND: Chronic myelogenous leukemia (CML) is a pluripotent hematopoietic stem cell disorder caused by the fusion of the BCR and ABL1 genes. Quantitative RT-PCR (qRT-PCR) is a routinely performed screening technique to identify BCR-ABL1 fusion genes, but a limitation of this method is its inability to recognize novel fusions that have not been previously characterized. Next-generation sequencing (NGS) is an effective and sensitive detection method for the determination of novel BCR-ABL1 fusion genes as well as previously characterized ones...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28523642/autosomal-recessive-nonsyndromic-arrhythmogenic-right-ventricular-cardiomyopathy-without-cutaneous-involvements-a-novel-mutation
#9
Mahdieh Soveizi, Bahareh Rabbani, Yousef Rezaei, Sedigheh Saedi, Nasim Najafi, Majid Maleki, Nejat Mahdieh
The arrhythmogenic right ventricular dysplasia/cardiomyopathy (ARVD/C) is a genetic disease frequently associated with desmosomal mutations, mainly attributed to dominant mutations in the Plakophilin-2 (PKP2) gene. Naxos and Carvajal are the syndromic forms of ARVD/C due to recessive mutations. Herein, we report an autosomal recessive form of nonsyndromic ARVD/C caused by a mutation in the PKP2 gene. After examination and implementation of diagnostic modalities, the definite diagnosis of ARVD/C was confirmed by detection of ventricular tachycardia with a left bundle branch configuration and a superior axis, T-wave inversion in right precordial leads (i...
May 19, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28523359/arginine-cga-codons-as-a-source-of-nonsense-mutations-a-possible-role-in-multivariant-gene-expression-control-of-mrna-quality-and-aging
#10
Georgy A Romanov, Victor S Sukhoverov
Methylation of cytosine residues in DNA of higher eukaryotes, including humans, creates "hot spots" of C→T transitions in the genome. The predominantly methylated sequence in mammalian DNAs is CG (CpG). Among CG-containing codons, CGA codons for arginine are unique due to their ability to create stop codons TGA (UGA in mRNA) upon epigenetic-mediated mutation. As such nonsense mutations can have a strong adverse effect on the cell and organism, we have performed a study, on the example of human genes, aimed to characterise the anticipated effects of epigenetic-mediated nonsense mutations CGA→TGA in somatic cells...
May 18, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28522861/comparative-analysis-of-dendrobium-plastomes-and-utility-of-plastomic-mutational-hotspots
#11
Niu Zhitao, Zhu Shuying, Pan Jiajia, Li Ludan, Sun Jing, Ding Xiaoyu
Dendrobium is one of the largest genera in Orchidaceae, comprising about 800-1500 species mainly distributed in tropical Asia, Australasia, and Australia. There are 74 species and two varieties of this genus in China. Because of their ornamental and commercial value, Dendrobium orchids have been studied at low taxonomic levels. However, structural changes and effective mutational hotspots of Dendrobium plastomes have rarely been documented. Here, 30 Dendrobium plastomes were compared, comprising 25 newly sequenced in this study and five previously published...
May 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28521877/cyp21a2-intronic-variants-causing-21-hydroxylase-deficiency
#12
REVIEW
Paola Concolino, Roberta Rizza, Alessandra Costella, Cinzia Carrozza, Cecilia Zuppi, Ettore Capoluongo
Congenital adrenal hyperplasia (CAH) is an autosomal recessive disorder mainly caused by defects in the steroid 21-hydroxylase gene (CYP21A2). Most of CYP21A2 mutations result from intergenic recombinations between CYP21A2 and closely linked CYP21A1P pseudogene. Rare mutations not generated by gene conversion account for 5-10% of 21-hydroxylase deficiency alleles. Intronic variants represent only a little part of these but their effect on the protein is generally deleterious. The aim of this paper is to provide a comprehensive literary review regarding all intronic CYP21A2 pathological variants reported to date...
June 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28520979/the-dead-box-helicase-mss116-plays-distinct-roles-in-mitochondrial-ribogenesis-and-mrna-specific-translation
#13
Dasmanthie De Silva, Sarah Poliquin, Rui Zeng, Angelica Zamudio-Ochoa, Natalie Marrero, Xochitl Perez-Martinez, Flavia Fontanesi, Antoni Barrientos
Members of the DEAD-box family are often multifunctional proteins involved in several RNA transactions. Among them, yeast Saccharomyces cerevisiae Mss116 participates in mitochondrial intron splicing and, under cold stress, also in mitochondrial transcription elongation. Here, we show that Mss116 interacts with the mitoribosome assembly factor Mrh4, is required for efficient mitoribosome biogenesis, and consequently, maintenance of the overall mitochondrial protein synthesis rate. Additionally, Mss116 is required for efficient COX1 mRNA translation initiation and elongation...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28515442/interplay-between-alternative-splicing-and-alternative-polyadenylation-defines-the-expression-outcome-of-the-plant-unique-oxidative-tolerant-6-gene
#14
Qingshun Q Li, Zhaoyang Liu, Wenjia Lu, Man Liu
Pre-mRNA alternative splicing and alternative polyadenylation have been implicated to play important roles during eukaryotic gene expression. However, much remains unknown regarding the regulatory mechanisms and the interactions of these two processes in plants. Here we focus on an Arabidopsis gene OXT6 (Oxidative Tolerant-6) that has been demonstrated to encode two proteins through alternative splicing and alternative polyadenylation. Specifically, alternative polyadenylation at Intron-2 of OXT6 produces a transcript coding for AtCPSF30, an Arabidopsis ortholog of 30 kDa subunit of the Cleavage and Polyadenylation Specificity Factor...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28515030/congenital-central-hypothyroidism-caused-by-a-novel-tsh-beta-subunit-gene-mutation-c-94g-a-in-two-siblings
#15
Bayram Özhan, Özlem Boz Anlaş, Bilge Sarıtepe, Burcu Albuz, Nur Gündüz Semerci
Congenital central hypothyroidism (C-CH) is a very rare disease. Alterations in genes included in pituitary development, mutations of the immunoglobulin superfamily member 1 (IGSF1) and transducin β-like protein 1(TBL1X ) can result in C-CH with multiple pituitary hormone deficiencies. However, mutations of the thyrotropin-releasing hormone receptor or TSH-beta (TSHB) gene are responsible for isolated congenital central hypothyroidism. In this paper, we present 2 patients from the same Turkish family with a novel mutation of TSHB...
May 17, 2017: Journal of Clinical Research in Pediatric Endocrinology
https://www.readbyqxmd.com/read/28513431/dissection-of-zebrafish-shha-function-using-site-specific-targeting-with-a-cre-dependent-genetic-switch
#16
Kotaro Sugimoto, Subhra P Hui, Delicia Z Sheng, Kazu Kikuchi
Despite the extensive use of zebrafish as a model organism in developmental biology and regeneration research, genetic techniques enabling conditional analysis of gene function are limited. In this study, we generated Zwitch, a Cre-dependent invertible gene-trap cassette, enabling the establishment of conditional alleles in zebrafish by generating intronic insertions via in vivo homologous recombination. To demonstrate the utility of Zwitch, we generated a conditional sonic hedgehog a (shha) allele. Homozygous shha mutants developed normally; however, shha mutant embryos globally expressing Cre exhibited strong reductions in endogenous shha and shha target gene mRNA levels and developmental defects associated with null shha mutations...
May 17, 2017: ELife
https://www.readbyqxmd.com/read/28510626/outcome-measures-for-clinical-trials-of-leber-congenital-amaurosis-caused-by-the-intronic-mutation-in-the-cep290-gene
#17
Samuel G Jacobson, Artur V Cideciyan, Alexander Sumaroka, Alejandro J Roman, Jason Charng, Monica Lu, Windy Choi, Rebecca Sheplock, Malgorzata Swider, Mychajlo S Kosyk, Sharon B Schwartz, Edwin M Stone, Gerald A Fishman
Purpose: To determine efficacy outcome measures for clinical trials of Leber congenital amaurosis (LCA) associated with a common intronic mutation in the CEP290 gene. Methods: CEP290-LCA patients (ages 5-48) with the intronic mutation (c.2991+1655A>G) were studied as a retrospective observational case series using clinical methods and with full-field sensitivity testing (FST), optical coherence tomography (OCT), autofluorescence imaging (NIR-RAFI), transient pupillary light reflex (TPLR), oculomotor control and instability (OCI), a mobility course, and a questionnaire (NEI-VFQ)...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28508085/intragenic-dok7-deletion-detected-by-whole-genome-sequencing-in-congenital-myasthenic-syndromes
#18
Yoshiteru Azuma, Ana Töpf, Teresinha Evangelista, Paulo José Lorenzoni, Andreas Roos, Pedro Viana, Hidehito Inagaki, Hiroki Kurahashi, Hanns Lochmüller
OBJECTIVE: To identify the genetic cause in a patient affected by ptosis and exercise-induced muscle weakness and diagnosed with congenital myasthenic syndromes (CMS) using whole-genome sequencing (WGS). METHODS: Candidate gene screening and WGS analysis were performed in the case. Allele-specific PCR was subsequently performed to confirm the copy number variation (CNV) that was suspected from the WGS results. RESULTS: In addition to the previously reported frameshift mutation c...
June 2017: Neurology. Genetics
https://www.readbyqxmd.com/read/28503307/clinical-significance-of-intronic-variants-in-braf-inhibitor-resistant-melanomas-with-altered-braf-transcript-splicing
#19
Gulietta M Pupo, Suzanah C Boyd, Carina Fung, Matteo S Carlino, Alexander M Menzies, Bernadette Pedersen, Peter Johansson, Nicholas K Hayward, Richard F Kefford, Richard A Scolyer, Georgina V Long, Helen Rizos
Alternate BRAF splicing is the most common mechanism of acquired resistance to BRAF inhibitor treatment in melanoma. Recently, alternate BRAF exon 4-8 splicing was shown to involve an intronic mutation, located 51 nucleotides upstream of BRAF exon 9 within a predicted splicing branch point. This intronic mutation was identified in a single cell line but has not been examined in vivo. Herein we demonstrate that in three melanomas biopsied from patients with acquired resistance to BRAF inhibitors, alternate BRAF exon 4-8 splicing is not associated with this intronic branch point mutation...
2017: Biomarker Research
https://www.readbyqxmd.com/read/28501715/mutations-in-the-hco-mptl-1-gene-in-a-field-derived-monepantel-resistant-isolate-of-haemonchus-contortus
#20
Neil H Bagnall, Angela Ruffell, Ali Raza, Timothy P Elliott, Jane Lamb, Peter W Hunt, Andrew C Kotze
Resistance to the anthelmintic drug monepantel (Zolvix(®)) has emerged in parasitic worms infecting sheep and goats. The mechanism of resistance in these cases is unknown. The drug targets nicotinic acetylcholine receptors belonging to the nematode-specific DEG-3 subfamily. We examined the receptor gene, Hco-mptl-1, in a highly Zolvix(®)-resistant and a -susceptible isolate of the parasitic nematode Haemonchus contortus. cDNA coding for the full length receptor protein (Hco-MPTL-1) was present in all clones prepared from a pool of susceptible larvae (21/21 clones) and approximately 50% of those from the resistant isolate (17/33)...
May 4, 2017: International Journal for Parasitology, Drugs and Drug Resistance
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