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Gene splicing

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https://www.readbyqxmd.com/read/29040385/a-benchmarking-of-workflows-for-detecting-differential-splicing-and-differential-expression-at-isoform-level-in-human-rna-seq-studies
#1
Gabriela A Merino, Ana Conesa, Elmer A Fernández
Over the last few years, RNA-seq has been used to study alterations in alternative splicing related to several diseases. Bioinformatics workflows used to perform these studies can be divided into two groups, those finding changes in the absolute isoform expression and those studying differential splicing. Many computational methods for transcriptomics analysis have been developed, evaluated and compared; however, there are not enough reports of systematic and objective assessment of processing pipelines as a whole...
October 13, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29036614/identification-of-a-candidate-mutation-in-the-col1a2-gene-of-a-chow-chow-with-osteogenesis-imperfecta
#2
E M Quist, R Doan, R R Pool, B F Porter, D L Bannasch, S V Dindot
Osteogenesis imperfecta (OI) is a genetic disease that occurs in humans and animals. Individuals with OI exhibit signs of extreme bone fragility and osteopenia with frequent fractures and perinatal lethality in severe cases. In this study, we report the clinical diagnosis of OI in a dog and the use targeted next-generation sequencing to identify a candidate autosomal dominant mutation in the COL1A2 gene. A five-month old male Chow Chow was examined with a fractured left humerus and resolving, bilateral femoral fractures...
September 19, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036566/the-role-of-alternative-splicing-and-differential-gene-expression-in-cichlid-adaptive-radiation
#3
Pooja Singh, Christine Börger, Heather More, Christian Sturmbauer
Species diverge eco-morphologically through the continuous action of natural selection on functionally important structures, producing alternative adaptive morphologies. In cichlid fishes, the oral and pharyngeal jaws are such key structures. Adaptive variation in jaw morphology contributes to trophic specialisation, which is hypothesised to fuel their rapid speciation in the East African Great Lakes. Much is known about the genes involved in cichlid jaw and craniofacial development. However, it is still unclear what salient sources of variation gave rise to trophic-niche specialisation, facilitating adaptive radiation...
September 27, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29035443/genetic-variants-of-pre-micrornas-a-499g-rs3746444-and-t-196a2c-rs11614913-with-ulcerative-colitis-uc-and-investigated-with-thiopurine-s-methyltransferase-tpmt-activity
#4
Farideh Ghobadi, Asad Vaisi-Raygani, Fariborz Bahrehmand, Maryam Tanhapour, Amir Kiani, Zohreh Rahimi, Tayebeh Pourmotabbed
BACKGROUND: Abnormal expression and different splicing of miRNAs are involved in several human inflammatory disorders. It has been suggested that gene variants of miRNAs may be associated with increased risk of ulcerative colitis (UC). We aimed to evaluate the association of two SNPs (miRNA-A-499G(rs3746444) and miRNA-T196a2C(rs11614913)) with the risk of UC and monitor their effect on thiopurine-S-methyltransferase (TPMT) activity in Kurdish population of Iran. METHODS: This case-control study was performed on 210 UC patients and 212 healthy individuals...
October 1, 2017: Clinical Laboratory
https://www.readbyqxmd.com/read/29034897/generation-of-ipsc-line-from-desmin-related-cardiomyopathy-patient-carrying-splice-site-mutation-of-des-gene
#5
Aleksandr Khudiakov, Daria Kostina, Anna Zlotina, Tatiana Nikulina, Alexey Sergushichev, Alexandra Gudkova, Alexey Tomilin, Anna Malashicheva, Anna Kostareva
Human iPSC line was generated from patient-specific adipose tissue-derived mesenchymal multipotent stromal cells carrying desmin (DES) gene heterozygous splice site mutation using non-integrative reprogramming method. Reprogramming factors OCT4, KLF4, SOX2, CMYC were delivered using Sendai viruses. iPSCs were characterized by sequencing, karyotype analysis, STR analysis, immunocytochemistry, RT-PCR and teratoma formation.
October 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29034641/-establishment-of-l-periaxin-gene-knock-out-rsc96-cell-line
#6
Min Liang, Tingting Peng, Yawei Shi
Periaxin, a protein of noncompact myelin, is specifically expressed in the peripheral nervous system (PNS). There are two protein isoform L-periaxin and S-Periaxin by alternative splicing of periaxin gene, playing an important role in the initiation of myelin formation. So far, 18 different mutation sites in L-periaxin gene have been found to induce the peripheral demyelinating neurological charcot-marie-tooth diseases subtype 4F (CMT4F). The technique of activation of transcription activator-like effector nucleases (TALENS) was used to knock out the L-periaxin gene in RSC 96 cell line of Rattus...
December 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29034245/handshakes-and-fights-the-regulatory-interplay-of-rna-binding-proteins
#7
REVIEW
Erik Dassi
What drives the flow of signals controlling the outcome of post-transcriptional regulation of gene expression? This regulatory layer, presiding to processes ranging from splicing to mRNA stability and localization, is a key determinant of protein levels and thus cell phenotypes. RNA-binding proteins (RBPs) form a remarkable army of post-transcriptional regulators, strong of more than 1,500 genes implementing this expression fine-tuning plan and implicated in both cell physiology and pathology. RBPs can bind and control a wide array of RNA targets...
2017: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29034140/regulation-of-gene-expression-by-translation-factor-eif5a-hypusine-modified-eif5a-enhances-nonsense-mediated-mrna-decay-in-human-cells
#8
Mainul Hoque, Ji Yeon Park, Yun-Juan Chang, Augusto D Luchessi, Tavane D Cambiaghi, Raghavendra Shamanna, Hartmut M Hanauske-Abel, Bart Holland, Tsafi Pe'ery, Bin Tian, Michael B Mathews
Nonsense-mediated mRNA decay (NMD) couples protein synthesis to mRNA turnover. It eliminates defective transcripts and controls the abundance of certain normal mRNAs. Our study establishes a connection between NMD and the translation factor eIF5A (eukaryotic initiation factor 5A) in human cells. eIF5A modulates the synthesis of groups of proteins (the eIF5A regulon), and undergoes a distinctive two-step post-translational modification (hypusination) catalyzed by deoxyhypusine synthase and deoxyhypusine hydroxylase...
2017: Translation
https://www.readbyqxmd.com/read/29034082/functional-characterizations-of-rare-uba1-variants-in-x-linked-spinal-muscular-atrophy
#9
Chris D Balak, Jesse M Hunter, Mary E Ahearn, David Wiley, Gennaro D'urso, Lisa Baumbach-Reardon
Background: X-linked spinal muscular atrophy (XL-SMA) results from mutations in the Ubiquitin-Like Modifier Activating Enzyme 1 ( UBA1). Previously, four novel closely clustered mutations have been shown to cause this fatal infantile disorder affecting only males. These mutations, three missense and one synonymous, all lie within Exon15 of the UBA1 gene, which contains the active adenylation domain (AAD). Methods: In this study, our group characterized the three known missense variants in vitro. Using a novel Uba1 assay and other methods, we investigated Uba1 adenylation, thioester, and transthioesterification reactions in vitro to determine possible biochemical effects of the missense variants...
2017: F1000Research
https://www.readbyqxmd.com/read/29033321/regulation-of-m-6-a-transcripts-by-the-3-%C3%A2-5-rna-helicase-ythdc2-is-essential-for-a-successful-meiotic-program-in-the-mammalian-germline
#10
Magdalena Natalia Wojtas, Radha Raman Pandey, Mateusz Mendel, David Homolka, Ravi Sachidanandam, Ramesh S Pillai
N(6)-methyladenosine (m(6)A) is an essential internal RNA modification that is critical for gene expression control in most organisms. Proteins with a YTH domain recognize m(6)A marks and are mediators of molecular functions like RNA splicing, mRNA decay, and translation control. Here we demonstrate that YTH domain-containing 2 (YTHDC2) is an m(6)A reader that is essential for male and female fertility in mice. High-throughput mapping of the m(6)A transcriptome and expression analysis in the Yhtdc2 mutant testes reveal an upregulation of m(6)A-enriched transcripts...
October 11, 2017: Molecular Cell
https://www.readbyqxmd.com/read/29031100/discovery-of-a-new-mechanism-for-regulation-of-plant-triacylglycerol-metabolism-the-peanut-diacylglycerol-acyltransferase-1-gene-family-transcriptome-is-highly-enriched-in-alternative-splicing-variants
#11
Ling Zheng, Jay Shockey, Feng Guo, Lingmin Shi, Xinguo Li, Lei Shan, Shubo Wan, Zhenying Peng
Triacylglycerols (TAGs) are the most important energy storage form in oilseed crops. Diacylglycerol acyltransferase (DGAT) catalyzes the rate-limiting step of the Kennedy pathway of TAG biosynthesis. To date, little is known about the regulation of DGAT activity in peanut (Arachis hypogaea), an agronomically important oilseed crop that is cultivated in many parts of the world. In this study, seven distinct forms of type 1 DGAT (AhDGAT1.1-AhDGAT1.7) were identified, cloned, and characterized. Comparisons of the nucleotide sequences and gene structures revealed many different splicing variants of AhDGAT1, some of which displayed different organ-specific expression patterns...
October 6, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29031026/genome-wide-characterization-of-differential-transcript-usage-in-arabidopsis-thaliana
#12
Dries Vaneechoutte, April R Estrada, Ying-Chen Lin, Ann E Loraine, Klaas Vandepoele
Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of Differential Transcript Usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes and have been linked to development and stress response...
October 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29030993/maternal-provision-of-non-sex-specific-transformer-messenger-rna-in-sex-determination-of-the-wasp-asobara-tabida
#13
E Geuverink, E C Verhulst, M van Leussen, L van de Zande, L W Beukeboom
In many insect species maternal provision of sex-specifically spliced messenger RNA (mRNA) of sex determination genes is an essential component of the sex determination mechanism. In haplodiploid Hymenoptera, maternal provision in combination with genomic imprinting has been shown for the parasitoid Nasonia vitripennis, known as maternal effect genomic imprinting sex determination (MEGISD). Here, we characterize the sex determination cascade of Asobara tabida, another hymenopteran parasitoid. We show the presence of the conserved sex determination genes doublesex (dsx), transformer (tra) and transformer-2 (tra2) orthologues in As...
October 14, 2017: Insect Molecular Biology
https://www.readbyqxmd.com/read/29029611/identification-of-15-candidate-structured-noncoding-rna-motifs-in-fungi-by-comparative-genomics
#14
Sanshu Li, Ronald R Breaker
BACKGROUND: With the development of rapid and inexpensive DNA sequencing, the genome sequences of more than 100 fungal species have been made available. This dataset provides an excellent resource for comparative genomics analyses, which can be used to discover genetic elements, including noncoding RNAs (ncRNAs). Bioinformatics tools similar to those used to uncover novel ncRNAs in bacteria, likewise, should be useful for searching fungal genomic sequences, and the relative ease of genetic experiments with some model fungal species could facilitate experimental validation studies...
October 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29029362/altered-tdp-43-dependent-splicing-in-hspb8-related-distal-hereditary-motor-neuropathy-and-myofibrillar-myopathy
#15
Andrea Cortese, Matilde Laurà, Carlo Casali, Ichizo Nishino, Yukiko K Hayashi, Stefania Magri, Franco Taroni, Cristiana Stuani, Paola Saveri, Maurizio Moggio, Michela Ripolone, A Prelle, C Pisciotta, A Sagnelli, Anna Pichiecchio, Mary M Reilly, Emanuele Buratti, Davide Pareyson
INTRODUCTION: Mutations in the small heat shock protein 22 gene (HSPB8) have been associated with Charcot-Marie-Tooth type 2L, distal hereditary motor neuropathy (dHMN) type IIa and, more recently, distal myopathy/myofibrillar myopathy (MFM) with protein aggregates and TDP-43 inclusions. OBJECTIVE: To report a novel family with HSPB8 (K141E) -related dHMN/MFM and to investigate, in a patient muscle biopsy, whether the presence of protein aggregates was paralleled by altered TDP-43 function...
October 13, 2017: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/29029327/the-exonization-and-functionalization-of-an-alu-j-element-in-the-protein-coding-region-of-glycoprotein-hormone-alpha-gene-represent-a-novel-mechanism-to-the-evolution-of-hemochorial-placentation-in-primates
#16
Haidi Chen, Li Chen, Yune Wu, Hao Shen, Guang Yang, Cheng Deng
Alu elements contribute considerably to gene regulation and genome evolution in primates. The generation of new exons from Alu elements has been found in various human genes, and the regulatory function of the Alu exon has been investigated in many studies. However, the functionalization of Alu elements in protein coding regions remains unknown. Here, we reported that an Alu-J element exonized in the glycoprotein hormone alpha (GPHA) gene and encoded an additional N-terminal peptide (Alu-J encoding peptide) of the mature GPHA peptide, leading to a splicing variant of Alu-GPHA in anthropoid primates approximately 35 million years ago...
September 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029073/clinical-genetics-and-outcome-of-left-ventricular-non-compaction-cardiomyopathy
#17
Farbod Sedaghat-Hamedani, Jan Haas, Feng Zhu, Christian Geier, Elham Kayvanpour, Martin Liss, Alan Lai, Karen Frese, Regina Pribe-Wolferts, Ali Amr, Daniel Tian Li, Omid Shirvani Samani, Avisha Carstensen, Diana Martins Bordalo, Marion Müller, Christine Fischer, Jing Shao, Jing Wang, Ming Nie, Li Yuan, Sabine Haßfeld, Christine Schwartz, Min Zhou, Zihua Zhou, Yanwen Shu, Min Wang, Kai Huang, Qiutang Zeng, Longxian Cheng, Tobias Fehlmann, Philipp Ehlermann, Andreas Keller, Christoph Dieterich, Katrin Streckfuß-Bömeke, Yuhua Liao, Michael Gotthardt, Hugo A Katus, Benjamin Meder
Aims: In this study, we aimed to clinically and genetically characterize LVNC patients and investigate the prevalence of variants in known and novel LVNC disease genes. Introduction: Left ventricular non-compaction cardiomyopathy (LVNC) is an increasingly recognized cause of heart failure, arrhythmia, thromboembolism, and sudden cardiac death. We sought here to dissect its genetic causes, phenotypic presentation and outcome. Methods and results: In our registry with follow-up of in the median 61 months, we analysed 95 LVNC patients (68 unrelated index patients and 27 affected relatives; definite familial LVNC = 23...
October 6, 2017: European Heart Journal
https://www.readbyqxmd.com/read/29028823/novel-mutations-in-darier-disease-and-association-to-self-reported-disease-severity
#18
Ivone U S Leong, Alexander Stuckey, Tara Ahanian, Martin Cederlöf, Jakob D Wikstrom
Darier disease is a rare and severe autosomal dominant skin disease characterised by malodorous keratotic papules in seborrheic areas of the skin. Darier disease affects up to 1 in 30 000 people and is caused by mutations in the ATP2A2 gene, which encodes to the sarco/endoplasmic reticulum calcium-ATPase isoform 2 that pumps calcium into the endoplasmic reticulum. Although many ATP2A2 variants have been described, it is not known if genotype correlates with phenotype, which could be important for prognosis and treatment...
2017: PloS One
https://www.readbyqxmd.com/read/29027761/oxidative-stress-and-mitochondrial-dynamics-malfunction-are-linked-in-pelizaeus-merzbacher-disease
#19
Montserrat Ruiz, Mélina Bégou, Nathalie Launay, Pablo Ranea-Robles, Patrizia Bianchi, Jone López-Erauskin, Laia Morató, Cristina Guilera, Bérengère Petit, Catherine Vaurs-Barriere, Céline Guéret-Gonthier, Marie-Noëlle Bonnet-Dupeyron, Stéphane Fourcade, Johan Auwerx, Odile Boespflug-Tanguy, Aurora Pujol
Pelizaeus-Merzbacher disease (PMD) is a fatal hypomyelinating disorder characterized by early impairment of motor development, nystagmus, choreoathetotic movements, ataxia and progressive spasticity. PMD is caused by variations in the proteolipid protein gene PLP1, which encodes the two major myelin proteins of the central nervous system, PLP and its spliced isoform DM20, in oligodendrocytes. Large duplications including the entire PLP1 gene are the most frequent causative mutation leading to the classical form of PMD...
October 13, 2017: Brain Pathology
https://www.readbyqxmd.com/read/29025893/disease-specific-biases-in-alternative-splicing-and-tissue-specific-dysregulation-revealed-by-multitissue-profiling-of-lymphocyte-gene-expression-in-type-1-diabetes
#20
Jeremy R B Newman, Ana Conesa, Matthew Mika, Felicia N New, Suna Onengut-Gumuscu, Mark A Atkinson, Stephen S Rich, Lauren M McIntyre, Patrick Concannon
Genome-wide association studies (GWAS) have identified multiple, shared allelic associations with many autoimmune diseases. However, the pathogenic contributions of variants residing in risk loci remain unresolved. The location of the majority of shared disease-associated variants in noncoding regions suggests they contribute to risk of autoimmunity through effects on gene expression in the immune system. In the current study, we test this hypothesis by applying RNA sequencing to CD4(+), CD8(+), and CD19(+) lymphocyte populations isolated from 81 subjects with type 1 diabetes (T1D)...
October 12, 2017: Genome Research
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