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Gene splicing

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https://www.readbyqxmd.com/read/29679569/ddx1-regulates-alternative-splicing-and-insulin-secretion-in-pancreatic-%C3%AE-cells
#1
Wen Zhong, Zonghong Li, Maoge Zhou, Tao Xu, You Wang
DEAD-box helicase 1 (DDX1) is a multifunction protein involved in diverse cellular processes including transcription, viral replication, mRNA/miRNA processing, and tRNA splicing. Here, we report a novel function of DDX1 in mRNA alternative splicing in pancreatic β cells. By performing integrated data analysis of high-throughput RNA sequencing (RNA-Seq), and cross-linking and immunoprecipitation coupled with deep sequencing (CLIP-Seq), we identify hundreds of alternative splicing genes that are targeted by DDX1...
April 18, 2018: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29678826/rna-binding-protein-hur-regulates-scn5a-expression-through-stabilizing-mef2c-transcription-factor-mrna
#2
Anyu Zhou, Guangbin Shi, Gyeoung-Jin Kang, An Xie, Hong Liu, Ning Jiang, Man Liu, Euy-Myoung Jeong, Samuel C Dudley
BACKGROUND: Although transcription is the initial process of gene expression, posttranscriptional gene expression regulation has also played a critical role for fine-tuning gene expression in a fast, precise, and cost-effective manner. Although the regulation of sodium channel α-subunit ( SCN5A ) mRNA expression has been studied at both transcriptional and pre-mRNA splicing levels, the molecular mechanisms governing SCN5A mRNA expression are far from clear. METHODS AND RESULTS: Herein, we show that, as evidenced by ribonucleoprotein immunoprecipitation assay, RNA binding protein Hu antigen R/ELAV like RNA binding protein 1 (HuR/ELAVL1) and myocyte enhancer factor-2C (MEF2C) transcription factor mRNA are associated...
April 20, 2018: Journal of the American Heart Association
https://www.readbyqxmd.com/read/29678492/hmga1a-induces-alternative-splicing-of-estrogen-receptor-alpha-in-mcf-7-human-breast-cancer-cells
#3
Kenji Ohe, Shinsuke Miyajima, Tomoko Tanaka, Yuriko Hamaguchi, Yoshihiro Harada, Yuta Horita, Yuki Beppu, Fumiaki Ito, Takafumi Yamasaki, Hiroki Terai, Masayoshi Mori, Yusuke Murata, Makito Tanabe, Kenji Ashida, Munechika Enjoji, Toshihiko Yanase, Nobuhiro Harada, Toshiaki Utsumi, Akila Mayeda
The high-mobility group A protein 1a (HMGA1a) protein is known as an oncogene whose expression level in cancer tissue correlates with the malignant potential, and known as a component of senescence-related structures connecting it to tumor suppressor networks in fibroblasts. HMGA1 protein binds to DNA, but recent studies have shown it exerts novel functions through RNA-binding. Our previous studies have shown that sequence-specific RNA-binding of HMGA1a induces exon-skipping of Presenilin-2 exon 5 in sporadic Alzheimer disease...
April 17, 2018: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/29677003/identification-of-a-novel-tcf4-isoform-in-the-human-corneal-endothelium
#4
Allen O Eghrari, Shivakumar Vasanth, Briana C Gapsis, Henry Bison, Ula Jurkunas, S Amer Riazuddin, John D Gottsch
PURPOSE: Alternative splice isoforms of TCF4, a gene implicated in Fuchs corneal dystrophy, have been identified in multiple human tissues outside of the eye. The aim of this study was to identify the transcriptional profile of TCF4 in the corneal endothelium. METHODS: We extracted RNA from the donor corneal endothelium and performed rapid amplification of cDNA ends. We tested the expression pattern of 1 newly identified isoform (7b) in a panel of cDNA derived from multiple human tissues and included cDNA from corneal endothelial (CE) and retinal pigment epithelial cell lines...
April 19, 2018: Cornea
https://www.readbyqxmd.com/read/29676859/a-novel-splicing-mutation-of-ectodysplasin-a-gene-responsible-for-hypohidrotic-ectodermal-dysplasia
#5
Guannan Liu, Xin Wang, Man Qin, Lisha Sun, Junxia Zhu
Hypohidrotic ectodermal dysplasia (HED) is characterized by hypohidrosis, hypodontia, sparse hair and characteristic facial features. This condition is caused by an ectodysplasin A (EDA) gene mutation. In this study, we examined two HED pedigrees and investigated the molecular genetics of the defect. Direct sequencing analysis revealed a previously unidentified mutation in the EDA splice donor site (c.526+1G>A). The function of the mutant EDA gene was predicted through online investigations and subsequently confirmed by splicing analysis in vitro...
April 20, 2018: Oral Diseases
https://www.readbyqxmd.com/read/29675420/regulation-of-long-noncoding-rnas-responsive-to-phytoplasma-infection-in-paulownia-tomentosa
#6
Guoqiang Fan, Yabing Cao, Zhe Wang
Paulownia witches' broom caused by phytoplasma infection affects the production of Paulownia trees worldwide. Emerging evidence showed that long noncoding RNAs (lncRNA) play a protagonist role in regulating the expression of genes in plants. So far, the identification of lncRNAs has been limited to a few model plant species, and their roles in mediating responses to Paulownia tomentosa that free of phytoplasma infection are yet to be characterized. Here, whole-genome identification of lncRNAs, based on strand-specific RNA sequencing, from four Paulownia tomentosa samples, was performed and identified 3689 lncRNAs...
2018: International Journal of Genomics
https://www.readbyqxmd.com/read/29674126/bbs9-gene-in-nonsyndromic-craniosynostosis-role-of-the-primary-cilium-in-the-aberrant-ossification-of-the-suture-osteogenic-niche
#7
Marta Barba, Lorena Di Pietro, Luca Massimi, Maria Concetta Geloso, Paolo Frassanito, Massimo Caldarelli, Fabrizio Michetti, Stefano Della Longa, Paul A Romitti, Concezio Di Rocco, Alessandro Arcovito, Ornella Parolini, Gianpiero Tamburrini, Camilla Bernardini, Simeon Antonov Boyadjiev, Wanda Lattanzi
Nonsyndromic craniosynostosis (NCS) is the premature ossification of skull sutures, without associated clinical features. Mutations in several genes account for a small number of NCS patients; thus, the molecular etiopathogenesis of NCS remains largely unclear. Our study aimed at characterizing the molecular signaling implicated in the aberrant ossification of sutures in NCS patients. Comparative gene expression profiling of NCS patient sutures identified a fused suture-specific signature, including 17 genes involved in primary cilium signaling and assembly...
April 16, 2018: Bone
https://www.readbyqxmd.com/read/29673323/indel-detection-from-dna-and-rna-sequencing-data-with-transindel
#8
Rendong Yang, Jamie L Van Etten, Scott M Dehm
BACKGROUND: Insertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indels from splicing events in RNA-seq data. RESULTS: Here, we developed transIndel, a splice-aware algorithm that parses the chimeric alignments predicted by a short read aligner and reconstructs the mid-sized insertions and large deletions based on the linear alignments of split reads from DNA-seq or RNA-seq data...
April 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29673180/accurate-classification-of-nf1-gene-variants-in-84-italian-patients-with-neurofibromatosis-type-1
#9
Alessandro Stella, Patrizia Lastella, Daria Carmela Loconte, Nenad Bukvic, Dora Varvara, Margherita Patruno, Rosanna Bagnulo, Rosaura Lovaglio, Nicola Bartolomeo, Gabriella Serio, Nicoletta Resta
Neurofibromatosis type 1 (NF1) is one of the most common autosomal dominant genetic diseases. It is caused by mutations in the NF1 gene encoding for the large protein, neurofibromin. Genetic testing of NF1 is cumbersome because 50% of cases are sporadic, and there are no mutation hot spots. In addition, the most recognizable NF1 clinical features—café-au-lait (CALs) spots and axillary and/or inguinal freckling—appear early in childhood but are rather non-specific. Thus, the identification of causative variants is extremely important for early diagnosis, especially in paediatric patients...
April 17, 2018: Genes
https://www.readbyqxmd.com/read/29672717/antisense-oligonucleotides-correct-the-familial-dysautonomia-splicing-defect-in-ikbkap-transgenic-mice
#10
Rahul Sinha, Young Jin Kim, Tomoki Nomakuchi, Kentaro Sahashi, Yimin Hua, Frank Rigo, C Frank Bennett, Adrian R Krainer
Familial dysautonomia (FD) is a rare inherited neurodegenerative disorder caused by a point mutation in the IKBKAP gene that results in defective splicing of its pre-mRNA. The mutation weakens the 5' splice site of exon 20, causing this exon to be skipped, thereby introducing a premature termination codon. Though detailed FD pathogenesis mechanisms are not yet clear, correcting the splicing defect in the relevant tissue(s), thus restoring normal expression levels of the full-length IKAP protein, could be therapeutic...
April 17, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29671950/comparative-transcriptomics-across-14-drosophila-species-reveals-signatures-of-longevity
#11
Siming Ma, Andrei S Avanesov, Emily Porter, Byung Cheon Lee, Marco Mariotti, Nadezhda Zemskaya, Roderic Guigo, Alexey A Moskalev, Vadim N Gladyshev
Lifespan varies dramatically among species, but the biological basis is not well understood. Previous studies in model organisms revealed the importance of nutrient sensing, mTOR, NAD/sirtuins, and insulin/IGF1 signaling in lifespan control. By studying life-history traits and transcriptomes of 14 Drosophila species differing more than sixfold in lifespan, we explored expression divergence and identified genes and processes that correlate with longevity. These longevity signatures suggested that longer-lived flies upregulate fatty acid metabolism, downregulate neuronal system development and activin signaling, and alter dynamics of RNA splicing...
April 19, 2018: Aging Cell
https://www.readbyqxmd.com/read/29670865/opposite-effects-of-two-human-atg10-isoforms-on-replication-of-a-hcv-sub-genomic-replicon-are-mediated-via-regulating-autophagy-flux-in-zebrafish
#12
Yu-Chen Li, Miao-Qing Zhang, Jing-Pu Zhang
Autophagy is a host mechanism for cellular homeostatic control. Intracellular stresses are symptoms of, and responses to, dysregulation of the physiological environment of the cell. Alternative gene transcription splicing is a mechanism potentially used by a host to respond to physiological or pathological challenges. Here, we aimed to confirm opposite effects of two isoforms of the human autophagy-related protein ATG10 on an HCV subgenomic replicon in zebrafish. A liver-specific HCV subreplicon model was established and exhibited several changes in gene expression typically induced by HCV infection, including overexpression of several HCV-dependent genes ( argsyn, leugpcr, rasgbd , and scaf-2 ), as well as overexpression of several ER stress related genes ( atf4, chop, atf6 , and bip )...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29669851/systemic-administration-of-the-antisense-oligonucleotide-ns-065-ncnp-01-for-skipping-of-exon-53-in-patients-with-duchenne-muscular-dystrophy
#13
Hirofumi Komaki, Tetsuya Nagata, Takashi Saito, Satoru Masuda, Eri Takeshita, Masayuki Sasaki, Hisateru Tachimori, Harumasa Nakamura, Yoshitsugu Aoki, Shin'ichi Takeda
Duchenne muscular dystrophy (DMD) is a lethal hereditary muscle disease caused by mutations in the gene encoding the muscle protein dystrophin. These mutations result in a shift in the open reading frame leading to loss of the dystrophin protein. Antisense oligonucleotides (ASOs) that induce exon skipping correct this frame shift during pre-mRNA splicing and partially restore dystrophin expression in mouse and dog models. We conducted a phase 1, open-label, dose-escalation clinical trial to determine the safety, pharmacokinetics, and activity of NS-065/NCNP-01, a morpholino ASO that enables skipping of exon 53...
April 18, 2018: Science Translational Medicine
https://www.readbyqxmd.com/read/29669480/tert-hras-and-eif1ax-mutations-in-a-patient-with-follicular-adenoma
#14
Michael C Topf, Zi-Xuan Wang, Madalina Tuluc, Edmund A Pribitkin
BACKGROUND: Molecular markers are increasingly used as diagnostic tools in the management of thyroid nodules. There is a paucity of studies evaluating the prevalence of molecular markers in benign lesions. PATIENT FINDINGS: A 68-year-old woman with hypothyroidism presented with a right thyroid nodule which was atypia of undetermined significance on cytology. The fine needle aspirate of the nodule was examined with next-generation sequencing and found to harbor a C228T mutation in the TERT gene, a Q61R mutation in the HRAS gene, and an A113_splice mutation in the EIF1AX gene...
April 19, 2018: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/29668310/human-splice-site-prediction-with-deep-neural-networks
#15
Tatsuhiko Naito
Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNNs) have achieved record-breaking results and often outperformed other supervised learning techniques. In this study, a new method of splice-site prediction using DNNs was proposed. The proposed system receives an input sequence data and returns an answer as to whether it is splice site...
April 18, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
https://www.readbyqxmd.com/read/29666783/development-of-neuroendocrine-prostate-cancers-by-the-ser-arg-repetitive-matrix-4-mediated-rna-splicing-network
#16
Ahn R Lee, Nicole Che, Jessica M Lovnicki, Xuesen Dong
While the use of next-generation androgen receptor pathway inhibition (ARPI) therapy has significantly increased the survival of patients with metastatic prostate adenocarcinoma (AdPC), several groups have reported a treatment-resistant mechanism, whereby cancer cells can become androgen receptor (AR) indifferent and gain a neuroendocrine (NE)-like phenotype. This subtype of castration-resistant prostate cancer has been termed "treatment-induced castration-resistant neuroendocrine prostate cancer" (CRPC-NE)...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29666342/unusual-structure-and-splicing-pattern-of-the-vertebrate-mitochondrial-solute-carrier-slc25a3-gene
#17
Rosa Calvello, Antonia Cianciulli, Maria A Panaro
The DNA sequence corresponding to the second exon of the SLC25A3 gene is duplicated in vertebrates. The second exon codes for the first transmembrane segment and parts of the immediately adjoining intermembrane and mitochondrial matrix segments. The two genomic exon 2 sequences are 84% similar in zebrafish (slc25a3b gene), 70% in chicken, 66% in mouse and 67% in human. The amino acid identity is 86% in zebrafish, 77% in chicken and 70% in mouse and human. The two copies of exon 2 are separated by an intronic interval...
March 2018: Journal of Genetics
https://www.readbyqxmd.com/read/29666160/most-human-introns-are-recognized-via-multiple-and-tissue-specific-branchpoints
#18
Jose Mario Bello Pineda, Robert K Bradley
Although branchpoint recognition is an essential component of intron excision during the RNA splicing process, the branchpoint itself is frequently assumed to be a basal, rather than regulatory, sequence feature. However, this assumption has not been systematically tested due to the technical difficulty of identifying branchpoints and quantifying their usage. Here, we analyzed ∼1.31 trillion reads from 17,164 RNA sequencing data sets to demonstrate that almost all human introns contain multiple branchpoints...
April 17, 2018: Genes & Development
https://www.readbyqxmd.com/read/29665929/-anti-cd36-mediated-platelet-transfusion-refractoriness-and-related-cases-after-stem-cell-transplantation
#19
Yan Zhou, Li-Lan Li, Zhou-Lin Zhong, Xue-Jun Liu, Jin-Lian Liu, Wei-Dong Shen, Guo-Guang Wu
OBJECTIVE: To analyse the cases of platelet transfusion refractoriness after received HLA-matched unrelated donor hematopoietic stem cell transplantation, to analyze and identify the phenotype and genotype of CD36 in both the patient and stem cell donor, as well as the characteristic of antibody induced platelet transfusion refractoriness, and to analyse the efficacy of matched CD36-deficiency platelets transfusions. METHODS: The CD36 expression on platelet and monocyte was analyzed by flow cytometry (FCM) in both patient and donor...
April 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/29665773/identification-and-characterization-of-functional-modules-reflecting-transcriptome-transition-during-human-neuron-maturation
#20
Zhisong He, Qianhui Yu
BACKGROUND: Neuron maturation is a critical process in neurogenesis, during which neurons gain their morphological, electrophysiological and molecular characteristics for their functions as the central components of the nervous system. RESULTS: To better understand the molecular changes during this process, we combined the protein-protein interaction network and public single cell RNA-seq data of mature and immature neurons to identify functional modules relevant to the neuron maturation process in humans...
April 17, 2018: BMC Genomics
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