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Alternative splicing

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https://www.readbyqxmd.com/read/28086949/nek2-promotes-aerobic-glycolysis-in-multiple-myeloma-through-regulating-splicing-of-pyruvate-kinase
#1
Zhimin Gu, Jiliang Xia, Hongwei Xu, Ivana Frech, Guido Tricot, Fenghuang Zhan
BACKGROUND: Aerobic glycolysis, a hallmark of cancer, is characterized by increased metabolism of glucose and production of lactate in normaxia. Recently, pyruvate kinase M2 (PKM2) has been identified as a key player for regulating aerobic glycolysis and promoting tumor cell proliferation and survival. METHODS: Tandem affinity purification followed up by mass spectrometry (TAP-MS) and co-immunoprecipitation (Co-IP) were used to study the interaction between NIMA (never in mitosis gene A)-related kinase 2 (NEK2) and heterogeneous nuclear ribonucleoproteins (hnRNP) A1/2...
January 13, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28077788/androgen-receptor-splice-variants-and-prostate-cancer-from-bench-to-bedside
#2
REVIEW
Kristine M Wadosky, Shahriar Koochekpour
Therapeutic interventions for advanced prostate cancer (PCa) center on inhibiting androgen receptor (AR) and downstream signaling pathways. Resistance to androgen deprivation therapy and/or AR antagonists is inevitable and molecular mechanisms driving castration-resistant PCa (CR-PCa) primarily involve alterations in AR expression and activity. Detailed molecular biology work over the past decade, discussed at length in this review article, has revealed several AR transcripts that result from alternative splicing...
January 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28077597/muscle-developmental-defects-in-heterogeneous-nuclear-ribonucleoprotein-a1-knockout-mice
#3
Ting-Yuan Liu, Yu-Chia Chen, Yuh-Jyh Jong, Huai-Jen Tsai, Chien-Chin Lee, Ya-Sian Chang, Jan-Gowth Chang, Yung-Fu Chang
Heterogeneous ribonucleoprotein A1 (hnRNP A1) is crucial for regulating alternative splicing. Its integrated function within an organism has not, however, been identified. We generated hnRNP A1 knockout mice to study the role of hnRNP A1 in vivo The knockout mice, hnRNP A1(-/-), showed embryonic lethality because of muscle developmental defects. The blood pressure and heart rate of the heterozygous mice were higher than those of the wild-type mice, indicating heart function defects. We performed mouse exon arrays to study the muscle development mechanism...
January 2017: Open Biology
https://www.readbyqxmd.com/read/28077579/neuron-enriched-rna-binding-proteins-regulate-pancreatic-beta-cell-function-and-survival
#4
Jon Agraves Juan-Mateu, Tatiana H Rech, Olatz Villate, Esther Lizarraga-Mollinedo, Anna Wendt, Jean-Valery Turatsinze, Leticia A Brondani, Tarlliza R Nardelli, Tatiane C Nogueira, Jonatan L S Esguerra, Maria In Ecircs Alvelos, Piero Marchetti, Lena Eliasson, D Eacutecio L Eizirik
Pancreatic beta cell failure is the central event leading to diabetes. Beta cells share many phenotypic traits with neurons, and proper beta cell function relies on the activation of several neuronal-like transcription programs. Regulation of gene expression by alternative splicing plays a pivotal role in brain, where it affects neuronal development, function and disease. The role of alternative splicing in beta cells remains unclear, but recent data indicate that splicing alterations modulated by both inflammation and susceptibility genes for diabetes contribute to beta cell dysfunction and death...
January 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28077248/alternative-splicing-at-exon-2-results-in-the-loss-of-the-catalytic-activity-of-mouse-dna-polymerase-iota-in-vitro
#5
Konstantin Y Kazachenko, Nataliya A Miropolskaya, Leonid V Gening, Vyacheslav Z Tarantul, Alena V Makarova
Y-family DNA polymerase iota (Pol ι) possesses both DNA polymerase and dRP lyase activities and was suggested to be involved in DNA translesion synthesis and base excision repair in mammals. The 129 strain of mice and its derivatives have a natural nonsense codon mutation in the second exon of the Pol ι gene resulting in truncation of the Pol ι protein. These mice were widely used as a Pol ι-null model for in vivo studies of the Pol ι function. However whether 129-derived strains of mice are fully deficient in the Pol ι functions was a subject of discussion since Pol ι mRNA undergoes alternative splicing at exon 2...
January 4, 2017: DNA Repair
https://www.readbyqxmd.com/read/28074037/developmental-pruning-of-excitatory-synaptic-inputs-to-parvalbumin-interneurons-in-monkey-prefrontal-cortex
#6
Daniel W Chung, Zachary P Wills, Kenneth N Fish, David A Lewis
Working memory requires efficient excitatory drive to parvalbumin-positive (PV) interneurons in the primate dorsolateral prefrontal cortex (DLPFC). Developmental pruning eliminates superfluous excitatory inputs, suggesting that working memory maturation during adolescence requires pruning of excitatory inputs to PV interneurons. Therefore, we tested the hypothesis that excitatory synapses on PV interneurons are pruned during adolescence. The density of excitatory synapses, defined by overlapping vesicular glutamate transporter 1-positive (VGlut1+) and postsynaptic density 95-positive (PSD95+) puncta, on PV interneurons was lower in postpubertal relative to prepubertal monkeys...
January 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28072465/splicing-regulation-and-dysregulation-of-cholinergic-genes-expressed-at-the-neuromuscular-junction
#7
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/28068922/functional-changes-in-mrna-expression-and-alternative-pre-mrna-splicing-associated-with-the-effects-of-nutrition-on-apoptosis-and-spermatogenesis-in-the-adult-testis
#8
Yongjuan Guan, Guanxiang Liang, Graeme B Martin, Le Luo Guan
BACKGROUND: The effects of nutrition on testis mass in the sexually mature male have long been known, however, the cellular and molecular processes of the testis response to nutrition was not fully understood. METHODS: We tested whether the defects in spermatogenesis and increases in germ cell apoptosis in the testis that are induced by under-nutrition are associated with changes in mRNA expression and pre-mRNA alternative splicing using groups of 8 male sheep fed for a 10% increase or 10% decrease in body mass over 65 days...
January 10, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28067669/targeting-deregulated-ampk-mtorc1-pathways-improves-muscle-function-in-myotonic-dystrophy-type-i
#9
Marielle Brockhoff, Nathalie Rion, Kathrin Chojnowska, Tatiana Wiktorowicz, Christopher Eickhorst, Beat Erne, Stephan Frank, Corrado Angelini, Denis Furling, Markus A Rüegg, Michael Sinnreich, Perrine Castets
Myotonic dystrophy type I (DM1) is a disabling multisystemic disease that predominantly affects skeletal muscle. It is caused by expanded CTG repeats in the 3'-UTR of the dystrophia myotonica protein kinase (DMPK) gene. RNA hairpins formed by elongated DMPK transcripts sequester RNA-binding proteins, leading to mis-splicing of numerous pre-mRNAs. Here, we have investigated whether DM1-associated muscle pathology is related to deregulation of central metabolic pathways, which may identify potential therapeutic targets for the disease...
January 9, 2017: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/28067534/molecular-cloning-alternative-splicing-and-mrna-expression-analysis-of-magi1-and-its-correlation-with-laying-performance-in-geese
#10
S Yu, M Xia, M A Alsiddig, H Liu, W Wei, J Chen
1. In a previous study, a laying-related single nucleotide polymorphism (SNP) Record-106975 (A-G) was found in the intron of Membrane-associated Guanylate Kinase with Inverted Domain Structure-1 gene (MAGI1) by restriction site-associated DNA sequencing. This study was performed to further identify the function of MAGI1 on laying performance in Yangzhou geese. 2. The complete MAGI1 cDNA sequence was cloned from the ovary of the Yangzhou goose. A total of 4 alternative splice variants were identified, and the characterisation of their nucleic acid and amino acid sequences were analysed...
January 9, 2017: British Poultry Science
https://www.readbyqxmd.com/read/28064309/-role-of-pre-mrna-secondary-structures-in-the-regulation-of-alternative-splicing
#11
P M Rubtsov
Alternative splicing of pre-mRNA is one of the main mechanisms regulating gene expression that generates multiple transcripts from one gene. The review considers the specific role that intramolecular secondary structures arising through the interaction of distant complementary regions of introns play in regulating alternative splicing. Examples where aberrant splicing associated with hereditary disorders is corrected by altering the pre-mRNA secondary structures are described. The advances and prospects in whole transcriptome analysis of structured RNA regions and studies of their role in regulating alternative splicing are discussed...
November 2016: Molekuliarnaia Biologiia
https://www.readbyqxmd.com/read/28064149/emerging-roles-for-rna-binding-proteins-as-effectors-and-regulators-of-cardiovascular-disease
#12
REVIEW
Ruben G de Bruin, Ton J Rabelink, Anton Jan van Zonneveld, Eric P van der Veer
The cardiovascular system comprises multiple cell types that possess the capacity to modulate their phenotype in response to acute or chronic injury. Transcriptional and post-transcriptional mechanisms play a key role in the regulation of remodelling and regenerative responses to damaged cardiovascular tissues. Simultaneously, insufficient regulation of cellular phenotype is tightly coupled with the persistence and exacerbation of cardiovascular disease. Recently, RNA-binding proteins such as Quaking, HuR, Muscleblind, and SRSF1 have emerged as pivotal regulators of these functional adaptations in the cardiovascular system by guiding a wide-ranging number of post-transcriptional events that dramatically impact RNA fate, including alternative splicing, stability, localization and translation...
January 6, 2017: European Heart Journal
https://www.readbyqxmd.com/read/28062691/activating-mutations-and-translocations-in-the-guanine-exchange-factor-vav1-in-peripheral-t-cell-lymphomas
#13
Francesco Abate, Ana C da Silva-Almeida, Sakellarios Zairis, Javier Robles-Valero, Lucile Couronne, Hossein Khiabanian, S Aidan Quinn, Mi-Yeon Kim, Maria Antonella Laginestra, Christine Kim, Danilo Fiore, Govind Bhagat, Miguel Angel Piris, Elias Campo, Izidore S Lossos, Olivier A Bernard, Giorgio Inghirami, Stefano Pileri, Xosé R Bustelo, Raul Rabadan, Adolfo A Ferrando, Teresa Palomero
Peripheral T-cell lymphomas (PTCLs) are a heterogeneous group of non-Hodgkin lymphomas frequently associated with poor prognosis and for which genetic mechanisms of transformation remain incompletely understood. Using RNA sequencing and targeted sequencing, here we identify a recurrent in-frame deletion (VAV1 Δ778-786) generated by a focal deletion-driven alternative splicing mechanism as well as novel VAV1 gene fusions (VAV1-THAP4, VAV1-MYO1F, and VAV1-S100A7) in PTCL. Mechanistically these genetic lesions result in increased activation of VAV1 catalytic-dependent (MAPK, JNK) and non-catalytic-dependent (nuclear factor of activated T cells, NFAT) VAV1 effector pathways...
January 6, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28062664/mapping-eqtls-with-rna-seq-reveals-novel-susceptibility-genes-non-coding-rnas-and-alternative-splicing-events-in-systemic-lupus-erythematosus
#14
Christopher A Odhams, Andrea Cortini, Lingyan Chen, Amy L Roberts, Ana Viñuela, Alfonso Buil, Kerrin S Small, Emmanouil T Dermitzakis, David L Morris, Timothy J Vyse, Deborah S Cunninghame Graham
Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines...
January 5, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28057797/prmt2-interacts-with-splicing-factors-and-regulates-the-alternative-splicing-of-bcl-x
#15
Mynol I Vhuiyan, Magnolia L Pak, Margaret A Park, Dylan Thomas, Ted M Lakowski, Charles E Chalfant, Adam Frankel
Protein arginine N-methyltransferase 2 (PRMT2) functions in JAK-STAT and Wnt/β-catenin signaling pathways, serves as a nuclear receptor-dependent transcriptional co-activator, and represses NF-κB and E2F1 transcription factor activities to promote apoptosis. We have previously demonstrated that PRMT2 interacts with PRMT1 and increases its activity. Here, we reveal associations using proteomics between the PRMT2 SH3 domain and splicing factors including Src-associated in mitosis 68 kDa protein (SAM68), a PRMT1 substrate and trans-acting factor that mediates BCL-X alternative splicing...
January 5, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/28056087/mita-sting-and-its-alternative-splicing-isoform-mrp-restrict-hepatitis-b-virus-replication
#16
Shuhui Liu, Kaitao Zhao, Xi Su, Lu Lu, He Zhao, Xianwen Zhang, Yun Wang, Chunchen Wu, Jizheng Chen, Yuan Zhou, Xue Hu, Yanyi Wang, Mengji Lu, Xinwen Chen, Rongjuan Pei
An efficient clearance of hepatitis B virus (HBV) requires the coordinated work of both the innate and adaptive immune responses. MITA/STING, an adapter protein of the innate immune signaling pathways, plays a key role in regulating innate and adaptive immune responses to DNA virus infection. Previously, we identified an alternatively spliced isoform of MITA/STING, called MITA-related protein (MRP), and found that MRP could specifically block MITA-mediated interferon (IFN) induction while retaining the ability to activate NF-κB...
2017: PloS One
https://www.readbyqxmd.com/read/28053119/short-intron-derived-ncrnas
#17
Florent Hubé, Damien Ulveling, Alain Sureau, Sabrina Forveille, Claire Francastel
Introns represent almost half of the human genome, although they are eliminated from transcripts through RNA splicing. Yet, different classes of non-canonical miRNAs have been proposed to originate directly from intron splicing. Here, we considered the alternative splicing of introns as an interesting source of miRNAs, compatible with a developmental switch. We report computational prediction of new Short Intron-Derived ncRNAs (SID), defined as precursors of smaller ncRNAs like miRNAs and snoRNAs produced directly by splicing, and tested their dependence on each key factor in canonical or alternative miRNAs biogenesis (Drosha, DGCR8, DBR1, snRNP70, U2AF65, PRP8, Dicer, Ago2)...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28053030/tau-isoforms-imbalance-impairs-the-axonal-transport-of-the-amyloid-precursor-protein-in-human-neurons
#18
Valentina Lacovich, Sonia L Espindola, Matías Alloatti, Victorio Pozo Devoto, Lucas E Cromberg, Mária E Čarná, Giancarlo Forte, Jean-Marc Gallo, Luciana Bruno, Gorazd B Stokin, M Elena Avale, Tomás L Falzone
: Tau, as a microtubule (MT)-associated protein, participates in key neuronal functions such as the regulation of MT dynamics, axonal transport, and neurite outgrowth. Alternative splicing of exon 10 in the tau primary transcript gives rise to protein isoforms with three (3R) or four (4R) MT binding repeats. Although tau isoforms are balanced in the normal adult human brain, imbalances in 3R:4R ratio have been tightly associated with the pathogenesis of several neurodegenerative disorders, yet the underlying molecular mechanisms remain elusive...
January 4, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28052020/the-rna-binding-protein-esrp1-promotes-human-colorectal-cancer-progression
#19
Sharmila Fagoonee, Gabriele Picco, Francesca Orso, Arrigo Arrigoni, Dario L Longo, Marco Forni, Irene Scarfò, Adele Cassenti, Roberto Piva, Paola Cassoni, Lorenzo Silengo, Emanuela Tolosano, Silvio Aime, Daniela Taverna, Pier Paolo Pandolfi, Mara Brancaccio, Enzo Medico, Fiorella Altruda
Epithelial splicing regulatory protein 1 (ESRP1) is an epithelial cell-specific RNA binding protein that controls several key cellular processes, like alternative splicing and translation. Previous studies have demonstrated a tumor suppressor role for this protein. Recently, however, a pro-metastatic function of ESRP1 has been reported. We thus aimed at clarifying the role of ESRP1 in Colorectal Cancer (CRC) by performing loss- and gain-of-function studies, and evaluating tumorigenesis and malignancy with in vitro and in vivo approaches...
December 28, 2016: Oncotarget
https://www.readbyqxmd.com/read/28050347/gene-expression-profiling-of-u2af2-dependent-rna-protein-interactions-during-cd4%C3%A2-t-cell-activation
#20
Thomas C Whisenant
CD4 T cell activation is a central component of the mammalian adaptive immune response and is underscored by a dramatic change in the gene expression profile in these cells. The changes in gene expression that occur during T cell activation are regulated in multiple ways including post-transcriptionally by complexes of RNA-binding proteins. Recently, our study explored the role of the RNA-binding protein U2AF2 and its interacting proteins in mediating posttranscriptional changes in constitutive and alternative splicing during T cell activation...
March 2017: Genomics Data
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