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Alternative splicing

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https://www.readbyqxmd.com/read/28651367/alternative-rna-splicing-associated-with-mammalian-neuronal-differentiation
#1
Jiancheng Liu, Anqi Geng, Xiwei Wu, Ren-Jang Lin, Qiang Lu
Alternative pre-mRNA splicing (AS) produces multiple isoforms of mRNAs and proteins from a single gene. It is most prevalent in the mammalian brain and is thought to contribute to the formation and/or maintenance of functional complexity of the brain. Increasing evidence has documented the significant changes of AS between different regions or different developmental stages of the brain, however, the dynamics of AS and the possible function of it during neural progenitor cell (NPC) differentiation is less well known...
June 23, 2017: Cerebral Cortex
https://www.readbyqxmd.com/read/28650318/tandem-hnrnp-a1-rna-recognition-motifs-act-in-concert-to-repress-the-splicing-of-survival-motor-neuron-exon-7
#2
Irene Beusch, Pierre Barraud, Ahmed Moursy, Antoine Cléry, Frédéric Hai-Trieu Allain
HnRNP A1 regulates many alternative splicing events by the recognition of splicing silencer elements. Here, we provide the solution structures of its two RNA recognition motifs (RRMs) in complex with short RNA. In addition, we show by NMR that both RRMs of hnRNP A1 can bind simultaneously to a single bipartite motif of the human intronic splicing silencer ISS-N1, which controls survival of motor neuron exon 7 splicing. RRM2 binds to the upstream motif and RRM1 to the downstream motif. Combining the insights from the structure with in cell splicing assays we show that the architecture and organization of the two RRMs is essential to hnRNP A1 function...
June 26, 2017: ELife
https://www.readbyqxmd.com/read/28649249/dscam1-in-pancrustacean-immunity-current-status-and-a-look-to-the-future
#3
Sophie A O Armitage, Joachim Kurtz, Daniela Brites, Yuemei Dong, Louis Du Pasquier, Han-Ching Wang
The Down syndrome cell adhesion molecule 1 (Dscam1) gene is an extraordinary example of diversity: by combining alternatively spliced exons, thousands of isoforms can be produced from just one gene. So far, such diversity in this gene has only been found in insects and crustaceans, and its essential part in neural wiring has been well-characterized for Drosophila melanogaster. Ten years ago evidence from D. melanogaster showed that the Dscam1 gene is involved in insect immune defense and work on Anopheles gambiae indicated that it is a hypervariable immune receptor...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28645112/tap63%C3%AE-and-%C3%AE-np63%C3%AE-are-regulated-by-rbm38-via-mrna-stability-and-have-an-opposing-function-in-growth-suppression
#4
Wensheng Yan, Yanhong Zhang, Xinbin Chen
The p63 gene is expressed as TAp63 from the P1 promoter and as ΔNp63 from the P2 promoter. Through alternative splicing, five TA and five ΔN isoforms (α-ε) are expressed. Isoforms α-β and δ share an identical 3' untranslated region (3'UTR) whereas isoform γ has a unique 3'UTR. Recently, we found that RBM38 RNA-binding protein is a target of p63 and RBM38 in turn regulates p63α/β expression via mRNA stability. However, it is uncertain whether p63γ has a unique biological activity and whether p63γ is regulated by RBM38...
June 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/28644774/cd33-splicing-polymorphism-determines-gemtuzumab-ozogamicin-response-in-de-novo-acute-myeloid-leukemia-report-from-randomized-phase-iii-children-s-oncology-group-trial-aaml0531
#5
Jatinder K Lamba, Lata Chauhan, Miyoung Shin, Michael R Loken, Jessica A Pollard, Yi-Cheng Wang, Rhonda E Ries, Richard Aplenc, Betsy A Hirsch, Susana C Raimondi, Roland B Walter, Irwin D Bernstein, Alan S Gamis, Todd A Alonzo, Soheil Meshinchi
Purpose Gemtuzumab ozogamicin (GO), a CD33-targeted immunoconjugate, is a re-emerging therapy for acute myeloid leukemia (AML). CD33 single nucleotide polymorphism rs12459419 C>T in the splice enhancer region regulates the expression of an alternatively spliced CD33 isoform lacking exon2 (D2-CD33), thus eliminating the CD33 IgV domain, which is the antibody-binding site for GO, as well as diagnostic immunophenotypic panels. We aimed to determine the impact of the genotype of this splicing polymorphism in patients with AML treated with GO-containing chemotherapy...
June 23, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28642487/hypoxia-is-a-key-driver-of-alternative-splicing-in-human-breast-cancer-cells
#6
Jian Han, Jia Li, Jolene Caifeng Ho, Grace Sushin Chia, Hiroyuki Kato, Sudhakar Jha, Henry Yang, Lorenz Poellinger, Kian Leong Lee
Adaptation to hypoxia, a hallmark feature of many tumors, is an important driver of cancer cell survival, proliferation and the development of resistance to chemotherapy. Hypoxia-induced stabilization of hypoxia-inducible factors (HIFs) leads to transcriptional activation of a network of hypoxia target genes involved in angiogenesis, cell growth, glycolysis, DNA damage repair and apoptosis. Although the transcriptional targets of hypoxia have been characterized, the alternative splicing of transcripts that occurs during hypoxia and the roles they play in oncogenesis are much less understood...
June 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28641998/construction-of-a-hepatitis-b-virus-neutralizing-chimeric-monoclonal-antibody-recognizing-escape-mutants-of-the-viral-surface-antigen-hbsag
#7
Forough Golsaz-Shirazi, Mohammad Mehdi Amiri, Samira Farid, Motahareh Bahadori, Felix Bohne, Sebastian Altstetter, Lisa Wolff, Tohid Kazemi, Jalal Khoshnoodi, Mohammad Hojjat-Farsangi, Michael Chudy, Mahmood Jeddi-Tehrani, Ulrike Protzer, Fazel Shokri
Hepatitis B virus (HBV) infection is a global burden on the health-care system and is considered as the tenth leading cause of death in the world. Over 248 million patients are currently suffering from chronic HBV infection worldwide and annual mortality rate of this infection is 686000. The "a" determinant is a hydrophilic region present in all antigenic subtypes of hepatitis B surface antigen (HBsAg), and antibodies against this region can neutralize the virus and are protective against all subtypes. We have recently generated a murine anti-HBs monoclonal antibody (4G4), which can neutralize HBV infection in HepaRG cells and recognize most of the escape mutant forms of HBsAg...
June 19, 2017: Antiviral Research
https://www.readbyqxmd.com/read/28640813/identification-of-a-sj%C3%A3-gren-s-syndrome-susceptibility-locus-at-oas1-that-influences-isoform-switching-protein-expression-and-responsiveness-to-type-i-interferons
#8
He Li, Tove Ragna Reksten, John A Ice, Jennifer A Kelly, Indra Adrianto, Astrid Rasmussen, Shaofeng Wang, Bo He, Kiely M Grundahl, Stuart B Glenn, Corinne Miceli-Richard, Simon Bowman, Sue Lester, Per Eriksson, Maija-Leena Eloranta, Johan G Brun, Lasse G Gøransson, Erna Harboe, Joel M Guthridge, Kenneth M Kaufman, Marika Kvarnström, Deborah S Cunninghame Graham, Ketan Patel, Adam J Adler, A Darise Farris, Michael T Brennan, James Chodosh, Rajaram Gopalakrishnan, Michael H Weisman, Swamy Venuturupalli, Daniel J Wallace, Kimberly S Hefner, Glen D Houston, Andrew J W Huang, Pamela J Hughes, David M Lewis, Lida Radfar, Evan S Vista, Contessa E Edgar, Michael D Rohrer, Donald U Stone, Timothy J Vyse, John B Harley, Patrick M Gaffney, Judith A James, Sean Turner, Ilias Alevizos, Juan-Manuel Anaya, Nelson L Rhodus, Barbara M Segal, Courtney G Montgomery, R Hal Scofield, Susan Kovats, Xavier Mariette, Lars Rönnblom, Torsten Witte, Maureen Rischmueller, Marie Wahren-Herlenius, Roald Omdal, Roland Jonsson, Wan-Fai Ng, Gunnel Nordmark, Christopher J Lessard, Kathy L Sivils
Sjögren's syndrome (SS) is a common, autoimmune exocrinopathy distinguished by keratoconjunctivitis sicca and xerostomia. Patients frequently develop serious complications including lymphoma, pulmonary dysfunction, neuropathy, vasculitis, and debilitating fatigue. Dysregulation of type I interferon (IFN) pathway is a prominent feature of SS and is correlated with increased autoantibody titers and disease severity. To identify genetic determinants of IFN pathway dysregulation in SS, we performed cis-expression quantitative trait locus (eQTL) analyses focusing on differentially expressed type I IFN-inducible transcripts identified through a transcriptome profiling study...
June 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28637762/differential-requirement-of-human-cytomegalovirus-ul112-113-protein-isoforms-for-viral-replication
#9
Tim Schommartz, Jiajia Tang, Rebekka Brost, Wolfram Brune
The UL112-113 gene is one of the few alternatively spliced genes of human cytomegalovirus (HCMV). It codes for four phosphoproteins, p34, p43, p50, and p84, all of which are expressed with early kinetics and accumulate at sites of viral DNA replication within the host cell nucleus. Although these proteins are known to play important, possibly essential, roles in the viral replication cycle, little is known about the contribution of individual UL112-113 protein products. Here we used splice site mutagenesis, intron deletion and substitution, and nonsense mutagenesis to prevent the individual expression of each UL112-113 protein isoform and to investigate the importance of each isoform for viral replication...
June 21, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28637711/the-exon-junction-complex-and-srp54-contribute-to-drosophila-hedgehog-signaling-via-ci-rna-splicing
#10
Elisa Garcia Garcia, Jamie C Little, Daniel Kalderon
Hedgehog (Hh) regulates the Cubitus interruptus (Ci) transcription factor in Drosophila melanogaster by activating full-length Ci-155 and blocking processing to Ci-75 repressor. However, the interplay between regulation of Ci-155 levels and activity, as well as processing-independent mechanisms that affect Ci-155 levels have not been explored extensively. Here we identified Mago Nashi (Mago) and Y14 core Exon Junction Complex (EJC) proteins, as well as the Srp54 splicing factor as modifiers of Hh pathway activity under sensitized conditions...
June 21, 2017: Genetics
https://www.readbyqxmd.com/read/28636946/ptbp2-controls-an-alternative-splicing-network-required-for-cell-communication-during-spermatogenesis
#11
Molly M Hannigan, Leah L Zagore, Donny D Licatalosi
Alternative splicing has essential roles in development. Remarkably, spermatogenic cells express more alternatively spliced RNAs compared to most whole tissues; however, regulation of these RNAs remains unclear. Here, we characterize the alternative splicing landscape during spermatogenesis and reveal an essential function for the RNA-binding protein Ptbp2 in this highly regulated developmental program. We found that Ptbp2 controls a network of genes involved in cell adhesion, migration, and polarity, suggesting that splicing regulation by Ptbp2 is critical for germ cell communication with Sertoli cells (multifunctional somatic cells necessary for spermatogenesis)...
June 20, 2017: Cell Reports
https://www.readbyqxmd.com/read/28634818/sg2na-is-a-regulator-of-endoplasmic-reticulum-er-homeostasis-as-its-depletion-leads-to-er-stress
#12
Buddhi Prakash Jain, Shweta Pandey, Nikhat Saleem, Goutam K Tanti, Shalini Mishra, Shyamal K Goswami
SG2NA belongs to a three-member striatin subfamily of WD40 repeat superfamily of proteins. It has multiple protein-protein interaction domains involved in assembling supramolecular signaling complexes. Earlier, we had demonstrated that there are at least five variants of SG2NA generated by alternative splicing, intron retention, and RNA editing. Such versatile and dynamic mode of regulation implicates it in tissue development. In order to shed light on its role in cell physiology, total proteome analysis was performed in NIH3T3 cells depleted of 78 kDa SG2NA, the only isoform expressing therein...
June 21, 2017: Cell Stress & Chaperones
https://www.readbyqxmd.com/read/28634384/alternative-splicing-regulates-distinct-subcellular-localization-of-epithelial-splicing-regulatory-protein-1-esrp1-isoforms
#13
Yueqin Yang, Russ P Carstens
Epithelial-Splicing-Regulatory-Protein 1 (Esrp1) is a cell-type specific RNA-binding protein (RBP) that is essential for mammalian development through maintenance of epithelial cell properties including barrier function. Esrp1 also regulates splicing during the epithelial to mesenchymal transition (EMT). It contains three highly conserved RNA recognition motifs (RRMs) in the absence of other clearly defined protein domains. Esrp1 itself is also alternatively spliced to produce multiple protein isoforms. Here we determined that two competing alternative 5' splice sites in exon 12 yield Esrp1 isoforms with differential nucleocytoplasmic localization...
June 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28631899/dual-molecular-diagnosis-contributes-to-atypical-prader-willi-phenotype-in-monozygotic-twins
#14
Fernanda S Jehee, Valdirene T de Oliveira, Juliana Gurgel-Giannetti, Rafaella X Pietra, Fernando V M Rubatino, Natália V Carobin, Gabrielle S Vianna, Mariana L de Freitas, Karla S Fernandes, Beatriz S V Ribeiro, Hennie T Brüggenwirth, Roza Ali-Amin, Janson J White, Zeynep C Akdemir, Shalini N Jhangiani, Richard A Gibbs, James R Lupski, Monica C Varela, Célia Koiffmann, Carla Rosenberg, Cláudia M B Carvalho
We describe monozygotic twin girls with genetic variation at two separate loci resulting in a blended phenotype of Prader-Willi syndrome and Pitt-Hopkins syndrome. These girls were diagnosed in early infancy with Prader-Willi syndrome, but developed an atypical phenotype, with apparent intellectual deficiency and lack of obesity. Array-comparative genomic hybridization confirmed a de novo paternal deletion of the 15q11.2q13 region and exome sequencing identified a second mutational event in both girls, which was a novel variant c...
June 20, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28630030/alzheimer-s-brains-show-inter-related-changes-in-rna-and-lipid-metabolism
#15
Shahar Barbash, Benjamin P Garfinkel, Rotem Maoz, Alon Simchovitz, Bettina Nadorp, Alessandro Guffanti, Estelle R Bennett, Courtney Nadeau, Andreas Türk, Lukas Paul, Torsten Reda, Yan Li, Aron S Buchman, David S Greenberg, Alexander Seitz, David A Bennett, Patrick Giavalisco, Hermona Soreq
Alzheimer's disease (AD) involves changes in both lipid and RNA metabolism, but it remained unknown if these differences associate with AD's cognition and/or post-mortem neuropathology indices. Here, we report RNA-sequencing evidence of inter-related associations between lipid processing, cognition level, and AD neuropathology. In two unrelated cohorts, we identified pathway-enriched facilitation of lipid processing and alternative splicing genes, including the neuronal-enriched NOVA1 and hnRNPA1. Specifically, this association emerged in temporal lobe tissue samples from donors where postmortem evidence demonstrated AD neuropathology, but who presented normal cognition proximate to death...
June 16, 2017: Neurobiology of Disease
https://www.readbyqxmd.com/read/28629792/alternative-splicing-and-start-sites-lessons-from-the-grainyhead-like-family
#16
REVIEW
Lee B Miles, Sebastian Dworkin, Charbel Darido
The two main mechanisms that expand the proteomic output of eukaryotic genes are alternative splicing and alternative translation initiation signals. Despite being essential to generate isoforms of gene products that create functional diversity during development, the impact of these mechanisms on fine-tuning regulatory gene networks is still underappreciated. In this review, we use the Grainyhead-like (Grhl) family as a case study to illustrate the importance of isoforms when investigating transcription factor family function during development and disease, and highlight the potential for differential modulation of downstream target genes...
June 16, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28629467/chromatin-marks-and-ambient-temperature-dependent-flowering-strike-up-a-novel-liaison
#17
Alexander Steffen, Dorothee Staiger
A distinct chromatin mark, H3K36me3, has been found to engage in temperature-dependent alternative splicing and ambient temperature-dependent flowering-time control in Arabidopsis.
June 19, 2017: Genome Biology
https://www.readbyqxmd.com/read/28627443/impact-of-the-bcr-abl1-fusion-transcripts-on-different-responses-to-imatinib-and-disease-recurrence-in-iranian-patients-with-chronic-myeloid-leukemia
#18
Golale Rostami, Mohammad Hamid, Hasan Jalaeikhoo
BACKGROUND: One genomic breakpoint can result in variable BCR-ABL1 transcript types due to alternative splicing. The influence of different BCR-ABL1 transcript types on clinical outcome is still controversial. AIM OF THE STUDY: The objective of this analysis was to determine the impact of transcript type on response, clinical outcome, recurrence risk after treatment with Imatinib mesylate in Chronic Myeloid Leukemia (CML) patients. METHODS: Sixty CML patients in chronic phase were analyzed by quantitative real-time polymerase chain reaction (qRT-PCR) and banding standard protocols...
June 13, 2017: Gene
https://www.readbyqxmd.com/read/28627382/bpag1-a-distinctive-role-in-skin-and-neurological-diseases
#19
REVIEW
Arshad Ali, Lifang Hu, Fan Zhao, Wuxia Qiu, Pai Wang, Xiaoli Ma, Yan Zhang, Lei Chen, Airong Qian
Spectraplakins are multifunctional cytoskeletal linker proteins that act as important communicators, connecting cytoskeletal components with each other and to cellular junctions. Bullous pemphigoid antigen 1 (BPAG1)/dystonin is a member of spectraplakin family and expressed in various tissues. Alternative splicing of BPAG1 gene produces various isoforms with unique structure and domains. BPAG1 plays crucial roles in numerous biological processes, such as cytoskeleton organization, cell polarization, cell adhesion, and cell migration as well as signaling transduction...
June 13, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/28626003/transcriptional-complexity-and-distinct-expression-patterns-of-auts2-paralogs-in-danio-rerio
#20
Igor Kondrychyn, Lena Robra, Vatsala Thirumalai
Several genes that have been implicated in autism spectrum disorders are large and have multiple transcripts. Neurons are especially enriched with longer transcripts compared to non-neural cell types. The human autism susceptibility candidate 2 (AUTS2) gene is ~1.2 Mb long and is implicated in a number of neurological disorders including autism, intellectual disability, addiction and developmental delay. Recent studies show AUTS2 to be important for activation of transcription of neural specific genes, neuronal migration and neurite outgrowth...
June 16, 2017: G3: Genes—Genomes—Genetics
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