Mechanism of Regulation of Spliceosome Activation by Brr2 And
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ARP36414 P050) Data Sheet
SNRNP200 antibody - N-terminal region (ARP36414_P050) Data Sheet Product Number ARP36414_P050 Product Name SNRNP200 antibody - N-terminal region (ARP36414_P050) Size 50ug Gene Symbol SNRNP200 Alias Symbols ASCC3L1; BRR2; FLJ11521; HELIC2; RP33; U5-200KD Nucleotide Accession# NM_014014 Protein Size (# AA) 2136 amino acids Molecular Weight 244kDa Product Format Lyophilized powder NCBI Gene Id 23020 Host Rabbit Clonality Polyclonal Official Gene Full Name Small nuclear ribonucleoprotein 200kDa (U5) This is a rabbit polyclonal antibody against SNRNP200. It was validated on Western Blot by Aviva Systems Biology. At Aviva Systems Biology we manufacture rabbit polyclonal antibodies on a large scale (200-1000 Description products/month) of high throughput manner. Our antibodies are peptide based and protein family oriented. We usually provide antibodies covering each member of a whole protein family of your interest. We also use our best efforts to provide you antibodies recognize various epitopes of a target protein. For availability of antibody needed for your experiment, please inquire (). Peptide Sequence Synthetic peptide located within the following region: GDEDVYGEVREEASDDDMEGDEAVVRCTLSANLVASGELMSSKKKDLHPR Pre-mRNA splicing is catalyzed by the spliceosome, a complex of specialized RNA and protein subunits that removes introns from a transcribed pre-mRNA segment. The spliceosome consists of small nuclear RNA proteins (snRNPs) U1, U2, U4, U5 and U6, together with approximately 80 conserved proteins. U5 snRNP Description of Target contains nine specific proteins. This gene encodes one of the U5 snRNP-specific proteins. This protein belongs to the DEXH-box family of putative RNA helicases. It is a core component of U4/U6-U5 snRNPs and appears to catalyze an ATP-dependent unwinding of U4/U6 RNA duplices. -
Supplementary File 2A Revised
Supplementary file 2A. Differentially expressed genes in aldosteronomas compared to all other samples, ranked according to statistical significance. Missing values were not allowed in aldosteronomas, but to a maximum of five in the other samples. Acc UGCluster Name Symbol log Fold Change P - Value Adj. P-Value B R99527 Hs.8162 Hypothetical protein MGC39372 MGC39372 2,17 6,3E-09 5,1E-05 10,2 AA398335 Hs.10414 Kelch domain containing 8A KLHDC8A 2,26 1,2E-08 5,1E-05 9,56 AA441933 Hs.519075 Leiomodin 1 (smooth muscle) LMOD1 2,33 1,3E-08 5,1E-05 9,54 AA630120 Hs.78781 Vascular endothelial growth factor B VEGFB 1,24 1,1E-07 2,9E-04 7,59 R07846 Data not found 3,71 1,2E-07 2,9E-04 7,49 W92795 Hs.434386 Hypothetical protein LOC201229 LOC201229 1,55 2,0E-07 4,0E-04 7,03 AA454564 Hs.323396 Family with sequence similarity 54, member B FAM54B 1,25 3,0E-07 5,2E-04 6,65 AA775249 Hs.513633 G protein-coupled receptor 56 GPR56 -1,63 4,3E-07 6,4E-04 6,33 AA012822 Hs.713814 Oxysterol bining protein OSBP 1,35 5,3E-07 7,1E-04 6,14 R45592 Hs.655271 Regulating synaptic membrane exocytosis 2 RIMS2 2,51 5,9E-07 7,1E-04 6,04 AA282936 Hs.240 M-phase phosphoprotein 1 MPHOSPH -1,40 8,1E-07 8,9E-04 5,74 N34945 Hs.234898 Acetyl-Coenzyme A carboxylase beta ACACB 0,87 9,7E-07 9,8E-04 5,58 R07322 Hs.464137 Acyl-Coenzyme A oxidase 1, palmitoyl ACOX1 0,82 1,3E-06 1,2E-03 5,35 R77144 Hs.488835 Transmembrane protein 120A TMEM120A 1,55 1,7E-06 1,4E-03 5,07 H68542 Hs.420009 Transcribed locus 1,07 1,7E-06 1,4E-03 5,06 AA410184 Hs.696454 PBX/knotted 1 homeobox 2 PKNOX2 1,78 2,0E-06 -
Aneuploidy: Using Genetic Instability to Preserve a Haploid Genome?
Health Science Campus FINAL APPROVAL OF DISSERTATION Doctor of Philosophy in Biomedical Science (Cancer Biology) Aneuploidy: Using genetic instability to preserve a haploid genome? Submitted by: Ramona Ramdath In partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biomedical Science Examination Committee Signature/Date Major Advisor: David Allison, M.D., Ph.D. Academic James Trempe, Ph.D. Advisory Committee: David Giovanucci, Ph.D. Randall Ruch, Ph.D. Ronald Mellgren, Ph.D. Senior Associate Dean College of Graduate Studies Michael S. Bisesi, Ph.D. Date of Defense: April 10, 2009 Aneuploidy: Using genetic instability to preserve a haploid genome? Ramona Ramdath University of Toledo, Health Science Campus 2009 Dedication I dedicate this dissertation to my grandfather who died of lung cancer two years ago, but who always instilled in us the value and importance of education. And to my mom and sister, both of whom have been pillars of support and stimulating conversations. To my sister, Rehanna, especially- I hope this inspires you to achieve all that you want to in life, academically and otherwise. ii Acknowledgements As we go through these academic journeys, there are so many along the way that make an impact not only on our work, but on our lives as well, and I would like to say a heartfelt thank you to all of those people: My Committee members- Dr. James Trempe, Dr. David Giovanucchi, Dr. Ronald Mellgren and Dr. Randall Ruch for their guidance, suggestions, support and confidence in me. My major advisor- Dr. David Allison, for his constructive criticism and positive reinforcement. -
Lineage-Specific Programming Target Genes Defines Potential for Th1 Temporal Induction Pattern of STAT4
Downloaded from http://www.jimmunol.org/ by guest on October 1, 2021 is online at: average * The Journal of Immunology published online 26 August 2009 from submission to initial decision 4 weeks from acceptance to publication J Immunol http://www.jimmunol.org/content/early/2009/08/26/jimmuno l.0901411 Temporal Induction Pattern of STAT4 Target Genes Defines Potential for Th1 Lineage-Specific Programming Seth R. Good, Vivian T. Thieu, Anubhav N. Mathur, Qing Yu, Gretta L. Stritesky, Norman Yeh, John T. O'Malley, Narayanan B. Perumal and Mark H. Kaplan Submit online. Every submission reviewed by practicing scientists ? is published twice each month by http://jimmunol.org/subscription Submit copyright permission requests at: http://www.aai.org/About/Publications/JI/copyright.html Receive free email-alerts when new articles cite this article. Sign up at: http://jimmunol.org/alerts http://www.jimmunol.org/content/suppl/2009/08/26/jimmunol.090141 1.DC1 Information about subscribing to The JI No Triage! Fast Publication! Rapid Reviews! 30 days* • Why • • Material Permissions Email Alerts Subscription Supplementary The Journal of Immunology The American Association of Immunologists, Inc., 1451 Rockville Pike, Suite 650, Rockville, MD 20852 Copyright © 2009 by The American Association of Immunologists, Inc. All rights reserved. Print ISSN: 0022-1767 Online ISSN: 1550-6606. This information is current as of October 1, 2021. Published August 26, 2009, doi:10.4049/jimmunol.0901411 The Journal of Immunology Temporal Induction Pattern of STAT4 Target Genes Defines Potential for Th1 Lineage-Specific Programming1 Seth R. Good,2* Vivian T. Thieu,2† Anubhav N. Mathur,† Qing Yu,† Gretta L. -
Next Generation Sequencing by Multiple Samples Pooling Reveals
Next generation sequencing of pooled samples reveals new SNRNP200 mutations associated with retinitis pigmentosa Paola Benaglio1, Terri L. McGee2, Leonardo P. Capelli1,3, Shyana Harper2, Eliot L. Berson2 and Carlo Rivolta1 1Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland 2The Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA 3Department of Genetics and Evolutionary Biology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil Correspondence to: Carlo Rivolta Department of Medical Genetics University of Lausanne Rue du Bugnon 27 1005 Lausanne Switzerland; Phone: +41(21) 692-5451 FAX: +41(21) 692-5455 email: [email protected] 1 ABSTRACT The gene SNRNP200 is composed of 45-exons and encodes a protein essential for pre- mRNA splicing, the 200 kDa helicase hBrr2. Despite the fact that complete lack of this protein is incompatible with cell survival, two independent heterozygous mutations in SNRNP200 have recently been found to be associated with the retinal degenerative disease retinitis pigmentosa (RP) in two families from China. In this work the entire 35-Kb SNRNP200 genomic region was analyzed in a cohort of 96 unrelated North American patients with autosomal dominant RP. To carry out this large-scale sequencing project, we performed ultra high-throughput sequencing of pooled, untagged PCR products and verified the presence of the detected DNA changes by Sanger sequencing of individual samples. One of the two previously known mutations (p.S1087L) was identified in 3 patients, and 4 new missense changes (p.R681C, p.R681H, p.V683L, p.Y689C) affecting highly conserved codons were identified in 6 unrelated individuals. -
Open Data for Differential Network Analysis in Glioma
International Journal of Molecular Sciences Article Open Data for Differential Network Analysis in Glioma , Claire Jean-Quartier * y , Fleur Jeanquartier y and Andreas Holzinger Holzinger Group HCI-KDD, Institute for Medical Informatics, Statistics and Documentation, Medical University Graz, Auenbruggerplatz 2/V, 8036 Graz, Austria; [email protected] (F.J.); [email protected] (A.H.) * Correspondence: [email protected] These authors contributed equally to this work. y Received: 27 October 2019; Accepted: 3 January 2020; Published: 15 January 2020 Abstract: The complexity of cancer diseases demands bioinformatic techniques and translational research based on big data and personalized medicine. Open data enables researchers to accelerate cancer studies, save resources and foster collaboration. Several tools and programming approaches are available for analyzing data, including annotation, clustering, comparison and extrapolation, merging, enrichment, functional association and statistics. We exploit openly available data via cancer gene expression analysis, we apply refinement as well as enrichment analysis via gene ontology and conclude with graph-based visualization of involved protein interaction networks as a basis for signaling. The different databases allowed for the construction of huge networks or specified ones consisting of high-confidence interactions only. Several genes associated to glioma were isolated via a network analysis from top hub nodes as well as from an outlier analysis. The latter approach highlights a mitogen-activated protein kinase next to a member of histondeacetylases and a protein phosphatase as genes uncommonly associated with glioma. Cluster analysis from top hub nodes lists several identified glioma-associated gene products to function within protein complexes, including epidermal growth factors as well as cell cycle proteins or RAS proto-oncogenes. -
Distinct Domains of Splicing Factor Prp8 Mediate Different Aspects of Spliceosome Activation
Distinct domains of splicing factor Prp8 mediate different aspects of spliceosome activation Andreas N. Kuhn*, Elizabeth M. Reichl†, and David A. Brow‡ Department of Biomolecular Chemistry, University of Wisconsin Medical School, Madison, WI 53706-1532 Communicated by James E. Dahlberg, University of Wisconsin Medical School, Madison, WI, May 21, 2002 (received for review March 25, 2002) Prp8 is the largest and most highly conserved protein in the splicing. Although Prp8 is two-thirds identical between yeast and spliceosome yet its mechanism of function is poorly understood. humans (21), it contains no recognizable structural motifs. To Our previous studies implicate Prp8 in control of spliceosome define domains important for the function of Prp8 in catalytic activation for the first catalytic step of splicing, because substitu- activation for the first transesterification reaction, we isolated tions in five distinct regions (a–e) of Prp8 suppress a cold-sensitive over 40 additional single amino acid substitutions in Prp8 that block to activation caused by a mutation in U4 RNA. Catalytic suppress U4-cs1 (11), here collectively called prp8-cat mutations, activation of the spliceosome is thought to require unwinding of because of their positive effect on catalytic activation. These the U1 RNA͞5 splice site and U4͞U6 RNA helices by the Prp28 and mutations cluster in five regions named a–e (see Fig. 4) and are Prp44͞Brr2 DExD͞H-box helicases, respectively. Here we show that distinct from mutations in Prp8 that suppress defects in the mutations in regions a, d, and e of Prp8 exhibit allele-specific second transesterification reaction. genetic interactions with mutations in Prp28, Prp44͞Brr2, and U6 We hypothesized that Prp8 regulates spliceosome activation RNA, respectively. -
The RNA Splicing Response to DNA Damage
Biomolecules 2015, 5, 2935-2977; doi:10.3390/biom5042935 OPEN ACCESS biomolecules ISSN 2218-273X www.mdpi.com/journal/biomolecules/ Review The RNA Splicing Response to DNA Damage Lulzim Shkreta and Benoit Chabot * Département de Microbiologie et d’Infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada; E-Mail: [email protected] * Author to whom correspondence should be addressed; E-Mail: [email protected]; Tel.: +1-819-821-8000 (ext. 75321); Fax: +1-819-820-6831. Academic Editors: Wolf-Dietrich Heyer, Thomas Helleday and Fumio Hanaoka Received: 12 August 2015 / Accepted: 16 October 2015 / Published: 29 October 2015 Abstract: The number of factors known to participate in the DNA damage response (DDR) has expanded considerably in recent years to include splicing and alternative splicing factors. While the binding of splicing proteins and ribonucleoprotein complexes to nascent transcripts prevents genomic instability by deterring the formation of RNA/DNA duplexes, splicing factors are also recruited to, or removed from, sites of DNA damage. The first steps of the DDR promote the post-translational modification of splicing factors to affect their localization and activity, while more downstream DDR events alter their expression. Although descriptions of molecular mechanisms remain limited, an emerging trend is that DNA damage disrupts the coupling of constitutive and alternative splicing with the transcription of genes involved in DNA repair, cell-cycle control and apoptosis. A better understanding of how changes in splice site selection are integrated into the DDR may provide new avenues to combat cancer and delay aging. -
Group II Intron Rnps and Reverse Transcriptases: from Retroelements to Research Tools
Downloaded from http://cshperspectives.cshlp.org/ on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Group II Intron RNPs and Reverse Transcriptases: From Retroelements to Research Tools Marlene Belfort1 and Alan M. Lambowitz2 1Department of Biological Sciences and RNA Institute, University at Albany, State University of New York, Albany, New York 12222 2Institute for Cellular and Molecular Biology and Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712 Correspondence: [email protected]; [email protected] SUMMARY Group II introns, self-splicing retrotransposons, serve as both targets of investigation into their structure, splicing, and retromobility and a source of tools for genome editing and RNA anal- ysis. Here, we describe the first cryo-electron microscopy (cryo-EM) structure determination, at 3.8–4.5 Å, of a group II intron ribozyme complexed with its encoded protein, containing a reverse transcriptase (RT), required for RNA splicing and retromobility. We also describe a method called RIG-seq using a retrotransposon indicator gene for high-throughput integration profiling of group II introns and other retrotransposons. Targetrons, RNA-guided gene targeting agents widely used for bacterial genome engineering, are described next. Finally, we detail thermostable group II intron RTs, which synthesize cDNAs with high accuracy and processiv- ity, for use in various RNA-seq applications and relate their properties to a 3.0-Å crystal structure of the protein poised for reverse transcription. Biological insights from these group II intron revelations are discussed. Outline 1 Introduction 5 Technique 4. RTs with novel enzymatic properties as potent research tools 2 Technique 1. -
Structural Studies of the Spliceosome: Zooming Into the Heart Of
Available online at www.sciencedirect.com ScienceDirect Structural studies of the spliceosome: zooming into the heart of the machine Wojciech P Galej, Thi Hoang Duong Nguyen, Andrew J Newman and Kiyoshi Nagai Spliceosomes are large, dynamic ribonucleoprotein complexes canonical subunits: U1, U2, U4, U5 and U6 small nuclear that catalyse the removal of introns from messenger RNA ribonucleoprotein particles (snRNPs) and various other precursors via a two-step splicing reaction. The recent crystal non-snRNP factors [2]. The assembly process begins with 0 0 structure of Prp8 has revealed Reverse Transcriptase-like, the recognition of the 5 splice site (5 SS) and the branch Linker and Endonuclease-like domains. The intron branch- point sequence (BP) by U1 and U2 snRNPs, respectively, point cross-link with the Linker domain of Prp8 in active and further recruitment of the U4/U6.U5 tri-snRNP leads 0 0 spliceosomes and together with suppressors of 5 and 3 splice to the formation of the pre-catalytic complex B. A major site mutations this unambiguously locates the active site cavity. remodeling event catalyzed by the two DExD/H box Structural and mechanistic similarities with group II self- helicases Prp28 and Brr2 [3] leads to formation of the splicing introns have encouraged the notion that the catalytically competent complex B*, in which the first spliceosome is at heart a ribozyme, and recently the ligands for step of splicing occurs. two catalytic magnesium ions were identified within U6 snRNA. They position catalytic divalent metal ions in the same way as The enormous complexity and highly dynamic nature of Domain V of group II intron RNA, suggesting that the the spliceosome present a formidable challenge for struc- spliceosome and group II intron use the same catalytic tural and mechanistic studies. -
Analysis of RP2 and RPGR Mutations in Five X-Linked Chinese Families
www.nature.com/scientificreports OPEN Analysis of RP2 and RPGR Mutations in Five X-Linked Chinese Families with Retinitis Pigmentosa Received: 07 December 2016 Jingjing Jiang1,*, Xiaofei Wu2,*, Di Shen3,*, Lijin Dong4, Xiaodong Jiao5, J. Fielding Hejtmancik5 Accepted: 08 February 2017 & Ningdong Li1,2,5 Published: 15 March 2017 Mutations in RP2 and RPGR genes are responsible for the X-linked retinitis pigmentosa (XLRP). In this study, we analyzed the RP2 and RPGR gene mutations in five Han Chinese families with XLRP. An approximately 17Kb large deletion including the exon 4 and exon 5 of RP2 gene was found in an XLRP family. In addition, four frameshift mutations including three novel mutations of c.1059 + 1 G > T, c.2002dupC and c.2236_2237del CT, as well as a previously reported mutation of c.2899delG were detected in the RPGR gene in the other four families. Our study further expands the mutation spectrum of RP2 and RPGR, and will be helpful for further study molecular pathogenesis of XLRP. Retinitis pigmentosa (RP) is a clinically and genetically heterogeneous group of retinal dystrophies characterized by photoreceptor cell degeneration. The prevalence of RP is about 1/4000 ~1/5000 according to studies in dif- ferent populations1. The clinical features comprise night blindness, progressive constriction of visual field with age, and fundus changes including attenuation of the retinal arterioles, bone spicule-like pigment deposits in the mid-peripheral retinal and waxy pallor of the optic disc. Affected individuals often have severely abnormal or non-detectable rod responses in the electroretinograms (ERG) recordings even in the early stage of the disease2. -
The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas Reinhardtii
cells Review The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii Ulrich Kück * and Olga Schmitt Allgemeine und Molekulare Botanik, Faculty for Biology and Biotechnology, Ruhr-Universität Bochum, Universitätsstraße 150, 44780 Bochum, Germany; [email protected] * Correspondence: [email protected]; Tel.: +49-234-32-28951 Abstract: In eukaryotes, RNA trans-splicing is a significant RNA modification process for the end-to- end ligation of exons from separately transcribed primary transcripts to generate mature mRNA. So far, three different categories of RNA trans-splicing have been found in organisms within a diverse range. Here, we review trans-splicing of discontinuous group II introns, which occurs in chloroplasts and mitochondria of lower eukaryotes and plants. We discuss the origin of intronic sequences and the evolutionary relationship between chloroplast ribonucleoprotein complexes and the nuclear spliceosome. Finally, we focus on the ribonucleoprotein supercomplex involved in trans-splicing of chloroplast group II introns from the green alga Chlamydomonas reinhardtii. This complex has been well characterized genetically and biochemically, resulting in a detailed picture of the chloroplast ribonucleoprotein supercomplex. This information contributes substantially to our understanding of the function of RNA-processing machineries and might provide a blueprint for other splicing complexes involved in trans- as well as cis-splicing of organellar intron RNAs. Keywords: group II intron; trans-splicing; ribonucleoprotein complex; chloroplast; Chlamydomonas reinhardtii Citation: Kück, U.; Schmitt, O. The Chloroplast Trans-Splicing RNA–Protein Supercomplex from the Green Alga Chlamydomonas reinhardtii. 1. Introduction Cells 2021, 10, 290. https://doi.org/ One of the unexpected and outstanding discoveries in 20th century biology was the 10.3390/cells10020290 identification of discontinuous eukaryotic genes [1,2].