(Bsc Zoology and Microbiology) Concept of Introns and Exons

Total Page:16

File Type:pdf, Size:1020Kb

(Bsc Zoology and Microbiology) Concept of Introns and Exons Unit-5 Molecular Biology (BSc Zoology and Microbiology) Concept of introns and exons Most of the portion of a gene in higher eukaryotes consists of noncoding DNA that interrupts the relatively short segments of coding DNA. The coding sequences are called exons. The noncoding sequences are called introns. Intron: An intron is a portion of a gene that does not code for amino acids An intron is any nucleotide sequence within a gene which is represented in the primary transcript of the gene, but not present in the final processed form. In other words, Introns are noncoding regions of an RNA transcript which are eliminated by splicing before translation. Sequences that are joined together in the final mature RNA after RNA splicing are exons. Introns are very large chunks of RNA within a messenger RNA molecule that interfere with the code of the exons. And these introns get removed from the RNA molecule to leave a string of exons attached to each other so that the appropriate amino acids can be encoded for. Introns are rare in genes of prokaryotes. #Look carefully at the diagram above, we have already discussed about the modification and processing of eukaryotic RNA. In which 5’ guanine cap and 3’poly A tail is added. So at that time, noncoding regions i.e. introns are removed. We hv done ths already. Ok Exon: The coding sequences are called Exon. An exon is the portion of a gene that codes for amino acids. In the cells of plants and animals, most gene sequences are broken up by one or more DNA sequences called introns. The parts of the gene sequence that are expressed in the protein are called exons, because they are expressed, while the parts of the gene sequence that are not expressed in the protein are called introns. split gene: An split gene (also called interrupted gene) is a gene that contains sections of DNA called exons, which are expressed as RNA and protein, interrupted by sections of DNA called introns, which are not expressed. RNA Splicing and Splicing mechanism: During splicing, introns (Non-coding regions) are removed and exons (Coding Regions) are joined together. Exons are coding sections of an RNA transcript that are translated into protein. Exons can be separated by intervening sections of DNA that do not code for proteins, known as introns. Following transcription, new, immature strands of messenger RNA, called pre-mRNA, may contain both introns and exons. These pre-mRNA molecules go through a modification process in the nucleus called splicing during which the noncoding introns are cut out and only the coding exons remain. Splicing produces a mature messenger RNA molecule that is then translated into a protein. 1. Alternative splicing (AS) is a common posttranscriptional process in eukaryotic organisms, by which multiple distinct functional transcripts are produced from a single gene. Alternative splicing is a process that enables a messenger RNA (mRNA) to direct synthesis of different protein variants (isoforms) that may have different cellular functions or properties. It occurs by rearranging the pattern of intron and exon elements that are joined by splicing to alter the mRNA coding sequence. During RNA splicing exons are either retained in the mRNA or targeted for removal in different combinations to create diverse mRNA from a single pre mRNA. This process is known as alternative RNA splicing 2. Exon Shuffling: Exon shuffling is a molecular mechanism for the formation of new genes. It is a process through which two or more exons from different genes can be brought together to create a new exon-intron structure. .
Recommended publications
  • News & Views Research
    NEWS & VIEWS RESEARCH may exhibit some tissue specificity in humans. Upstream intron Downstream intron a Sibley et al. found that genes with long introns sequence sequence tend to be expressed in the human nervous Precursor RNA system, and they identified recursively spliced 3' Splice 5' Splice RNAs expressed in the human brain6. Duff site site First step et al. detected some selectivity for recursive splicing in the brain in a screen of 20 human tissues (including fetal brain and adult cerebel- Second step lum), but this may partly reflect the difficulty of detecting recursively spliced RNAs in tis- Mature mRNA sues that express such RNAs at low levels. It will be important to determine whether this b RS exon specificity, if real, results from the tendency of recursively spliced genes to be expressed in the brain, or whether cells in the nervous system have factors that promote recursive Competing 5' splice sites First step splicing. Many genes that have long introns, including those that undergo recursive splicing, are linked to neurological diseases and to Second step 9–11 Second step autism . Whether these conditions are sometimes triggered by errors in the multi- step recursive RNA-splicing process will be an exciting avenue for future studies. ■ NMD Heidi Cook-Andersen and Miles F. Wilkinson are in the Department of Reproductive Medicine, University of Figure 1 | Mechanisms of recursive splicing. a, In recursive splicing, long intron sequences of precursor California, San Diego, La Jolla, California, RNA are removed in a stepwise process mediated by juxtaposed internal 3ʹ and 5ʹ splice sites. In the first step, 92093, USA.
    [Show full text]
  • Current Perspectives in Intronic Micro Rnas (Mirnas)
    Journal of Biomedical Science (2006) 13:5–15 5 DOI 10.1007/s11373-005-9036-8 Current perspectives in intronic micro RNAs (miRNAs) Shao-Yao Ying & Shi-Lung Lin Department of Cell & Neurobiology, Keck School of Medicine, BMT-403, University of Southern California, 1333 San Pablo Street, Los Angeles, CA, 90033, USA Received 27 May 2005; accepted 14 September 2005 Ó 2005 National Science Council, Taipei Key words: fine-tuning of gene function, functional/structural genomics, gene expression, genetic regula- tion, intronic microRNA, miRNA biogenesis, miRNA, post-translational modification, regulatory gene Summary MicroRNAs (miRNAs), small single-stranded regulatory RNAs capable of interfering with intracellular messenger RNAs (mRNAs) that contain either complete or partial complementarity, are useful for the design of new therapies against cancer polymorphism and viral mutation. Numerous miRNAs have been reported to induce RNA interference (RNAi), a post-transcriptional gene silencing mechanism. Intronic miRNAs, derived from introns by RNA splicing and Dicer processing, can interfere with intracellular mRNAs to silence that gene expression. The intronic miRNAs differ uniquely from previously described intergenic miRNAs in the requirement of type II RNA polymerases (Pol-II) and spliceosomal components for its biogenesis. Several kinds of intronic miRNAs have been identified in Caenorhabditis elegans, mouse and human cells; however, neither their function nor application has been reported. To this day, the computer searching program for miRNA seldom include the intronic portion of protein-coding RNAs. The functional significance of artificially generated intronic miRNAs has been successfully ascertained in several biological systems such as zebrafishes, chicken embryos and adult mice, indicating the evolutionary pres- ervation of this gene regulation system in vivo.
    [Show full text]
  • RNA Splice Sites Classification Using Convolutional Neural Network Models
    RNA Splice Sites Classification Using Convolutional Neural Network Models Thanyathorn Thanapattheerakul Worrawat Engchuan Daniele Merico School of Information Technology, The Centre for Applied Genomics, Molecular Diagnostics, King Mongkut’s University of Genetics and Genome Biology, The Deep Genomics, Technology Thonburi, Hospital for Sick Children, Toronto, Ontario, Canada Bangkok, Thailand Toronto, Ontario, Canada [email protected] [email protected] [email protected] Narumol Doungpan Kiyota Hashimoto Jonathan H. Chan Faculty of Engineering, Faculty of Technology and School of Information Technology, King Mongkut’s University of Environment, King Mongkut’s University of Technology Thonburi, Prince of Songkla University, Technology Thonburi, Bangkok, Thailand Phuket, Thailand Bangkok, Thailand [email protected] [email protected] [email protected] Abstract—RNA splicing refers to the elimination of non- completely make it loss of function. The alternative splicing coding region on transcribed pre-messenger ribonucleic acid can produce different functional proteins, which could lead (RNA). Identifying splicing site is an essential step which can to causing abnormal states in human [3]. be used to gain novel insights of alternative splicing as well as Many studies have proposed models to recognize the splicing defects, potentially cause malfunction of protein splice sites to reveal which splice sites contain a mutation resulting from mutations at splice site. In this work, we that may cause a splicing error. One common method to propose a data preprocessing step applying to RNA sequences recognize binding sites in motif sequences is called Position- and the models leveraging Convolutional Neural Network (CNN). The preprocessing step includes reducing sequence Weight-Matrix (PWM).
    [Show full text]
  • The CTD Role in Cotranscriptional RNA Processing and Surveillance
    CORE Metadata, citation and similar papers at core.ac.uk Provided by Elsevier - Publisher Connector FEBS Letters 582 (2008) 1971–1976 Minireview The CTD role in cotranscriptional RNA processing and surveillance Se´rgio F. de Almeida, Maria Carmo-Fonseca* Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal Received 4 April 2008; revised 13 April 2008; accepted 14 April 2008 Available online 22 April 2008 Edited by Ulrike Kutay proteins specific to each snRNP. The selection of specific splice Abstract In higher eukaryotes, the production of mature mes- senger RNA that exits the nucleus to be translated into protein sites (ss) on a particular pre-mRNA substrate relies on an intri- requires precise and extensive processing of the nascent tran- cate interplay involving the cooperative binding of trans-acting script. The processing steps include 50-end capping, splicing, splicing proteins to cis-acting sequence elements in the pre- and 30-end formation. Pre-mRNA processing is coupled to tran- mRNA. In mammals, an intron is defined by four short and scription by mechanisms that are not well understood but involve poorly conserved consensus sequences: the exon–intron junc- the carboxyl-terminal domain (CTD) of the largest subunit of tions (50ss and 30ss); the branch point sequence; and the poly- RNA polymerase II. This review focuses on recent findings that pyrimidine tract (Table 1). These sequences are recognized by provide novel insight into the role of the CTD in promoting RNA base pairing with the spliceosomal snRNAs (Fig. 1). In addi- processing and surveillance. tion, both exons and introns contain weak binding sites for a Ó 2008 Federation of European Biochemical Societies.
    [Show full text]
  • Chapter 19: RNA Splicing and Processing
    Chapter 19: RNA Splicing and Processing Chapter Opener: © Laguna Design/Getty Images. CHAPTER OUTLINE 19.1 Introduction 19.2 The 5′ End of Eukaryotic mRNA Is Capped 19.3 Nuclear Splice Sites Are Short Sequences 19.4 Splice Sites Are Read in Pairs 19.5 Pre-mRNA Splicing Proceeds Through a Lariat 19.6 snRNAs Are Required for Splicing 19.7 Commitment of Pre-mRNA to the Splicing Pathway booksmedicos.org 19.8 The Spliceosome Assembly Pathway 19.9 An Alternative Spliceosome Uses Different snRNPs to Process the Minor Class of Introns 19.10 Pre-mRNA Splicing Likely Shares the Mechanism with Group II Autocatalytic Introns 19.11 Splicing Is Temporally and Functionally Coupled with Multiple Steps in Gene Expression 19.12 Alternative Splicing Is a Rule, Rather Than an Exception, in Multicellular Eukaryotes 19.13 Splicing Can Be Regulated by Exonic and Intronic Splicing Enhancers and Silencers 19.14 trans-Splicing Reactions Use Small RNAs 19.15 The 3′ Ends of mRNAs Are Generated by Cleavage and Polyadenylation 19.16 3′ mRNA End Processing Is Critical for Termination of Transcription 19.17 The 3′ End Formation of Histone mRNA Requires U7 snRNA 19.18 tRNA Splicing Involves Cutting and Rejoining in Separate Reactions 19.19 The Unfolded Protein Response Is Related to tRNA Splicing 19.20 Production of rRNA Requires Cleavage Events and Involves Small RNAs 19.1 Introduction booksmedicos.org RNA is a central player in gene expression. It was first characterized as an intermediate in protein synthesis, but since then many other RNAs that play structural or functional roles at various stages of gene expression have been discovered.
    [Show full text]
  • Glossary of Terms Note: Words in Bold in a Definition Indicate Terms Also Defined in This Glossary
    Glossary of Terms Note: Words in bold in a definition indicate terms also defined in this Glossary Term Definition “3 prime”; Refers to carbon 3 of the nucleic acid sugar component (either ribose in RNA or deoxyribose in DNA) to which additional nucleotides may be added by 3' polymerase, often used to refer to that end of a single-stranded DNA or RNA molecule where the 3' carbon retains its hydroxyl group (-OH) and no further nucleotides are bonded. “5 prime”; Refers to carbon 5 of the nucleic acid sugar component (either ribose in RNA or deoxyribose in DNA), to which the triphosphate is attached in a nucleotide 5' triphosphate, often used to refer to that end of a single-stranded DNA or RNA molecule where the 5' carbon's phosphate group(s) is/are unattached to a preceding nucleotide. The inclusion or exclusion of certain exons in the splicing reactions that determine the sequences included in the final mRNA product. This mechanism is utilized to generate a series of closely related protein isoforms, which differ by the inclusion alternative splicing or exclusion of the particular protein regions encoded by those exons. Alternative splicing is directed by RNA-binding proteins that may block, or stimulate, utilization of a particular splice site. The basic building block of proteins, a small molecule with a -C-C- core, an amine group (-NH2) at one end and a carboxylic acid group (-COOH) at the other end. The amino acid general structure can be represented as NH2-CHR-COOH, where R can be any of 20 different functional groups of acidic, basic, or nonpolar character.
    [Show full text]
  • Protein-Synthesis.Pdf
    Protein Synthesis Contents Introduction ........................................................................................................................ 1 DNA Transcription ............................................................................................................... 1 The Primary Transcript ........................................................................................................ 4 Translation .......................................................................................................................... 7 Protein Structure............................................................................................................... 11 References ........................................................................................................................ 11 Resources .......................................................................................................................... 11 Introduction The genetic message carried on the DNA molecule is a code. This code is ultimately translated into a sequence of amino acids that, when complete, becomes a protein. Proteins carry out the “business” of the cell. Some proteins are used as structural components of cells, some are used to transport other molecules, still others are charged with directing chemical reactions. The latter class of proteins is the enzymes. Regardless of the role played by a protein in the cell one aspect is the same, they are all encoded in the base sequences of DNA. The path from DNA sequence to protein
    [Show full text]
  • 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].
    [Show full text]
  • Alternatively Spliced Genes
    1 Alternatively Spliced Genes Jane Y. Wu1,2,LiyaYuan1 and Necat Havlioglu1 1Washington University School of Medicine, St. Louis, MO, USA 2John F. Kennedy Center for Research on Human Development, Vanderbilt University Medical Center, Nashville, TN, USA 1 Pre-mRNA Splicing and Splicing Machinery 3 1.1 Splicing Machinery: Spliceosome 3 1.2 Splicing Signals 4 1.3 Spliceosomal UsnRNP Biogenesis 12 1.4 Spliceosome Assembly 13 1.5 Biochemical Mechanisms of pre-mRNA Splicing 17 2 Alternative pre-mRNA Splicing 17 2.1 Alternative Splicing and its Role in Regulating Gene Activities and Generating Genetic Diversity 17 2.1.1 Different Patterns of Alternative Splicing 17 2.1.2 Alternative Splicing and Genetic Diversity 18 2.2 Mechanisms Underlying Alternative Splicing Regulation 19 2.2.1 Splicing Signals and Splicing Regulatory Elements 20 2.2.2 Trans-acting Splicing Regulators 23 2.3 Tissue-specific and Developmentally Regulated Alternative Splicing 26 2.4 Regulation of Alternative Splicing in Response to Extracellular Stimuli 27 3 Pre-mRNA Splicing and Human Diseases 28 3.1 Splicing Defects in Human Diseases 28 3.2 Molecular Mechanisms Underlying Splicing Defects Associated with Disease 33 4 Perspectives on Diagnosis and Treatment of Diseases Caused by pre-mRNA Splicing Defects 36 4.1 Diagnosis of Human Diseases Caused by Splicing Defects 36 2 Alternatively Spliced Genes 4.2 Potential Therapeutic Approaches 37 4.2.1 Oligonucleotide-based Approaches: Antisense, RNAi, and Chimeric Molecules 37 4.2.2 Ribozymes 37 4.2.3 SMaRT 38 4.2.4 Chemical Compounds 38 5 Concluding Remarks 38 Acknowledgment 39 Bibliography 39 Books and Reviews 39 Keywords Pre-mRNA Nascent transcripts that are precursors of mature messenger RNAs.
    [Show full text]
  • Spliceosomal Pre-Mrna Splicing Methods and Protocols M ETHODS in MOLECULAR BIOLOGY
    Methods in Molecular Biology 1126 Klemens J. Hertel Editor Spliceosomal Pre-mRNA Splicing Methods and Protocols M ETHODS IN MOLECULAR BIOLOGY Series Editor John M. Walker School of Life Sciences University of Hertfordshire Hat fi eld, Hertfordshire, AL10 9AB, UK For further volumes: http://www.springer.com/series/7651 Spliceosomal Pre-mRNA Splicing Methods and Protocols Edited by Klemens J. Hertel Department of Microbiology & Molecular Genetics, University of California, Irvine, CA, USA Editor Klemens J. Hertel Department of Microbiology & Molecular Genetics University of California Irvine , CA , USA ISSN 1064-3745 ISSN 1940-6029 (electronic) ISBN 978-1-62703-979-6 ISBN 978-1-62703-980-2 (eBook) DOI 10.1007/978-1-62703-980-2 Springer New York Heidelberg Dordrecht London Library of Congress Control Number: 2014931088 © Springer Science+Business Media, LLC 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifi cally for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer.
    [Show full text]
  • The Role of Histone Modifications in the Regulation of Alternative Splicing During Epithelial-To-Mesenchymal Transition Alexandre Segelle
    The role of histone modifications in the regulation of alternative splicing during epithelial-to-mesenchymal transition Alexandre Segelle To cite this version: Alexandre Segelle. The role of histone modifications in the regulation of alternative splicing during epithelial-to-mesenchymal transition. Agricultural sciences. Université Montpellier, 2020. English. NNT : 2020MONTT017. tel-03137009 HAL Id: tel-03137009 https://tel.archives-ouvertes.fr/tel-03137009 Submitted on 10 Feb 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THÈSE POUR OBTENIR LE GRADE DE DOCTEUR DE L’UNIVERSITÉ DE M ONTPELLIER En Biologie Moléculaire et Cellulaire École doctorale Sciences Chimiques et Biologiques pour la Santé (ED CBS2 168) Unité de recherche UMR9002 CNRS-UM – Institut de Génétique Humaine (IGH) The role of histone modifications in the regulation of alternative splicing during the epithelial-to-mesenchymal transition Présentée par Alexandre Segelle Le 28 Septembre 2020 Sous la direction de Reini Fernandez de Luco Devant le jury composé de Anne-Marie MARTINEZ,
    [Show full text]
  • Sequential Splicing of a Group II Twintron in the Marine Cyanobacterium Trichodesmium Received: 02 July 2015 Accepted: 20 October 2015 Ulrike Pfreundt & Wolfgang R
    www.nature.com/scientificreports OPEN Sequential splicing of a group II twintron in the marine cyanobacterium Trichodesmium Received: 02 July 2015 Accepted: 20 October 2015 Ulrike Pfreundt & Wolfgang R. Hess Published: 18 November 2015 The marine cyanobacterium Trichodesmium is unusual in its genomic architecture as 40% of the genome is occupied by non-coding DNA. Although the majority of it is transcribed into RNA, it is not well understood why such a large non-coding genome fraction is maintained. Mobile genetic elements can contribute to genome expansion. Many bacteria harbor introns whereas twintrons, introns-in-introns, are rare and not known to interrupt protein-coding genes in bacteria. Here we show the sequential in vivo splicing of a 5400 nt long group II twintron interrupting a highly conserved gene that is associated with RNase HI in some cyanobacteria, but free-standing in others, including Trichodesmium erythraeum. We show that twintron splicing results in a putatively functional mRNA. The full genetic arrangement was found conserved in two geospatially distinct metagenomic datasets supporting its functional relevance. We further show that splicing of the inner intron yields the free intron as a true circle. This reaction requires the spliced exon reopening (SER) reaction to provide a free 5′ exon. The fact that Trichodesmium harbors a functional twintron fits in well with the high intron load of these genomes, and suggests peculiarities in its genetic machinery permitting such arrangements. The diazotrophic Trichodesmium is a tropical marine cyanobacterium of global importance1. Trichodesmium is unusual in its genomic architecture, characterized by the presence of a large non-coding fraction, encompassing about 40% of the total genome length, compared to the cyanobacterial aver- age of only 15%2,3.
    [Show full text]