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Xu B, Meng Y, Jin Y. RNA structures in alternative splicing and back-splicing. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1626. [PMID: 32929887 DOI: 10.1002/wrna.1626] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/14/2020] [Accepted: 08/22/2020] [Indexed: 12/12/2022]
Abstract
Alternative splicing greatly expands the transcriptomic and proteomic diversities related to physiological and developmental processes in higher eukaryotes. Splicing of long noncoding RNAs, and back- and trans- splicing further expanded the regulatory repertoire of alternative splicing. RNA structures were shown to play an important role in regulating alternative splicing and back-splicing. Application of novel sequencing technologies made it possible to identify genome-wide RNA structures and interaction networks, which might provide new insights into RNA splicing regulation in vitro to in vivo. The emerging transcription-folding-splicing paradigm is changing our understanding of RNA alternative splicing regulation. Here, we review the insights into the roles and mechanisms of RNA structures in alternative splicing and back-splicing, as well as how disruption of these structures affects alternative splicing and then leads to human diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.
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Affiliation(s)
- Bingbing Xu
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
| | - Yijun Meng
- College of Life and Environmental Sciences, Hangzhou Normal University, Zhejiang, Hangzhou, China
| | - Yongfeng Jin
- MOE Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, College of Life Sciences, Zhejiang University, Zhejiang, Hangzhou, China
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2
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Xu B, Shi Y, Wu Y, Meng Y, Jin Y. Role of RNA secondary structures in regulating Dscam alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194381. [DOI: 10.1016/j.bbagrm.2019.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 12/19/2022]
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3
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Haussmann IU, Ustaoglu P, Brauer U, Hemani Y, Dix TC, Soller M. Plasmid-based gap-repair recombineered transgenes reveal a central role for introns in mutually exclusive alternative splicing in Down Syndrome Cell Adhesion Molecule exon 4. Nucleic Acids Res 2019; 47:1389-1403. [PMID: 30541104 PMCID: PMC6379703 DOI: 10.1093/nar/gky1254] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/22/2018] [Accepted: 12/03/2018] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing is a key feature of human genes, yet studying its regulation is often complicated by large introns. The Down Syndrome Cell Adhesion Molecule (Dscam) gene from Drosophila is one of the most complex genes generating vast molecular diversity by mutually exclusive alternative splicing. To resolve how alternative splicing in Dscam is regulated, we first developed plasmid-based UAS reporter genes for the Dscam variable exon 4 cluster and show that its alternative splicing is recapitulated by GAL4-mediated expression in neurons. We then developed gap-repair recombineering to very efficiently manipulate these large reporter plasmids in Escherichia coli using restriction enzymes or sgRNA/Cas9 DNA scission to capitalize on the many benefits of plasmids in phiC31 integrase-mediated transgenesis. Using these novel tools, we show that inclusion of Dscam exon 4 variables differs little in development and individual flies, and is robustly determined by sequences harbored in variable exons. We further show that introns drive selection of both proximal and distal variable exons. Since exon 4 cluster introns lack conserved sequences that could mediate robust long-range base-pairing to bring exons into proximity for splicing, our data argue for a central role of introns in mutually exclusive alternative splicing of Dscam exon 4 cluster.
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Affiliation(s)
- Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.,School of Life Science, CSELS, Coventry University, Coventry CV1 5FB, UK
| | - Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Ulrike Brauer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Yash Hemani
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Thomas C Dix
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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Abstract
Pre-mRNA splicing is a key post-transcriptional regulation process in which introns are excised and exons are ligated together. A novel class of structured intron was recently discovered in fish. Simple expansions of complementary AC and GT dimers at opposite boundaries of an intron were found to form a bridging structure, thereby enforcing correct splice site pairing across the intron. In some fish introns, the RNA structures are strong enough to bypass the need of regulatory protein factors for splicing. Here, we discuss the prevalence and potential functions of highly structured introns. In humans, structured introns usually arise through the co-occurrence of C and G-rich repeats at intron boundaries. We explore the potentially instructive example of the HLA receptor genes. In HLA pre-mRNA, structured introns flank the exons that encode the highly polymorphic β sheet cleft, making the processing of the transcript robust to variants that disrupt splicing factor binding. While selective forces that have shaped HLA receptor are fairly atypical, numerous other highly polymorphic genes that encode receptors contain structured introns. Finally, we discuss how the elevated mutation rate associated with the simple repeats that often compose structured intron can make structured introns themselves rapidly evolving elements.
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Affiliation(s)
- Chien-Ling Lin
- a Molecular Biology, Cell Biology and Biochemistry, Brown University , Providence , RI , USA
| | - Allison J Taggart
- a Molecular Biology, Cell Biology and Biochemistry, Brown University , Providence , RI , USA
| | - William G Fairbrother
- a Molecular Biology, Cell Biology and Biochemistry, Brown University , Providence , RI , USA.,b Center for Computational Molecular Biology, Brown University , Providence , RI , USA.,c Hassenfeld Child Health Innovation Institute of Brown University , Providence , RI , USA
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Yue Y, Meng Y, Ma H, Hou S, Cao G, Hong W, Shi Y, Guo P, Liu B, Shi F, Yang Y, Jin Y. A large family of Dscam genes with tandemly arrayed 5' cassettes in Chelicerata. Nat Commun 2016; 7:11252. [PMID: 27080167 PMCID: PMC4835542 DOI: 10.1038/ncomms11252] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 03/07/2016] [Indexed: 02/04/2023] Open
Abstract
Drosophila Dscam1 (Down Syndrome Cell Adhesion Molecules) and vertebrate clustered protocadherins (Pcdhs) are two classic examples of the extraordinary isoform diversity from a single genomic locus. Dscam1 encodes 38,016 distinct isoforms via mutually exclusive splicing in D. melanogaster, while the vertebrate clustered Pcdhs utilize alternative promoters to generate isoform diversity. Here we reveal a shortened Dscam gene family with tandemly arrayed 5' cassettes in Chelicerata. These cassette repeats generally comprise two or four exons, corresponding to variable Immunoglobulin 7 (Ig7) or Ig7-8 domains of Drosophila Dscam1. Furthermore, extraordinary isoform diversity has been generated through a combination of alternating promoter and alternative splicing. These sDscams have a high sequence similarity with Drosophila Dscam1, and share striking organizational resemblance to the 5' variable regions of vertebrate clustered Pcdhs. Hence, our findings have important implications for understanding the functional similarities between Drosophila Dscam1 and vertebrate Pcdhs, and may provide further mechanistic insights into the regulation of isoform diversity.
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Affiliation(s)
- Yuan Yue
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yijun Meng
- College of Life and Environmental Sciences; Hangzhou Normal University, Hangzhou, Zhejiang ZJ310036, China
| | - Hongru Ma
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Shouqing Hou
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Guozheng Cao
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Weiling Hong
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yang Shi
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Pengjuan Guo
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Baoping Liu
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Feng Shi
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yun Yang
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
| | - Yongfeng Jin
- Institute of Biochemistry, Innovation Center for Signaling Network, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang ZJ310058, China
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Lin CL, Taggart AJ, Lim KH, Cygan KJ, Ferraris L, Creton R, Huang YT, Fairbrother WG. RNA structure replaces the need for U2AF2 in splicing. Genome Res 2016; 26:12-23. [PMID: 26566657 PMCID: PMC4691745 DOI: 10.1101/gr.181008.114] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2014] [Accepted: 11/10/2015] [Indexed: 01/21/2023]
Abstract
RNA secondary structure plays an integral role in catalytic, ribosomal, small nuclear, micro, and transfer RNAs. Discovering a prevalent role for secondary structure in pre-mRNAs has proven more elusive. By utilizing a variety of computational and biochemical approaches, we present evidence for a class of nuclear introns that relies upon secondary structure for correct splicing. These introns are defined by simple repeat expansions of complementary AC and GT dimers that co-occur at opposite boundaries of an intron to form a bridging structure that enforces correct splice site pairing. Remarkably, this class of introns does not require U2AF2, a core component of the spliceosome, for its processing. Phylogenetic analysis suggests that this mechanism was present in the ancestral vertebrate lineage prior to the divergence of tetrapods from teleosts. While largely lost from land dwelling vertebrates, this class of introns is found in 10% of all zebrafish genes.
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Affiliation(s)
- Chien-Ling Lin
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Allison J Taggart
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kian Huat Lim
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Kamil J Cygan
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
| | - Luciana Ferraris
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Robbert Creton
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Yen-Tsung Huang
- Departments of Epidemiology and Biostatistics, Brown University, Providence, Rhode Island 02912, USA
| | - William G Fairbrother
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island 02912, USA; Center for Computational Molecular Biology, Brown University, Providence, Rhode Island 02912, USA
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Brites D, Du Pasquier L. Somatic and Germline Diversification of a Putative Immunoreceptor within One Phylum: Dscam in Arthropods. Results Probl Cell Differ 2015; 57:131-158. [PMID: 26537380 DOI: 10.1007/978-3-319-20819-0_6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Arthropod Dscam, the homologue of the human Down Syndrome cell adhesion molecule, is a receptor used by the nervous and immune systems. Unlike in vertebrates, evolutionary pressure has selected and maintained a vast Dscam diversity of isoforms, known to specifying neuronal identity during the nervous system differentiation. This chapter examines the different modes of Dscam diversification in the context of arthropods' evolution and that of their immune system, where its role is controversial. In the single Dscam gene of insects and crustaceans, mutually exclusive alternative splicing affects three clusters of duplicated exons encoding the variable parts of the receptor. The Dscam gene produces over 10,000 isoforms. In the more basal arthropods such as centipedes, Dscam diversity results from a combination of many germline genes (over 80) with, in about half of those, the possibility of alternative splicing affecting only one exon cluster. In the even more basal arthropods, such as chelicerates, no splicing possibility is detected, but there exist dozens of germline Dscam genes. Compared to controlling the expression of multiple germline genes, the somatic mutually alternative splicing within a single gene may offer a simplified way of expressing a large Dscam repertoire. Expressed by hemocytes, Dscam is considered a phagocytic receptor but is also encountered in solution. More information is necessary about its binding to pathogens, its role in phagocytosis, its possible role in specifying hemocyte identity, its kinetics of expression, and the regulation of its RNA splicing to understand how its diversity is linked to immunity.
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Affiliation(s)
- Daniela Brites
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.
| | - Louis Du Pasquier
- Institute of Zoology and Evolutionary Biology, University of Basel, Vesalgasse 1, 4051, Basel, Switzerland.
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Majeske AJ, Oren M, Sacchi S, Smith LC. Single sea urchin phagocytes express messages of a single sequence from the diverse Sp185/333 gene family in response to bacterial challenge. THE JOURNAL OF IMMUNOLOGY 2014; 193:5678-88. [PMID: 25355922 DOI: 10.4049/jimmunol.1401681] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Immune systems in animals rely on fast and efficient responses to a wide variety of pathogens. The Sp185/333 gene family in the purple sea urchin, Strongylocentrotus purpuratus, consists of an estimated 50 (±10) members per genome that share a basic gene structure but show high sequence diversity, primarily due to the mosaic appearance of short blocks of sequence called elements. The genes show significantly elevated expression in three subpopulations of phagocytes responding to marine bacteria. The encoded Sp185/333 proteins are highly diverse and have central effector functions in the immune system. In this study we report the Sp185/333 gene expression in single sea urchin phagocytes. Sea urchins challenged with heat-killed marine bacteria resulted in a typical increase in coelomocyte concentration within 24 h, which included an increased proportion of phagocytes expressing Sp185/333 proteins. Phagocyte fractions enriched from coelomocytes were used in limiting dilutions to obtain samples of single cells that were evaluated for Sp185/333 gene expression by nested RT-PCR. Amplicon sequences showed identical or nearly identical Sp185/333 amplicon sequences in single phagocytes with matches to six known Sp185/333 element patterns, including both common and rare element patterns. This suggested that single phagocytes show restricted expression from the Sp185/333 gene family and infers a diverse, flexible, and efficient response to pathogens. This type of expression pattern from a family of immune response genes in single cells has not been identified previously in other invertebrates.
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Affiliation(s)
- Audrey J Majeske
- Department of Biological Sciences, George Washington University, Washington, DC 20052
| | - Matan Oren
- Department of Biological Sciences, George Washington University, Washington, DC 20052
| | - Sandro Sacchi
- Department of Biological Sciences, George Washington University, Washington, DC 20052
| | - L Courtney Smith
- Department of Biological Sciences, George Washington University, Washington, DC 20052
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10
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Yang Y, Sun F, Wang X, Yue Y, Wang W, Zhang W, Zhan L, Tian N, shi F, Jin Y. Conservation and regulation of alternative splicing by dynamic inter- and intra-intron base pairings in Lepidoptera 14-3-3z pre-mRNAs. RNA Biol 2014; 9:691-700. [DOI: 10.4161/rna.20205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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Pervouchine DD. IRBIS: a systematic search for conserved complementarity. RNA (NEW YORK, N.Y.) 2014; 20:1519-31. [PMID: 25142064 PMCID: PMC4174434 DOI: 10.1261/rna.045088.114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/26/2014] [Indexed: 05/28/2023]
Abstract
IRBIS is a computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences. Unlike other methods, it follows the "first-fold-then-align" principle in which all possible combinations of complementary k-mers are searched for simultaneous conservation. The novel trimming procedure reduces the size of the search space and improves the performance to the point where large-scale analyses of intra- and intermolecular RNA-RNA interactions become possible. In this article, I provide a rigorous description of the method, benchmarking on simulated and real data, and a set of stringent predictions of intramolecular RNA structure in placental mammals, drosophilids, and nematodes. I discuss two particular cases of long-range RNA structures that are likely to have a causal effect on single- and multiple-exon skipping, one in the mammalian gene Dystonin and the other in the insect gene Ca-α1D. In Dystonin, one of the two complementary boxes contains a binding site of Rbfox protein similar to one recently described in Enah gene. I also report that snoRNAs and long noncoding RNAs (lncRNAs) have a high capacity of base-pairing to introns of protein-coding genes, suggesting possible involvement of these transcripts in splicing regulation. I also find that conserved sequences that occur equally likely on both strands of DNA (e.g., transcription factor binding sites) contribute strongly to the false-discovery rate and, therefore, would confound every such analysis. IRBIS is an open-source software that is available at http://genome.crg.es/~dmitri/irbis/.
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Affiliation(s)
- Dmitri D Pervouchine
- Centre for Genomic Regulation and UPF, Barcelona 08003, Spain Faculty of Bioengineering and Bioinformatics, Moscow State University, 119992 Moscow, Russia
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12
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Abstract
Post-transcriptional pre-mRNA splicing has emerged as a critical step in the gene expression cascade greatly influencing diversification and spatiotemporal control of the proteome in many developmental processes. The percentage of genes targeted by alternative splicing (AS) is shown to be over 95% in humans and 60% in Drosophila. Therefore, it is evident that deregulation of this process underlies many genetic diseases. Among all tissues, the brain shows the highest transcriptome diversity, which is not surprising in view of the complex inter- and intracellular networks underlying the development of this organ. Reports of isoforms known to function at different steps during Drosophila nervous system development are rapidly increasing as well as knowledge on their regulation and function, highlighting the role of AS during neuronal development in Drosophila.
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Affiliation(s)
- Carmen Mohr
- Institute of Human Genetics, University Medical Center Freiburg , Freiburg , Germany
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Lovci MT, Ghanem D, Marr H, Arnold J, Gee S, Parra M, Liang TY, Stark TJ, Gehman LT, Hoon S, Massirer KB, Pratt GA, Black DL, Gray JW, Conboy JG, Yeo GW. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol 2013; 20:1434-42. [PMID: 24213538 DOI: 10.1038/nsmb.2699] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 09/19/2013] [Indexed: 02/08/2023]
Abstract
Alternative splicing (AS) enables programmed diversity of gene expression across tissues and development. We show here that binding in distal intronic regions (>500 nucleotides (nt) from any exon) by Rbfox splicing factors important in development is extensive and is an active mode of splicing regulation. Similarly to exon-proximal sites, distal sites contain evolutionarily conserved GCATG sequences and are associated with AS activation and repression upon modulation of Rbfox abundance in human and mouse experimental systems. As a proof of principle, we validated the activity of two specific Rbfox enhancers in KIF21A and ENAH distal introns and showed that a conserved long-range RNA-RNA base-pairing interaction (an RNA bridge) is necessary for Rbfox-mediated exon inclusion in the ENAH gene. Thus we demonstrate a previously unknown RNA-mediated mechanism for AS control by distally bound RNA-binding proteins.
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Affiliation(s)
- Michael T Lovci
- 1] Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA. [2] Stem Cell Program, University of California, San Diego, La Jolla, California, USA. [3] Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, USA
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Munding EM, Shiue L, Katzman S, Donohue JP, Ares M. Competition between pre-mRNAs for the splicing machinery drives global regulation of splicing. Mol Cell 2013; 51:338-48. [PMID: 23891561 PMCID: PMC3771316 DOI: 10.1016/j.molcel.2013.06.012] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 05/18/2013] [Accepted: 06/18/2013] [Indexed: 01/08/2023]
Abstract
During meiosis in yeast, global splicing efficiency increases and then decreases. Here we provide evidence that splicing improves due to reduced competition for the splicing machinery. The timing of this regulation corresponds to repression and reactivation of ribosomal protein genes (RPGs) during meiosis. In vegetative cells, RPG repression by rapamycin treatment also increases splicing efficiency. Downregulation of the RPG-dedicated transcription factor gene IFH1 genetically suppresses two spliceosome mutations, prp11-1 and prp4-1, and globally restores splicing efficiency in prp4-1 cells. We conclude that the splicing apparatus is limiting and that pre-messenger RNAs compete. Splicing efficiency of a pre-mRNA therefore depends not just on its own concentration and affinity for limiting splicing factor(s), but also on those of competing pre-mRNAs. Competition between RNAs for limiting processing factors appears to be a general condition in eukaryotes for a variety of posttranscriptional control mechanisms including microRNA (miRNA) repression, polyadenylation, and splicing.
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Affiliation(s)
- Elizabeth M. Munding
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Lily Shiue
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Sol Katzman
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - John Paul Donohue
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
| | - Manuel Ares
- Center for Molecular Biology of RNA, Department of Molecular, Cell & Developmental Biology, Sinsheimer Laboratories, University of California, Santa Cruz, Santa Cruz, CA 95064
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15
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Brites D, Brena C, Ebert D, Du Pasquier L. More than one way to produce protein diversity: duplication and limited alternative splicing of an adhesion molecule gene in basal arthropods. Evolution 2013; 67:2999-3011. [PMID: 24094349 DOI: 10.1111/evo.12179] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2013] [Accepted: 05/27/2013] [Indexed: 01/12/2023]
Abstract
Exon duplication and alternative splicing evolved multiple times in metazoa and are of overall importance in shaping genomes and allowing organisms to produce many fold more proteins than there are genes in the genome. No other example is as striking as the one of the Down syndrome cell adhesion molecule (Dscam) of insects and crustaceans (pancrustaceans) involved in the nervous system differentiation and in the immune system. To elucidate the evolutionary history of this extraordinary gene, we investigated Dscam homologs in two basal arthropods, the myriapod Strigamia maritima and the chelicerate Ixodes scapularis. In both, Dscam diversified extensively by whole gene duplications resulting in multigene expansions. Within some of the S. maritima genes, exons coding for one of the immunoglobulin domains (Ig7) duplicated and are mutually exclusively alternatively spliced. Our results suggest that Dscam diversification was selected independently in chelicerates, myriapods, and pancrustaceans and that the usage of Dscam diversity by immune cells evolved for the first time in basal arthropods. We propose an evolutionary scenario for the appearance of the highly variable Dscam gene of pancrustaceans, adding to the understanding of how alternative splicing, exon, and gene duplication contribute to create molecular diversity associated with potentially new cellular functions.
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Affiliation(s)
- Daniela Brites
- Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland; Swiss Tropical and Public Health Institute, Socinstrasse 57, PO Box 4002, Basel.
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Ultra-deep profiling of alternatively spliced Drosophila Dscam isoforms by circularization-assisted multi-segment sequencing. EMBO J 2013; 32:2029-38. [PMID: 23792425 DOI: 10.1038/emboj.2013.144] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 05/27/2013] [Indexed: 12/30/2022] Open
Abstract
The Drosophila melanogaster gene Dscam (Down syndrome cell adhesion molecule) can generate thousands of different ectodomains via mutual exclusive splicing of three large exon clusters. The isoform diversity plays a profound role in both neuronal wiring and pathogen recognition. However, the isoform expression pattern at the global level remained unexplored. Here, we developed a novel method that allows for direct quantification of the alternatively spliced exon combinations from over hundreds of millions of Dscam transcripts in one sequencing run. With unprecedented sequencing depth, we detected a total of 18,496 isoforms, out of 19,008 theoretically possible combinations. Importantly, we demonstrated that alternative splicing between different clusters is independent. Moreover, the isoforms were expressed across a broad dynamic range, with significant bias in cell/tissue and developmental stage-specific patterns. Hitherto underappreciated, such bias can dramatically reduce the ability of neurons to display unique surface receptor codes. Therefore, the seemingly excessive diversity encoded in the Dscam locus might nevertheless be essential for a robust self and non-self discrimination in neurons.
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Wang X, Li G, Yang Y, Wang W, Zhang W, Pan H, Zhang P, Yue Y, Lin H, Liu B, Bi J, Shi F, Mao J, Meng Y, Zhan L, Jin Y. An RNA architectural locus control region involved in Dscam mutually exclusive splicing. Nat Commun 2013; 3:1255. [PMID: 23212384 PMCID: PMC3535345 DOI: 10.1038/ncomms2269] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/07/2012] [Indexed: 11/25/2022] Open
Abstract
The most striking example of alternative splicing in a Drosophila melanogaster gene is observed in the Down syndrome cell adhesion molecule, which can generate 38,016 different isoforms. RNA secondary structures are thought to direct the mutually exclusive splicing of Down syndrome cell adhesion molecule, but the underlying mechanisms are poorly understood. Here we describe a locus control region that can activate the exon 6 cluster and specifically allow for the selection of only one exon variant in combination with docking site selector sequence interactions. Combining comparative genomic studies of 63 species with mutational analysis reveals that intricate, tandem multi-‘subunit’ RNA structures within the locus control region activate species-appropriate alternative variants. Importantly, strengthening the weak splice sites of the target exon can remove the locus control region dependence. Our findings not only provide a locus control region-dependent mechanism for mutually exclusive splicing, but also suggest a model for the evolution of increased complexity in a long-range RNA molecular machine. Alternative splicing at the Drosophila Down syndrome cell adhesion molecule gene generates 38,016 isoforms, and underlies self-avoidance of growing neurons. Wang et al. identify a structure in the DSCAM mRNA that ensures mutually exclusive splicing and observe expansion of the structure with increasing number of exons during arthropod evolution.
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Affiliation(s)
- Xuebin Wang
- Institute of Biochemistry, College of Life Sciences, Zhejiang University (Zijingang Campus), Hangzhou, Zhejiang ZJ310058, China
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18
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Coelho Ribeiro MDL, Espinosa J, Islam S, Martinez O, Thanki JJ, Mazariegos S, Nguyen T, Larina M, Xue B, Uversky VN. Malleable ribonucleoprotein machine: protein intrinsic disorder in the Saccharomyces cerevisiae spliceosome. PeerJ 2013; 1:e2. [PMID: 23638354 PMCID: PMC3628832 DOI: 10.7717/peerj.2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 12/01/2012] [Indexed: 12/29/2022] Open
Abstract
Recent studies revealed that a significant fraction of any given proteome is presented by proteins that do not have unique 3D structures as a whole or in significant parts. These intrinsically disordered proteins possess dramatic structural and functional variability, being especially enriched in signaling and regulatory functions since their lack of fixed structure defines their ability to be involved in interaction with several proteins and allows them to be re-used in multiple pathways. Among recognized disorder-based protein functions are interactions with nucleic acids and multi-target binding; i.e., the functions ascribed to many spliceosomal proteins. Therefore, the spliceosome, a multimegadalton ribonucleoprotein machine catalyzing the excision of introns from eukaryotic pre-mRNAs, represents an attractive target for the focused analysis of the abundance and functionality of intrinsic disorder in its proteinaceous components. In yeast cells, spliceosome consists of five small nuclear RNAs (U1, U2, U4, U5, and U6) and a range of associated proteins. Some of these proteins constitute cores of the corresponding snRNA-protein complexes known as small nuclear ribonucleoproteins (snRNPs). Other spliceosomal proteins have various auxiliary functions. To gain better understanding of the functional roles of intrinsic disorder, we have studied the prevalence of intrinsically disordered proteins in the yeast spliceosome using a wide array of bioinformatics methods. Our study revealed that similar to the proteins associated with human spliceosomes (Korneta & Bujnicki, 2012), proteins found in the yeast spliceosome are enriched in intrinsic disorder.
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Affiliation(s)
- Maria de Lourdes Coelho Ribeiro
- Cancer Imaging Metabolism, H. Lee Moffitt Cancer Center & Research Institute , United States ; Department of Molecular Medicine, University of South Florida , Tampa, Florida , United States
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19
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Abstract
Alternative splicing of pre-mRNA is a major mechanism to increase protein diversity in higher eukaryotes. Dscam, the Drosophila homologue of human DSCAM (Down's syndrome cell adhesion molecule), generates up to 38016 isoforms through mutually exclusive splicing in four variable exon clusters. This enormous molecular diversity is functionally important for wiring of the nervous system and phagocytosis of invading pathogens. Current models explaining this complex splicing regulation include a default repressed state of the variable exon clusters to prevent the splicing together of adjacent exons, the presence of RNA secondary structures important for the release of one specific variable exon from the repressed state and combinatorial interaction of RNA-binding proteins for choosing a specific exon.
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20
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Shi L, Lee T. Molecular Diversity of Dscam and Self-Recognition. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2012; 739:262-75. [DOI: 10.1007/978-1-4614-1704-0_17] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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21
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Verma A, Sengupta S, Lakhotia SC. DNApol-ϵ gene is indispensable for the survival and growth of Drosophila melanogaster. Genesis 2011; 50:86-101. [PMID: 21898761 DOI: 10.1002/dvg.20791] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Revised: 08/12/2011] [Accepted: 08/14/2011] [Indexed: 11/08/2022]
Abstract
Based on deletion and complementation mapping and DNA sequencing, a new recessive fully penetrant mutation (DNApol-ϵpl10R), causing prolonged larval life and larval/early pupal lethality, is identified as the first mutant allele of the DNApol-ϵ (CG6768) gene of Drosophila melanogaster. A same-sense base pair substitution in exon 1 of the DNApol-ϵ gene is associated with retention of the first intron and significant reduction in DNApol-ϵ transcripts in DNApol-ϵpl10R homozygotes. Homozygous mutant larvae show small imaginal discs with fewer cells and reduced polyteny in salivary glands, presumably because of the compromised DNA polymerase function following exhaustion of the maternal contribution. Extremely small and rare DNApol-ϵpl10R homozygous somatic clones in DNApol-ϵpl10R/+imaginal discs confirm their poor mitotic activity. The DNApol-ϵpl10R homozygotes, like those expressing DNApol-ϵ-RNAi transgene, show high sensitivity to DNA damaging agents. The first mutant allele of the DNApol-ϵ gene will facilitate functional characterization of this enzyme in the genetically tractable Drosophila model.
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Affiliation(s)
- Akanksha Verma
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, India
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22
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Ghosh J, Lun CM, Majeske AJ, Sacchi S, Schrankel CS, Smith LC. Invertebrate immune diversity. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2011; 35:959-974. [PMID: 21182860 DOI: 10.1016/j.dci.2010.12.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2010] [Revised: 12/13/2010] [Accepted: 12/14/2010] [Indexed: 05/30/2023]
Abstract
The arms race between hosts and pathogens (and other non-self) drives the molecular diversification of immune response genes in the host. Over long periods of evolutionary time, many different defense strategies have been employed by a wide variety of invertebrates. We review here penaeidins and crustins in crustaceans, the allorecognition system encoded by fuhc, fester and Uncle fester in a colonial tunicate, Dscam and PGRPs in arthropods, FREPs in snails, VCBPs in protochordates, and the Sp185/333 system in the purple sea urchin. Comparisons among immune systems, including those reviewed here have not identified an immune specific regulatory "genetic toolkit", however, repeatedly identified sequences (or "building materials" on which the tools act) are present in a broad range of immune systems. These include a Toll/TLR system, a primitive complement system, an LPS binding protein, and a RAG core/Transib element. Repeatedly identified domains and motifs that function in immune proteins include NACHT, LRR, Ig, death, TIR, lectin domains, and a thioester motif. In addition, there are repeatedly identified mechanisms (or "construction methods") that generate sequence diversity in genes with immune function. These include genomic instability, duplications and/or deletions of sequences and the generation of clusters of similar genes or exons that appear as families, gene recombination, gene conversion, retrotransposition, alternative splicing, multiple alleles for single copy genes, and RNA editing. These commonly employed "materials and methods" for building and maintaining an effective immune system that might have been part of that ancestral system appear now as a fragmented and likely incomplete set, likely due to the rapid evolutionary change (or loss) of host genes that are under pressure to keep pace with pathogen diversity.
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Affiliation(s)
- Julie Ghosh
- Department of Biological Sciences, George Washington University, Washington, DC, United States
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23
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Mirtrons: microRNA biogenesis via splicing. Biochimie 2011; 93:1897-904. [PMID: 21712066 DOI: 10.1016/j.biochi.2011.06.017] [Citation(s) in RCA: 187] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Accepted: 06/14/2011] [Indexed: 01/08/2023]
Abstract
A well-defined mechanism governs the maturation of most microRNAs (miRNAs) in animals, via stepwise cleavage of precursor hairpin transcripts by the Drosha and Dicer RNase III enzymes. Recently, several alternative miRNA biogenesis pathways were elucidated, the most prominent of which substitutes Drosha cleavage with splicing. Such short hairpin introns are known as mirtrons, and their study has uncovered related pathways that combine splicing with other ribonucleolytic machinery to yield Dicer substrates for miRNA biogenesis. In this review, we consider the mechanisms of splicing-mediated miRNA biogenesis, computational strategies for mirtron discovery, and the evolutionary implications of the existence of multiple miRNA biogenesis pathways. Altogether, the features of mirtron pathways illustrate unexpected flexibility in combining RNA processing pathways, and highlight how multiple functions can be encoded by individual transcripts.
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24
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RNA structure and the mechanisms of alternative splicing. Curr Opin Genet Dev 2011; 21:373-9. [PMID: 21530232 DOI: 10.1016/j.gde.2011.04.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 04/01/2011] [Indexed: 01/11/2023]
Abstract
Alternative splicing is a widespread means of increasing protein diversity and regulating gene expression in eukaryotes. Much progress has been made in understanding the proteins involved in regulating alternative splicing, the sequences they bind to, and how these interactions lead to changes in splicing patterns. However, several recent studies have identified other players involved in regulating alternative splicing. A major theme emerging from these studies is that RNA secondary structures play an under appreciated role in the regulation of alternative splicing. This review provides an overview of the basic aspects of splicing regulation and highlights recent progress in understanding the role of RNA secondary structure in this process.
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25
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Li X, Quon G, Lipshitz HD, Morris Q. Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA (NEW YORK, N.Y.) 2010; 16:1096-107. [PMID: 20418358 PMCID: PMC2874161 DOI: 10.1261/rna.2017210] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
While many RNA-binding proteins (RBPs) bind RNA in a sequence-specific manner, their sequence preferences alone do not distinguish known target RNAs from other potential targets that are coexpressed and contain the same sequence motifs. Recently, the mRNA targets of dozens of RNA-binding proteins have been identified, facilitating a systematic study of the features of target transcripts. Using these data, we demonstrate that calculating the predicted structural accessibility of a putative RBP binding site allows one to significantly improve the accuracy of predicting in vivo binding for the majority of sequence-specific RBPs. In our new in silico approach, accessibility is predicted based solely on the mRNA sequence without consideration of the locations of bound trans-factors; as such, our results suggest a greater than previously anticipated role for intrinsic mRNA secondary structure in determining RBP binding target preference. Target site accessibility aids in predicting target transcripts and the binding sites for RBPs with a range of RNA-binding domains and subcellular functions. Based on this work, we introduce a new motif-finding algorithm that identifies accessible sequence-specific RBP motifs from in vivo binding data.
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Affiliation(s)
- Xiao Li
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1E3, Canada
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26
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Lee C, Kim N, Roy M, Graveley BR. Massive expansions of Dscam splicing diversity via staggered homologous recombination during arthropod evolution. RNA (NEW YORK, N.Y.) 2010; 16:91-105. [PMID: 19934230 PMCID: PMC2802040 DOI: 10.1261/rna.1812710] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2009] [Accepted: 09/15/2009] [Indexed: 05/26/2023]
Abstract
The arthropod Down syndrome cell adhesion molecule (Dscam) gene can generate tens of thousands of protein isoforms via combinatorial splicing of numerous alternative exons encoding immunoglobulin variable domains organized into three clusters referred to as the exon 4, 6, and 9 clusters. Dscam protein diversity is important for nervous system development and immune functions. We have performed extensive phylogenetic analyses of Dscam from 20 arthropods (each containing between 46 and 96 alternative exons) to reconstruct the detailed history of exon duplication and loss events that built this remarkable system over 450 million years of evolution. Whereas the structure of the exon 4 cluster is ancient, the exon 6 and 9 clusters have undergone massive, independent expansions in each insect lineage. An analysis of nearly 2000 duplicated exons enabled detailed reconstruction of the timing, location, and boundaries of these duplication events. These data clearly show that new Dscam exons have arisen continuously throughout arthropod evolution and that this process is still occurring in the exon 6 and 9 clusters. Recently duplicated regions display boundaries corresponding to a single exon and the adjacent intron. The boundaries, homology, location, clustering, and relative frequencies of these duplication events strongly suggest that staggered homologous recombination is the major mechanism by which new Dscam exons evolve. These data provide a remarkably detailed picture of how complex gene structure evolves and reveal the molecular mechanism behind this process.
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Affiliation(s)
- Christopher Lee
- Department of Chemistry and Biochemistry, Center for Computational Biology, Institute for Genomics and Proteomics, Molecular BiologyInstitute, University of California at Los Angeles, Los Angeles, California 90095-1570, USA.
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27
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Warf MB, Berglund JA. Role of RNA structure in regulating pre-mRNA splicing. Trends Biochem Sci 2009; 35:169-78. [PMID: 19959365 DOI: 10.1016/j.tibs.2009.10.004] [Citation(s) in RCA: 217] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 10/16/2009] [Accepted: 10/19/2009] [Indexed: 01/06/2023]
Abstract
Pre-mRNA splicing involves removing non-coding introns from RNA transcripts. It is carried out by the spliceosome, along with other auxiliary factors. In general, research in splicing has focused on the sequences within the pre-mRNA, without considering the structures that these sequences might form. We propose that the role of RNA structure deserves more consideration when thinking about splicing mechanisms. RNA structures can inhibit or aid binding of spliceosomal components to the pre-mRNA, or can increase splicing efficiency by bringing important sequences into close proximity. Recent reports have identified proteins and small molecules that can regulate splicing by modulating RNA structures, thereby expanding our knowledge of the mechanisms used to regulate splicing.
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Affiliation(s)
- M Bryan Warf
- Institute of Molecular Biology, and Department of Chemistry, University of Oregon, Eugene, Oregon 97403, USA
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28
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Raker VA, Mironov AA, Gelfand MS, Pervouchine DD. Modulation of alternative splicing by long-range RNA structures in Drosophila. Nucleic Acids Res 2009; 37:4533-44. [PMID: 19465384 PMCID: PMC2724269 DOI: 10.1093/nar/gkp407] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Accurate and efficient recognition of splice sites during pre-mRNA splicing is essential for proper transcriptome expression. Splice site usage can be modulated by secondary structures, but it is unclear if this type of modulation is commonly used or occurs to a significant degree with secondary structures forming over long distances. Using phlyogenetic comparisons of intronic sequences among 12 Drosophila genomes, we elucidated a group of 202 highly conserved pairs of sequences, each at least nine nucleotides long, capable of forming stable stem structures. This set was highly enriched in alternatively spliced introns and introns with weak acceptor sites and long introns, and most occurred over long distances (>150 nucleotides). Experimentally, we analyzed the splicing of several of these introns using mini-genes in Drosophila S2 cells. Wild-type splicing patterns were changed by mutations that opened the stem structure, and restored by compensatory mutations that re-established the base-pairing potential, demonstrating that these secondary structures were indeed implicated in the splice site choice. Mechanistically, the RNA structures masked splice sites, brought together distant splice sites and/or looped out introns. Thus, base-pairing interactions within introns, even those occurring over long distances, are more frequent modulators of alternative splicing than is currently assumed.
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Affiliation(s)
- Veronica A Raker
- Center for Genomic Regulation (CRG), Dr. Aiguader, 88, 08003 Barcelona, Spain.
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29
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Schmucker D, Chen B. Dscam and DSCAM: complex genes in simple animals, complex animals yet simple genes. Genes Dev 2009; 23:147-56. [DOI: 10.1101/gad.1752909] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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Venables JP, Koh CS, Froehlich U, Lapointe E, Couture S, Inkel L, Bramard A, Paquet ER, Watier V, Durand M, Lucier JF, Gervais-Bird J, Tremblay K, Prinos P, Klinck R, Elela SA, Chabot B. Multiple and specific mRNA processing targets for the major human hnRNP proteins. Mol Cell Biol 2008; 28:6033-43. [PMID: 18644864 PMCID: PMC2547008 DOI: 10.1128/mcb.00726-08] [Citation(s) in RCA: 122] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2008] [Revised: 05/30/2008] [Accepted: 07/11/2008] [Indexed: 12/22/2022] Open
Abstract
Alternative splicing is a key mechanism regulating gene expression, and it is often used to produce antagonistic activities particularly in apoptotic genes. Heterogeneous nuclear ribonucleoparticle (hnRNP) proteins form a family of RNA-binding proteins that coat nascent pre-mRNAs. Many but not all major hnRNP proteins have been shown to participate in splicing control. The range and specificity of hnRNP protein action remain poorly documented, even for those affecting splice site selection. We used RNA interference and a reverse transcription-PCR screening platform to examine the implications of 14 of the major hnRNP proteins in the splicing of 56 alternative splicing events in apoptotic genes. Out of this total of 784 alternative splicing reactions tested in three human cell lines, 31 responded similarly to a knockdown in at least two different cell lines. On the other hand, the impact of other hnRNP knockdowns was cell line specific. The broadest effects were obtained with hnRNP K and C, two proteins whose role in alternative splicing had not previously been firmly established. Different hnRNP proteins affected distinct sets of targets with little overlap even between closely related hnRNP proteins. Overall, our study highlights the potential contribution of all of these major hnRNP proteins in alternative splicing control and shows that the targets for individual hnRNP proteins can vary in different cellular contexts.
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Affiliation(s)
- Julian P Venables
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine et des Sciences de la Santé, 3001, 12th Avenue Nord, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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31
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Smith DJ, Query CC, Konarska MM. "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing. Mol Cell 2008; 30:657-66. [PMID: 18570869 DOI: 10.1016/j.molcel.2008.04.013] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Indexed: 11/18/2022]
Abstract
The spliceosome is both compositionally and conformationally dynamic. Each transition along the splicing pathway presents an opportunity for progression, pausing, or discard, allowing splice site choice to be regulated throughout both the assembly and catalytic phases of the reaction.
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32
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Abstract
Background Recent evidence suggests that the number and variety of functional RNAs (ncRNAs as well as cis-acting RNA elements within mRNAs ) is much higher than previously thought; thus, the ability to computationally predict and analyze RNAs has taken on new importance. We have computationally studied the secondary structures in an alignment of six Aspergillus genomes. Little is known about the RNAs present in this set of fungi, and this diverse set of genomes has an optimal level of sequence conservation for observing the correlated evolution of base-pairs seen in RNAs. Methodology/Principal Findings We report the results of a whole-genome search for evolutionarily conserved secondary structures, as well as the results of clustering these predicted secondary structures by structural similarity. We find a total of 7450 predicted secondary structures, including a new predicted ∼60 bp long hairpin motif found primarily inside introns. We find no evidence for microRNAs. Different types of genomic regions are over-represented in different classes of predicted secondary structures. Exons contain the longest motifs (primarily long, branched hairpins), 5′ UTRs primarily contain groupings of short hairpins located near the start codon, and 3′ UTRs contain very little secondary structure compared to other regions. There is a large concentration of short hairpins just inside the boundaries of exons. The density of predicted intronic RNAs increases with the length of introns, and the density of predicted secondary structures within mRNA coding regions increases with the number of introns in a gene. Conclusions/Sigificance There are many conserved, high-confidence RNAs of unknown function in these Aspergillus genomes, as well as interesting spatial distributions of predicted secondary structures. This study increases our knowledge of secondary structure in these aspergillus organisms.
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Affiliation(s)
- Abigail Manson McGuire
- The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (AMM); (JEG)
| | - James E. Galagan
- The Broad Institute of M.I.T. and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (AMM); (JEG)
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Brites D, McTaggart S, Morris K, Anderson J, Thomas K, Colson I, Fabbro T, Little TJ, Ebert D, Du Pasquier L. The Dscam Homologue of the Crustacean Daphnia Is Diversified by Alternative Splicing Like in Insects. Mol Biol Evol 2008; 25:1429-39. [DOI: 10.1093/molbev/msn087] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Haj Khelil A, Deguillien M, Morinière M, Ben Chibani J, Baklouti F. Cryptic splicing sites are differentially utilized in vivo. FEBS J 2008; 275:1150-62. [PMID: 18266765 DOI: 10.1111/j.1742-4658.2008.06276.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
It has long been considered that cryptic splice sites are ignored by the splicing machinery in the context of intact genuine splice sites. In the present study, it is shown that cryptic splice sites are utilized in all circumstances, when the authentic site is intact, partially functional or completely abolished. Their use would therefore contribute to a background lack of fidelity in the context of the wild-type sequence. We also found that a mutation at the 5' splice site of beta-globin intron 1 accommodates multiple cryptic splicing pathways, including three previously reported pathways. Focusing on the two major cryptic 5' splice sites within beta-globin exon 1, we show that cryptic splice site selection ex vivo varies depending upon: (a) the cell stage of development during terminal erythroid differentiation; (b) the nature of the mutation at the authentic 5' splice site; and (c) the nature of the promoter. Finally, we found that the two major cryptic 5' splice sites are utilized with differential efficiencies in two siblings sharing the same beta-globin chromosome haplotype in the homozygous state. Collectively, these data suggest that intrinsic, sequence specific factors and cell genetic background factors both contribute to promote a subtle differential use of cryptic splice sites in vivo.
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Affiliation(s)
- Amel Haj Khelil
- CNRS UMR 5534, Centre de Génétique Moléculaire et Cellulaire, Université Lyon 1, 16 rue Raphael Dubois, Villeurbanne Cedex, France
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35
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Abstract
Alternative pre-mRNA splicing has an important role in the control of neuronal gene expression. Many neuronal proteins are structurally diversified through the differential inclusion and exclusion of sequences in the final spliced mRNA. Here, we discuss common mechanisms of splicing regulation and provide examples of how alternative splicing has important roles in neuronal development and mature neuron function. Finally, we describe regulatory proteins that control the splicing of some neuronally expressed transcripts.
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Affiliation(s)
- Qin Li
- Howard Hughes Medical Institute, University of California, Los Angeles, 6-762 MacDonald Research Laboratories, 675 Charles E. Young Drive South, Los Angeles, California 90095, USA
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36
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Buratti E, Dhir A, Lewandowska MA, Baralle FE. RNA structure is a key regulatory element in pathological ATM and CFTR pseudoexon inclusion events. Nucleic Acids Res 2007; 35:4369-83. [PMID: 17580311 PMCID: PMC1935003 DOI: 10.1093/nar/gkm447] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Genomic variations deep in the intronic regions of pre-mRNA molecules are increasingly reported to affect splicing events. However, there is no general explanation why apparently similar variations may have either no effect on splicing or cause significant splicing alterations. In this work we have examined the structural architecture of pseudoexons previously described in ATM and CFTR patients. The ATM case derives from the deletion of a repressor element and is characterized by an aberrant 5′ss selection despite the presence of better alternatives. The CFTR pseudoexon instead derives from the creation of a new 5′ss that is used while a nearby pre-existing donor-like sequence is never selected. Our results indicate that RNA structure is a major splicing regulatory factor in both cases. Furthermore, manipulation of the original RNA structures can lead to pseudoexon inclusion following the exposure of unused 5′ss already present in their wild-type intronic sequences and prevented to be recognized because of their location in RNA stem structures. Our data show that intrinsic structural features of introns must be taken into account to understand the mechanism of pseudoexon activation in genetic diseases. Our observations may help to improve diagnostics prediction programmes and eventual therapeutic targeting.
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Abstract
Alternative splicing is a powerful means of controlling gene expression and increasing protein diversity. Most genes express a limited number of mRNA isoforms, but there are several examples of genes that use alternative splicing to generate hundreds, thousands and even tens of thousands of isoforms. Collectively such genes are considered to undergo complex alternative splicing. The best example is the Drosophila Down syndrome cell adhesion molecule (Dscam) gene, which can generate 38,016 isoforms by the alternative splicing of 95 variable exons. In this review, we will describe several genes that use complex alternative splicing to generate large repertoires of mRNAs and what is known about the mechanisms by which they do so.
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38
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Xing Y, Lee C. Relating alternative splicing to proteome complexity and genome evolution. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:36-49. [PMID: 18380339 DOI: 10.1007/978-0-387-77374-2_3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Prior to genomics, studies of alternative splicing primarily focused on the function and mechanism of alternative splicing in individual genes and exons. This has changed dramatically since the late 1990s. High-throughput genomics technologies, such as EST sequencing and microarrays designed to detect changes in splicing, led to genome-wide discoveries and quantification of alternative splicing in a wide range of species from human to Arabidopsis. Consensus estimates of AS frequency in the human genome grew from less than 5% in mid-1990s to as high as 60-74% now. The rapid growth in sequence and microarray data for alternative splicing has made it possible to look into the global impact of alternative splicing on protein function and evolution of genomes. In this chapter, we review recent research on alternative splicing's impact on proteomic complexity and its role in genome evolution.
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Affiliation(s)
- Yi Xing
- Department of Internal Medicine, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, USA
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Zipursky SL, Wojtowicz WM, Hattori D. Got diversity? Wiring the fly brain with Dscam. Trends Biochem Sci 2006; 31:581-8. [PMID: 16919957 DOI: 10.1016/j.tibs.2006.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2006] [Revised: 07/17/2006] [Accepted: 08/03/2006] [Indexed: 10/24/2022]
Abstract
The Drosophila gene Dscam, encoding Down syndrome cell-adhesion molecule, is required for the development of neural circuits. Alternative splicing of Dscam mRNA potentially generates 38016 isoforms of a cell-surface recognition protein of the immunoglobulin superfamily. These isoforms include 19008 different ectodomains joined to one of two alternative transmembrane segments. Each ectodomain comprises a unique combination of three variable immunoglobulin domains. Biochemical studies support a model in which each isoform preferentially binds to the same isoform on opposing cell surfaces. This homophilic binding requires matching at all three variable immunoglobulin domains. These findings raise the intriguing possibility that specificity of binding by the Dscam isoforms mediates cell-surface recognition events required for wiring the fly brain.
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Affiliation(s)
- S Lawrence Zipursky
- Department of Biological Chemistry, Howard Hughes Medical Institute, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1662, USA.
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Buratti E, Baralle M, Baralle FE. Defective splicing, disease and therapy: searching for master checkpoints in exon definition. Nucleic Acids Res 2006; 34:3494-510. [PMID: 16855287 PMCID: PMC1524908 DOI: 10.1093/nar/gkl498] [Citation(s) in RCA: 164] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2006] [Revised: 06/27/2006] [Accepted: 06/28/2006] [Indexed: 12/25/2022] Open
Abstract
The number of aberrant splicing processes causing human disease is growing exponentially and many recent studies have uncovered some aspects of the unexpectedly complex network of interactions involved in these dysfunctions. As a consequence, our knowledge of the various cis- and trans-acting factors playing a role on both normal and aberrant splicing pathways has been enhanced greatly. However, the resulting information explosion has also uncovered the fact that many splicing systems are not easy to model. In fact we are still unable, with certainty, to predict the outcome of a given genomic variation. Nonetheless, in the midst of all this complexity some hard won lessons have been learned and in this survey we will focus on the importance of the wide sequence context when trying to understand why apparently similar mutations can give rise to different effects. The examples discussed in this summary will highlight the fine 'balance of power' that is often present between all the various regulatory elements that define exon boundaries. In the final part, we shall then discuss possible therapeutic targets and strategies to rescue genetic defects of complex splicing systems.
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Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 9934012 Trieste, Italy
| | - Marco Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 9934012 Trieste, Italy
| | - Francisco E. Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 9934012 Trieste, Italy
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Xing Y, Lee C. Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. Nat Rev Genet 2006; 7:499-509. [PMID: 16770337 DOI: 10.1038/nrg1896] [Citation(s) in RCA: 206] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genome-wide analyses of alternative splicing have established its nearly ubiquitous role in gene regulation in many organisms. Genome sequencing and comparative genomics have made it possible to look in detail at the evolutionary history of specific alternative exons or splice sites, resulting in a flurry of publications in recent years. Here, we consider how alternative splicing has contributed to the evolution of modern genomes, and discuss constraints on evolution associated with alternative splicing that might have important medical implications.
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Affiliation(s)
- Yi Xing
- Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
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Chen BE, Kondo M, Garnier A, Watson FL, Püettmann-Holgado R, Lamar DR, Schmucker D. The Molecular Diversity of Dscam Is Functionally Required for Neuronal Wiring Specificity in Drosophila. Cell 2006; 125:607-20. [PMID: 16678102 DOI: 10.1016/j.cell.2006.03.034] [Citation(s) in RCA: 144] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2006] [Revised: 03/19/2006] [Accepted: 03/29/2006] [Indexed: 11/28/2022]
Abstract
Alternative splicing of Dscam generates an enormous molecular diversity with maximally 38,016 different receptors. Whether this large diversity is required in vivo is currently unclear. We examined the role of Dscam in neuron-target recognition of single mechanosensory neurons, which connect with different target cells through multiple axonal branches. Analysis of Dscam null neurons demonstrated an essential role of Dscam for growth and directed extension of axon branches. Expression of randomly chosen single isoforms could not rescue connectivity but did restore basic axonal extension and rudimentary branching. Moreover, two Dscam alleles were generated that each reduced the maximally possible Dscam diversity to 22,176 isoforms. Reduction of Dscam diversity resulted in specific connectivity defects of mechanosensory neurons. Furthermore, the observed allele-specific phenotypes suggest functional differences among isoforms. Our findings provide evidence that a very large number of structurally unique receptor isoforms is required to ensure fidelity and precision of neuronal connectivity.
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Affiliation(s)
- Brian E Chen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
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Xing Y, Lee C. Can RNA selection pressure distort the measurement of Ka/Ks? Gene 2006; 370:1-5. [PMID: 16488091 DOI: 10.1016/j.gene.2005.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2005] [Revised: 12/15/2005] [Accepted: 12/20/2005] [Indexed: 11/24/2022]
Abstract
Recently, an interesting question has emerged in the evolutionary interpretation of sequence substitution data as evidence of amino acid selection pressure. Specifically, the Ka/Ks metric was designed to measure selection pressure on amino acid substitutions, assuming that the synonymous substitution rate Ks reflects the neutral nucleotide substitution rate. However, there is increasing evidence for selection pressure at silent sites due to constraints of RNA splicing. Is Ka/Ks an appropriate metric for selection pressure on amino acid substitutions, in the presence of other selection pressures acting only at the RNA level (such as selection for exonic splicing enhancers)? Or can the resulting decreases in Ks from such selection pressures introduce bias into the Ka/Ks metric, so that it no longer gives an accurate measure of amino acid level selection pressure? In this review, we present both mathematical models and empirical evidence for these divergent points of view.
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Affiliation(s)
- Yi Xing
- Molecular Biology Institute, Center for Genomics and Proteomics, Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA
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