1
|
Masson E, Maestri S, Bordeau V, Cooper DN, Férec C, Chen JM. Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a disease-causing mechanism. Am J Hum Genet 2024:S0002-9297(24)00302-1. [PMID: 39265574 DOI: 10.1016/j.ajhg.2024.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/14/2024] Open
Abstract
We previously identified a homozygous Alu insertion variant (Alu_Ins) in the 3'-untranslated region (3'-UTR) of SPINK1 as the cause of severe infantile isolated exocrine pancreatic insufficiency. Although we established that Alu_Ins leads to the complete loss of SPINK1 mRNA expression, the precise mechanisms remained elusive. Here, we aimed to elucidate these mechanisms through a hypothesis-driven approach. Initially, we speculated that, owing to its particular location, Alu_Ins could independently disrupt mRNA 3' end formation and/or affect other post-transcriptional processes such as nuclear export and translation. However, employing a 3'-UTR luciferase reporter assay, Alu_Ins was found to result in only an ∼50% reduction in luciferase activity compared to wild type, which is insufficient to account for the severe pancreatic deficiency in the Alu_Ins homozygote. We then postulated that double-stranded RNA (dsRNA) structures formed between Alu elements, an upstream mechanism regulating gene expression, might be responsible. Using RepeatMasker, we identified two Alu elements within SPINK1's third intron, both oriented oppositely to Alu_Ins. Through RNAfold predictions and full-length gene expression assays, we investigated orientation-dependent interactions between these Alu repeats. We provide compelling evidence to link the detrimental effect of Alu_Ins to extensive dsRNA structures formed between Alu_Ins and pre-existing intronic Alu sequences, including the restoration of SPINK1 mRNA expression by aligning all three Alu elements in the same orientation. Given the widespread presence of Alu elements in the human genome and the potential for new Alu insertions at almost any locus, our findings have important implications for detecting and interpreting Alu insertions in disease genes.
Collapse
Affiliation(s)
- Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France; CHRU Brest, 29200 Brest, France
| | - Sandrine Maestri
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France; CHRU Brest, 29200 Brest, France
| | - Valérie Bordeau
- Inserm U1230 BRM (Bacterial RNAs and Medicine), Université de Rennes, 35043 Rennes, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, 29200 Brest, France.
| |
Collapse
|
2
|
Long-read technologies identify a hidden inverted duplication in a family with choroideremia. HGG ADVANCES 2021; 2:100046. [PMID: 35047838 PMCID: PMC8756506 DOI: 10.1016/j.xhgg.2021.100046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/01/2021] [Indexed: 12/03/2022] Open
Abstract
The lack of molecular diagnoses in rare genetic diseases can be explained by limitations of current standard genomic technologies. Upcoming long-read techniques have complementary strengths to overcome these limitations, with a particular strength in identifying structural variants. By using optical genome mapping and long-read sequencing, we aimed to identify the pathogenic variant in a large family with X-linked choroideremia. In this family, aberrant splicing of exon 12 of the choroideremia gene CHM was detected in 2003, but the underlying genomic defect remained elusive. Optical genome mapping and long-read sequencing approaches now revealed an intragenic 1,752 bp inverted duplication including exon 12 and surrounding regions, located downstream of the wild-type copy of exon 12. Both breakpoint junctions were confirmed with Sanger sequencing and segregate with the X-linked inheritance in the family. The breakpoint junctions displayed sequence microhomology suggestive for an erroneous replication mechanism as the origin of the structural variant. The inverted duplication is predicted to result in a hairpin formation of the pre-mRNA with the wild-type exon 12, leading to exon skipping in the mature mRNA. The identified inverted duplication is deemed the hidden pathogenic cause of disease in this family. Our study shows that optical genome mapping and long-read sequencing have significant potential for the identification of (hidden) structural variants in rare genetic diseases.
Collapse
|
3
|
Saldi T, Riemondy K, Erickson B, Bentley DL. Alternative RNA structures formed during transcription depend on elongation rate and modify RNA processing. Mol Cell 2021; 81:1789-1801.e5. [PMID: 33631106 DOI: 10.1016/j.molcel.2021.01.040] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/24/2022]
Abstract
Most RNA processing occurs co-transcriptionally. We interrogated nascent pol II transcripts by chemical and enzymatic probing and determined how the "nascent RNA structureome" relates to splicing, A-I editing and transcription speed. RNA folding within introns and steep structural transitions at splice sites are associated with efficient co-transcriptional splicing. A slow pol II mutant elicits extensive remodeling into more folded conformations with increased A-I editing. Introns that become more structured at their 3' splice sites get co-transcriptionally excised more efficiently. Slow pol II altered folding of intronic Alu elements where cryptic splicing and intron retention are stimulated, an outcome mimicked by UV, which decelerates transcription. Slow transcription also remodeled RNA folding around alternative exons in distinct ways that predict whether skipping or inclusion is favored, even though it occurs post-transcriptionally. Hence, co-transcriptional RNA folding modulates post-transcriptional alternative splicing. In summary, the plasticity of nascent transcripts has widespread effects on RNA processing.
Collapse
Affiliation(s)
- Tassa Saldi
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Kent Riemondy
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - Benjamin Erickson
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA
| | - David L Bentley
- RNA Bioscience Initiative, Department Biochemistry and Molecular Genetics, University of Colorado School of Medicine, PO Box 6511, Aurora, CO 80045, USA.
| |
Collapse
|
4
|
Neil CR, Fairbrother WG. Intronic RNA: Ad'junk' mediator of post-transcriptional gene regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194439. [PMID: 31682938 DOI: 10.1016/j.bbagrm.2019.194439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 09/30/2019] [Indexed: 01/23/2023]
Abstract
RNA splicing, the process through which intervening segments of noncoding RNA (introns) are excised from pre-mRNAs to allow for the formation of a mature mRNA product, has long been appreciated for its capacity to add complexity to eukaryotic proteomes. However, evidence suggests that the utility of this process extends beyond protein output and provides cells with a dynamic tool for gene regulation. In this review, we aim to highlight the role that intronic RNA plays in mediating specific splicing outcomes in pre-mRNA processing, as well as explore an emerging class of stable intronic sequences that have been observed to act in gene expression control. Building from underlying flexibility in both sequence and structure, intronic RNA provides mechanisms for post-transcriptional gene regulation that are amenable to the tissue and condition specific needs of eukaryotic cells. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
Collapse
Affiliation(s)
- Christopher R Neil
- Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States of America
| | - William G Fairbrother
- Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States of America; Center for Computational Molecular Biology, Brown University, Providence, RI, United States of America.
| |
Collapse
|
5
|
β-Mannosidosis caused by a novel homozygous intragenic inverted duplication in MANBA. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003954. [PMID: 30886116 PMCID: PMC6549551 DOI: 10.1101/mcs.a003954] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/04/2019] [Indexed: 11/25/2022] Open
Abstract
β-Mannosidosis is a lysosomal storage disorder characterized by accumulation of disaccharides due to deficiency of the lysosomal enzyme β-mannosidase. The disease is caused by mutations in MANBA and is extremely rare in humans. Although the clinical presentation is heterogeneous, common symptoms include various degrees of developmental delay, behavioral disturbances, hearing loss, and frequent infections. We report a 15-yr-old girl presenting with mild intellectual disability, sensorineural hearing loss, severe behavioral disturbances, dysmorphic traits, and evolving angiokeratomas. Copy-number variation analysis of next-generation sequencing (NGS) data indicated increased coverage in exons 8-11 of MANBA Low β-mannosidase activity (1 µkatal/kg protein, refv 25-40) established the diagnosis of β-mannosidosis. Whole-genome sequencing (WGS) and cDNA analysis revealed a novel homozygous intragenic inverted duplication in MANBA, where a 13.1-kb region between introns 7 and 11 was duplicated and inserted in an inverted orientation, creating a 67-base nonduplicated gap at the insertion point. Both junctions showed microhomology regions. The inverted duplication resulted in exon skipping of exons 8-9 or 8-10. Our report highlights the importance of copy-number variation analysis of data from NGS and in particular the power of WGS in the identification and characterization of copy-number variants.
Collapse
|
6
|
Ungerleider N, Flemington E. SpliceV: analysis and publication quality printing of linear and circular RNA splicing, expression and regulation. BMC Bioinformatics 2019; 20:231. [PMID: 31068132 PMCID: PMC6507234 DOI: 10.1186/s12859-019-2865-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 04/30/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND In eukaryotes, most genes code for multiple transcript isoforms that are generated through the complex and tightly regulated process of RNA splicing. Despite arising from identical precursor transcripts, alternatively spliced RNAs can have dramatically different functions. Transcriptome complexity is elevated further by the production of circular RNAs (circRNAs), another class of mature RNA that results from the splicing of a downstream splice donor to an upstream splice acceptor. While there has been a rapid expansion of circRNA catalogs in the last few years through the utilization of next generation sequencing approaches, our understanding of the mechanisms and regulation of circular RNA biogenesis, the impact that circRNA generation has on parental transcript processing, and the functions carried out by circular RNAs remains limited. RESULTS Here, we present a visualization and analysis tool, SpliceV, that rapidly plots all relevant forward- and back-splice data, with exon and single nucleotide level coverage information from RNA-seq experiments in a publication quality format. SpliceV also integrates analysis features that assist investigations into splicing regulation and transcript functions through the display of predicted RNA binding protein sites and the configuration of repetitive elements along the primary transcript. CONCLUSIONS SpliceV is an easy-to-use splicing visualization tool, compatible with both Python 2.7 and 3+, and distributed under the GNU Public License. The source code is freely available for download at https://github.com/flemingtonlab/SpliceV and can be installed from PyPI using pip.
Collapse
Affiliation(s)
- Nathan Ungerleider
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA
| | - Erik Flemington
- Department of Pathology, Tulane Cancer Center, Tulane University School of Medicine, New Orleans, LA, 70112, USA.
| |
Collapse
|
7
|
Zhang L, Vielle A, Espinosa S, Zhao R. RNAs in the spliceosome: Insight from cryoEM structures. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1523. [PMID: 30729694 DOI: 10.1002/wrna.1523] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 12/12/2018] [Accepted: 12/28/2018] [Indexed: 12/28/2022]
Abstract
Pre-mRNA splicing is catalyzed by the spliceosome, a multimegadalton RNA-protein complex. The spliceosome undergoes dramatic compositional and conformational changes through the splicing cycle, forming at least 10 distinct complexes. Recent high-resolution cryoEM structures of various spliceosomal complexes revealed unprecedented details of this large molecular machine. This review highlights insight into the structure and function of the spliceosomal RNA components obtained from these new structures, with a focus on the yeast spliceosome. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics, and Chemistry RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
Collapse
Affiliation(s)
- Lingdi Zhang
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Anne Vielle
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Sara Espinosa
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, Anschutz Medical Campus, University of Colorado Denver, Aurora, Colorado
| |
Collapse
|
8
|
Azibani F, Brull A, Arandel L, Beuvin M, Nelson I, Jollet A, Ziat E, Prudhon B, Benkhelifa-Ziyyat S, Bitoun M, Lorain S, Bonne G, Bertrand AT. Gene Therapy via Trans-Splicing for LMNA-Related Congenital Muscular Dystrophy. MOLECULAR THERAPY. NUCLEIC ACIDS 2017; 10:376-386. [PMID: 29499949 PMCID: PMC5862133 DOI: 10.1016/j.omtn.2017.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 12/20/2017] [Accepted: 12/20/2017] [Indexed: 11/28/2022]
Abstract
We assessed the potential of Lmna-mRNA repair by spliceosome-mediated RNA trans-splicing as a therapeutic approach for LMNA-related congenital muscular dystrophy. This gene therapy strategy leads to reduction of mutated transcript expression for the benefit of corresponding wild-type (WT) transcripts. We developed 5′-RNA pre-trans-splicing molecules containing the first five exons of Lmna and targeting intron 5 of Lmna pre-mRNA. Among nine pre-trans-splicing molecules, differing in the targeted sequence in intron 5 and tested in C2C12 myoblasts, three induced trans-splicing events on endogenous Lmna mRNA and confirmed at protein level. Further analyses performed in primary myotubes derived from an LMNA-related congenital muscular dystrophy (L-CMD) mouse model led to a partial rescue of the mutant phenotype. Finally, we tested this approach in vivo using adeno-associated virus (AAV) delivery in newborn mice and showed that trans-splicing events occurred in WT mice 50 days after AAV delivery, although at a low rate. Altogether, while these results provide the first evidence for reprogramming LMNA mRNA in vitro, strategies to improve the rate of trans-splicing events still need to be developed for efficient application of this therapeutic approach in vivo.
Collapse
Affiliation(s)
- Feriel Azibani
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Astrid Brull
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Ludovic Arandel
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Maud Beuvin
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Isabelle Nelson
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Arnaud Jollet
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Esma Ziat
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Bernard Prudhon
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | | | - Marc Bitoun
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Stéphanie Lorain
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Gisèle Bonne
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France
| | - Anne T Bertrand
- Sorbonne Université, INSERM UMRS_974, Center of Research in Myology, 75013 Paris, France.
| |
Collapse
|
9
|
Soemedi R, Cygan KJ, Rhine CL, Glidden DT, Taggart AJ, Lin CL, Fredericks AM, Fairbrother WG. The effects of structure on pre-mRNA processing and stability. Methods 2017; 125:36-44. [PMID: 28595983 DOI: 10.1016/j.ymeth.2017.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Pre-mRNA molecules can form a variety of structures, and both secondary and tertiary structures have important effects on processing, function and stability of these molecules. The prediction of RNA secondary structure is a challenging problem and various algorithms that use minimum free energy, maximum expected accuracy and comparative evolutionary based methods have been developed to predict secondary structures. However, these tools are not perfect, and this remains an active area of research. The secondary structure of pre-mRNA molecules can have an enhancing or inhibitory effect on pre-mRNA splicing. An example of enhancing structure can be found in a novel class of introns in zebrafish. About 10% of zebrafish genes contain a structured intron that forms a bridging hairpin that enforces correct splice site pairing. Negative examples of splicing include local structures around splice sites that decrease splicing efficiency and potentially cause mis-splicing leading to disease. Splicing mutations are a frequent cause of hereditary disease. The transcripts of disease genes are significantly more structured around the splice sites, and point mutations that increase the local structure often cause splicing disruptions. Post-splicing, RNA secondary structure can also affect the stability of the spliced intron and regulatory RNA interference pathway intermediates, such as pre-microRNAs. Additionally, RNA secondary structure has important roles in the innate immune defense against viruses. Finally, tertiary structure can also play a large role in pre-mRNA splicing. One example is the G-quadruplex structure, which, similar to secondary structure, can either enhance or inhibit splicing through mechanisms such as creating or obscuring RNA binding protein sites.
Collapse
Affiliation(s)
- Rachel Soemedi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Kamil J Cygan
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Christy L Rhine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - David T Glidden
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Allison J Taggart
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - Chien-Ling Lin
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - Alger M Fredericks
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
A Phylogenetic Survey on the Structure of the HIV-1 Leader RNA Domain That Encodes the Splice Donor Signal. Viruses 2016; 8:v8070200. [PMID: 27455303 PMCID: PMC4974535 DOI: 10.3390/v8070200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 11/16/2022] Open
Abstract
RNA splicing is a critical step in the human immunodeficiency virus type 1 (HIV-1) replication cycle because it controls the expression of the complex viral proteome. The major 5′ splice site (5′ss) that is positioned in the untranslated leader of the HIV-1 RNA transcript is of particular interest because it is used for the production of the more than 40 differentially spliced subgenomic mRNAs. HIV-1 splicing needs to be balanced tightly to ensure the proper levels of all viral proteins, including the Gag-Pol proteins that are translated from the unspliced RNA. We previously presented evidence that the major 5′ss is regulated by a repressive local RNA structure, the splice donor (SD) hairpin, that masks the 11 nucleotides (nts) of the 5′ss signal for recognition by U1 small nuclear RNA (snRNA) of the spliceosome machinery. A strikingly different multiple-hairpin RNA conformation was recently proposed for this part of the HIV-1 leader RNA. We therefore inspected the sequence of natural HIV-1 isolates in search for support, in the form of base pair (bp) co-variations, for the different RNA conformations.
Collapse
|
12
|
Meyer F. Viral interactions with components of the splicing machinery. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 142:241-68. [PMID: 27571697 DOI: 10.1016/bs.pmbts.2016.05.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Eukaryotic genes are often interrupted by stretches of sequence with no protein coding potential or obvious function. After transcription, these interrupting sequences must be removed to give rise to the mature messenger RNA. This fundamental process is called RNA splicing and is achieved by complicated machinery made of protein and RNA that assembles around the RNA to be edited. Viruses also use RNA splicing to maximize their coding potential and economize on genetic space, and use clever strategies to manipulate the splicing machinery to their advantage. This article gives an overview of the splicing process and provides examples of viral strategies that make use of various components of the splicing system to promote their replicative cycle. Representative virus families have been selected to illustrate the interaction with various regulatory proteins and ribonucleoproteins. The unifying theme is fine regulation through protein-protein and protein-RNA interactions with the spliceosome components and associated factors to promote or prevent spliceosome assembly on given splice sites, in addition to a strong influence from cis-regulatory sequences on viral transcripts. Because there is an intimate coupling of splicing with the processes that direct mRNA biogenesis, a description of how these viruses couple the regulation of splicing with the retention or stability of mRNAs is also included. It seems that a unique balance of suppression and activation of splicing and nuclear export works optimally for each family of viruses.
Collapse
Affiliation(s)
- F Meyer
- Department of Biochemistry & Molecular Biology, Entomology & Plant Pathology, Mississippi State University, Starkville, MS, USA.
| |
Collapse
|
13
|
Vandivier LE, Anderson SJ, Foley SW, Gregory BD. The Conservation and Function of RNA Secondary Structure in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2016; 67:463-88. [PMID: 26865341 PMCID: PMC5125251 DOI: 10.1146/annurev-arplant-043015-111754] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance (NMR) imaging to chemical and nuclease probing methods. Combining these latter methods with high-throughput sequencing has enabled them to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure.
Collapse
Affiliation(s)
- Lee E Vandivier
- Department of Biology, School of Arts and Sciences, and
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | | | - Shawn W Foley
- Department of Biology, School of Arts and Sciences, and
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| | - Brian D Gregory
- Department of Biology, School of Arts and Sciences, and
- Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
| |
Collapse
|
14
|
Sohail M, Xie J. Diverse regulation of 3' splice site usage. Cell Mol Life Sci 2015; 72:4771-93. [PMID: 26370726 PMCID: PMC11113787 DOI: 10.1007/s00018-015-2037-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/12/2015] [Accepted: 09/03/2015] [Indexed: 01/13/2023]
Abstract
The regulation of splice site (SS) usage is important for alternative pre-mRNA splicing and thus proper expression of protein isoforms in cells; its disruption causes diseases. In recent years, an increasing number of novel regulatory elements have been found within or nearby the 3'SS in mammalian genes. The diverse elements recruit a repertoire of trans-acting factors or form secondary structures to regulate 3'SS usage, mostly at the early steps of spliceosome assembly. Their mechanisms of action mainly include: (1) competition between the factors for RNA elements, (2) steric hindrance between the factors, (3) direct interaction between the factors, (4) competition between two splice sites, or (5) local RNA secondary structures or longer range loops, according to the mode of protein/RNA interactions. Beyond the 3'SS, chromatin remodeling/transcription, posttranslational modifications of trans-acting factors and upstream signaling provide further layers of regulation. Evolutionarily, some of the 3'SS elements seem to have emerged in mammalian ancestors. Moreover, other possibilities of regulation such as that by non-coding RNA remain to be explored. It is thus likely that there are more diverse elements/factors and mechanisms that influence the choice of an intron end. The diverse regulation likely contributes to a more complex but refined transcriptome and proteome in mammals.
Collapse
Affiliation(s)
- Muhammad Sohail
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
- Department of Biochemistry and Medical Genetics, College of Medicine, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
| |
Collapse
|
15
|
Mueller N, Berkhout B, Das AT. HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5' splice site. J Gen Virol 2015; 96:1906-17. [PMID: 25779589 DOI: 10.1099/vir.0.000122] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The 5' leader region of the human immunodeficiency virus 1 (HIV-1) RNA genome contains the major 5' splice site (ss) that is used in the production of the many spliced viral RNAs. This splice-donor (SD) region can fold into a stable stem-loop structure and the thermodynamic stability of this RNA hairpin influences splicing efficiency. In addition, splicing may be modulated by binding of splicing regulatory (SR) proteins, in particular SF2/ASF (SRSF1), SC35 (SRSF2), SRp40 (SRSF5) and SRp55 (SRSF6), to sequence elements in the SD region. The role of RNA structure and SR protein binding in splicing control was previously studied by functional analysis of mutant SD sequences. The interpretation of these studies was complicated by the fact that most mutations simultaneously affect both structure and sequence elements. We therefore tried to disentangle the contribution of these two variables by designing more precise SD region mutants with a single effect on either the sequence or the structure. The current analysis indicates that HIV-1 splicing at the major 5'ss is modulated by both the stability of the local RNA structure and the binding of splicing regulatory proteins.
Collapse
Affiliation(s)
- Nancy Mueller
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands
| |
Collapse
|
16
|
Leija-Martínez N, Casas-Flores S, Cadena-Nava RD, Roca JA, Mendez-Cabañas JA, Gomez E, Ruiz-Garcia J. The separation between the 5'-3' ends in long RNA molecules is short and nearly constant. Nucleic Acids Res 2014; 42:13963-8. [PMID: 25428360 PMCID: PMC4267660 DOI: 10.1093/nar/gku1249] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
RNA molecules play different roles in coding, decoding and gene expression regulation. Such roles are often associated to the RNA secondary or tertiary structures. The folding dynamics lead to multiple secondary structures of long RNA molecules, since an RNA molecule might fold into multiple distinct native states. Despite an ensemble of different structures, it has been theoretically proposed that the separation between the 5′ and 3′ ends of long single-stranded RNA molecules (ssRNA) remains constant, independent of their base content and length. Here, we present the first experimental measurements of the end-to-end separation in long ssRNA molecules. To determine this separation, we use single molecule Fluorescence Resonance Energy Transfer of fluorescently end-labeled ssRNA molecules ranging from 500 to 5500 nucleotides in length, obtained from two viruses and a fungus. We found that the end-to-end separation is indeed short, within 5–9 nm. It is remarkable that the separation of the ends of all RNA molecules studied remains small and similar, despite the origin, length and differences in their secondary structure. This implies that the ssRNA molecules are ‘effectively circularized’ something that might be a general feature of RNAs, and could result in fine-tuning for translation and gene expression regulation.
Collapse
Affiliation(s)
- Nehemías Leija-Martínez
- Biological Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, S.L.P. 78290, México
| | - Sergio Casas-Flores
- División de Biología Molecular, IPICYT, Camino a la Presa San Jose s/n, San Luis Potosí, SLP 78216, México
| | - Rubén D Cadena-Nava
- Center for Nanociences and Nanotechnology, Universidad Nacional Autónoma de México, Km. 107 Carretera Tijuana-Ensenada s/n, Baja California 22800, México
| | - Joan A Roca
- Centre de Desenvolupament de Sensors, Instrumentación i Sistemes, Universitat Politecnica de Catalunya, Rambla de Sant Nebridi 10, E-0822, Terrasa, España
| | - José A Mendez-Cabañas
- Molecular Biophysics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, SLP 78290, México
| | - Eduardo Gomez
- Biological Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, S.L.P. 78290, México
| | - Jaime Ruiz-Garcia
- Biological Physics Laboratory, Physics Institute, Universidad Autónoma de San Luis Potosí, Alvaro Obregon 64, San Luis Potosí, S.L.P. 78290, México
| |
Collapse
|
17
|
Gandolfi B, Daniel RJ, O'Brien DP, Guo LT, Youngs MD, Leach SB, Jones BR, Shelton GD, Lyons LA. A novel mutation in CLCN1 associated with feline myotonia congenita. PLoS One 2014; 9:e109926. [PMID: 25356766 PMCID: PMC4214686 DOI: 10.1371/journal.pone.0109926] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/05/2014] [Indexed: 12/30/2022] Open
Abstract
Myotonia congenita (MC) is a skeletal muscle channelopathy characterized by inability of the muscle to relax following voluntary contraction. Worldwide population prevalence in humans is 1∶100,000. Studies in mice, dogs, humans and goats confirmed myotonia associated with functional defects in chloride channels and mutations in a skeletal muscle chloride channel (CLCN1). CLCN1 encodes for the most abundant chloride channel in the skeletal muscle cell membrane. Five random bred cats from Winnipeg, Canada with MC were examined. All cats had a protruding tongue, limited range of jaw motion and drooling with prominent neck and proximal limb musculature. All cats had blepharospasm upon palpebral reflex testing and a short-strided gait. Electromyograms demonstrated myotonic discharges at a mean frequency of 300 Hz resembling the sound of a ‘swarm of bees’. Muscle histopathology showed hypertrophy of all fiber types. Direct sequencing of CLCN1 revealed a mutation disrupting a donor splice site downstream of exon 16 in only the affected cats. In vitro translation of the mutated protein predicted a premature truncation and partial lack of the highly conserved CBS1 (cystathionine β-synthase) domain critical for ion transport activity and one dimerization domain pivotal in channel formation. Genetic screening of the Winnipeg random bred population of the cats' origin identified carriers of the mutation. A genetic test for population screening is now available and carrier cats from the feral population can be identified.
Collapse
Affiliation(s)
- Barbara Gandolfi
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
- * E-mail:
| | - Rob J. Daniel
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
| | - Dennis P. O'Brien
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
| | - Ling T. Guo
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | | | - Stacey B. Leach
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
| | - Boyd R. Jones
- Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand
| | - G. Diane Shelton
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Leslie A. Lyons
- Department of Veterinary Medicine and Surgery, School of Veterinary Medicine, University of Missouri – Columbia, Columbia, Missouri, United States of America
| |
Collapse
|
18
|
Mueller N, van Bel N, Berkhout B, Das AT. HIV-1 splicing at the major splice donor site is restricted by RNA structure. Virology 2014; 468-470:609-620. [PMID: 25305540 DOI: 10.1016/j.virol.2014.09.018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 08/11/2014] [Accepted: 09/19/2014] [Indexed: 11/29/2022]
Abstract
The 5' leader region of the HIV-1 RNA contains the major 5' splice site (ss) that is used in the production of all spliced viral RNAs. This splice-donor (SD) region can fold a stem-loop structure. We demonstrate that whereas stabilization of this SD hairpin reduces splicing efficiency, destabilization increases splicing. Both stabilization and destabilization reduce viral fitness. These results demonstrate that the stability of the SD hairpin can modulate the level of splicing, most likely by controlling the accessibility of the 5'ss for the splicing machinery. The natural stability of the SD hairpin restricts splicing and this stability seems to be fine-tuned to reach the optimal balance between unspliced and spliced RNAs for efficient virus replication. The 5'ss region of different HIV-1 isolates and the related SIVmac239 can fold a similar structure. This evolutionary conservation supports the importance of this structure in viral replication.
Collapse
Affiliation(s)
- Nancy Mueller
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Nikki van Bel
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Ben Berkhout
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| | - Atze T Das
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, The Netherlands.
| |
Collapse
|
19
|
Mao R, Raj Kumar PK, Guo C, Zhang Y, Liang C. Comparative analyses between retained introns and constitutively spliced introns in Arabidopsis thaliana using random forest and support vector machine. PLoS One 2014; 9:e104049. [PMID: 25110928 PMCID: PMC4128822 DOI: 10.1371/journal.pone.0104049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/06/2014] [Indexed: 01/04/2023] Open
Abstract
One of the important modes of pre-mRNA post-transcriptional modification is alternative splicing. Alternative splicing allows creation of many distinct mature mRNA transcripts from a single gene by utilizing different splice sites. In plants like Arabidopsis thaliana, the most common type of alternative splicing is intron retention. Many studies in the past focus on positional distribution of retained introns (RIs) among different genic regions and their expression regulations, while little systematic classification of RIs from constitutively spliced introns (CSIs) has been conducted using machine learning approaches. We used random forest and support vector machine (SVM) with radial basis kernel function (RBF) to differentiate these two types of introns in Arabidopsis. By comparing coordinates of introns of all annotated mRNAs from TAIR10, we obtained our high-quality experimental data. To distinguish RIs from CSIs, We investigated the unique characteristics of RIs in comparison with CSIs and finally extracted 37 quantitative features: local and global nucleotide sequence features of introns, frequent motifs, the signal strength of splice sites, and the similarity between sequences of introns and their flanking regions. We demonstrated that our proposed feature extraction approach was more accurate in effectively classifying RIs from CSIs in comparison with other four approaches. The optimal penalty parameter C and the RBF kernel parameter in SVM were set based on particle swarm optimization algorithm (PSOSVM). Our classification performance showed F-Measure of 80.8% (random forest) and 77.4% (PSOSVM). Not only the basic sequence features and positional distribution characteristics of RIs were obtained, but also putative regulatory motifs in intron splicing were predicted based on our feature extraction approach. Clearly, our study will facilitate a better understanding of underlying mechanisms involved in intron retention.
Collapse
Affiliation(s)
- Rui Mao
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, China
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
- Department of Biology, Miami University, Oxford, Ohio, United States of America
| | | | - Cheng Guo
- Department of Biology, Miami University, Oxford, Ohio, United States of America
| | - Yang Zhang
- College of Mechanical and Electronic Engineering, Northwest A&F University, Yangling, Shaanxi, China
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail: (YZ); (CL)
| | - Chun Liang
- Department of Biology, Miami University, Oxford, Ohio, United States of America
- Department of Computer Sciences and Software Engineering, Miami University, Oxford, Ohio, United States of America
- * E-mail: (YZ); (CL)
| |
Collapse
|
20
|
Glauser DA. The multiplicity of alternative splicing decisions in Caenorhabditis elegans is linked to specific intronic regulatory motifs and minisatellites. BMC Genomics 2014; 15:364. [PMID: 24884695 PMCID: PMC4039745 DOI: 10.1186/1471-2164-15-364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 04/15/2014] [Indexed: 11/28/2022] Open
Abstract
Background Alternative splicing diversifies the pool of messenger RNA molecules encoded by individual genes. This diversity is particularly high when multiple splicing decisions cause a combinatorial arrangement of several alternate exons. We know very little on how the multiple decisions occurring during the maturation of single transcripts are coordinated and whether specific sequence elements might be involved. Results Here, the Caenorhabditis elegans genome was surveyed in order to identify sequence elements that might play a specific role in the regulation of multiple splicing decisions. The introns flanking alternate exons in transcripts whose maturation involves multiple alternative splicing decisions were compared to those whose maturation involves a single decision. Fifty-eight penta-, hexa-, and hepta-meric elements, clustered in 17 groups, were significantly over-represented in genes subject to multiple alternative splicing decisions. Most of these motifs relate to known splicing regulatory elements and appear to be well conserved in the related species Caenorhabditis briggsae. The usage of specific motifs is not linked to the gene product function, but rather depends on the gene structure, since it is influenced by the distance separating the multiple splicing decision sites. Two of these motifs are part of the CeRep25B minisatellite, which is also over-represented at the vicinity of alternative splicing regions. Most of the remaining motifs are not part of repeated sequence elements, but tend to occur in specific heterologous pairs in genes subject to multiple alternative splicing decisions. Conclusions The existence of specific intronic sequence elements linked to multiple alternative splicing decisions is intriguing and suggests that these elements might have some specialized regulatory role during splicing. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-364) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Dominique A Glauser
- Department of Biology, University of Fribourg, Chemin du Musée 10, 1700 Fribourg, Switzerland.
| |
Collapse
|
21
|
Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature 2013; 505:696-700. [DOI: 10.1038/nature12756] [Citation(s) in RCA: 587] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 10/09/2013] [Indexed: 12/18/2022]
|
22
|
Roca X, Krainer AR, Eperon IC. Pick one, but be quick: 5' splice sites and the problems of too many choices. Genes Dev 2013; 27:129-44. [PMID: 23348838 DOI: 10.1101/gad.209759.112] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Splice site selection is fundamental to pre-mRNA splicing and the expansion of genomic coding potential. 5' Splice sites (5'ss) are the critical elements at the 5' end of introns and are extremely diverse, as thousands of different sequences act as bona fide 5'ss in the human transcriptome. Most 5'ss are recognized by base-pairing with the 5' end of the U1 small nuclear RNA (snRNA). Here we review the history of research on 5'ss selection, highlighting the difficulties of establishing how base-pairing strength determines splicing outcomes. We also discuss recent work demonstrating that U1 snRNA:5'ss helices can accommodate noncanonical registers such as bulged duplexes. In addition, we describe the mechanisms by which other snRNAs, regulatory proteins, splicing enhancers, and the relative positions of alternative 5'ss contribute to selection. Moreover, we discuss mechanisms by which the recognition of numerous candidate 5'ss might lead to selection of a single 5'ss and propose that protein complexes propagate along the exon, thereby changing its physical behavior so as to affect 5'ss selection.
Collapse
Affiliation(s)
- Xavier Roca
- School of Biological Sciences, Division of Molecular Genetics and Cell Biology, Nanyang Technological University, Singapore.
| | | | | |
Collapse
|
23
|
Li S, Breaker RR. Eukaryotic TPP riboswitch regulation of alternative splicing involving long-distance base pairing. Nucleic Acids Res 2013; 41:3022-31. [PMID: 23376932 PMCID: PMC3597705 DOI: 10.1093/nar/gkt057] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Thiamin pyrophosphate (TPP) riboswitches are found in organisms from all three domains of life. Examples in bacteria commonly repress gene expression by terminating transcription or by blocking ribosome binding, whereas most eukaryotic TPP riboswitches are predicted to regulate gene expression by modulating RNA splicing. Given the widespread distribution of eukaryotic TPP riboswitches and the diversity of their locations in precursor messenger RNAs (pre-mRNAs), we sought to examine the mechanism of alternative splicing regulation by a fungal TPP riboswitch from Neurospora crassa, which is mostly located in a large intron separating protein-coding exons. Our data reveal that this riboswitch uses a long-distance (∼530-nt separation) base-pairing interaction to regulate alternative splicing. Specifically, a portion of the TPP-binding aptamer can form a base-paired structure with a conserved sequence element (α) located near a 5′ splice site, which greatly increases use of this 5′ splice site and promotes gene expression. Comparative sequence analyses indicate that many fungal species carry a TPP riboswitch with similar intron architecture, and therefore the homologous genes in these fungi are likely to use the same mechanism. Our findings expand the scope of genetic control mechanisms relying on long-range RNA interactions to include riboswitches.
Collapse
Affiliation(s)
- Sanshu Li
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | | |
Collapse
|
24
|
Zaphiropoulos PG. Genetic variations and alternative splicing: the Glioma associated oncogene 1, GLI1. Front Genet 2012; 3:119. [PMID: 22833753 PMCID: PMC3400943 DOI: 10.3389/fgene.2012.00119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 06/13/2012] [Indexed: 02/01/2023] Open
Abstract
Alternative splicing is a post-transcriptional regulatory process that is attaining stronger recognition as a modulator of gene expression. Alternative splicing occurs when the primary RNA transcript is differentially processed into more than one mature RNAs. This is the result of a variable definition/inclusion of the exons, the sequences that are excised from the primary RNA to form the mature RNAs. Consequently, RNA expression can generate a collection of differentially spliced RNAs, which may distinctly influence subsequent biological events, such as protein synthesis or other biomolecular interactions. Still the mechanisms that control exon definition and exon inclusion are not fully clarified. This mini-review highlights advances in this field as well as the impact of single nucleotide polymorphisms in affecting splicing decisions. The Glioma-associated oncogene 1, GLI1, is taken as an example in addressing the role of nucleotide substitutions for splicing regulation.
Collapse
|
25
|
Pervouchine DD, Khrameeva EE, Pichugina MY, Nikolaienko OV, Gelfand MS, Rubtsov PM, Mironov AA. Evidence for widespread association of mammalian splicing and conserved long-range RNA structures. RNA (NEW YORK, N.Y.) 2012; 18:1-15. [PMID: 22128342 PMCID: PMC3261731 DOI: 10.1261/rna.029249.111] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Pre-mRNA structure impacts many cellular processes, including splicing in genes associated with disease. The contemporary paradigm of RNA structure prediction is biased toward secondary structures that occur within short ranges of pre-mRNA, although long-range base-pairings are known to be at least as important. Recently, we developed an efficient method for detecting conserved RNA structures on the genome-wide scale, one that does not require multiple sequence alignments and works equally well for the detection of local and long-range base-pairings. Using an enhanced method that detects base-pairings at all possible combinations of splice sites within each gene, we now report RNA structures that could be involved in the regulation of splicing in mammals. Statistically, we demonstrate strong association between the occurrence of conserved RNA structures and alternative splicing, where local RNA structures are generally more frequent at alternative donor splice sites, while long-range structures are more associated with weak alternative acceptor splice sites. As an example, we validated the RNA structure in the human SF1 gene using minigenes in the HEK293 cell line. Point mutations that disrupted the base-pairing of two complementary boxes between exons 9 and 10 of this gene altered the splicing pattern, while the compensatory mutations that reestablished the base-pairing reverted splicing to that of the wild-type. There is statistical evidence for a Dscam-like class of mammalian genes, in which mutually exclusive RNA structures control mutually exclusive alternative splicing. In sum, we propose that long-range base-pairings carry an important, yet unconsidered part of the splicing code, and that, even by modest estimates, there must be thousands of such potentially regulatory structures conserved throughout the evolutionary history of mammals.
Collapse
Affiliation(s)
- Dmitri D Pervouchine
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, 119992, GSP-2 Russia.
| | | | | | | | | | | | | |
Collapse
|
26
|
Al-Balool HH, Weber D, Liu Y, Wade M, Guleria K, Nam PLP, Clayton J, Rowe W, Coxhead J, Irving J, Elliott DJ, Hall AG, Santibanez-Koref M, Jackson MS. Post-transcriptional exon shuffling events in humans can be evolutionarily conserved and abundant. Genome Res 2011; 21:1788-99. [PMID: 21948523 PMCID: PMC3205564 DOI: 10.1101/gr.116442.110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 07/28/2011] [Indexed: 12/31/2022]
Abstract
In silico analyses have established that transcripts from some genes can be processed into RNAs with rearranged exon order relative to genomic structure (post-transcriptional exon shuffling, or PTES). Although known to contribute to transcriptome diversity in some species, to date the structure, distribution, abundance, and functional significance of human PTES transcripts remains largely unknown. Here, using high-throughput transcriptome sequencing, we identify 205 putative human PTES products from 176 genes. We validate 72 out of 112 products analyzed using RT-PCR, and identify additional PTES products structurally related to 61% of validated targets. Sequencing of these additional products reveals GT-AG dinucleotides at >95% of the splice junctions, confirming that they are processed by the spliceosome. We show that most PTES transcripts are expressed in a wide variety of human tissues, that they can be polyadenylated, and that some are conserved in mouse. We also show that they can extend into 5' and 3' UTRs, consistent with formation via trans-splicing of independent pre-mRNA molecules. Finally, we use real-time PCR to compare the abundance of PTES exon junctions relative to canonical exon junctions within the transcripts from seven genes. PTES exon junctions are present at <0.01% to >90% of the levels of canonical junctions, with transcripts from MAN1A2, PHC3, TLE4, and CDK13 exhibiting the highest levels. This is the first systematic experimental analysis of PTES in human, and it suggests both that the phenomenon is much more widespread than previously thought and that some PTES transcripts could be functional.
Collapse
Affiliation(s)
- Haya H. Al-Balool
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - David Weber
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Yilei Liu
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Mark Wade
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Kamlesh Guleria
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Pitsien Lang Ping Nam
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Jake Clayton
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - William Rowe
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Jonathan Coxhead
- NewGene Limited, Bioscience Building, International Centre for Life, Newcastle upon Tyne NE1 4EP, United Kingdom
| | - Julie Irving
- NewGene Limited, Bioscience Building, International Centre for Life, Newcastle upon Tyne NE1 4EP, United Kingdom
| | - David J. Elliott
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| | - Andrew G. Hall
- Northern Institute for Cancer Research, Paul O'Gorman Building, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Michael S. Jackson
- Institute of Genetic Medicine, Newcastle University, Newcastle NE1 3BZ, United Kingdom
| |
Collapse
|
27
|
Wang Z, Xu J. A conditional random fields method for RNA sequence-structure relationship modeling and conformation sampling. ACTA ACUST UNITED AC 2011; 27:i102-10. [PMID: 21685058 PMCID: PMC3117333 DOI: 10.1093/bioinformatics/btr232] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Accurate tertiary structures are very important for the functional study of non-coding RNA molecules. However, predicting RNA tertiary structures is extremely challenging, because of a large conformation space to be explored and lack of an accurate scoring function differentiating the native structure from decoys. The fragment-based conformation sampling method (e.g. FARNA) bears shortcomings that the limited size of a fragment library makes it infeasible to represent all possible conformations well. A recent dynamic Bayesian network method, BARNACLE, overcomes the issue of fragment assembly. In addition, neither of these methods makes use of sequence information in sampling conformations. Here, we present a new probabilistic graphical model, conditional random fields (CRFs), to model RNA sequence–structure relationship, which enables us to accurately estimate the probability of an RNA conformation from sequence. Coupled with a novel tree-guided sampling scheme, our CRF model is then applied to RNA conformation sampling. Experimental results show that our CRF method can model RNA sequence–structure relationship well and sequence information is important for conformation sampling. Our method, named as TreeFolder, generates a much higher percentage of native-like decoys than FARNA and BARNACLE, although we use the same simple energy function as BARNACLE. Contact:zywang@ttic.edu; j3xu@ttic.edu Supplementary Information:Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Zhiyong Wang
- Toyota Technological Institute at Chicago, IL, USA.
| | | |
Collapse
|
28
|
Gahura O, Hammann C, Valentová A, Půta F, Folk P. Secondary structure is required for 3' splice site recognition in yeast. Nucleic Acids Res 2011; 39:9759-67. [PMID: 21893588 PMCID: PMC3239191 DOI: 10.1093/nar/gkr662] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Higher order RNA structures can mask splicing signals, loop out exons, or constitute riboswitches all of which contributes to the complexity of splicing regulation. We identified a G to A substitution between branch point (BP) and 3′ splice site (3′ss) of Saccharomyces cerevisiae COF1 intron, which dramatically impaired its splicing. RNA structure prediction and in-line probing showed that this mutation disrupted a stem in the BP-3′ss region. Analyses of various COF1 intron modifications revealed that the secondary structure brought about the reduction of BP to 3′ss distance and masked potential 3′ss. We demonstrated the same structural requisite for the splicing of UBC13 intron. Moreover, RNAfold predicted stable structures for almost all distant BP introns in S. cerevisiae and for selected examples in several other Saccharomycotina species. The employment of intramolecular structure to localize 3′ss for the second splicing step suggests the existence of pre-mRNA structure-based mechanism of 3′ss recognition.
Collapse
Affiliation(s)
- Ondřej Gahura
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | | | | | | | | |
Collapse
|
29
|
Cherny D, Gooding C, Eperon GE, Coelho MB, Bagshaw CR, Smith CWJ, Eperon IC. Stoichiometry of a regulatory splicing complex revealed by single-molecule analyses. EMBO J 2010; 29:2161-72. [PMID: 20502437 PMCID: PMC2905242 DOI: 10.1038/emboj.2010.103] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 05/05/2010] [Indexed: 12/17/2022] Open
Abstract
Splicing is regulated by complex interactions of numerous RNA-binding proteins. The molecular mechanisms involved remain elusive, in large part because of ignorance regarding the numbers of proteins in regulatory complexes. Polypyrimidine tract-binding protein (PTB), which regulates tissue-specific splicing, represses exon 3 of alpha-tropomyosin through distant pyrimidine-rich tracts in the flanking introns. Current models for repression involve either PTB-mediated looping or the propagation of complexes between tracts. To test these models, we used single-molecule approaches to count the number of bound PTB molecules both by counting the number of bleaching steps of GFP molecules linked to PTB within complexes and by analysing their total emissions. Both approaches showed that five or six PTB molecules assemble. Given the domain structures, this suggests that the molecules occupy primarily multiple overlapping potential sites in the polypyrimidine tracts, excluding propagation models. As an alternative to direct looping, we propose that repression involves a multistep process in which PTB binding forms small local loops, creating a platform for recruitment of other proteins that bring these loops into close proximity.
Collapse
Affiliation(s)
- Dmitry Cherny
- Department of Biochemistry, University of Leicester, Leicester, UK
| | | | | | | | | | | | | |
Collapse
|
30
|
Zychlinski D, Erkelenz S, Melhorn V, Baum C, Schaal H, Bohne J. Limited complementarity between U1 snRNA and a retroviral 5' splice site permits its attenuation via RNA secondary structure. Nucleic Acids Res 2010; 37:7429-40. [PMID: 19854941 PMCID: PMC2794156 DOI: 10.1093/nar/gkp694] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Multiple types of regulation are used by cells and viruses to control alternative splicing. In murine leukemia virus, accessibility of the 5′ splice site (ss) is regulated by an upstream region, which can fold into a complex RNA stem–loop structure. The underlying sequence of the structure itself is negligible, since most of it could be functionally replaced by a simple heterologous RNA stem–loop preserving the wild-type splicing pattern. Increasing the RNA duplex formation between U1 snRNA and the 5′ss by a compensatory mutation in position +6 led to enhanced splicing. Interestingly, this mutation affects splicing only in the context of the secondary structure, arguing for a dynamic interplay between structure and primary 5′ss sequence. The reduced 5′ss accessibility could also be counteracted by recruiting a splicing enhancer domain via a modified MS2 phage coat protein to a single binding site at the tip of the simple RNA stem–loop. The mechanism of 5′ss attenuation was revealed using hyperstable U1 snRNA mutants, showing that restricted U1 snRNP access is the cause of retroviral alternative splicing.
Collapse
Affiliation(s)
- Daniela Zychlinski
- Institute for Virology, Hannover Medical School, 30625 Hannover, Germany
| | | | | | | | | | | |
Collapse
|
31
|
Abstract
SummaryInsulin plays an important role in maintaining the whole organism’s homeostasis. The presence of insulin receptors in all vertebrates and invertebrates cells reflects the diversity of regulatory processes in which this hormone is involved. Furthermore, many different factors may influence the level of insulin receptor expression. These factors include e.g. the sole insulin or stage of development. Mutations in the receptor may lead to the development of insulin resistance. These mutations differ in the level of severity and are frequently associated with diabetes mellitus, hypertension, cardiovascular disorders, heart failure, metabolic syndrome and infertility in women. More than 50 mutations in insulin receptor gene have already been characterized. These mutations are associated with rare forms of insulin resistance like leprechaunism, insulin resistance type A or Rabson-Mendenhall syndrome. Molecular analysis of insulin receptor gene may lead to a better understanding of molecular mechanisms underlying various types of insulin resistance and help to develop more efficient treatment.
Collapse
|
32
|
Schwartz S, Gal-Mark N, Kfir N, Oren R, Kim E, Ast G. Alu exonization events reveal features required for precise recognition of exons by the splicing machinery. PLoS Comput Biol 2009; 5:e1000300. [PMID: 19266014 PMCID: PMC2639721 DOI: 10.1371/journal.pcbi.1000300] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2008] [Accepted: 01/23/2009] [Indexed: 12/12/2022] Open
Abstract
Despite decades of research, the question of how the mRNA splicing machinery precisely identifies short exonic islands within the vast intronic oceans remains to a large extent obscure. In this study, we analyzed Alu exonization events, aiming to understand the requirements for correct selection of exons. Comparison of exonizing Alus to their non-exonizing counterparts is informative because Alus in these two groups have retained high sequence similarity but are perceived differently by the splicing machinery. We identified and characterized numerous features used by the splicing machinery to discriminate between Alu exons and their non-exonizing counterparts. Of these, the most novel is secondary structure: Alu exons in general and their 5′ splice sites (5′ss) in particular are characterized by decreased stability of local secondary structures with respect to their non-exonizing counterparts. We detected numerous further differences between Alu exons and their non-exonizing counterparts, among others in terms of exon–intron architecture and strength of splicing signals, enhancers, and silencers. Support vector machine analysis revealed that these features allow a high level of discrimination (AUC = 0.91) between exonizing and non-exonizing Alus. Moreover, the computationally derived probabilities of exonization significantly correlated with the biological inclusion level of the Alu exons, and the model could also be extended to general datasets of constitutive and alternative exons. This indicates that the features detected and explored in this study provide the basis not only for precise exon selection but also for the fine-tuned regulation thereof, manifested in cases of alternative splicing. A typical human gene consists of 9 exons around 150 nucleotides in length, separated by introns that are ∼3,000 nucleotides long. The challenge of the splicing machinery is to precisely identify and ligate the exons, while removing the introns. We aimed to understand how the splicing machinery meets this momentous challenge, based on Alu exonization events. Alus are transposable elements, of which approximately one million copies exist in the human genome, a large portion of which within introns. Throughout evolution, some intronic Alus accumulated mutations and became recognized by the splicing machinery as exons, a process termed exonization. Such Alus remain highly similar to their non-exonizing counterparts but are perceived as different by the splicing machinery. By comparing exonizing Alus to their non-exonizing counterparts, we were able to identify numerous features in which they differ and which presumably lead to the recognition only of the former by the splicing machinery. Our findings reveal insights regarding the role of local RNA secondary structures, exon–intron architecture constraints, and splicing regulatory signals. We integrated these features in a computational model, which was able to successfully mimic the function of the splicing machinery and discriminate between true Alu exons and their intronic counterparts, highlighting the functional importance of these features.
Collapse
Affiliation(s)
- Schraga Schwartz
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Tel Aviv, Israel
| | | | | | | | | | | |
Collapse
|
33
|
Lev-Maor G, Ram O, Kim E, Sela N, Goren A, Levanon EY, Ast G. Intronic Alus influence alternative splicing. PLoS Genet 2008; 4:e1000204. [PMID: 18818740 PMCID: PMC2533698 DOI: 10.1371/journal.pgen.1000204] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2008] [Accepted: 08/20/2008] [Indexed: 01/25/2023] Open
Abstract
Examination of the human transcriptome reveals higher levels of RNA editing than in any other organism tested to date. This is indicative of extensive double-stranded RNA (dsRNA) formation within the human transcriptome. Most of the editing sites are located in the primate-specific retrotransposed element called Alu. A large fraction of Alus are found in intronic sequences, implying extensive Alu-Alu dsRNA formation in mRNA precursors. Yet, the effect of these intronic Alus on splicing of the flanking exons is largely unknown. Here, we show that more Alus flank alternatively spliced exons than constitutively spliced ones; this is especially notable for those exons that have changed their mode of splicing from constitutive to alternative during human evolution. This implies that Alu insertions may change the mode of splicing of the flanking exons. Indeed, we demonstrate experimentally that two Alu elements that were inserted into an intron in opposite orientation undergo base-pairing, as evident by RNA editing, and affect the splicing patterns of a downstream exon, shifting it from constitutive to alternative. Our results indicate the importance of intronic Alus in influencing the splicing of flanking exons, further emphasizing the role of Alus in shaping of the human transcriptome.
Collapse
Affiliation(s)
- Galit Lev-Maor
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oren Ram
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Eddo Kim
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Noa Sela
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amir Goren
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Erez Y. Levanon
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Gil Ast
- Department of Human Molecular Genetics, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| |
Collapse
|
34
|
Kim DS, Gusti V, Dery KJ, Gaur RK. Ligand-induced sequestering of branchpoint sequence allows conditional control of splicing. BMC Mol Biol 2008; 9:23. [PMID: 18267036 PMCID: PMC2275289 DOI: 10.1186/1471-2199-9-23] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2007] [Accepted: 02/12/2008] [Indexed: 12/24/2022] Open
Abstract
Background Despite tremendous progress in understanding the mechanisms of constitutive and alternative splicing, an important and widespread step along the gene expression pathway, our ability to deliberately regulate gene expression at this step remains rudimentary. The present study was performed to investigate whether a theophylline-dependent "splice switch" that sequesters the branchpoint sequence (BPS) within RNA-theophylline complex can regulate alternative splicing. Results We constructed a series of pre-mRNAs in which the BPS was inserted within theophylline aptamer. We show that theophylline-induced sequestering of BPS inhibits pre-mRNA splicing both in vitro and in vivo in a dose-dependent manner. Several lines of evidence suggest that theophylline-dependent inhibition of splicing is highly specific, and thermodynamic stability of RNA-theophylline complex as well as the location of BPS within this complex affects the efficiency of splicing inhibition. Finally, we have constructed an alternative splicing model pre-mRNA substrate in which theophylline caused exon skipping both in vitro and in vivo, suggesting that a small molecule-RNA interaction can modulate alternative splicing. Conclusion These findings provide the ability to control splicing pattern at will and should have important implications for basic, biotechnological, and biomedical research.
Collapse
Affiliation(s)
- Dong-Suk Kim
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
| | | | | | | |
Collapse
|
35
|
Wang P, Lyman RF, Shabalina SA, Mackay TFC, Anholt RRH. Association of polymorphisms in odorant-binding protein genes with variation in olfactory response to benzaldehyde in Drosophila. Genetics 2007; 177:1655-65. [PMID: 17720903 PMCID: PMC2147940 DOI: 10.1534/genetics.107.079731] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Adaptive evolution of animals depends on behaviors that are essential for their survival and reproduction. The olfactory system of Drosophila melanogaster has emerged as one of the best characterized olfactory systems, which in addition to a family of odorant receptors, contains an approximately equal number of odorant-binding proteins (OBPs), encoded by a multigene family of 51 genes. Despite their abundant expression, little is known about their role in chemosensation, largely due to the lack of available mutations in these genes. We capitalized on naturally occurring mutations (polymorphisms) to gain insights into their functions. We analyzed the sequences of 13 Obp genes in two chromosomal clusters in a population of wild-derived inbred lines, and asked whether polymorphisms in these genes are associated with variation in olfactory responsiveness. Four polymorphisms in 3 Obp genes exceeded the statistical permutation threshold for association with responsiveness to benzaldehyde, suggesting redundancy and/or combinatorial recognition by these OBPs of this odorant. Model predictions of alternative pre-mRNA secondary structures associated with polymorphic sites suggest that alterations in Obp mRNA structure could contribute to phenotypic variation in olfactory behavior.
Collapse
Affiliation(s)
- Ping Wang
- Department of Genetics, North Carolina State University, Raleigh, North Carolina 27695, USA
| | | | | | | | | |
Collapse
|
36
|
Simon R, Starlinger P. Transposable element Ds2 of Zea mays influences polyadenylation and splice site selection. ACTA ACUST UNITED AC 2006; 209:198-9. [PMID: 17186624 DOI: 10.1007/bf00329859] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the allele adh1-2F11 of Zea mays the 1.3 kb transposable element Ds2 is inserted in the fourth exon of Adh1. Two major RNAs of 3.0 and 1.6 kb are transcribed from this allele. While the 3.0 kb transcript also contains the Ds2 sequences, the 1.6 kb transcript has lost the Ds2 sequences by an alternative splicing process. In this process, a normal 5' splice site is joined to a cryptic 3' splice site located within exon 4. This cryptic 3' splice site is not used in a wild-type Adh1F allele. Other minor transcripts of adh1-2F11 are prematurely terminated and polyadenylated.
Collapse
Affiliation(s)
- R Simon
- Institut für Genetik, Universität zu Köln, D-5000 Köln 41, Federal Republic of Germany
| | | |
Collapse
|
37
|
Kim DS, Gusti V, Pillai SG, Gaur RK. An artificial riboswitch for controlling pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2005; 11:1667-77. [PMID: 16244133 PMCID: PMC1370853 DOI: 10.1261/rna.2162205] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Riboswitches, as previously reported, are natural RNA aptamers that regulate the expression of numerous bacterial metabolic genes in response to small molecule ligands. It has recently been shown that these RNA genetic elements are also present near the splice site junctions of plant and fungal introns, thus raising the possibility of their involvement in regulating mRNA splicing. Here it is shown for the first time that a riboswitch can be engineered to regulate pre-mRNA splicing in vitro. We show that insertion of a high-affinity theophylline binding aptamer into the 3' splice site (3' ss) region of a model pre-mRNA (AdML-Theo29AG) enables its splicing to be repressed by the addition theophylline. Our results indicate that the location of 3' ss AG within the aptamer plays a crucial role in conferring theophylline-dependent control of pre-mRNA splicing. We also show that theophylline-mediated control of pre-mRNA splicing is highly specific by first demonstrating that a small molecule ligand similar in shape and size to theophylline had no effect on the splicing of AdML-Theo29AG pre-mRNA. Second, theophylline failed to exert any influence on the splicing of a pre-mRNA that does not contain its binding site. Third, theophylline specifically blocks the step II of the splicing reaction. Finally, we provide evidence that theophylline-dependent control of pre-mRNA splicing is functionally relevant.
Collapse
Affiliation(s)
- Dong-Suk Kim
- Division of Molecular Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | | | | | | |
Collapse
|
38
|
McAlinden A, Havlioglu N, Liang L, Davies SR, Sandell LJ. Alternative splicing of type II procollagen exon 2 is regulated by the combination of a weak 5' splice site and an adjacent intronic stem-loop cis element. J Biol Chem 2005; 280:32700-11. [PMID: 16076844 DOI: 10.1074/jbc.m505940200] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative splicing of the type II procollagen gene (COL2A1) is developmentally regulated during chondrogenesis. Chondroprogenitor cells produce the type IIA procollagen isoform by splicing (including) exon 2 during pre-mRNA processing, whereas differentiated chondrocytes synthesize the type IIB procollagen isoform by exon 2 skipping (exclusion). Using a COL2A1 mini-gene and chondrocytes at various stages of differentiation, we identified a non-classical consensus splicing sequence in intron 2 adjacent to the 5' splice site, which is essential in regulating exon 2 splicing. RNA mapping confirmed this region contains secondary structure in the form of a stem-loop. Mutational analysis identified three cis elements within the conserved double-stranded stem region that are functional only in the context of the natural weak 5' splice site of exon 2; they are 1) a uridine-rich enhancer element in all cell types tested except differentiated chondrocytes; 2) an adenine-rich silencer element, and 3) an enhancer cis element functional in the context of secondary structure. This is the first report identifying key cis elements in the COL2A1 gene that modulate the cell type-specific alternative splicing switch of exon 2 during cartilage development.
Collapse
Affiliation(s)
- Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St Louis, Missouri 63110, USA.
| | | | | | | | | |
Collapse
|
39
|
Haddrill PR, Charlesworth B, Halligan DL, Andolfatto P. Patterns of intron sequence evolution in Drosophila are dependent upon length and GC content. Genome Biol 2005; 6:R67. [PMID: 16086849 PMCID: PMC1273634 DOI: 10.1186/gb-2005-6-8-r67] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2005] [Revised: 04/25/2005] [Accepted: 06/29/2005] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Introns comprise a large fraction of eukaryotic genomes, yet little is known about their functional significance. Regulatory elements have been mapped to some introns, though these are believed to account for only a small fraction of genome wide intronic DNA. No consistent patterns have emerged from studies that have investigated general levels of evolutionary constraint in introns. RESULTS We examine the relationship between intron length and levels of evolutionary constraint by analyzing inter-specific divergence at 225 intron fragments in Drosophila melanogaster and Drosophila simulans, sampled from a broad distribution of intron lengths. We document a strongly negative correlation between intron length and divergence. Interestingly, we also find that divergence in introns is negatively correlated with GC content. This relationship does not account for the correlation between intron length and divergence, however, and may simply reflect local variation in mutational rates or biases. CONCLUSION Short introns make up only a small fraction of total intronic DNA in the genome. Our finding that long introns evolve more slowly than average implies that, while the majority of introns in the Drosophila genome may experience little or no selective constraint, most intronic DNA in the genome is likely to be evolving under considerable constraint. Our results suggest that functional elements may be ubiquitous within longer introns and that these introns may have a more general role in regulating gene expression than previously appreciated. Our finding that GC content and divergence are negatively correlated in introns has important implications for the interpretation of the correlation between divergence and levels of codon bias observed in Drosophila.
Collapse
Affiliation(s)
- Penelope R Haddrill
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Daniel L Halligan
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Peter Andolfatto
- Section of Ecology, Behavior and Evolution, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
40
|
Glazov EA, Pheasant M, McGraw EA, Bejerano G, Mattick JS. Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res 2005; 15:800-8. [PMID: 15899965 PMCID: PMC1142470 DOI: 10.1101/gr.3545105] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2004] [Accepted: 03/29/2005] [Indexed: 12/19/2022]
Abstract
Recently, we identified a large number of ultraconserved (uc) sequences in noncoding regions of human, mouse, and rat genomes that appear to be essential for vertebrate and amniote ontogeny. Here, we used similar methods to identify ultraconserved genomic regions between the insect species Drosophila melanogaster and Drosophila pseudoobscura, as well as the more distantly related Anopheles gambiae. As with vertebrates, ultraconserved sequences in insects appear to occur primarily in intergenic and intronic sequences, and at intron-exon junctions. The sequences are significantly associated with genes encoding developmental regulators and transcription factors, but are less frequent and are smaller in size than in vertebrates. The longest identical, nongapped orthologous match between the three genomes was found within the homothorax (hth) gene. This sequence spans an internal exon-intron junction, with the majority located within the intron, and is predicted to form a highly stable stem-loop RNA structure. Real-time quantitative PCR analysis of different hth splice isoforms and Northern blotting showed that the conserved element is associated with a high incidence of intron retention in hth pre-mRNA, suggesting that the conserved intronic element is critically important in the post-transcriptional regulation of hth expression in Diptera.
Collapse
Affiliation(s)
- Evgeny A Glazov
- ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | | | | | | | | |
Collapse
|
41
|
Affiliation(s)
- Emanuele Buratti
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, 34012 Trieste, Italy
| | | |
Collapse
|
42
|
Ng AK, Block TM, Aiamkitsumrit B, Wang M, Clementi E, Wu TT, Taylor JM, Su YH. Construction of a herpes simplex virus type 1 mutant with only a three-nucleotide change in the branchpoint region of the latency-associated transcript (LAT) and the stability of its two-kilobase LAT intron. J Virol 2004; 78:12097-106. [PMID: 15507596 PMCID: PMC525071 DOI: 10.1128/jvi.78.22.12097-12106.2004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Previous studies using a eukaryotic expression system indicated that the unusual stability of the latency-associated transcript (LAT) intron was due to its nonconsensus branchpoint sequence (T.-T Wu, Y.-H. Su, T. M. Block, and J. M. Taylor, Virology, 243:140-149, 1998). The present study investigated the role of the branchpoint sequence in the stability of the intron expressed from the herpes simplex virus type 1 (HSV-1) genome and the role of LAT intron stability in the HSV-1 life cycle. A branchpoint mutant called Sy2 and the corresponding rescued viruses, SyRA and SyRB, were constructed. To preserve the coding sequence of the immediate early gene icp0, which overlaps with the branchpoint region of the 2-kb LAT, a 3-nucleotide mutation into the branchpoint region of the 2-kb LAT was introduced, resulting in a branchpoint that is 85% identical to the consensus intron branchpoint sequence of eukaryotic cells. As anticipated, there was a 90- to 96-fold reduction in 2-kb LAT accumulation following productive infection in tissue culture and latent infection in mice with Sy2, as determined by Northern blot analysis. These results clearly suggest that the accumulation of the 2-kb intron in tissue culture and in vivo is, at least in part, due to the nonconsensus branchpoint sequence of the LAT intron. Interestingly, a failure to accumulate LAT was associated with greater progeny production of Sy2 at a low multiplicity of infection (0.01) in tissue culture, but not in mice. However, the ability of mutant Sy2 to reactivate from trigeminal ganglia (TG) derived from latently infected mice was indistinguishable from that of wild-type virus, as assayed in the mouse TG explant reactivation system.
Collapse
Affiliation(s)
- Alan K Ng
- Department of Biochemistry and Molecular Pharmacology, Jefferson Center for Biomedical Research, Thomas Jefferson University, 700 E. Butler Avenue, Doylestown, PA 18901-2697, USA
| | | | | | | | | | | | | | | |
Collapse
|
43
|
Buchroithner B, Klausegger A, Ebschner U, Anton-Lamprecht I, Pohla-Gubo G, Lanschuetzer CM, Laimer M, Hintner H, Bauer JW. Analysis of the LAMB3 gene in a junctional epidermolysis bullosa patient reveals exonic splicing and allele-specific nonsense-mediated mRNA decay. J Transl Med 2004; 84:1279-88. [PMID: 15311214 DOI: 10.1038/labinvest.3700164] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
How splicing, the process of intron removal in pre-messenger RNA (mRNA), is carried out with such fidelity in human cells is still not understood, although some general rules are being proposed mainly by in vitro experiments. These rules are currently being redefined by analysis of splicing mechanisms in patients presenting splicing defects. We analysed material of a patient suffering from junctional epidermolysis bullosa, a heritable blistering skin disease. Absence of laminin-5 protein together with hypoplastic hemidesmosomes at the dermo-epidermal junction in the patient's skin was shown by immunohistochemical analysis and immunoelectron microscopy. Subsequent DNA analysis revealed heterozygosity for the mutations R635X and 3009C-->T in the LAMB3 gene. The latter did not alter codon translation, but introduced an exonic splice site in exon 20. Interestingly, this exonic splice site, which presented a splice score of only 68.6, was preferentially used by the spliceosome over the wild-type splice site at the exon 20-intron 20 border, which showed a splice score of 92.2. LAMB3 mRNA was still detectable in RT-PCR analysis although the aberrantly spliced mRNA leads to a stop codon in exon 21, 5' of the commonly assumed 3' border for nonsense-mediated mRNA decay. These results describe an exception to the proposed rules of pre-mRNA splicing and RNA degradation.
Collapse
Affiliation(s)
- Birgit Buchroithner
- Department of Dermatology, Paracelsus Private Medical University of Salzburg, Salzburg, Austria
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Cabello-Villegas J, Giles KE, Soto AM, Yu P, Mougin A, Beemon KL, Wang YX. Solution structure of the pseudo-5' splice site of a retroviral splicing suppressor. RNA (NEW YORK, N.Y.) 2004; 10:1388-1398. [PMID: 15317975 PMCID: PMC1370626 DOI: 10.1261/rna.7020804] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2004] [Accepted: 06/09/2004] [Indexed: 05/24/2023]
Abstract
Control of Rous sarcoma virus RNA splicing depends in part on the interaction of U1 and U11 snRNPs with an intronic RNA element called the negative regulator of splicing (NRS). A 23mer RNA hairpin (NRS23) of the NRS directly binds U1 and U11 snRNPs. Mutations that disrupt base-pairing between the loop of NRS23 and U1 snRNA abolish its negative control of splicing. We have determined the solution structure of NRS23 using NOEs, torsion angles, and residual dipolar couplings that were extracted from multidimensional heteronuclear NMR spectra. Our structure showed that the 6-bp stem of NRS23 adopts a nearly A-form duplex conformation. The loop, which consists of 11 residues according to secondary structure probing, was in a closed conformation. U913, the first residue in the loop, was bulged out or dynamic, and loop residues G914-C923, G915-U922, and U916-A921 were base-paired. The remaining UUGU tetraloop sequence did not adopt a stable structure and appears flexible in solution. This tetraloop differs from the well-known classes of tetraloops (GNRA, CUYG, UNCG) in terms of its stability, structure, and function. Deletion of the bulged U913, which is not complementary to U1 snRNA, increased the melting temperature of the RNA hairpin. This hyperstable hairpin exhibited a significant decrease in binding to U1 snRNP. Thus, the structure of the NRS RNA, as well as its sequence, is important for interaction with U1 snRNP and for splicing suppression.
Collapse
Affiliation(s)
- Javier Cabello-Villegas
- Protein-Nucleic Acid Interaction Section, Structural Biophysics Laboratory, CCR, National Cancer Institute-Frederick, National Institutes of Health, MD 21702, USA
| | | | | | | | | | | | | |
Collapse
|
45
|
Scamborova P, Wong A, Steitz JA. An intronic enhancer regulates splicing of the twintron of Drosophila melanogaster prospero pre-mRNA by two different spliceosomes. Mol Cell Biol 2004; 24:1855-69. [PMID: 14966268 PMCID: PMC350559 DOI: 10.1128/mcb.24.5.1855-1869.2004] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We have examined the alternative splicing of the Drosophila melanogaster prospero twintron, which contains splice sites for both the U2- and U12-type spliceosome and generates two forms of mRNA, pros-L (U2-type product) and pros-S (U12-type product). We find that twintron splicing is developmentally regulated: pros-L is abundant in early embryogenesis while pros-S displays the opposite pattern. We have established a Kc cell in vitro splicing system that accurately splices a minimal pros substrate containing the twintron and have examined the sequence requirements for pros twintron splicing. Systematic deletion and mutation analysis of intron sequences established that twintron splicing requires a 46-nucleotide purine-rich element located 32 nucleotides downstream of the U2-type 5' splice site. While this element regulates both splicing pathways, its alteration showed the severest effects on the U2-type splicing pathway. Addition of an RNA competitor containing the wild-type purine-rich element to the Kc extract abolished U2-type splicing and slightly repressed U12-type splicing, suggesting that a trans-acting factor(s) binds the enhancer element to stimulate twintron splicing. Thus, we have identified an intron region critical for prospero twintron splicing as a first step towards elucidating the molecular mechanism of splicing regulation involving competition between the two kinds of spliceosomes.
Collapse
Affiliation(s)
- Petra Scamborova
- Department of Molecular Biophysics and Biochemistry, Yale University Howard Hughes Medical Institute, New Haven, Connecticut 06536-9812, USA
| | | | | |
Collapse
|
46
|
Chabot B, LeBel C, Hutchison S, Nasim FH, Simard MJ. Heterogeneous nuclear ribonucleoprotein particle A/B proteins and the control of alternative splicing of the mammalian heterogeneous nuclear ribonucleoprotein particle A1 pre-mRNA. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2003; 31:59-88. [PMID: 12494763 DOI: 10.1007/978-3-662-09728-1_3] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Affiliation(s)
- B Chabot
- Département de Microbiologie et d'Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
| | | | | | | | | |
Collapse
|
47
|
Muh SJ, Hovhannisyan RH, Carstens RP. A Non-sequence-specific double-stranded RNA structural element regulates splicing of two mutually exclusive exons of fibroblast growth factor receptor 2 (FGFR2). J Biol Chem 2002; 277:50143-54. [PMID: 12393912 DOI: 10.1074/jbc.m207409200] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Alternative splicing of fibroblast growth factor receptor 2 (FGFR2) mutually exclusive exons IIIb and IIIc represents a tightly regulated and functionally relevant example of post-transcriptional gene regulation. Rat prostate cancer DT3 and AT3 cell lines demonstrate exclusive selection of either exon IIIb or exon IIIc, respectively, and have been used to characterize regulatory FGFR2 RNA cis-elements that are required for splicing regulation. Two sequences termed ISE-2 and ISAR are located in the intron between exons IIIb and IIIc and are required for cell-type specific exon IIIb. Previous studies suggest that the function of these elements involves formation of an RNA stem structure, even though they are separated by more than 700 nucleotides. Using transfected minigenes, we performed a systematic analysis of the sequence and structural components of ISE-2 and ISAR that are required for their ability to regulate FGFR2 splicing. We found that the primary sequence of these elements can be replaced by completely unrelated sequences, provided that they are also predicted to form an RNA stem structure. Thus, a nonsequence-specific double stranded RNA stem constitutes a functional element required for FGFR2 splicing; suggesting that a double-stranded RNA binding protein is a component of the splicing regulatory machinery.
Collapse
MESH Headings
- Alternative Splicing
- Animals
- Base Sequence
- Cells, Cultured
- Conserved Sequence
- Exons
- Gene Expression Regulation
- Humans
- Introns
- Mice
- Models, Biological
- Models, Genetic
- Molecular Sequence Data
- Mutation
- Nucleic Acid Conformation
- Plasmids/metabolism
- RNA/metabolism
- RNA Splicing
- RNA, Double-Stranded/chemistry
- Rats
- Receptor Protein-Tyrosine Kinases/biosynthesis
- Receptor Protein-Tyrosine Kinases/genetics
- Receptor, Fibroblast Growth Factor, Type 1
- Receptor, Fibroblast Growth Factor, Type 2
- Receptors, Fibroblast Growth Factor/biosynthesis
- Receptors, Fibroblast Growth Factor/genetics
- Reverse Transcriptase Polymerase Chain Reaction
- Transfection
- Tumor Cells, Cultured
- Xenopus
- Xenopus Proteins
Collapse
Affiliation(s)
- Stephanie J Muh
- Renal-Electrolyte and Hypertension Division, Department of Medicine, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6144, USA
| | | | | |
Collapse
|
48
|
Abstract
Transcription and pre-mRNA splicing are tightly coupled gene expression events in eukaryotic cells. An interaction between the carboxy-terminal domain of the largest subunit of RNA polymerase (Pol) II and components of the splicing machinery is postulated to mediate this coupling. Here, we show that splicing factors function directly to promote transcriptional elongation, demonstrating that transcription is more intimately coupled to splicing than previously thought. The spliceosomal U small nuclear ribonucleoproteins (snRNPs) interact with human transcription elongation factor TAT-SF1 (refs 6,7,8,9) and strongly stimulate polymerase elongation when directed to an intron-free human immunodeficiency virus-1 (HIV-1) template. This effect is likely to be mediated through the binding of TAT-SF1 to elongation factor P-TEFb, a proposed component of the transcription elongation complex. Inclusion of splicing signals in the nascent transcript further stimulates transcription, supporting the notion that the recruitment of U snRNPs near the elongating polymerase is important for transcription. Because the TAT-SF1-U snRNP complex also stimulates splicing in vitro, it may serve as a dual-function factor to couple transcription and splicing and to facilitate their reciprocal activation.
Collapse
Affiliation(s)
- Y W Fong
- Department of Molecular Biology, University of California at Berkeley, California, 94720-3206, USA
| | | |
Collapse
|
49
|
Franchina M, Hooper J, Kay PH. Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes. Int J Biochem Cell Biol 2001; 33:1104-15. [PMID: 11551826 DOI: 10.1016/s1357-2725(01)00074-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Alternative splicing of RNA molecules transcribed from DNA (cytosine-5) methyltransferases has been proposed as a mechanism by which methylation is able to effect diverse biological processes in higher eukaryotes. This study has investigated transcriptional versatility of DNA (cytosine-5) methyltransferase 2, which may methylate cytosine residues within 5'-CCTGG-3' pentanucleotides in regions of the human genome devoid of 5'-CG-3' methylation. Five novel splice variants of DNA (cytosine-5) methyltransferase 2 were identified in the peripheral blood leukocytes of healthy subjects following cloning and sequencing of RT-PCR products amplified using gene specific oligodeoxyribonucleotide primers. The generation of some of these splice variants may be influenced by the formation of secondary structures within pre-mRNA due to the repetition of sequences flanking alternatively spliced exons in a reverse and complementary orientation on the same strand. These findings enable novel approaches to investigate the role of RNA secondary structures in alternative splicing. The DNA (cytosine-5) methyltransferase 2 splice variants are generated in all the major cell types of peripheral blood, as well as in neoplastic lymphoid cells indicating that they are unlikely to generate proteins involved in control of the cell cycle or cellular differentiation. Interestingly, the gene products generated by some splice variants completely or partially lack highly conserved amino acid motifs shown to be important for the catalysis of cytosine methylation. The possibility cannot be excluded, therefore, that alternative splicing of DNA (cytosine-5) methyltransferase 2 pre-mRNA may generate protein isoforms which have different methylating capabilities or which are involved in biological processes other than the catalysis of cytosine methylation.
Collapse
Affiliation(s)
- M Franchina
- Molecular Pathology Laboratory, Department of Pathology, The University of Western Australia, WA 6907, Nedlands, Australia
| | | | | |
Collapse
|
50
|
Hummel HS, Gillespie RD, Swindle J. Mutational analysis of 3' splice site selection during trans-splicing. J Biol Chem 2000; 275:35522-31. [PMID: 10938269 DOI: 10.1074/jbc.m002424200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
trans-Splicing is essential for mRNA maturation in trypanosomatids. A conserved AG dinucleotide serves as the 3' splice acceptor site, and analysis of native processing sites suggests that selection of this site is determined according to a 5'-3' scanning model. A series of stable gene replacement lines were generated that carried point mutations at or near the 3' splice site within the intergenic region separating CUB2.65, the calmodulin-ubiquitin associated gene, and FUS1, the ubiquitin fusion gene of Trypanosoma cruzi. In one stable line, the elimination of the native 3' splice acceptor site led to the accumulation of Y-branched splicing intermediates, which served as templates for mapping the first trans-splicing branch points in T. cruzi. In other lines, point mutations shifted the position of the first consensus AG dinucleotide either upstream or downstream of the wild-type 3' splice acceptor site in this intergenic region. Consistent with the scanning model, the first AG dinucleotide downstream of the branch points was used as the predominant 3' splice acceptor site. In all of the stable lines, the point mutations affected splicing efficiency in this region.
Collapse
Affiliation(s)
- H S Hummel
- Department of Microbiology and Immunology, University of Tennessee, Memphis, Tennessee 38163, USA
| | | | | |
Collapse
|