1
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Lee S, Aubee JI, Lai EC. Regulation of alternative splicing and polyadenylation in neurons. Life Sci Alliance 2023; 6:e202302000. [PMID: 37793776 PMCID: PMC10551640 DOI: 10.26508/lsa.202302000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
Cell-type-specific gene expression is a fundamental feature of multicellular organisms and is achieved by combinations of regulatory strategies. Although cell-restricted transcription is perhaps the most widely studied mechanism, co-transcriptional and post-transcriptional processes are also central to the spatiotemporal control of gene functions. One general category of expression control involves the generation of multiple transcript isoforms from an individual gene, whose balance and cell specificity are frequently tightly regulated via diverse strategies. The nervous system makes particularly extensive use of cell-specific isoforms, specializing the neural function of genes that are expressed more broadly. Here, we review regulatory strategies and RNA-binding proteins that direct neural-specific isoform processing. These include various classes of alternative splicing and alternative polyadenylation events, both of which broadly diversify the neural transcriptome. Importantly, global alterations of splicing and alternative polyadenylation are characteristic of many neural pathologies, and recent genetic studies demonstrate how misregulation of individual neural isoforms can directly cause mutant phenotypes.
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Affiliation(s)
- Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Joseph I Aubee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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2
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Xie J, Wang L, Lin RJ. Variations of intronic branchpoint motif: identification and functional implications in splicing and disease. Commun Biol 2023; 6:1142. [PMID: 37949953 PMCID: PMC10638238 DOI: 10.1038/s42003-023-05513-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023] Open
Abstract
The branchpoint (BP) motif is an essential intronic element for spliceosomal pre-mRNA splicing. In mammals, its sequence composition, distance to the downstream exon, and number of BPs per 3´ splice site are highly variable, unlike the GT/AG dinucleotides at the intron ends. These variations appear to provide evolutionary advantages for fostering alternative splicing, satisfying more diverse cellular contexts, and promoting resilience to genetic changes, thus contributing to an extra layer of complexity for gene regulation. Importantly, variants in the BP motif itself or in genes encoding BP-interacting factors cause human genetic diseases or cancers, highlighting the critical function of BP motif and the need to precisely identify functional BPs for faithful interpretation of their roles in splicing. In this perspective, we will succinctly summarize the major findings related to BP motif variations, discuss the relevant issues/challenges, and provide our insights.
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Affiliation(s)
- Jiuyong Xie
- Department of Physiology & Pathophysiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, R3E 0J9, Canada.
| | - Lili Wang
- Department of Systems Biology, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
| | - Ren-Jang Lin
- Center for RNA Biology & Therapeutics, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA.
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3
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Hoppe ER, Udy DB, Bradley RK. Recursive splicing discovery using lariats in total RNA sequencing. Life Sci Alliance 2023; 6:e202201889. [PMID: 37137707 PMCID: PMC10156609 DOI: 10.26508/lsa.202201889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023] Open
Abstract
Recursive splicing is a non-canonical splicing mechanism in which an intron is removed in segments via multiple splicing reactions. Relatively few recursive splice sites have been identified with high confidence in human introns, and more comprehensive analyses are needed to better characterize where recursive splicing happens and whether or not it has a regulatory function. In this study, we use an unbiased approach using intron lariats to search for recursive splice sites in constitutive introns and alternative exons in the human transcriptome. We find evidence for recursive splicing in a broader range of intron sizes than previously reported and detail a new location for recursive splicing at the distal ends of cassette exons. In addition, we identify evidence for the conservation of these recursive splice sites among higher vertebrates and the use of these sites to influence alternative exon exclusion. Together, our data demonstrate the prevalence of recursive splicing and its potential influence on gene expression through alternatively spliced isoforms.
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Affiliation(s)
- Emma R Hoppe
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dylan B Udy
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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4
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Transcriptome-Wide Detection of Intron/Exon Definition in the Endogenous Pre-mRNA Transcripts of Mammalian Cells and Its Regulation by Depolarization. Int J Mol Sci 2022; 23:ijms231710157. [PMID: 36077555 PMCID: PMC9456152 DOI: 10.3390/ijms231710157] [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: 08/11/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/23/2022] Open
Abstract
Pairing of splice sites across an intron or exon is the central point of intron or exon definition in pre-mRNA splicing with the latter mode proposed for most mammalian exons. However, transcriptome-wide pairing within endogenous transcripts has not been examined for the prevalence of each mode in mammalian cells. Here we report such pairings in rat GH3 pituitary cells by measuring the relative abundance of nuclear RNA-Seq reads at the intron start or end (RISE). Interestingly, RISE indexes are positively correlated between 5′ and 3′ splice sites specifically across introns or exons but inversely correlated with the usage of adjacent exons. Moreover, the ratios between the paired indexes were globally modulated by depolarization, which was disruptible by 5-aza-Cytidine. The nucleotide matrices of the RISE-positive splice sites deviate significantly from the rat consensus, and short introns or exons are enriched with the cross-intron or -exon RISE pairs, respectively. Functionally, the RISE-positive genes cluster for basic cellular processes including RNA binding/splicing, or more specifically, hormone production if regulated by depolarization. Together, the RISE analysis identified the transcriptome-wide regulation of either intron or exon definition between weak splice sites of short introns/exons in mammalian cells. The analysis also provides a way to further track the splicing intermediates and intron/exon definition during the dynamic regulation of alternative splicing by extracellular factors.
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5
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Pitolli C, Marini A, Sette C, Pagliarini V. Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer. Int J Mol Sci 2022; 23:ijms23052811. [PMID: 35269953 PMCID: PMC8911335 DOI: 10.3390/ijms23052811] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
The advance of experimental and computational techniques has allowed us to highlight the existence of numerous different mechanisms of RNA maturation, which have been so far unknown. Besides canonical splicing, consisting of the removal of introns from pre-mRNA molecules, non-canonical splicing events may occur to further increase the regulatory and coding potential of the human genome. Among these, splicing of microexons, recursive splicing and biogenesis of circular and chimeric RNAs through back-splicing and trans-splicing processes, respectively, all contribute to expanding the repertoire of RNA transcripts with newly acquired regulatory functions. Interestingly, these non-canonical splicing events seem to occur more frequently in the central nervous system, affecting neuronal development and differentiation programs with important implications on brain physiology. Coherently, dysregulation of non-canonical RNA processing events is associated with brain disorders, including brain tumours. Herein, we summarize the current knowledge on molecular and regulatory mechanisms underlying canonical and non-canonical splicing events with particular emphasis on cis-acting elements and trans-acting factors that all together orchestrate splicing catalysis reactions and decisions. Lastly, we review the impact of non-canonical splicing on brain physiology and pathology and how unconventional splicing mechanisms may be targeted or exploited for novel therapeutic strategies in cancer.
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Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Alberto Marini
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
- Correspondence:
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6
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Prudêncio P, Savisaar R, Rebelo K, Martinho RG, Carmo-Fonseca M. Transcription and splicing dynamics during early Drosophila development. RNA (NEW YORK, N.Y.) 2022; 28:139-161. [PMID: 34667107 PMCID: PMC8906543 DOI: 10.1261/rna.078933.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/23/2021] [Indexed: 05/03/2023]
Abstract
Widespread cotranscriptional splicing has been demonstrated from yeast to human. However, most studies to date addressing the kinetics of splicing relative to transcription used either Saccharomyces cerevisiae or metazoan cultured cell lines. Here, we adapted native elongating transcript sequencing technology (NET-seq) to measure cotranscriptional splicing dynamics during the early developmental stages of Drosophila melanogaster embryos. Our results reveal the position of RNA polymerase II (Pol II) when both canonical and recursive splicing occur. We found heterogeneity in splicing dynamics, with some RNAs spliced immediately after intron transcription, whereas for other transcripts no splicing was observed over the first 100 nt of the downstream exon. Introns that show splicing completion before Pol II has reached the end of the downstream exon are necessarily intron-defined. We studied the splicing dynamics of both nascent pre-mRNAs transcribed in the early embryo, which have few and short introns, as well as pre-mRNAs transcribed later in embryonic development, which contain multiple long introns. As expected, we found a relationship between the proportion of spliced reads and intron size. However, intron definition was observed at all intron sizes. We further observed that genes transcribed in the early embryo tend to be isolated in the genome whereas genes transcribed later are often overlapped by a neighboring convergent gene. In isolated genes, transcription termination occurred soon after the polyadenylation site, while in overlapped genes, Pol II persisted associated with the DNA template after cleavage and polyadenylation of the nascent transcript. Taken together, our data unravel novel dynamic features of Pol II transcription and splicing in the developing Drosophila embryo.
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Affiliation(s)
- Pedro Prudêncio
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
| | - Rosina Savisaar
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Kenny Rebelo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Rui Gonçalo Martinho
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Department of Medical Sciences and Institute for Biomedicine (iBiMED), Universidade de Aveiro, 3810-193 Aveiro, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
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7
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Moon S, Zhao YT. Recursive splicing is a rare event in the mouse brain. PLoS One 2022; 17:e0263082. [PMID: 35089962 PMCID: PMC8797253 DOI: 10.1371/journal.pone.0263082] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/11/2022] [Indexed: 11/18/2022] Open
Abstract
Recursive splicing (RS) is a splicing mechanism to remove long introns from messenger RNA precursors of long genes. Compared to the hundreds of RS events identified in humans and drosophila, only ten RS events have been reported in mice. To further investigate RS in mice, we analyzed RS in the mouse brain, a tissue that is enriched in the expression of long genes. We found that nuclear total RNA sequencing is an efficient approach to investigate RS events. We analyzed 1.15 billion uniquely mapped reads from the nuclear total RNA sequencing data in the mouse cerebral cortex. Unexpectedly, we only identified 20 RS sites, suggesting that RS is a rare event in the mouse brain. We also identified that RS is constitutive between excitatory and inhibitory neurons and between sexes in the mouse cerebral cortex. In addition, we found that the primary sequence context is associated with RS splicing intermediates and distinguishes RS AGGT site from non-RS AGGT sites, indicating the importance of the primary sequence context in RS sites. Moreover, we discovered that cryptic exons may use an RS-like mechanism for splicing. Overall, we provide novel findings about RS in long genes in the mouse brain.
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Affiliation(s)
- Sohyun Moon
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, United States of America
| | - Ying-Tao Zhao
- Department of Biomedical Sciences, New York Institute of Technology College of Osteopathic Medicine, Old Westbury, New York, United States of America
- * E-mail:
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8
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Kumari A, Sedehizadeh S, Brook JD, Kozlowski P, Wojciechowska M. Differential fates of introns in gene expression due to global alternative splicing. Hum Genet 2021; 141:31-47. [PMID: 34907472 PMCID: PMC8758631 DOI: 10.1007/s00439-021-02409-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023]
Abstract
The discovery of introns over four decades ago revealed a new vision of genes and their interrupted arrangement. Throughout the years, it has appeared that introns play essential roles in the regulation of gene expression. Unique processing of excised introns through the formation of lariats suggests a widespread role for these molecules in the structure and function of cells. In addition to rapid destruction, these lariats may linger on in the nucleus or may even be exported to the cytoplasm, where they remain stable circular RNAs (circRNAs). Alternative splicing (AS) is a source of diversity in mature transcripts harboring retained introns (RI-mRNAs). Such RNAs may contain one or more entire retained intron(s) (RIs), but they may also have intron fragments resulting from sequential excision of smaller subfragments via recursive splicing (RS), which is characteristic of long introns. There are many potential fates of RI-mRNAs, including their downregulation via nuclear and cytoplasmic surveillance systems and the generation of new protein isoforms with potentially different functions. Various reports have linked the presence of such unprocessed transcripts in mammals to important roles in normal development and in disease-related conditions. In certain human neurological-neuromuscular disorders, including myotonic dystrophy type 2 (DM2), frontotemporal dementia/amyotrophic lateral sclerosis (FTD/ALS) and Duchenne muscular dystrophy (DMD), peculiar processing of long introns has been identified and is associated with their pathogenic effects. In this review, we discuss different mechanisms involved in the processing of introns during AS and the functions of these large sections of the genome in our biology.
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Affiliation(s)
- Anjani Kumari
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Saam Sedehizadeh
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - John David Brook
- Queen's Medical Centre, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marzena Wojciechowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland. .,Department of Rare Human Diseases, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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9
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Joseph B, Scala C, Kondo S, Lai EC. Molecular and genetic dissection of recursive splicing. Life Sci Alliance 2021; 5:5/1/e202101063. [PMID: 34759052 PMCID: PMC8605326 DOI: 10.26508/lsa.202101063] [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: 02/22/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 11/24/2022] Open
Abstract
Intronic ratchet points (RPs) are abundant within long introns in the Drosophila genome and consist of juxtaposed splice acceptor and splice donor (SD) sites. Although they appear to encompass zero-nucleotide exons, we recently clarified that intronic recursive splicing (RS) requires a cryptic exon at the RP (an RS-exon), which is subsequently always skipped and thus absent from mRNA. In addition, Drosophila encodes a smaller set of expressed exons bearing features of RS. Here, we investigate mechanisms that regulate the choice between RP and RS-exon SDs. First, analysis of Drosophila RP SD mutants demonstrates that SD competition suppresses inclusion of cryptic exons in endogenous contexts. Second, characterization of RS-exon reporters implicates exonic sequences as influencing choice of RS-exon usage. Using RS-exon swap and mutagenesis assays, we show exonic sequences can determine RS-exon inclusion. Finally, we provide evidence that splicing can suppress utilization of RP SDs to enable RS-exon expression. Overall, multiple factors can influence splicing of Drosophila RS-exons, which usually result in their complete suppression as zero-nucleotide RPs, but occasionally yield translated RS-exons.
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Affiliation(s)
- Brian Joseph
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA .,Louis V Gerstner, Jr Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Chaz Scala
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Shu Kondo
- Research Building 11F, Tokyo University of Science, Tokyo, Japan
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
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10
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Ustaoglu P, Gill JK, Doubovetzky N, Haussmann IU, Dix TC, Arnold R, Devaud JM, Soller M. Dynamically expressed single ELAV/Hu orthologue elavl2 of bees is required for learning and memory. Commun Biol 2021; 4:1234. [PMID: 34711922 PMCID: PMC8553928 DOI: 10.1038/s42003-021-02763-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 10/09/2021] [Indexed: 12/16/2022] Open
Abstract
Changes in gene expression are a hallmark of learning and memory consolidation. Little is known about how alternative mRNA processing, particularly abundant in neuron-specific genes, contributes to these processes. Prototype RNA binding proteins of the neuronally expressed ELAV/Hu family are candidates for roles in learning and memory, but their capacity to cross-regulate and take over each other's functions complicate substantiation of such links. Honey bees Apis mellifera have only one elav/Hu family gene elavl2, that has functionally diversified by increasing alternative splicing including an evolutionary conserved microexon. RNAi knockdown demonstrates that ELAVL2 is required for learning and memory in bees. ELAVL2 is dynamically expressed with altered alternative splicing and subcellular localization in mushroom bodies, but not in other brain regions. Expression and alternative splicing of elavl2 change during memory consolidation illustrating an alternative mRNA processing program as part of a local gene expression response underlying memory consolidation.
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Affiliation(s)
- Pinar Ustaoglu
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jatinder Kaur Gill
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Nicolas Doubovetzky
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, 31062, France
| | - Irmgard U Haussmann
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Department of Life Science, Faculty of Health, Education and Life Sciences, Birmingham City University, Birmingham, B15 3TN, UK
| | - Thomas C Dix
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Roland Arnold
- Birmingham Centre for Genome Biology, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Cancer and Genomics Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Jean-Marc Devaud
- Research Center on Animal Cognition (CRCA), Center for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, 31062, France
| | - Matthias Soller
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- Institute of Cancer and Genomics Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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11
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Wan Y, Anastasakis DG, Rodriguez J, Palangat M, Gudla P, Zaki G, Tandon M, Pegoraro G, Chow CC, Hafner M, Larson DR. Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and stochastic splice site selection. Cell 2021; 184:2878-2895.e20. [PMID: 33979654 DOI: 10.1016/j.cell.2021.04.012] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 11/12/2020] [Accepted: 04/08/2021] [Indexed: 01/06/2023]
Abstract
The activities of RNA polymerase and the spliceosome are responsible for the heterogeneity in the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. We find that all observed genes show transcriptional bursting. We also observe large kinetic variation in intron removal for single introns in single cells, which is inconsistent with deterministic splice site selection. Transcriptome-wide footprinting of the U2AF complex, nascent RNA profiling, long-read sequencing, and lariat sequencing further reveal widespread stochastic recursive splicing within introns. We propose and validate a unified theoretical model to explain the general features of transcription and pervasive stochastic splice site selection.
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Affiliation(s)
- Yihan Wan
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Dimitrios G Anastasakis
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA
| | | | - Murali Palangat
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Prabhakar Gudla
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - George Zaki
- Biomedical Informatics and Data Science Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mayank Tandon
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Gianluca Pegoraro
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carson C Chow
- Laboratory of Biological Modeling, NIDDK, Bethesda, MD, USA
| | - Markus Hafner
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA.
| | - Daniel R Larson
- Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
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12
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Joseph B, Lai EC. The Exon Junction Complex and intron removal prevent re-splicing of mRNA. PLoS Genet 2021; 17:e1009563. [PMID: 34033644 PMCID: PMC8184009 DOI: 10.1371/journal.pgen.1009563] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 06/07/2021] [Accepted: 04/26/2021] [Indexed: 01/23/2023] Open
Abstract
Accurate splice site selection is critical for fruitful gene expression. Recently, the mammalian EJC was shown to repress competing, cryptic, splice sites (SS). However, the evolutionary generality of this remains unclear. Here, we demonstrate the Drosophila EJC suppresses hundreds of functional cryptic SS, even though most bear weak splicing motifs and are seemingly incompetent. Mechanistically, the EJC directly conceals cryptic splicing elements by virtue of its position-specific recruitment, preventing aberrant SS definition. Unexpectedly, we discover the EJC inhibits scores of regenerated 5' and 3' recursive SS on segments that have already undergone splicing, and that loss of EJC regulation triggers faulty resplicing of mRNA. An important corollary is that certain intronless cDNA constructs yield unanticipated, truncated transcripts generated by resplicing. We conclude the EJC has conserved roles to defend transcriptome fidelity by (1) repressing illegitimate splice sites on pre-mRNAs, and (2) preventing inadvertent activation of such sites on spliced segments.
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Affiliation(s)
- Brian Joseph
- Developmental Biology Program, Sloan Kettering Institute, New York, New York, United States of America
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Eric C. Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, New York, United States of America
- Louis V. Gerstner, Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
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13
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Conboy JG. Unannotated splicing regulatory elements in deep intron space. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 12:e1656. [PMID: 33887804 DOI: 10.1002/wrna.1656] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/14/2021] [Accepted: 03/23/2021] [Indexed: 12/21/2022]
Abstract
Deep intron space harbors a diverse array of splicing regulatory elements that cooperate with better-known exon-proximal elements to enforce proper tissue-specific and development-specific pre-mRNA processing. Many deep intron elements have been highly conserved through vertebrate evolution, yet remain poorly annotated in the human genome. Recursive splicing exons (RS-exons) and intraexons promote noncanonical, multistep resplicing pathways in long introns, involving transient intermediate structures that are greatly underrepresented in RNA-seq datasets. Decoy splice sites and decoy exons act at a distance to inhibit splicing catalysis at annotated splice sites, with functional consequences such as exon skipping and intron retention. RNA:RNA bridges can juxtapose distant sequences within or across introns to activate deep intron splicing enhancers and silencers, to loop out exons to be skipped, or to select one member of a mutually exclusive set of exons. Similarly, protein bridges mediated by interactions among transcript-bound RNA binding proteins (RBPs) can modulate splicing outcomes. Experimental disruption of deep intron elements serving any of these functions can abrogate normal splicing, strongly suggesting that natural mutations of deep intron elements can do likewise to cause human disease. Understanding noncanonical splicing pathways and discovering deep intron regulatory signals, many of which map hundreds to many thousands of nucleotides from annotated splice junctions, is of great academic interest for basic scientists studying alternative splicing mechanisms. Hopefully, this knowledge coupled with increased analysis of deep intron sequences will also have important medical applications, as better interpretation of deep intron mutations may reveal new disease mechanisms and suggest new therapies. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- John G Conboy
- Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, California, USA
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14
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Gehring NH, Roignant JY. Anything but Ordinary – Emerging Splicing Mechanisms in Eukaryotic Gene Regulation. Trends Genet 2021; 37:355-372. [DOI: 10.1016/j.tig.2020.10.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/14/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022]
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15
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Gong M, Zhang X, Wang Y, Mao G, Ou Y, Wei C, Hu X, Xiang S. DDX21 interacts with nuclear AGO2 and regulates the alternative splicing of SMN2. Biosci Biotechnol Biochem 2021; 85:272-279. [PMID: 33604619 DOI: 10.1093/bbb/zbaa029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/17/2020] [Indexed: 01/30/2023]
Abstract
AGO2 is the only member of mammalian Ago protein family that possesses the catalytic activity and plays a central role in gene silencing. Recently researches reported that multiple gene silencing factors, including AGO2, function in the nuclei. The molecular mechanisms of the gene silencing factors functioning in nuclei are conducive to comprehend the roles of gene silencing in pretranslational regulation of gene expression. Here, we report that AGO2 interacts with DDX21 indirectly in an RNA-dependent manner by Co-IP and GST-Pulldown assays and the 2 proteins present nuclei foci in the immunofluorescence experiments. We found that DDX21 up-regulated the protein level of AGO2 and participated in target gene, SNM2, alternative splicing involved in AGO2 by the indirect interaction with AGO2, which produced different transcripts of SMN2 in discrepant expression level. This study laid important experiment foundation for the further analysis of the nuclear functions of gene silencing components.
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Affiliation(s)
- Mengting Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China.,College of Physical Education, Hunan University of Finance and Economics, Changsha, China
| | - Xi Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yaru Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Guiyan Mao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Yangqi Ou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chenxi Wei
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xiang Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shuanglin Xiang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, China
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16
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Schott G, Galarza-Muñoz G, Trevino N, Chen X, Weirauch M, Gregory SG, Bradrick SS, Garcia-Blanco MA. U2AF2 binds IL7R exon 6 ectopically and represses its inclusion. RNA (NEW YORK, N.Y.) 2021; 27:rna.078279.120. [PMID: 33568552 PMCID: PMC8051268 DOI: 10.1261/rna.078279.120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/02/2021] [Indexed: 06/03/2023]
Abstract
Interleukin 7 receptor α-chain is crucial for the development and maintenance of T cells and is genetically associated with autoimmune disorders including multiple sclerosis (MS), a demyelinating disease of the CNS. Exon 6 of IL7R encodes for the transmembrane domain of the receptor and is regulated by alternative splicing: inclusion or skipping of IL7R exon 6 results in membrane-bound or soluble IL7R isoforms, respectively. We previously identified a SNP (rs6897932) in IL7R exon 6, strongly associated with MS risk and showed that the risk allele (C) increases skipping of the exon, resulting in elevated levels of sIL7R. This has important pathological consequences as elevated levels of sIL7R has been shown to exacerbate the disease in the experimental autoimmune encephalomyelitis mouse model of MS. Understanding the regulation of exon 6 splicing provides important mechanistic insights into the pathogenesis of MS. Here we report two mechanisms by which IL7R exon 6 is controlled. First, a competition between PTBP1 and U2AF2 at the polypyrimidine tract (PPT) of intron 5, and second, an unexpected U2AF2-mediated assembly of spicing factors in the exon. We noted the presence of a branchpoint sequence (BPS) (TACTAAT or TACTAAC) within exon 6, which is stronger with the C allele. We also noted that the BPS is followed by a PPT and conjectured that silencing could be mediated by the binding of U2AF2 to that tract. In support of this model, we show that evolutionary conservation of the exonic PPT correlates well with the degree of alternative splicing of exon 6 in two non-human primate species and that U2AF2 binding to this PPT recruits U2 snRNP components to the exon. These observations provide the first explanation for the stronger silencing of IL7R exon 6 with the disease associated C allele at rs6897932.
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17
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Xue W, Ma XK, Yang L. Fast and furious: insights of back splicing regulation during nascent RNA synthesis. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1050-1061. [PMID: 33580425 DOI: 10.1007/s11427-020-1881-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022]
Abstract
Alternative splicing of eukaryotic precursor (messenger) RNAs in the nucleus not only increases transcriptomic complexity, but also expands proteomic and functional diversity. In addition to basic types of alternative splicing, recent transcriptome-wide analyses have also suggested other new types of non-canonical splicing, such as back splicing and recursive splicing, and their widespread expression across species Increasing lines of evidence have suggested mechanisms for back splicing, including insights from analyses of nascent RNA sequencing. In this review, we discuss our current understanding of back splicing regulation, and highlight its distinct characteristics in processing during nascent RNA synthesis by taking advantage of metabolic tagging nascent RNA sequencing. Features of recursive splicing are also discussed in the perspective of nascent RNA sequencing.
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Affiliation(s)
- Wei Xue
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xu-Kai Ma
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Li Yang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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18
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Lv Q, Qiu J, Liu J, Li Z, Zhang W, Wang Q, Fang J, Pan J, Chen Z, Cheng W, Barker MS, Huang X, Wei X, Cheng K. The Chimonanthus salicifolius genome provides insight into magnoliid evolution and flavonoid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1910-1923. [PMID: 32524692 DOI: 10.1111/tpj.14874] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 05/25/2020] [Accepted: 06/02/2020] [Indexed: 05/11/2023]
Abstract
Chimonanthus salicifolius, a member of the Calycanthaceae of magnoliids, is one of the most famous medicinal plants in Eastern China. Here, we report a chromosome-level genome assembly of C. salicifolius, comprising 820.1 Mb of genomic sequence with a contig N50 of 2.3 Mb and containing 36 651 annotated protein-coding genes. Phylogenetic analyses revealed that magnoliids were sister to the eudicots. Two rounds of ancient whole-genome duplication were inferred in the C. salicifolious genome. One is shared by Calycanthaceae after its divergence with Lauraceae, and the other is in the ancestry of Magnoliales and Laurales. Notably, long genes with > 20 kb in length were much more prevalent in the magnoliid genomes compared with other angiosperms, which could be caused by the length expansion of introns inserted by transposon elements. Homologous genes within the flavonoid pathway for C. salicifolius were identified, and correlation of the gene expression and the contents of flavonoid metabolites revealed potential critical genes involved in flavonoids biosynthesis. This study not only provides an additional whole-genome sequence from the magnoliids, but also opens the door to functional genomic research and molecular breeding of C. salicifolius.
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Affiliation(s)
- Qundan Lv
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
| | - Wenting Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Qin Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Fang
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Junjie Pan
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Zhengdao Chen
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Wenliang Cheng
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Kejun Cheng
- Chemical Biology Center, Lishui Institute of Agriculture and Forestry Sciences, Lishui, China
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19
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Parra M, Zhang W, Vu J, DeWitt M, Conboy JG. Antisense targeting of decoy exons can reduce intron retention and increase protein expression in human erythroblasts. RNA (NEW YORK, N.Y.) 2020; 26:996-1005. [PMID: 32312846 PMCID: PMC7373989 DOI: 10.1261/rna.075028.120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 04/10/2020] [Indexed: 06/11/2023]
Abstract
The decoy exon model has been proposed to regulate a subset of intron retention (IR) events involving predominantly larger introns (>1 kb). Splicing reporter studies have shown that decoy splice sites are essential for activity, suggesting that decoys act by engaging intron-terminal splice sites and competing with cross-intron interactions required for intron excision. The decoy model predicts that antisense oligonucleotides may be able to block decoy splice sites in endogenous pre-mRNA, thereby reducing IR and increasing productive gene expression. Indeed, we now demonstrate that targeting a decoy 5' splice site in the O-GlcNAc transferase (OGT) gene reduced IR from ∼80% to ∼20% in primary human erythroblasts, accompanied by increases in spliced OGT RNA and OGT protein expression. The remaining OGT IR was refractory to antisense treatment and might be mediated by independent mechanism(s). In contrast, other retained introns were strongly dependent on decoy function, since antisense targeting of decoy 5' splice sites greatly reduced (SNRNP70) or nearly eliminated (SF3B1) IR in two widely expressed splicing factors, and also greatly reduced IR in transcripts encoding the erythroid-specific structural protein, α-spectrin (SPTA1). These results show that modulating decoy exon function can dramatically alter IR and suggest that dynamic regulation of decoy exons could be a mechanism to fine-tune gene expression post-transcriptionally in many cell types.
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Affiliation(s)
- Marilyn Parra
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Weiguo Zhang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jonathan Vu
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - Mark DeWitt
- Innovative Genomics Institute, University of California, Berkeley, California, USA
| | - John G Conboy
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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20
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Cao S, Luo X, Xie L, Gao C, Wang D, Holt BF, Lin H, Chu C, Xia X. The florigen interactor BdES43 represses flowering in the model temperate grass Brachypodium distachyon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:262-275. [PMID: 31782581 DOI: 10.1111/tpj.14622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 10/25/2019] [Accepted: 11/05/2019] [Indexed: 06/10/2023]
Abstract
FLOWERING LOCUS T (FT) protein, physiologically florigen, has been identified as a system integrator of numerous flowering time pathways in many studies, and its homologs are found throughout the plant lineage. It is important to uncover how precisely florigenic homologs contribute to flowering initiation and how these factors interact genetically. Here we dissected the function of Brachypodium FT orthologs BdFTL1 and BdFTL2 using overexpression and gene-editing experiments. Transgenic assays showed that both BdFTL1 and BdFTL2 could promote flowering, whereas BdFTL2 was essential for flowering initiation. Notably, BdFTL1 is subject to alternative splicing (AS), and its transcriptional level and AS are significantly affected by BdFTL2. Additionally, BdFTL2 could bind with the PHD-containing protein BdES43, an H3K4me3 reader. Furthermore, BdES43 was antagonistic to BdFTL2 in flowering initiation in a transcription-dependent manner and significantly affected BdFTL1 expression. BdFTL2, BdES43 and H3K4me3 also had highly similar distribution patterns within the BdFTL1 locus, indicating their interplay in regulating target genes. Taken together, florigen BdFTL2 functions as a potential epigenetic effector of BdFTL1 by interacting with a BdES43-H3K4me3 complex. This finding provides an additional insight for the regulatory mechanism underlying the multifaceted roles of florigen.
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Affiliation(s)
- Shuanghe Cao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xumei Luo
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Li Xie
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Caixia Gao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Daowen Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Ben F Holt
- Department of Microbiology and Plant Biology, University of Oklahoma, 770 Van Vleet Oval, Norman, OK, 73019, USA
| | - Hao Lin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Chengcai Chu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences (CAS), No. 1 West Beichen Road, Chaoyang District, Beijing, 100101, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
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21
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Abstract
High-throughput sequencing-based methods and their applications in the study of transcriptomes have revolutionized our understanding of alternative splicing. Networks of functionally coordinated and biologically important alternative splicing events continue to be discovered in an ever-increasing diversity of cell types in the context of physiologically normal and disease states. These studies have been complemented by efforts directed at defining sequence codes governing splicing and their cognate trans-acting factors, which have illuminated important combinatorial principles of regulation. Additional studies have revealed critical roles of position-dependent, multivalent protein-RNA interactions that direct splicing outcomes. Investigations of evolutionary changes in RNA binding proteins, splice variants, and associated cis elements have further shed light on the emergence, mechanisms, and functions of splicing networks. Progress in these areas has emphasized the need for a coordinated, community-based effort to systematically address the functions of individual splice variants associated with normal and disease biology.
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22
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Pasquier C, Agnel S, Robichon A. Transcriptome-wide-scale-predicted dsRNAs potentially involved in RNA homoeostasis are remarkably excluded from genes with no/very low expression in all developmental stages. RNA Biol 2020; 17:554-570. [PMID: 31971862 DOI: 10.1080/15476286.2020.1717154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
RNA interference (RNAi) refers to a conserved posttranscriptional mechanism for the degradation of RNA by short dsRNAs. A genome-wide analysis of mRNAs that are complementary to RNAs of variable length that are transcribed from the full transcriptome and susceptible to being loaded onto Argonaute type 2 was performed through computational searches in the Drosophila model. We report the segments of RNAs that are complementary to mRNAs originating from introns, the exons of mRNAs and lncRNAs as a potential source of siRNAs. A full catalogue of the mRNAs that fulfill these criteria is presented, along with the quantification of multiple annealing. The catalogue was assessed for biological validation using three published lists: two for Ago2-associated RNAs and one for dsRNAs isolated from a crude extract. A broad spectrum of mRNAs were found to theoretically form intermolecular segmental dsRNAs, which should qualify them as Dicer/Ago2 substrates if they exist in vivo. These results suggest a genome-wide scale of mRNA homoeostasis via RNAi metabolism and could extend the known roles of canonical miRNAs and hairpin RNAs. The distribution of the genes for which transcripts are engaged in intermolecular segmental pairing is largely lacking in the gene collections defined as showing no expression in each individual developmental stage from early embryos to adulthood. This trend was also observed for the genes showing very low expression from the 8-12-hour embryonic to larval stage 2. This situation was also suggested by the 3 lists generated with minimal 20-, 25- and 30-base pairing lengths.
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Affiliation(s)
- Claude Pasquier
- Laboratoire d'informatique, signaux et système (I3S) CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Sandra Agnel
- Agrobiotech Institute (ISA)INRA, CNRS, Université Côte d'Azur, Sophia Antipolis, France
| | - Alain Robichon
- Agrobiotech Institute (ISA)INRA, CNRS, Université Côte d'Azur, Sophia Antipolis, France
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23
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Maita H, Nakagawa S. What is the switch for coupling transcription and splicing? RNA Polymerase II C‐terminal domain phosphorylation, phase separation and beyond. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 11:e1574. [DOI: 10.1002/wrna.1574] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 01/12/2023]
Affiliation(s)
- Hiroshi Maita
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences Hokkaido University Sapporo Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences Hokkaido University Sapporo Japan
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24
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Davis-Turak J, Johnson TL, Hoffmann A. Mathematical modeling identifies potential gene structure determinants of co-transcriptional control of alternative pre-mRNA splicing. Nucleic Acids Res 2019; 46:10598-10607. [PMID: 30272246 PMCID: PMC6237756 DOI: 10.1093/nar/gky870] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 09/17/2018] [Indexed: 01/22/2023] Open
Abstract
The spliceosome catalyzes the removal of introns from pre-messenger RNA (mRNA) and subsequent pairing of exons with remarkable fidelity. Some exons are known to be skipped or included in the mature mRNA in a cell type- or context-dependent manner (cassette exons), thereby contributing to the diversification of the human proteome. Interestingly, splicing is initiated (and sometimes completed) co-transcriptionally. Here, we develop a kinetic mathematical modeling framework to investigate alternative co-transcriptional splicing (CTS) and, specifically, the control of cassette exons' inclusion. We show that when splicing is co-transcriptional, default splice patterns of exon inclusion are more likely than when splicing is post-transcriptional, and that certain exons are more likely to be regulatable (i.e. cassette exons) than others, based on the exon-intron structure context. For such regulatable exons, transcriptional elongation rates may affect splicing outcomes. Within the CTS paradigm, we examine previously described hypotheses of co-operativity between splice sites of short introns (i.e. 'intron definition') or across short exons (i.e. 'exon definition'), and find that models encoding these faithfully recapitulate observations in the fly and human genomes, respectively.
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Affiliation(s)
- Jeremy Davis-Turak
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, La Jolla, CA 92093, USA
| | - Tracy L Johnson
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, La Jolla, CA 92093, USA.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.,Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Alexander Hoffmann
- San Diego Center for Systems Biology (SDCSB), University of California, San Diego, La Jolla, CA 92093, USA.,Molecular Biology Institute (MBI), University of California, Los Angeles, Los Angeles, CA 90095, USA.,Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, CA 90095, USA.,Institute for Quantitative and Computational Biosciences (QCB) University of California, Los Angeles, Los Angeles, CA 90095, USA
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25
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Blazquez L, Emmett W, Faraway R, Pineda JMB, Bajew S, Gohr A, Haberman N, Sibley CR, Bradley RK, Irimia M, Ule J. Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing. Mol Cell 2018; 72:496-509.e9. [PMID: 30388411 PMCID: PMC6224609 DOI: 10.1016/j.molcel.2018.09.033] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/24/2018] [Accepted: 09/27/2018] [Indexed: 01/13/2023]
Abstract
Recursive splicing (RS) starts by defining an "RS-exon," which is then spliced to the preceding exon, thus creating a recursive 5' splice site (RS-5ss). Previous studies focused on cryptic RS-exons, and now we find that the exon junction complex (EJC) represses RS of hundreds of annotated, mainly constitutive RS-exons. The core EJC factors, and the peripheral factors PNN and RNPS1, maintain RS-exon inclusion by repressing spliceosomal assembly on RS-5ss. The EJC also blocks 5ss located near exon-exon junctions, thus repressing inclusion of cryptic microexons. The prevalence of annotated RS-exons is high in deuterostomes, while the cryptic RS-exons are more prevalent in Drosophila, where EJC appears less capable of repressing RS. Notably, incomplete repression of RS also contributes to physiological alternative splicing of several human RS-exons. Finally, haploinsufficiency of the EJC factor Magoh in mice is associated with skipping of RS-exons in the brain, with relevance to the microcephaly phenotype and human diseases.
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Affiliation(s)
- Lorea Blazquez
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Warren Emmett
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; University College London Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Rupert Faraway
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Jose Mario Bello Pineda
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Simon Bajew
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Andre Gohr
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Nejc Haberman
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christopher R Sibley
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Robert K Bradley
- Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain
| | - Jernej Ule
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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26
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Numerous recursive sites contribute to accuracy of splicing in long introns in flies. PLoS Genet 2018; 14:e1007588. [PMID: 30148878 PMCID: PMC6110457 DOI: 10.1371/journal.pgen.1007588] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/24/2018] [Indexed: 01/10/2023] Open
Abstract
Recursive splicing, a process by which a single intron is removed from pre-mRNA transcripts in multiple distinct segments, has been observed in a small subset of Drosophila melanogaster introns. However, detection of recursive splicing requires observation of splicing intermediates that are inherently unstable, making it difficult to study. Here we developed new computational approaches to identify recursively spliced introns and applied them, in combination with existing methods, to nascent RNA sequencing data from Drosophila S2 cells. These approaches identified hundreds of novel sites of recursive splicing, expanding the catalog of recursively spliced fly introns by 4-fold. A subset of recursive sites were validated by RT-PCR and sequencing. Recursive sites occur in most very long (> 40 kb) fly introns, including many genes involved in morphogenesis and development, and tend to occur near the midpoints of introns. Suggesting a possible function for recursive splicing, we observe that fly introns with recursive sites are spliced more accurately than comparably sized non-recursive introns. The splicing of RNA transcripts is an essential step in the production of mature mRNA molecules, involving removal of intron sequences and joining of flanking exon sequences. Introns are usually removed as a single unit in a two-step catalytic reaction. However, a small subset of introns in flies are removed via splicing of multiple distinct consecutive segments in a process known as recursive splicing. This pathway was thought to be quite rare since intermediates of recursive splicing are seldom detected. In this study, we developed three new computational approaches to identify sequence reads, read pairs and patterns of read accumulation indicative of recursive splicing in Drosophila melanogaster cells using data from sequencing of nascent RNA captured within minutes after transcription. We used these methods to identify hundreds of previously unknown sites of recursive splicing, occurring commonly in fly introns longer than 40kb and often in genes involved in morphogenesis and development. We observed that recursive splicing is associated with increased splicing accuracy of long introns, which are otherwise often spliced inaccurately, potentially explaining its widespread occurrence in long fly introns.
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Zhang XO, Fu Y, Mou H, Xue W, Weng Z. The temporal landscape of recursive splicing during Pol II transcription elongation in human cells. PLoS Genet 2018; 14:e1007579. [PMID: 30148885 PMCID: PMC6110456 DOI: 10.1371/journal.pgen.1007579] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/20/2018] [Indexed: 01/28/2023] Open
Abstract
Recursive splicing (RS) is an evolutionarily conserved process of removing long introns via multiple steps of splicing. It was first discovered in Drosophila and recently proven to occur also in humans. The detailed mechanism of recursive splicing is not well understood, in particular, whether it is kinetically coupled with transcription. To investigate the dynamic process that underlies recursive splicing, we systematically characterized 342 RS sites in three human cell types using published time-series data that monitored synchronized Pol II elongation and nascent RNA production with 4-thiouridine labeling. We found that half of the RS events occurred post-transcriptionally with long delays. For at least 18-47% RS introns, we detected RS junction reads only after detecting canonical splicing junction reads, supporting the notion that these introns were removed by both recursive splicing and canonical splicing. Furthermore, the choice of which splicing mechanism was used showed cell type specificity. Our results suggest that recursive splicing supplements, rather than replaces, canonical splicing for removing long introns.
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Affiliation(s)
- Xiao-Ou Zhang
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Yu Fu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Haiwei Mou
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Wen Xue
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
| | - Zhiping Weng
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America
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28
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Short cryptic exons mediate recursive splicing in Drosophila. Nat Struct Mol Biol 2018; 25:365-371. [PMID: 29632374 DOI: 10.1038/s41594-018-0052-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 03/02/2018] [Indexed: 01/11/2023]
Abstract
Many long Drosophila introns are processed by an unusual recursive strategy. The presence of ~200 adjacent splice acceptor and splice donor sites, termed ratchet points (RPs), were inferred to reflect 'zero-nucleotide exons', whose sequential processing subdivides removal of long host introns. We used CRISPR-Cas9 to disrupt several intronic RPs in Drosophila melanogaster, some of which recapitulated characteristic loss-of-function phenotypes. Unexpectedly, selective disruption of RP splice donors revealed constitutive retention of unannotated short exons. Assays using functional minigenes confirm that unannotated cryptic splice donor sites are critical for recognition of intronic RPs, demonstrating that recursive splicing involves the recognition of cryptic RP exons. This appears to be a general mechanism, because canonical, conserved splice donors are specifically enriched in a 40-80-nt window downstream of known and newly annotated intronic RPs and exhibit similar properties to a broadly expanded class of expressed RP exons. Overall, these studies unify the mechanism of Drosophila recursive splicing with that in mammals.
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Alternative Splicing in Genetic Diseases: Improved Diagnosis and Novel Treatment Options. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2017; 335:85-141. [PMID: 29305015 DOI: 10.1016/bs.ircmb.2017.07.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Alternative splicing is an important mechanism to regulate gene expression and to expand the repertoire of gene products in order to accommodate an increase in complexity of multicellular organisms. It needs to be precisely regulated, which is achieved via RNA structure, splicing factors, transcriptional regulation, and chromatin. Changes in any of these factors can lead to disease. These may include the core spliceosome, splicing enhancer/repressor sequences and their interacting proteins, the speed of transcription by RNA polymerase II, and histone modifications. While the basic principle of splicing is well understood, it is still very difficult to predict splicing outcome, due to the multiple levels of regulation. Current molecular diagnostics mainly uses Sanger sequencing of exons, or next-generation sequencing of gene panels or the whole exome. Functional analysis of potential splicing variants is scarce, and intronic variants are often not considered. This likely results in underestimation of the percentage of splicing variants. Understanding how sequence variants may affect splicing is not only crucial for confirmation of diagnosis and for genetic counseling, but also for the development of novel treatment options. These include small molecules, transsplicing, antisense oligonucleotides, and gene therapy. Here we review the current state of molecular mechanisms of splicing regulation and how deregulation can lead to human disease, diagnostics to detect splicing variants, and novel treatment options based on splicing correction.
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Ramanouskaya TV, Grinev VV. The determinants of alternative RNA splicing in human cells. Mol Genet Genomics 2017; 292:1175-1195. [PMID: 28707092 DOI: 10.1007/s00438-017-1350-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/06/2017] [Indexed: 12/29/2022]
Abstract
Alternative splicing represents an important level of the regulation of gene function in eukaryotic organisms. It plays a critical role in virtually every biological process within an organism, including regulation of cell division and cell death, differentiation of tissues in the embryo and the adult organism, as well as in cellular response to diverse environmental factors. In turn, studies of the last decade have shown that alternative splicing itself is controlled by different mechanisms. Unfortunately, there is no clear understanding of how these diverse mechanisms, or determinants, regulate and constrain the set of alternative RNA species produced from any particular gene in every cell of the human body. Here, we provide a consolidated overview of alternative splicing determinants including RNA-protein interactions, epigenetic regulation via chromatin remodeling, coupling of transcription-to-alternative splicing, effect of secondary structures in pre-RNA, and function of the RNA quality control systems. We also extensively and critically discuss some mechanistic insights on coordinated inclusion/exclusion of exons during the formation of mature RNA molecules. We conclude that the final structure of RNA is pre-determined by a complex interplay between cis- and trans-acting factors. Altogether, currently available empirical data significantly expand our understanding of the functioning of the alternative splicing machinery of cells in normal and pathological conditions. On the other hand, there are still many blind spots that require further deep investigations.
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31
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Deep intronic mutations and human disease. Hum Genet 2017; 136:1093-1111. [DOI: 10.1007/s00439-017-1809-4] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 05/05/2017] [Indexed: 12/22/2022]
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Bangru S, Kalsotra A. Advances in analyzing RNA diversity in eukaryotic transcriptomes: peering through the Omics lens. F1000Res 2016; 5:2668. [PMID: 27909578 PMCID: PMC5112568 DOI: 10.12688/f1000research.9511.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/08/2016] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing, polyadenylation, and chemical modifications of RNA generate astonishing complexity within eukaryotic transcriptomes. The last decade has brought numerous advances in sequencing technologies that allow biologists to investigate these phenomena with greater depth and accuracy while reducing time and cost. A commensurate development in biochemical techniques for the enrichment and analysis of different RNA variants has accompanied the advancement of global sequencing analysis platforms. Here, we present a detailed overview of the latest biochemical methods, along with bioinformatics pipelines that have aided in identifying different RNA variants. We also highlight the ongoing developments and challenges associated with RNA variant detection and quantification, including sample heterogeneity and isolation, as well as 'Omics' big data handling.
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Affiliation(s)
- Sushant Bangru
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Illinois, USA; Institute of Genomic Biology, University of Illinois at Urbana-Champaign, Illinois, USA; College of Medicine, University of Illinois at Urbana-Champaign, Illinois, USA
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Suzuki H, Aoki Y, Kameyama T, Saito T, Masuda S, Tanihata J, Nagata T, Mayeda A, Takeda S, Tsukahara T. Endogenous Multiple Exon Skipping and Back-Splicing at the DMD Mutation Hotspot. Int J Mol Sci 2016; 17:ijms17101722. [PMID: 27754374 PMCID: PMC5085753 DOI: 10.3390/ijms17101722] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 09/26/2016] [Accepted: 09/30/2016] [Indexed: 12/15/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe muscular disorder. It was reported that multiple exon skipping (MES), targeting exon 45–55 of the DMD gene, might improve patients’ symptoms because patients who have a genomic deletion of all these exons showed very mild symptoms. Thus, exon 45–55 skipping treatments for DMD have been proposed as a potential clinical cure. Herein, we detected the expression of endogenous exons 44–56 connected mRNA transcript of the DMD using total RNAs derived from human normal skeletal muscle by reverse transcription polymerase chain reaction (RT-PCR), and identified a total of eight types of MES products around the hotspot. Surprisingly, the 5′ splice sites of recently reported post-transcriptional introns (remaining introns after co-transcriptional splicing) act as splicing donor sites for MESs. We also tested exon combinations to generate DMD circular RNAs (circRNAs) and determined the preferential splice sites of back-splicing, which are involved not only in circRNA generation, but also in MESs. Our results fit the current circRNA-generation model, suggesting that upstream post-transcriptional introns trigger MES and generate circRNA because its existence is critical for the intra-intronic interaction or for extremely distal splicing.
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Affiliation(s)
- Hitoshi Suzuki
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan.
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8502, Japan.
| | - Toshiki Kameyama
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
| | - Takashi Saito
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8502, Japan.
| | - Satoru Masuda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8502, Japan.
| | - Jun Tanihata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8502, Japan.
| | - Tetsuya Nagata
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8502, Japan.
- Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyoku, Tokyo 113-0034, Japan.
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan.
| | - Shin'ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Kodaira, Tokyo 187-8502, Japan.
| | - Toshifumi Tsukahara
- School of Materials Science, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa 923-1292, Japan.
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Abstract
Introns inserted within introns are commonly referred to as twintrons, however the original definition for twintron implied that splicing of the external member of the twintron could only proceed upon splicing of the internal member. This review examines the various types of twintron-like arrangements that have been reported and assigns them to either nested or twintron categories that are subdivided further into subtypes based on differences of their mode of splicing. Twintron-like arrangements evolved independently by fortuitous events among different types of introns but once formed they offer opportunities for the evolution of new regulatory strategies and/or novel genetic elements.
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Affiliation(s)
- Mohamed Hafez
- a Department of Biochemistry ; Faculty of Medicine; University of Montreal ; Montréal , QC Canada.,b Department of Botany and Microbiology ; Faculty of Science; Suez University ; Suez , Egypt
| | - Georg Hausner
- c Department of Microbiology ; University of Manitoba ; Winnipeg , MB Canada
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35
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Abstract
Recent improvements in experimental and computational techniques that are used to study the transcriptome have enabled an unprecedented view of RNA processing, revealing many previously unknown non-canonical splicing events. This includes cryptic events located far from the currently annotated exons and unconventional splicing mechanisms that have important roles in regulating gene expression. These non-canonical splicing events are a major source of newly emerging transcripts during evolution, especially when they involve sequences derived from transposable elements. They are therefore under precise regulation and quality control, which minimizes their potential to disrupt gene expression. We explain how non-canonical splicing can lead to aberrant transcripts that cause many diseases, and also how it can be exploited for new therapeutic strategies.
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36
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Warnefors M, Hartmann B, Thomsen S, Alonso CR. Combinatorial Gene Regulatory Functions Underlie Ultraconserved Elements in Drosophila. Mol Biol Evol 2016; 33:2294-306. [PMID: 27247329 PMCID: PMC4989106 DOI: 10.1093/molbev/msw101] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ultraconserved elements (UCEs) are discrete genomic elements conserved across large evolutionary distances. Although UCEs have been linked to multiple facets of mammalian gene regulation their extreme evolutionary conservation remains largely unexplained. Here, we apply a computational approach to investigate this question in Drosophila, exploring the molecular functions of more than 1,500 UCEs shared across the genomes of 12 Drosophila species. Our data indicate that Drosophila UCEs are hubs for gene regulatory functions and suggest that UCE sequence invariance originates from their combinatorial roles in gene control. We also note that the gene regulatory roles of intronic and intergenic UCEs (iUCEs) are distinct from those found in exonic UCEs (eUCEs). In iUCEs, transcription factor (TF) and epigenetic factor binding data strongly support iUCE roles in transcriptional and epigenetic regulation. In contrast, analyses of eUCEs indicate that they are two orders of magnitude more likely than the expected to simultaneously include protein-coding sequence, TF-binding sites, splice sites, and RNA editing sites but have reduced roles in transcriptional or epigenetic regulation. Furthermore, we use a Drosophila cell culture system and transgenic Drosophila embryos to validate the notion of UCE combinatorial regulatory roles using an eUCE within the Hox gene Ultrabithorax and show that its protein-coding region also contains alternative splicing regulatory information. Taken together our experiments indicate that UCEs emerge as a result of combinatorial gene regulatory roles and highlight common features in mammalian and insect UCEs implying that similar processes might underlie ultraconservation in diverse animal taxa.
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Affiliation(s)
- Maria Warnefors
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Britta Hartmann
- Institute of Human Genetics, Freiburg, Germany BIOSS Centre for Biological Signaling Studies, University Medical Center Freiburg, Freiburg, Germany
| | - Stefan Thomsen
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Claudio R Alonso
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
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37
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Voorter CEM, Gerritsen KEH, Groeneweg M, Wieten L, Tilanus MGJ. The role of gene polymorphism in HLA class I splicing. Int J Immunogenet 2016; 43:65-78. [PMID: 26920492 DOI: 10.1111/iji.12256] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/28/2016] [Accepted: 02/04/2016] [Indexed: 01/15/2023]
Abstract
Among the large number of human leucocyte antigen (HLA) alleles, only a few have been identified with a nucleotide polymorphism impairing correct splicing. Those alleles show aberrant expression levels, due to either a direct effect of the polymorphism on the normal splice site or to the creation of an alternative splice site. Furthermore, in several studies, the presence of alternatively spliced HLA transcripts co-expressed with the mature spliced transcripts was reported. We evaluated the splice site sequences of all known HLA class I alleles and found that, beside the consensus GT and AG sequences at the intron borders, there were some other highly conserved nucleotides for the different class I genes. In this review, we summarize the splicing mechanism and evaluate what is known today about alternative splicing of HLA class I genes.
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Affiliation(s)
- C E M Voorter
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - K E H Gerritsen
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - M Groeneweg
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - L Wieten
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - M G J Tilanus
- Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Centre, Maastricht, the Netherlands
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38
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Qin D, Huang L, Wlodaver A, Andrade J, Staley JP. Sequencing of lariat termini in S. cerevisiae reveals 5' splice sites, branch points, and novel splicing events. RNA (NEW YORK, N.Y.) 2016; 22:237-53. [PMID: 26647463 PMCID: PMC4712674 DOI: 10.1261/rna.052829.115] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 11/04/2015] [Indexed: 05/23/2023]
Abstract
Pre-mRNA splicing is a central step in the shaping of the eukaryotic transcriptome and in the regulation of gene expression. Yet, due to a focus on fully processed mRNA, common approaches for defining pre-mRNA splicing genome-wide are suboptimal-especially with respect to defining the branch point sequence, a key cis-element that initiates the chemistry of splicing. Here, we report a complementary intron-centered approach designed to more efficiently, simply, and directly define splicing events genome-wide. Specifically, we developed a method distinguished by deep sequencing of lariat intron termini (LIT-seq). In a test of LIT-seq using the budding yeast Saccharomyces cerevisiae, we not only successfully captured the majority of annotated, expressed splicing events but also uncovered 45 novel splicing events, establishing the sensitivity of LIT-seq. Moreover, our libraries were highly enriched with reads that reported on splice sites; by a simple and direct inspection of sequencing reads, we empirically defined both 5' splice sites and branch sites, as well as their consensus sequences, with nucleotide resolution. Additionally, our study revealed that the 3' termini of lariat introns are subject to nontemplated addition of adenosines, characteristic of signals sensed by 3' to 5' RNA turnover machinery. Collectively, this work defines a novel, genome-wide approach for analyzing splicing with unprecedented depth, specificity, and resolution.
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Affiliation(s)
- Daoming Qin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Lei Huang
- Center for Research Informatics, University of Chicago, Chicago, Illinois 60637, USA
| | - Alissa Wlodaver
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
| | - Jorge Andrade
- Center for Research Informatics, University of Chicago, Chicago, Illinois 60637, USA
| | - Jonathan P Staley
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois 60637, USA
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Gazzoli I, Pulyakhina I, Verwey NE, Ariyurek Y, Laros JFJ, 't Hoen PAC, Aartsma-Rus A. Non-sequential and multi-step splicing of the dystrophin transcript. RNA Biol 2015; 13:290-305. [PMID: 26670121 PMCID: PMC4829307 DOI: 10.1080/15476286.2015.1125074] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The dystrophin protein encoding DMD gene is the longest human gene. The 2.2 Mb long human dystrophin transcript takes 16 hours to be transcribed and is co-transcriptionally spliced. It contains long introns (24 over 10kb long, 5 over 100kb long) and the heterogeneity in intron size makes it an ideal transcript to study different aspects of the human splicing process. Splicing is a complex process and much is unknown regarding the splicing of long introns in human genes. Here, we used ultra-deep transcript sequencing to characterize splicing of the dystrophin transcripts in 3 different human skeletal muscle cell lines, and explored the order of intron removal and multi-step splicing. Coverage and read pair analyses showed that around 40% of the introns were not always removed sequentially. Additionally, for the first time, we report that non-consecutive intron removal resulted in 3 or more joined exons which are flanked by unspliced introns and we defined these joined exons as an exon block. Lastly, computational and experimental data revealed that, for the majority of dystrophin introns, multistep splicing events are used to splice out a single intron. Overall, our data show for the first time in a human transcript, that multi-step intron removal is a general feature of mRNA splicing.
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Affiliation(s)
- Isabella Gazzoli
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
| | - Irina Pulyakhina
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
| | - Nisha E Verwey
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
| | - Yavuz Ariyurek
- b Leiden Genome Technology Center, Leiden University Medical Center , Leiden , The Netherlands
| | - Jeroen F J Laros
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands.,b Leiden Genome Technology Center, Leiden University Medical Center , Leiden , The Netherlands
| | - Peter A C 't Hoen
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
| | - Annemieke Aartsma-Rus
- a Department of Human Genetics , Leiden University Medical Center , Leiden , the Netherlands
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40
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Guo L, Liu CM. A single-nucleotide exon found in Arabidopsis. Sci Rep 2015; 5:18087. [PMID: 26657562 PMCID: PMC4674806 DOI: 10.1038/srep18087] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 11/11/2015] [Indexed: 01/09/2023] Open
Abstract
The presence of introns in gene-coding regions is one of the most mysterious evolutionary inventions in eukaryotic organisms. It has been proposed that, although sequences involved in intron recognition and splicing are mainly located in introns, exonic sequences also contribute to intron splicing. The smallest constitutively spliced exon known so far has 6 nucleotides, and the smallest alternatively spliced exon has 3 nucleotides. Here we report that the Anaphase Promoting Complex subunit 11 (APC11) gene in Arabidopsis thaliana carries a constitutive single-nucleotide exon. In vivo transcription and translation assays performed using APC11-Green Fluorescence Protein (GFP) fusion constructs revealed that intron splicing surrounding the single-nucleotide exon is effective in both Arabidopsis and rice. This discovery warrants attention to genome annotations in the future.
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Affiliation(s)
- Lei Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chun-Ming Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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41
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Geyer A, Koltsaki I, Hessinger C, Renner S, Rogulja-Ortmann A. Impact of Ultrabithorax alternative splicing on Drosophila embryonic nervous system development. Mech Dev 2015; 138 Pt 2:177-189. [PMID: 26299253 DOI: 10.1016/j.mod.2015.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 11/17/2022]
Abstract
Hox genes control divergent segment identities along the anteroposterior body axis of bilateral animals by regulating a large number of processes in a cell context-specific manner. How Hox proteins achieve this functional diversity is a long-standing question in developmental biology. In this study we investigate the role of alternative splicing in functional specificity of the Drosophila Hox gene Ultrabithorax (Ubx). We focus specifically on the embryonic central nervous system (CNS) and provide a description of temporal expression patterns of three major Ubx isoforms during development of this tissue. These analyses imply distinct functions for individual isoforms in different stages of neural development. We also examine the set of Ubx isoforms expressed in two isoform-specific Ubx mutant strains and analyze for the first time the effects of splicing defects on regional neural stem cell (neuroblast) identity. Our findings support the notion of specific isoforms having different effects in providing individual neuroblasts with positional identity along the anteroposterior body axis, as well as being involved in regulation of progeny cell fate.
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Affiliation(s)
- Aenne Geyer
- Institute of Genetics, University of Mainz, Mainz, Germany
| | | | | | - Simone Renner
- Institute of Genetics, University of Mainz, Mainz, Germany
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42
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Sibley CR, Emmett W, Blazquez L, Faro A, Haberman N, Briese M, Trabzuni D, Ryten M, Weale ME, Hardy J, Modic M, Curk T, Wilson SW, Plagnol V, Ule J. Recursive splicing in long vertebrate genes. Nature 2015; 521:371-375. [PMID: 25970246 PMCID: PMC4471124 DOI: 10.1038/nature14466] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 04/09/2015] [Indexed: 12/13/2022]
Abstract
It is generally believed that splicing removes introns as single units from precursor messenger RNA transcripts. However, some long Drosophila melanogaster introns contain a cryptic site, known as a recursive splice site (RS-site), that enables a multi-step process of intron removal termed recursive splicing. The extent to which recursive splicing occurs in other species and its mechanistic basis have not been examined. Here we identify highly conserved RS-sites in genes expressed in the mammalian brain that encode proteins functioning in neuronal development. Moreover, the RS-sites are found in some of the longest introns across vertebrates. We find that vertebrate recursive splicing requires initial definition of an 'RS-exon' that follows the RS-site. The RS-exon is then excluded from the dominant mRNA isoform owing to competition with a reconstituted 5' splice site formed at the RS-site after the first splicing step. Conversely, the RS-exon is included when preceded by cryptic promoters or exons that fail to reconstitute an efficient 5' splice site. Most RS-exons contain a premature stop codon such that their inclusion can decrease mRNA stability. Thus, by establishing a binary splicing switch, RS-sites demarcate different mRNA isoforms emerging from long genes by coupling cryptic elements with inclusion of RS-exons.
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Affiliation(s)
- Christopher R Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Warren Emmett
- University College London Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Lorea Blazquez
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Ana Faro
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Nejc Haberman
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Michael Briese
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Institute for Clinical Neurobiology, University of Würzburg, Versbacherstr. 5, 97078, Würzburg, Germany
| | - Daniah Trabzuni
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mina Ryten
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Department of Medical &Molecular Genetics, King’s College London, Guy’s Hospital, London, UK
| | - Michael E Weale
- King’s College London, Department of Medical & Molecular Genetics, Guy’s Hospital, London SE1 9RT, UK
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Miha Modic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
- Institute of Stem Cell Research, German Research Center for Environmental Health, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Tomaž Curk
- Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia
| | - Stephen W Wilson
- Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Vincent Plagnol
- University College London Genetics Institute, Gower Street, London WC1E 6BT, UK
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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Genome-wide identification of zero nucleotide recursive splicing in Drosophila. Nature 2015; 521:376-9. [PMID: 25970244 PMCID: PMC4529404 DOI: 10.1038/nature14475] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 04/16/2015] [Indexed: 01/23/2023]
Abstract
Recursive splicing is a process in which large introns are removed in multiple steps by resplicing at ratchet points - 5′ splice sites recreated after splicing1. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene1 and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing2,3. Here, we identify 197 zero nucleotide exon ratchet points in 130 introns of 115 Drosophila genes from total RNA sequencing data generated from developmental time points, dissected tissues, and cultured cells. The sequential nature of recursive splicing was confirmed by identification of lariat introns generated by splicing to and from the ratchet points. We also show that recursive splicing is a constitutive process, that depletion of U2AF inhibits recursive splicing, and that the sequence and function of ratchet points are evolutionarily conserved in Drosophila. Finally, we identified four recursively spliced human genes, one of which is also recursively spliced in Drosophila. Together these results indicate that recursive splicing is commonly used in Drosophila, occurs in human and provides insight into the mechanisms by which some large introns are removed.
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Lannoy N, Bandelier C, Grisart B, Reginster M, Ronge-Collard E, Vikkula M, Hermans C. Tandem inversion duplication withinF8Intron 1 associated with mild haemophilia A. Haemophilia 2015; 21:516-22. [DOI: 10.1111/hae.12675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2015] [Indexed: 12/16/2022]
Affiliation(s)
- N. Lannoy
- Center of Human Genetics UCLouvain; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
- Institut de Recherche Expérimentale et Clinique (IREC); Université Catholique de Louvain; Bruxelles Belgium
| | - C. Bandelier
- Center of Human Genetics UCLouvain; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
| | - B. Grisart
- Center of Human Genetics; Institut de Pathologie et de Génétique (IPG); Charleroi (Gosselies) Belgium
| | - M. Reginster
- Department of Hemato-oncology; Centre Hospitalier Regional de Huy; Huy Belgium
| | - E. Ronge-Collard
- Hemostasis Laboratory; Department of Biological Chemistry; Centre Hospitalier Regional de Liège; Liege Belgium
| | - M. Vikkula
- Laboratory of Human Molecular Genetics de Duve Institute; Université Catholique de Louvain; Bruxelles Belgium
| | - C. Hermans
- Institut de Recherche Expérimentale et Clinique (IREC); Université Catholique de Louvain; Bruxelles Belgium
- Haemostasis and Thrombosis Unit; Haemophilia Clinic; Division of Haematology; Cliniques Universitaires Saint-Luc; Bruxelles Belgium
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46
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Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity. Genome Res 2015; 25:995-1007. [PMID: 25934563 PMCID: PMC4484396 DOI: 10.1101/gr.186585.114] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 04/30/2015] [Indexed: 11/25/2022]
Abstract
Alternative splicing (AS) diversifies transcriptomes and proteomes and is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events in Arabidopsis, we found unusual AS events inside annotated protein-coding exons. Here, we also identify such AS events in human and use these two sets to analyse their features, regulation, functional impact, and evolutionary origin. As these events involve introns with features of both introns and protein-coding exons, we name them exitrons (exonic introns). Though exitrons were detected as a subset of retained introns, they are clearly distinguishable, and their splicing results in transcripts with different fates. About half of the 1002 Arabidopsis and 923 human exitrons have sizes of multiples of 3 nucleotides (nt). Splicing of these exitrons results in internally deleted proteins and affects protein domains, disordered regions, and various post-translational modification sites, thus broadly impacting protein function. Exitron splicing is regulated across tissues, in response to stress and in carcinogenesis. Intriguingly, annotated intronless genes can be also alternatively spliced via exitron usage. We demonstrate that at least some exitrons originate from ancestral coding exons. Based on our findings, we propose a “splicing memory” hypothesis whereby upon intron loss imprints of former exon borders defined by vestigial splicing regulatory elements could drive the evolution of exitron splicing. Altogether, our studies show that exitron splicing is a conserved strategy for increasing proteome plasticity in plants and animals, complementing the repertoire of AS events.
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Kelly S, Georgomanolis T, Zirkel A, Diermeier S, O'Reilly D, Murphy S, Längst G, Cook PR, Papantonis A. Splicing of many human genes involves sites embedded within introns. Nucleic Acids Res 2015; 43:4721-32. [PMID: 25897131 PMCID: PMC4482092 DOI: 10.1093/nar/gkv386] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Accepted: 04/12/2015] [Indexed: 02/03/2023] Open
Abstract
The conventional model for splicing involves excision of each intron in one piece; we demonstrate this inaccurately describes splicing in many human genes. First, after switching on transcription of SAMD4A, a gene with a 134 kb-long first intron, splicing joins the 3′ end of exon 1 to successive points within intron 1 well before the acceptor site at exon 2 is made. Second, genome-wide analysis shows that >60% of active genes yield products generated by such intermediate intron splicing. These products are present at ∼15% the levels of primary transcripts, are encoded by conserved sequences similar to those found at canonical acceptors, and marked by distinctive structural and epigenetic features. Finally, using targeted genome editing, we demonstrate that inhibiting the formation of these splicing intermediates affects efficient exon–exon splicing. These findings greatly expand the functional and regulatory complexity of the human transcriptome.
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Affiliation(s)
- Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, United Kingdom
| | | | - Anne Zirkel
- Centre for Molecular Medicine, University of Cologne, Cologne D-50931, Germany
| | - Sarah Diermeier
- Institut für Biochemie III, University of Regensburg, Regensburg D-93053, Germany
| | - Dawn O'Reilly
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Shona Murphy
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Gernot Längst
- Institut für Biochemie III, University of Regensburg, Regensburg D-93053, Germany
| | - Peter R Cook
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Argyris Papantonis
- Centre for Molecular Medicine, University of Cologne, Cologne D-50931, Germany
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Pulyakhina I, Gazzoli I, 't Hoen PAC, Verwey N, den Dunnen JT, den Dunnen J, Aartsma-Rus A, Laros JFJ. SplicePie: a novel analytical approach for the detection of alternative, non-sequential and recursive splicing. Nucleic Acids Res 2015; 43:e80. [PMID: 25800735 PMCID: PMC4499118 DOI: 10.1093/nar/gkv242] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 03/09/2015] [Indexed: 11/20/2022] Open
Abstract
Alternative splicing is a powerful mechanism present in eukaryotic cells to obtain a wide range of transcripts and protein isoforms from a relatively small number of genes. The mechanisms regulating (alternative) splicing and the paradigm of consecutive splicing have recently been challenged, especially for genes with a large number of introns. RNA-Seq, a powerful technology using deep sequencing in order to determine transcript structure and expression levels, is usually performed on mature mRNA, therefore not allowing detailed analysis of splicing progression. Sequencing pre-mRNA at different stages of splicing potentially provides insight into mRNA maturation. Although the number of tools that analyze total and cytoplasmic RNA in order to elucidate the transcriptome composition is rapidly growing, there are no tools specifically designed for the analysis of nuclear RNA (which contains mixtures of pre- and mature mRNA). We developed dedicated algorithms to investigate the splicing process. In this paper, we present a new classification of RNA-Seq reads based on three major stages of splicing: pre-, intermediate- and post-splicing. Applying this novel classification we demonstrate the possibility to analyze the order of splicing. Furthermore, we uncover the potential to investigate the multi-step nature of splicing, assessing various types of recursive splicing events. We provide the data that gives biological insight into the order of splicing, show that non-sequential splicing of certain introns is reproducible and coinciding in multiple cell lines. We validated our observations with independent experimental technologies and showed the reliability of our method. The pipeline, named SplicePie, is freely available at: https://github.com/pulyakhina/splicing_analysis_pipeline. The example data can be found at: https://barmsijs.lumc.nl/HG/irina/example_data.tar.gz.
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Affiliation(s)
- Irina Pulyakhina
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Isabella Gazzoli
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A C 't Hoen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Nisha Verwey
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Johan den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke Aartsma-Rus
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands Leiden Genome Technology Center, Leiden University Medical Center, Leiden, The Netherlands
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Ruden DM, Cingolani PE, Sen A, Qu W, Wang L, Senut MC, Garfinkel MD, Sollars VE, Lu X. Epigenetics as an answer to Darwin's "special difficulty," Part 2: natural selection of metastable epialleles in honeybee castes. Front Genet 2015; 6:60. [PMID: 25759717 PMCID: PMC4338822 DOI: 10.3389/fgene.2015.00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 02/08/2015] [Indexed: 11/15/2022] Open
Abstract
In a recent perspective in this journal, Herb (2014) discussed how epigenetics is a possible mechanism to circumvent Charles Darwin's "special difficulty" in using natural selection to explain the existence of the sterile-fertile dimorphism in eusocial insects. Darwin's classic book "On the Origin of Species by Means of Natural Selection" explains how natural selection of the fittest individuals in a population can allow a species to adapt to a novel or changing environment. However, in bees and other eusocial insects, such as ants and termites, there exist two or more castes of genetically similar females, from fertile queens to multiple sub-castes of sterile workers, with vastly different phenotypes, lifespans, and behaviors. This necessitates the selection of groups (or kin) rather than individuals in the evolution of honeybee hives, but group and kin selection theories of evolution are controversial and mechanistically uncertain. Also, group selection would seem to be prohibitively inefficient because the effective population size of a colony is reduced from thousands to a single breeding queen. In this follow-up perspective, we elaborate on possible mechanisms for how a combination of both epigenetics, specifically, the selection of metastable epialleles, and genetics, the selection of mutations generated by the selected metastable epialleles, allows for a combined means for selection amongst the fertile members of a species to increase colony fitness. This "intra-caste evolution" hypothesis is a variation of the epigenetic directed genetic error hypothesis, which proposes that selected metastable epialleles increase genetic variability by directing mutations specifically to the epialleles. Natural selection of random metastable epialleles followed by a second round of natural selection of random mutations generated by the metastable epialleles would allow a way around the small effective population size of eusocial insects.
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Affiliation(s)
- Douglas M. Ruden
- Department of Obstetrics and Gynecology, C. S. Mott Center for Human Growth and Development and Center for Urban Responses to Environmental Stressors, Institute of Environmental Health Sciences, Wayne State UniversityDetroit, MI, USA
| | - Pablo E. Cingolani
- School of Computer Science and Genome Quebec Innovation Centre, McGill UniversityMontreal, QC, Canada
| | - Arko Sen
- Department of Pharmacology, Wayne State UniversityDetroit, MI, USA
| | - Wen Qu
- Department of Pharmacology, Wayne State UniversityDetroit, MI, USA
| | - Luan Wang
- Institute of Environmental Health Sciences, Wayne State UniversityDetroit, MI, USA
| | - Marie-Claude Senut
- Institute of Environmental Health Sciences, Wayne State UniversityDetroit, MI, USA
| | - Mark D. Garfinkel
- Department of Biological Sciences, University of Alabama in HuntsvilleHuntsville, AL, USA
| | - Vincent E. Sollars
- Department of Biochemistry and Microbiology, Joan C. Edwards School of Medicine, Marshall UniversityHuntington, WV, USA
| | - Xiangyi Lu
- Institute of Environmental Health Sciences, Wayne State UniversityDetroit, MI, USA
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Mammalian introns: when the junk generates molecular diversity. Int J Mol Sci 2015; 16:4429-52. [PMID: 25710723 PMCID: PMC4394429 DOI: 10.3390/ijms16034429] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 02/06/2015] [Accepted: 02/11/2015] [Indexed: 01/14/2023] Open
Abstract
Introns represent almost half of the human genome, yet their vast majority is eliminated from eukaryotic transcripts through RNA splicing. Nevertheless, they feature key elements and functions that deserve further interest. At the level of DNA, introns are genomic segments that can shelter independent transcription units for coding and non-coding RNAs which transcription may interfere with that of the host gene, and regulatory elements that can influence gene expression and splicing itself. From the RNA perspective, some introns can be subjected to alternative splicing. Intron retention appear to provide some plasticity to the nature of the protein produced, its distribution in a given cell type and timing of its translation. Intron retention may also serve as a switch to produce coding or non-coding RNAs from the same transcription unit. Conversely, splicing of introns has been directly implicated in the production of small regulatory RNAs. Hence, splicing of introns also appears to provide plasticity to the type of RNA produced from a genetic locus (coding, non-coding, short or long). We addressed these aspects to add to our understanding of mechanisms that control the fate of introns and could be instrumental in regulating genomic output and hence cell fate.
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