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Olthof A, Schwoerer C, Girardini K, Weber A, Doggett K, Mieruszynski S, Heath J, Moore T, Biran J, Kanadia R. Taxonomy of introns and the evolution of minor introns. Nucleic Acids Res 2024; 52:9247-9266. [PMID: 38943346 PMCID: PMC11347168 DOI: 10.1093/nar/gkae550] [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: 11/30/2023] [Revised: 06/05/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024] Open
Abstract
Classification of introns, which is crucial to understanding their evolution and splicing, has historically been binary and has resulted in the naming of major and minor introns that are spliced by their namesake spliceosome. However, a broad range of intron consensus sequences exist, leading us to here reclassify introns as minor, minor-like, hybrid, major-like, major and non-canonical introns in 263 species across six eukaryotic supergroups. Through intron orthology analysis, we discovered that minor-like introns are a transitory node for intron conversion across evolution. Despite close resemblance of their consensus sequences to minor introns, these introns possess an AG dinucleotide at the -1 and -2 position of the 5' splice site, a salient feature of major introns. Through combined analysis of CoLa-seq, CLIP-seq for major and minor spliceosome components, and RNAseq from samples in which the minor spliceosome is inhibited we found that minor-like introns are also an intermediate class from a splicing mechanism perspective. Importantly, this analysis has provided insight into the sequence elements that have evolved to make minor-like introns amenable to recognition by both minor and major spliceosome components. We hope that this revised intron classification provides a new framework to study intron evolution and splicing.
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Affiliation(s)
- Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Charles F Schwoerer
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Kaitlin N Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Audrey L Weber
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
| | - Karen Doggett
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Stephen Mieruszynski
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Joan K Heath
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Timothy E Moore
- Statistical Consulting Services, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT, USA
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon, Israel
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
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2
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Powell-Rodgers G, Pirzada MUR, Richee J, Jungers CF, Colijn S, Stratman AN, Djuranovic S. Role of U11/U12 minor spliceosome gene ZCRB1 in Ciliogenesis and WNT Signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607392. [PMID: 39149385 PMCID: PMC11326282 DOI: 10.1101/2024.08.09.607392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Despite the fact that 0.5% of human introns are processed by the U11/U12 minor spliceosome, the latter influences gene expression across multiple cellular processes. The ZCRB1 protein is a recently described core component of the U12 mono-snRNP minor spliceosome, but its functional significance to minor splicing, gene regulation, and biological signaling cascades is poorly understood. Using CRISPR-Cas9 and siRNA targeted knockout and knockdown strategies, we show that human cell lines with a partial reduction in ZCRB1 expression exhibit significant dysregulation of the splicing and expression of U12-type genes, primarily due to dysregulation of U12 mono-snRNA. RNA-Seq and targeted analyses of minor intron-containing genes indicate a downregulation in the expression of genes involved in ciliogenesis, and consequentially an upregulation in WNT signaling. Additionally, zcrb1 CRISPR-Cas12a knockdown in zebrafish embryos led to gross developmental and body axis abnormalities, disrupted ciliogenesis, and upregulated WNT signaling, complementing our human cell studies. This work highlights a conserved and essential biological role of the minor spliceosome in general, and the ZCRB1 protein specifically in cellular and developmental processes across species, shedding light on the multifaceted relationship between splicing regulation, ciliogenesis, and WNT signaling.
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Affiliation(s)
- Geralle Powell-Rodgers
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Mujeeb Ur Rehman Pirzada
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Jahmiera Richee
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Courtney F. Jungers
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Sarah Colijn
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Amber N. Stratman
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
| | - Sergej Djuranovic
- Washington University in St. Louis, School of Medicine, Cell Biology and Physiology, St. Louis, MO
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3
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Li C, Liang S, Huang Q, Zhou Z, Ding Z, Long N, Wi K, Li L, Jiang X, Fan Y, Xu Y. Minor Spliceosomal 65K/RNPC3 Interacts with ANKRD11 and Mediates HDAC3-Regulated Histone Deacetylation and Transcription. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307804. [PMID: 38837887 PMCID: PMC11304329 DOI: 10.1002/advs.202307804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/12/2024] [Indexed: 06/07/2024]
Abstract
RNA splicing is crucial in the multilayer regulatory networks for gene expression, making functional interactions with DNA- and other RNA-processing machineries in the nucleus. However, these established couplings are all major spliceosome-related; whether the minor spliceosome is involved remains unclear. Here, through affinity purification using Drosophila lysates, an interaction is identified between the minor spliceosomal 65K/RNPC3 and ANKRD11, a cofactor of histone deacetylase 3 (HDAC3). Using a CRISPR/Cas9 system, Deletion strains are constructed and found that both Dm65KΔ/Δ and Dmankrd11Δ/Δ mutants have reduced histone deacetylation at Lys9 of histone H3 (H3K9) and Lys5 of histone H4 (H4K5) in their heads, exhibiting various neural-related defects. The 65K-ANKRD11 interaction is also conserved in human cells, and the HsANKRD11 middle-uncharacterized domain mediates Hs65K association with HDAC3. Cleavage under targets and tagmentation (CUT&Tag) assays revealed that HsANKRD11 is a bridging factor, which facilitates the synergistic common chromatin-binding of HDAC3 and Hs65K. Knockdown (KD) of HsANKRD11 simultaneously decreased their common binding, resulting in reduced deacetylation of nearby H3K9. Ultimately, this study demonstrates that expression changes of many genes caused by HsANKRD11-KD are due to the decreased common chromatin-binding of HDAC3 and Hs65K and subsequently reduced deacetylation of H3K9, illustrating a novel and conserved coupling mechanism that links the histone deacetylation with minor spliceosome for the regulation of gene expression.
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Affiliation(s)
- Chen‐Hui Li
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Shao‐Bo Liang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Qi‐Wei Huang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Zhen‐Zhen Zhou
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Zhan Ding
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
- Key Laboratory of Insect Developmental and Evolutionary BiologyCenter for Excellence in Molecular Plant SciencesChinese Academy of SciencesUniversity of Chinese Academy of SciencesShanghai200032China
| | - Ni Long
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Kwang‐Chon Wi
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Liang Li
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Xi‐Ping Jiang
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Yu‐Jie Fan
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
| | - Yong‐Zhen Xu
- RNA InstituteState Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisCollege of Life ScienceTaiKang Center for Life and Medical SciencesWuhan UniversityHubei430072China
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4
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Jacquemin V, Versbraegen N, Duerinckx S, Massart A, Soblet J, Perazzolo C, Deconinck N, Brischoux-Boucher E, De Leener A, Revencu N, Janssens S, Moorgat S, Blaumeiser B, Avela K, Touraine R, Abou Jaoude I, Keymolen K, Saugier-Veber P, Lenaerts T, Abramowicz M, Pirson I. Congenital hydrocephalus: new Mendelian mutations and evidence for oligogenic inheritance. Hum Genomics 2023; 17:16. [PMID: 36859317 PMCID: PMC9979489 DOI: 10.1186/s40246-023-00464-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Congenital hydrocephalus is characterized by ventriculomegaly, defined as a dilatation of cerebral ventricles, and thought to be due to impaired cerebrospinal fluid (CSF) homeostasis. Primary congenital hydrocephalus is a subset of cases with prenatal onset and absence of another primary cause, e.g., brain hemorrhage. Published series report a Mendelian cause in only a minority of cases. In this study, we analyzed exome data of PCH patients in search of novel causal genes and addressed the possibility of an underlying oligogenic mode of inheritance for PCH. MATERIALS AND METHODS We sequenced the exome in 28 unrelated probands with PCH, 12 of whom from families with at least two affected siblings and 9 of whom consanguineous, thereby increasing the contribution of genetic causes. Patient exome data were first analyzed for rare (MAF < 0.005) transmitted or de novo variants. Population stratification of unrelated PCH patients and controls was determined by principle component analysis, and outliers identified using Mahalanobis distance 5% as cutoff. Patient and control exome data for genes biologically related to cilia (SYScilia database) were analyzed by mutation burden test. RESULTS In 18% of probands, we identify a causal (pathogenic or likely pathogenic) variant of a known hydrocephalus gene, including genes for postnatal, syndromic hydrocephalus, not previously reported in isolated PCH. In a further 11%, we identify mutations in novel candidate genes. Through mutation burden tests, we demonstrate a significant burden of genetic variants in genes coding for proteins of the primary cilium in PCH patients compared to controls. CONCLUSION Our study confirms the low contribution of Mendelian mutations in PCH and reports PCH as a phenotypic presentation of some known genes known for syndromic, postnatal hydrocephalus. Furthermore, this study identifies novel Mendelian candidate genes, and provides evidence for oligogenic inheritance implicating primary cilia in PCH.
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Affiliation(s)
- Valerie Jacquemin
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium.
| | - Nassim Versbraegen
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium ,grid.4989.c0000 0001 2348 0746Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium
| | - Sarah Duerinckx
- grid.4989.c0000 0001 2348 0746Service de Neuropédiatrie, Hôpital Universitaire de Bruxelles and CUB Hôpital Erasme and Université Libre de Bruxelles, Brussels, Belgium
| | - Annick Massart
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium ,grid.411414.50000 0004 0626 3418Department of Nephrology, University Hospital of Antwerp, Edegem, Belgium
| | - Julie Soblet
- grid.412157.40000 0000 8571 829XHuman Genetics Department, CUB Hôpital Erasme, Brussels, Belgium
| | - Camille Perazzolo
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
| | - Nicolas Deconinck
- grid.412209.c0000 0004 0578 1002Hopital Universitaire des Enfants Reine Fabiola and Hopital Universitaire de Bruxelles and Université Libre de Bruxelles, Brussels, Belgium
| | - Elise Brischoux-Boucher
- grid.493090.70000 0004 4910 6615Centre de génétique humaine - CHU de Besançon, Université de Bourgogne-Franche-Comté, Besançon, France
| | - Anne De Leener
- grid.48769.340000 0004 0461 6320Centre de Génétique Humaine, Cliniques Universitaires Saint-Luc et Université Catholique de Louvain, Brussels, Belgium
| | - Nicole Revencu
- grid.48769.340000 0004 0461 6320Centre de Génétique Humaine, Cliniques Universitaires Saint-Luc et Université Catholique de Louvain, Brussels, Belgium
| | - Sandra Janssens
- grid.410566.00000 0004 0626 3303Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Stèphanie Moorgat
- grid.452439.d0000 0004 0578 0894Centre de Génétique Humaine, Institut de Pathologie et de Génétique, Gosselies, Belgium
| | - Bettina Blaumeiser
- grid.411414.50000 0004 0626 3418Center of Medical Genetics, Antwerp University and Antwerp University Hospital, Edegem, Belgium
| | - Kristiina Avela
- grid.15485.3d0000 0000 9950 5666Department of Clinical Genetics, Helsinki University Hospital, Helsinki, Finland
| | - Renaud Touraine
- grid.412954.f0000 0004 1765 1491Génétique Clinique Chromosomique et Moléculaire, CHU de Saint-Etienne, St-Priest-en-Jarez, France
| | - Imad Abou Jaoude
- Department of Gynecology and Obstetrics, Abou Jaoude Hospital, Jal El Dib, Lebanon
| | - Kathelijn Keymolen
- grid.411326.30000 0004 0626 3362Center for Medical Genetics, UZ Brussels, Jette, Belgium
| | - Pascale Saugier-Veber
- grid.10400.350000 0001 2108 3034Department of Genetics and Reference Center for Developmental Disorders, Université Rouen Normandie, Inserm U1245 and CHU Rouen, Rouen, France
| | - Tom Lenaerts
- grid.4989.c0000 0001 2348 0746Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, Brussels, Belgium ,grid.4989.c0000 0001 2348 0746Machine Learning Group, Université Libre de Bruxelles, Brussels, Belgium ,grid.8767.e0000 0001 2290 8069Artificial Intelligence Lab, Vrije Universiteit Brussel, Brussels, Belgium
| | - Marc Abramowicz
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium. .,Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.
| | - Isabelle Pirson
- grid.4989.c0000 0001 2348 0746Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire, Université Libre de Bruxelles, Brussels, Belgium
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5
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Morgan KJ, Doggett K, Geng F, Mieruszynski S, Whitehead L, Smith KA, Hogan BM, Simons C, Baillie GJ, Molania R, Papenfuss AT, Hall TE, Ober EA, Stainier DYR, Gong Z, Heath JK. ahctf1 and kras mutations combine to amplify oncogenic stress and restrict liver overgrowth in a zebrafish model of hepatocellular carcinoma. eLife 2023; 12:73407. [PMID: 36648336 PMCID: PMC9897728 DOI: 10.7554/elife.73407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
The nucleoporin (NUP) ELYS, encoded by AHCTF1, is a large multifunctional protein with essential roles in nuclear pore assembly and mitosis. Using both larval and adult zebrafish models of hepatocellular carcinoma (HCC), in which the expression of an inducible mutant kras transgene (krasG12V) drives hepatocyte-specific hyperplasia and liver enlargement, we show that reducing ahctf1 gene dosage by 50% markedly decreases liver volume, while non-hyperplastic tissues are unaffected. We demonstrate that in the context of cancer, ahctf1 heterozygosity impairs nuclear pore formation, mitotic spindle assembly, and chromosome segregation, leading to DNA damage and activation of a Tp53-dependent transcriptional programme that induces cell death and cell cycle arrest. Heterozygous expression of both ahctf1 and ranbp2 (encoding a second nucleoporin), or treatment of heterozygous ahctf1 larvae with the nucleocytoplasmic transport inhibitor, Selinexor, completely blocks krasG12V-driven hepatocyte hyperplasia. Gene expression analysis of patient samples in the liver hepatocellular carcinoma (LIHC) dataset in The Cancer Genome Atlas shows that high expression of one or more of the transcripts encoding the 10 components of the NUP107-160 subcomplex, which includes AHCTF1, is positively correlated with worse overall survival. These results provide a strong and feasible rationale for the development of novel cancer therapeutics that target ELYS function and suggest potential avenues for effective combinatorial treatments.
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Affiliation(s)
- Kimberly J Morgan
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Karen Doggett
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Fansuo Geng
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Stephen Mieruszynski
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
| | - Lachlan Whitehead
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Centre for Dynamic Imaging, Advanced Technology and Biology Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Kelly A Smith
- Department of Physiology, University of MelbourneParkvilleAustralia
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Benjamin M Hogan
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
- Peter MacCallum Cancer CentreMelbourneAustralia
| | - Cas Simons
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
- Murdoch Children's Research InstituteParkvilleAustralia
| | - Gregory J Baillie
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Ramyar Molania
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Anthony T Papenfuss
- Department of Medical Biology, University of MelbourneParkvilleAustralia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
| | - Thomas E Hall
- Institute for Molecular Biosciences, University of QueenslandQueenslandAustralia
| | - Elke A Ober
- Danish Stem Cell Center, University of CopenhagenCopenhagenDenmark
| | - Didier YR Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung ResearchBad NauheimGermany
| | - Zhiyuan Gong
- Department of Biological Science, National University of SingaporeSingaporeSingapore
| | - Joan K Heath
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical ResearchParkvilleAustralia
- Department of Medical Biology, University of MelbourneParkvilleAustralia
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6
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Ding Z, Meng YR, Fan YJ, Xu YZ. Roles of minor spliceosome in intron recognition and the convergence with the better understood major spliceosome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1761. [PMID: 36056453 DOI: 10.1002/wrna.1761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 06/06/2022] [Accepted: 08/06/2022] [Indexed: 01/31/2023]
Abstract
Catalyzed by spliceosomes in the nucleus, RNA splicing removes intronic sequences from precursor RNAs in eukaryotes to generate mature RNA, which also significantly increases proteome complexity and fine-tunes gene expression. Most metazoans have two coexisting spliceosomes; the major spliceosome, which removes >99.5% of introns, and the minor spliceosome, which removes far fewer introns (only 770 at present have been predicted in the human genome). Both spliceosomes are large and dynamic machineries, each consisting of five small nuclear RNAs (snRNAs) and more than 100 proteins. However, the dynamic assembly, catalysis, and protein composition of the minor spliceosome are still poorly understood. With different splicing signals, minor introns are rare and usually distributed alone and flanked by major introns in genes, raising questions of how they are recognized by the minor spliceosome and how their processing deals with the splicing of neighboring major introns. Due to large numbers of introns and close similarities between the two machinery, cooperative, and competitive recognition by the two spliceosomes has been investigated. Functionally, many minor-intron-containing genes are evolutionarily conserved and essential. Mutations in the minor spliceosome exhibit a variety of developmental defects in plants and animals and are linked to numerous human diseases. Here, we review recent progress in the understanding of minor splicing, compare currently known components of the two spliceosomes, survey minor introns in a wide range of organisms, discuss cooperation and competition of the two spliceosomes in splicing of minor-intron-containing genes, and contributions of minor splicing mutations in development and diseases. This article is categorized under: RNA Processing > Processing of Small RNAs RNA Processing > Splicing Mechanisms RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Zhan Ding
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yan-Ran Meng
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, and Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, Hubei, China
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7
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Yang JY, Wang WQ, Han MY, Huang SS, Wang GJ, Su Y, Xu JC, Fu Y, Kang DY, Yang K, Zhang X, Liu X, Gao X, Yuan YY, Dai P. Addition of an affected family member to a previously ascertained autosomal recessive nonsyndromic hearing loss pedigree and systematic phenotype-genotype analysis of splice-site variants in MYO15A. BMC Med Genomics 2022; 15:241. [PMCID: PMC9673454 DOI: 10.1186/s12920-022-01368-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/29/2022] [Indexed: 11/19/2022] Open
Abstract
Pathogenic variants in MYO15A are known to cause autosomal recessive nonsyndromic hearing loss (ARNSHL), DFNB3. We have previously reported on one ARNSHL family including two affected siblings and identified MYO15A c.5964+3G > A and c.8375 T > C (p.Val2792Ala) as the possible deafness-causing variants. Eight year follow up identified one new affected individual in this family, who also showed congenital, severe to profound sensorineural hearing loss. By whole exome sequencing, we identified a new splice-site variant c.5531+1G > C (maternal allele), in a compound heterozygote with previously identified missense variant c.8375 T > C (p.Val2792Ala) (paternal allele) in MYO15A as the disease-causing variants. The new affected individual underwent unilateral cochlear implantation at the age of 1 year, and 5 year follow-up showed satisfactory speech and language outcomes. Our results further indicate that MYO15A-associated hearing loss is good candidates for cochlear implantation, which is in accordance with previous report. In light of our findings and review of the literatures, 58 splice-site variants in MYO15A are correlated with a severe deafness phenotype, composed of 46 canonical splice-site variants and 12 non-canonical splice-site variants.
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Affiliation(s)
- Jin-Yuan Yang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Wei-Qian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ming-Yu Han
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Sha-Sha Huang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Guo-Jian Wang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Yu Su
- Department of Otolaryngology, Head and Neck Surgery, Chinese PLA General Hospital Affiliated Hainan Hospital, Jianglin Road, Sanya, 572013 People’s Republic of China ,Hainan Province Clinical Research Center for Otolaryngologic and Head and Neck Diseases, Jianglin Road, Sanya, 572013 People’s Republic of China
| | - Jin-Cao Xu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Ying Fu
- grid.27255.370000 0004 1761 1174Department of Otorhinolaryngology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, 758 Hefei Road, Qingdao, 266035 Shandong People’s Republic of China
| | - Dong-Yang Kang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Kun Yang
- grid.488137.10000 0001 2267 2324Postgraduate Training Base of Jinzhou Medical University, The PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xin Zhang
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Xing Liu
- grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Xue Gao
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China ,grid.488137.10000 0001 2267 2324Department of Otolaryngology, PLA Rocket Force Characteristic Medical Center, 16# XinWai Da Jie, Beijing, 100088 People’s Republic of China
| | - Yong-Yi Yuan
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
| | - Pu Dai
- grid.488137.10000 0001 2267 2324College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, 28 Fuxing Road, Beijing, 100853 People’s Republic of China ,grid.419897.a0000 0004 0369 313XNational Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People’s Republic of China ,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People’s Republic of China
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8
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Emerging Roles of RNA-Binding Proteins in Inner Ear Hair Cell Development and Regeneration. Int J Mol Sci 2022; 23:ijms232012393. [PMID: 36293251 PMCID: PMC9604452 DOI: 10.3390/ijms232012393] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/07/2022] [Accepted: 10/14/2022] [Indexed: 11/05/2022] Open
Abstract
RNA-binding proteins (RBPs) regulate gene expression at the post-transcriptional level. They play major roles in the tissue- and stage-specific expression of protein isoforms as well as in the maintenance of protein homeostasis. The inner ear is a bi-functional organ, with the cochlea and the vestibular system required for hearing and for maintaining balance, respectively. It is relatively well documented that transcription factors and signaling pathways are critically involved in the formation of inner ear structures and in the development of hair cells. Accumulating evidence highlights emerging functions of RBPs in the post-transcriptional regulation of inner ear development and hair cell function. Importantly, mutations of splicing factors of the RBP family and defective alternative splicing, which result in inappropriate expression of protein isoforms, lead to deafness in both animal models and humans. Because RBPs are critical regulators of cell proliferation and differentiation, they present the potential to promote hair cell regeneration following noise- or ototoxin-induced damage through mitotic and non-mitotic mechanisms. Therefore, deciphering RBP-regulated events during inner ear development and hair cell regeneration can help define therapeutic strategies for treatment of hearing loss. In this review, we outline our evolving understanding of the implications of RBPs in hair cell formation and hearing disease with the aim of promoting future research in this field.
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9
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Olthof AM, White AK, Kanadia RN. The emerging significance of splicing in vertebrate development. Development 2022; 149:dev200373. [PMID: 36178052 PMCID: PMC9641660 DOI: 10.1242/dev.200373] [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] [Indexed: 01/19/2023]
Abstract
Splicing is a crucial regulatory node of gene expression that has been leveraged to expand the proteome from a limited number of genes. Indeed, the vast increase in intron number that accompanied vertebrate emergence might have aided the evolution of developmental and organismal complexity. Here, we review how animal models for core spliceosome components have provided insights into the role of splicing in vertebrate development, with a specific focus on neuronal, neural crest and skeletal development. To this end, we also discuss relevant spliceosomopathies, which are developmental disorders linked to mutations in spliceosome subunits. Finally, we discuss potential mechanisms that could underlie the tissue-specific phenotypes often observed upon spliceosome inhibition and identify gaps in our knowledge that, we hope, will inspire further research.
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Affiliation(s)
- Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen 2200, Denmark
| | - Alisa K. White
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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10
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Siebert AE, Corll J, Paige Gronevelt J, Levine L, Hobbs LM, Kenney C, Powell CLE, Battistuzzi FU, Davenport R, Mark Settles A, Brad Barbazuk W, Westrick RJ, Madlambayan GJ, Lal S. Genetic analysis of human RNA binding motif protein 48 (RBM48) reveals an essential role in U12-type intron splicing. Genetics 2022; 222:iyac129. [PMID: 36040194 PMCID: PMC9526058 DOI: 10.1093/genetics/iyac129] [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: 05/13/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
U12-type or minor introns are found in most multicellular eukaryotes and constitute ∼0.5% of all introns in species with a minor spliceosome. Although the biological significance for the evolutionary conservation of U12-type introns is debated, mutations disrupting U12 splicing cause developmental defects in both plants and animals. In human hematopoietic stem cells, U12 splicing defects disrupt proper differentiation of myeloid lineages and are associated with myelodysplastic syndrome, predisposing individuals to acute myeloid leukemia. Mutants in the maize ortholog of RNA binding motif protein 48 (RBM48) have aberrant U12-type intron splicing. Human RBM48 was recently purified biochemically as part of the minor spliceosome and shown to recognize the 5' end of the U6atac snRNA. In this report, we use CRISPR/Cas9-mediated ablation of RBM48 in human K-562 cells to show the genetic function of RBM48. RNA-seq analysis comparing wild-type and mutant K-562 genotypes found that 48% of minor intron-containing genes have significant U12-type intron retention in RBM48 mutants. Comparing these results to maize rbm48 mutants defined a subset of minor intron-containing genes disrupted in both species. Mutations in the majority of these orthologous minor intron-containing genes have been reported to cause developmental defects in both plants and animals. Our results provide genetic evidence that the primary defect of human RBM48 mutants is aberrant U12-type intron splicing, while a comparison of human and maize RNA-seq data identifies candidate genes likely to mediate mutant phenotypes of U12-type splicing defects.
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Affiliation(s)
- Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - J Paige Gronevelt
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Laurel Levine
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Linzi M Hobbs
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Catalina Kenney
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Christopher L E Powell
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Fabia U Battistuzzi
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - A Mark Settles
- Horticultural Sciences Department and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Randal J Westrick
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Gerard J Madlambayan
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester Hills, MI 48309, USA
- Department of Bioengineering, Oakland University, Rochester Hills, MI 48309, USA
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11
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Weinstein R, Bishop K, Broadbridge E, Yu K, Carrington B, Elkahloun A, Zhen T, Pei W, Burgess SM, Liu P, Bresciani E, Sood R. Zrsr2 Is Essential for the Embryonic Development and Splicing of Minor Introns in RNA and Protein Processing Genes in Zebrafish. Int J Mol Sci 2022; 23:10668. [PMID: 36142581 PMCID: PMC9501576 DOI: 10.3390/ijms231810668] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/12/2022] [Indexed: 11/30/2022] Open
Abstract
ZRSR2 (zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2) is an essential splicing factor involved in 3' splice-site recognition as a component of both the major and minor spliceosomes that mediate the splicing of U2-type (major) and U12-type (minor) introns, respectively. Studies of ZRSR2-depleted cell lines and ZRSR2-mutated patient samples revealed its essential role in the U12-dependent minor spliceosome. However, the role of ZRSR2 during embryonic development is not clear, as its function is compensated for by Zrsr1 in mice. Here, we utilized the zebrafish model to investigate the role of zrsr2 during embryonic development. Using CRISPR/Cas9 technology, we generated a zrsr2-knockout zebrafish line, termed zrsr2hg129/hg129 (p.Trp167Argfs*9) and examined embryo development in the homozygous mutant embryos. zrsr2hg129/hg129 embryos displayed multiple developmental defects starting at 4 days post fertilization (dpf) and died after 8 dpf, suggesting that proper Zrsr2 function is required during embryonic development. The global transcriptome analysis of 3 dpf zrsr2hg129/hg129 embryos revealed that the loss of Zrsr2 results in the downregulation of essential metabolic pathways and the aberrant retention of minor introns in about one-third of all minor intron-containing genes in zebrafish. Overall, our study has demonstrated that the role of Zrsr2 as a component of the minor spliceosome is conserved and critical for proper embryonic development in zebrafish.
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Affiliation(s)
- Rachel Weinstein
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth Broadbridge
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kai Yu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdel Elkahloun
- Microarray Core, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tao Zhen
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M. Burgess
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Liu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erica Bresciani
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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12
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Gómez-Redondo I, Pericuesta E, Navarrete-Lopez P, Ramos-Ibeas P, Planells B, Fonseca-Balvís N, Vaquero-Rey A, Fernández-González R, Laguna-Barraza R, Horiuchi K, Gutiérrez-Adán A. Zrsr2 and functional U12-dependent spliceosome are necessary for follicular development. iScience 2022; 25:103860. [PMID: 35198906 PMCID: PMC8850803 DOI: 10.1016/j.isci.2022.103860] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 12/13/2022] Open
Abstract
ZRSR2 is a splicing factor involved in recognition of 3'-intron splice sites that is frequently mutated in myeloid malignancies and several tumors; however, the role of mutations of Zrsr2 in other tissues has not been analyzed. To explore the biological role of ZRSR2, we generated three Zrsr2 mutant mouse lines. All Zrsr2 mutant lines exhibited blood cell anomalies, and in two lines, oogenesis was blocked at the secondary follicle stage. RNA-seq of Zrsr2 mu secondary follicles showed aberrations in gene expression and showed altered alternative splicing (AS) events involving enrichment of U12-type intron retention (IR), supporting the functional Zrsr2 action in minor spliceosomes. IR events were preferentially associated with centriole replication, protein phosphorylation, and DNA damage checkpoint. Notably, we found alterations in AS events of 50 meiotic genes. These results indicate that ZRSR2 mutations alter splicing mainly in U12-type introns, which may affect peripheral blood cells, and impede oogenesis and female fertility.
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Affiliation(s)
- Isabel Gómez-Redondo
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Eva Pericuesta
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Paula Navarrete-Lopez
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Priscila Ramos-Ibeas
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Benjamín Planells
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Noelia Fonseca-Balvís
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Aida Vaquero-Rey
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Raúl Fernández-González
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Ricardo Laguna-Barraza
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Keiko Horiuchi
- Department of Protein-Protein Interaction Research, Institute for Advanced Medical Sciences, Nippon Medical School, 1-396 Kosugi-cho, Nakahara-ku, Kawasaki, Kanagawa 211-8533, Japan
| | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, INIA-CSIC, Avda. Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
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13
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Öther-Gee Pohl S, Myant KB. Alternative RNA splicing in tumour heterogeneity, plasticity and therapy. Dis Model Mech 2022; 15:dmm049233. [PMID: 35014671 PMCID: PMC8764416 DOI: 10.1242/dmm.049233] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a process by which a single gene is able to encode multiple different protein isoforms. It is regulated by the inclusion or exclusion of introns and exons that are joined in different patterns prior to protein translation, thus enabling transcriptomic and proteomic diversity. It is now widely accepted that alternative splicing is dysregulated across nearly all cancer types. This widespread dysregulation means that nearly all cellular processes are affected - these include processes synonymous with the hallmarks of cancer - evasion of apoptosis, tissue invasion and metastasis, altered cellular metabolism, genome instability and drug resistance. Emerging evidence indicates that the dysregulation of alternative splicing also promotes a permissive environment for increased tumour heterogeneity and cellular plasticity. These are fundamental regulators of a patient's response to therapy. In this Review, we introduce the mechanisms of alternative splicing and the role of aberrant splicing in cancer, with particular focus on newfound evidence of alternative splicing promoting tumour heterogeneity, cellular plasticity and altered metabolism. We discuss recent in vivo models generated to study alternative splicing and the importance of these for understanding complex tumourigenic processes. Finally, we review the effects of alternative splicing on immune evasion, cell death and genome instability, and how targeting these might enhance therapeutic efficacy.
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Affiliation(s)
| | - Kevin B. Myant
- Cancer Research UK Edinburgh Centre, Institute of Genetics of Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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14
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Minor Intron Splicing from Basic Science to Disease. Int J Mol Sci 2021; 22:ijms22116062. [PMID: 34199764 PMCID: PMC8199999 DOI: 10.3390/ijms22116062] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 01/14/2023] Open
Abstract
Pre-mRNA splicing is an essential step in gene expression and is catalyzed by two machineries in eukaryotes: the major (U2 type) and minor (U12 type) spliceosomes. While the majority of introns in humans are U2 type, less than 0.4% are U12 type, also known as minor introns (mi-INTs), and require a specialized spliceosome composed of U11, U12, U4atac, U5, and U6atac snRNPs. The high evolutionary conservation and apparent splicing inefficiency of U12 introns have set them apart from their major counterparts and led to speculations on the purpose for their existence. However, recent studies challenged the simple concept of mi-INTs splicing inefficiency due to low abundance of their spliceosome and confirmed their regulatory role in alternative splicing, significantly impacting the expression of their host genes. Additionally, a growing list of minor spliceosome-associated diseases with tissue-specific pathologies affirmed the importance of minor splicing as a key regulatory pathway, which when deregulated could lead to tissue-specific pathologies due to specific alterations in the expression of some minor-intron-containing genes. Consequently, uncovering how mi-INTs splicing is regulated in a tissue-specific manner would allow for better understanding of disease pathogenesis and pave the way for novel therapies, which we highlight in this review.
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15
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Gourain V, Armant O, Lübke L, Diotel N, Rastegar S, Strähle U. Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury. Front Neurosci 2021; 15:671249. [PMID: 34054419 PMCID: PMC8162057 DOI: 10.3389/fnins.2021.671249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/16/2021] [Indexed: 12/14/2022] Open
Abstract
Zebrafish is an attractive model to investigate regeneration of the nervous system. Despite major progress in our understanding of the underlying processes, the transcriptomic changes are largely unknown. We carried out a computational analysis of the transcriptome of the regenerating telencephalon integrating changes in the expression of mRNAs, their splice variants and investigated the putative role of regulatory RNAs in the modulation of these transcriptional changes. Profound changes in the expression of genes and their splice variants engaged in many distinct processes were observed. Differential transcription and splicing are important processes in response to injury of the telencephalon. As exemplified by the coordinated regulation of the cholesterol synthesizing enzymes and transporters, the genome responded to injury of the telencephalon in a multi-tiered manner with distinct and interwoven changes in expression of enzymes, transporters and their regulatory molecules. This coordinated genomic response involved a decrease of the mRNA of the key transcription factor SREBF2, induction of microRNAs (miR-182, miR-155, miR-146, miR-31) targeting cholesterol genes, shifts in abundance of splice variants as well as regulation of long non-coding RNAs. Cholesterol metabolism appears to be switched from synthesis to relocation of cholesterol. Based on our in silico analyses, this switch involves complementary and synergistic inputs by different regulatory principles. Our studies suggest that adaptation of cholesterol metabolism is a key process involved in regeneration of the injured zebrafish brain.
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Affiliation(s)
- Victor Gourain
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,UMR 1064 Centre de Recherche en Transplantation en Immunologie, Nantes, France
| | - Olivier Armant
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,PSE-ENV/SRTE/LECO, Institut de Radioprotection et de Sûreté Nucléaire (IRSN), Cadarache, Saint-Paul-Lez-Durance, France
| | - Luisa Lübke
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Nicolas Diotel
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,UMR 1188, Diabète Athérothrombose Thérapies Réunion Océan Indien CYROI, Saint-Denis, France
| | - Sepand Rastegar
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Uwe Strähle
- Institute of Biological and Chemical Systems-Biological Information Processing (IBCS-BIP), Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany.,COS, University Heidelberg, Heidelberg, Germany
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16
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Olthof AM, White AK, Mieruszynski S, Doggett K, Lee MF, Chakroun A, Abdel Aleem AK, Rousseau J, Magnani C, Roifman CM, Campeau PM, Heath JK, Kanadia RN. Disruption of exon-bridging interactions between the minor and major spliceosomes results in alternative splicing around minor introns. Nucleic Acids Res 2021; 49:3524-3545. [PMID: 33660780 PMCID: PMC8034651 DOI: 10.1093/nar/gkab118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/11/2022] Open
Abstract
Vertebrate genomes contain major (>99.5%) and minor (<0.5%) introns that are spliced by the major and minor spliceosomes, respectively. Major intron splicing follows the exon-definition model, whereby major spliceosome components first assemble across exons. However, since most genes with minor introns predominately consist of major introns, formation of exon-definition complexes in these genes would require interaction between the major and minor spliceosomes. Here, we report that minor spliceosome protein U11-59K binds to the major spliceosome U2AF complex, thereby supporting a model in which the minor spliceosome interacts with the major spliceosome across an exon to regulate the splicing of minor introns. Inhibition of minor spliceosome snRNAs and U11-59K disrupted exon-bridging interactions, leading to exon skipping by the major spliceosome. The resulting aberrant isoforms contained a premature stop codon, yet were not subjected to nonsense-mediated decay, but rather bound to polysomes. Importantly, we detected elevated levels of these alternatively spliced transcripts in individuals with minor spliceosome-related diseases such as Roifman syndrome, Lowry–Wood syndrome and early-onset cerebellar ataxia. In all, we report that the minor spliceosome informs splicing by the major spliceosome through exon-definition interactions and show that minor spliceosome inhibition results in aberrant alternative splicing in disease.
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Affiliation(s)
- Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA
| | - Alisa K White
- Physiology and Neurobiology Department, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA
| | - Stephen Mieruszynski
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Karen Doggett
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Madisen F Lee
- Physiology and Neurobiology Department, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA
| | | | | | - Justine Rousseau
- CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Cinzia Magnani
- Neonatology and Neonatal Intensive Care Unit, Maternal and Child Department, University of Parma, Parma, 43121, Italy
| | - Chaim M Roifman
- Division of Immunology and Allergy, Department of Pediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, ON M5G 1X8, Canada.,The Canadian Centre for Primary Immunodeficiency and The Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Philippe M Campeau
- Department of Pediatrics, University of Montreal, Montreal, QC H4A 3J1, Canada
| | - Joan K Heath
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, 75 N. Eagleville Road, Storrs, CT 06269, USA.,Institute for System Genomics, University of Connecticut, Storrs, CT 06269, USA
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17
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Inoue D, Polaski JT, Taylor J, Castel P, Chen S, Kobayashi S, Hogg SJ, Hayashi Y, Pineda JMB, El Marabti E, Erickson C, Knorr K, Fukumoto M, Yamazaki H, Tanaka A, Fukui C, Lu SX, Durham BH, Liu B, Wang E, Mehta S, Zakheim D, Garippa R, Penson A, Chew GL, McCormick F, Bradley RK, Abdel-Wahab O. Minor intron retention drives clonal hematopoietic disorders and diverse cancer predisposition. Nat Genet 2021; 53:707-718. [PMID: 33846634 PMCID: PMC8177065 DOI: 10.1038/s41588-021-00828-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/24/2021] [Indexed: 12/13/2022]
Abstract
Most eukaryotes harbor two distinct pre-mRNA splicing machineries: the major spliceosome, which removes >99% of introns, and the minor spliceosome, which removes rare, evolutionarily conserved introns. Although hypothesized to serve important regulatory functions, physiologic roles of the minor spliceosome are not well understood. For example, the minor spliceosome component ZRSR2 is subject to recurrent, leukemia-associated mutations, yet functional connections among minor introns, hematopoiesis and cancers are unclear. Here, we identify that impaired minor intron excision via ZRSR2 loss enhances hematopoietic stem cell self-renewal. CRISPR screens mimicking nonsense-mediated decay of minor intron-containing mRNA species converged on LZTR1, a regulator of RAS-related GTPases. LZTR1 minor intron retention was also discovered in the RASopathy Noonan syndrome, due to intronic mutations disrupting splicing and diverse solid tumors. These data uncover minor intron recognition as a regulator of hematopoiesis, noncoding mutations within minor introns as potential cancer drivers and links among ZRSR2 mutations, LZTR1 regulation and leukemias.
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Affiliation(s)
- Daichi Inoue
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Jacob T Polaski
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Justin Taylor
- Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Pau Castel
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Sisi Chen
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Susumu Kobayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
- Division of Cellular Therapy, The Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Simon J Hogg
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Yasutaka Hayashi
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Jose Mario Bello Pineda
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Ettaib El Marabti
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Caroline Erickson
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Katherine Knorr
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Miki Fukumoto
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Hiromi Yamazaki
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Atsushi Tanaka
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
- Department of Immunology, Institute for Frontier Medical Sciences, Kyoto University, Kyoto, Japan
| | - Chie Fukui
- Department of Hematology-Oncology, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Japan
| | - Sydney X Lu
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Benjamin H Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Eric Wang
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Sanjoy Mehta
- Gene Editing & Screening Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Zakheim
- Gene Editing & Screening Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Garippa
- Gene Editing & Screening Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alex Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA
| | - Guo-Liang Chew
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Frank McCormick
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert K Bradley
- Public Health Sciences and Basic Sciences Divisions, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan KetterAbsolute numbers of live mature hematopoietic cellsing Cancer Center, New York, NY, USA.
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18
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McElderry J, Carrington B, Bishop K, Kim E, Pei W, Chen Z, Ramanagoudr-Bhojappa R, Prakash A, Burgess SM, Liu PP, Sood R. Splicing factor DHX15 affects tp53 and mdm2 expression via alternate splicing and promoter usage. Hum Mol Genet 2020; 28:4173-4185. [PMID: 31691804 DOI: 10.1093/hmg/ddz261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 10/18/2019] [Accepted: 10/24/2019] [Indexed: 12/21/2022] Open
Abstract
DHX15, a DEAH box containing RNA helicase, is a splicing factor required for the last step of splicing. Recent studies identified a recurrent mutational hotspot, R222G, in DHX15 in ∼ 6% of acute myeloid leukemia (AML) patients that carry the fusion protein RUNX1-RUNX1T1 produced by t (8;21) (q22;q22). Studies using yeast mutants showed that substitution of G for the residue equivalent to R222 leads to loss of its helicase function, suggesting that it is a loss-of-function mutation. To elucidate the role of DHX15 during development, we established the first vertebrate knockout model with CRISPR/Cas9 in zebrafish. Our data showed that dhx15 expression is enriched in the brain, eyes, pectoral fin primordia, liver and intestinal bulb during embryonic development. Dhx15 deficiency leads to pleiotropic morphological phenotypes in homozygous mutant embryos starting at 3 days post fertilization (dpf) that result in lethality by 7 dpf, revealing an essential role during embryonic development. RNA-seq analysis suggested important roles of Dhx15 in chromatin and nucleosome assembly and regulation of the Mdm2-p53 pathway. Interestingly, exons corresponding to the alternate transcriptional start sites for tp53 and mdm2 were preferentially expressed in the mutant embryos, leading to significant upregulation of their alternate isoforms, Δ113p53 (orthologous to Δ133p53 isoform in human) and mdm2-P2 (isoform using distal promoter P2), respectively. We speculate that these alterations in the Mdm2-p53 pathway contribute to the development of AML in patients with t(8;21) and somatically mutated DHX15.
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Affiliation(s)
- John McElderry
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Blake Carrington
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kevin Bishop
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Erika Kim
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wuhong Pei
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zelin Chen
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ramanagouda Ramanagoudr-Bhojappa
- Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anupam Prakash
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Shawn M Burgess
- Developmental Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - P Paul Liu
- Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Raman Sood
- Zebrafish Core, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Oncogenesis and Development Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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19
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Osman EY, Van Alstyne M, Yen PF, Lotti F, Feng Z, Ling KK, Ko CP, Pellizzoni L, Lorson CL. Minor snRNA gene delivery improves the loss of proprioceptive synapses on SMA motor neurons. JCI Insight 2020; 5:130574. [PMID: 32516136 DOI: 10.1172/jci.insight.130574] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Spinal muscular atrophy (SMA) is an inherited neuromuscular disorder caused by reduced expression of the survival motor neuron (SMN) protein. SMN has key functions in multiple RNA pathways, including the biogenesis of small nuclear ribonucleoproteins that are essential components of both major (U2-dependent) and minor (U12-dependent) spliceosomes. Here we investigated the specific contribution of U12 splicing dysfunction to SMA pathology through selective restoration of this RNA pathway in mouse models of varying phenotypic severity. We show that virus-mediated delivery of minor snRNA genes specifically improves select U12 splicing defects induced by SMN deficiency in cultured mammalian cells, as well as in the spinal cord and dorsal root ganglia of SMA mice without increasing SMN expression. This approach resulted in a moderate amelioration of several parameters of the disease phenotype in SMA mice, including survival, weight gain, and motor function. Importantly, minor snRNA gene delivery improved aberrant splicing of the U12 intron-containing gene Stasimon and rescued the severe loss of proprioceptive sensory synapses on SMA motor neurons, which are early signatures of motor circuit dysfunction in mouse models. Taken together, these findings establish the direct contribution of U12 splicing dysfunction to synaptic deafferentation and motor circuit pathology in SMA.
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Affiliation(s)
- Erkan Y Osman
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Meaghan Van Alstyne
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Pei-Fen Yen
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
| | - Francesco Lotti
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Zhihua Feng
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Karen Ky Ling
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Chien-Ping Ko
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Livio Pellizzoni
- Center for Motor Neuron Biology and Disease, Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Christian L Lorson
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, Missouri, USA
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20
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Gómez-Redondo I, Ramos-Ibeas P, Pericuesta E, Fernández-González R, Laguna-Barraza R, Gutiérrez-Adán A. Minor Splicing Factors Zrsr1 and Zrsr2 Are Essential for Early Embryo Development and 2-Cell-Like Conversion. Int J Mol Sci 2020; 21:E4115. [PMID: 32527007 PMCID: PMC7312986 DOI: 10.3390/ijms21114115] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 12/18/2022] Open
Abstract
Minor splicing plays an important role in vertebrate development. Zrsr1 and Zrsr2 paralog genes have essential roles in alternative splicing, mainly participating in the recognition of minor (U12) introns. To further explore their roles during early embryo development, we produced Zrsr1mu and Zrsr2mu mutant mice, containing truncating mutations within the second zinc finger domain. Both homozygous mutant mice were viable with a normal lifespan. When we crossed a homozygous Zrsr2mu/mu female with Zrsr1mu/mu male, the double heterozygotes were non-viable, giving rise to embryos that stopped developing mainly between the 2- and 4-cell stages, just after zygotic gene activation. RNA-seq analysis of Zrsr1/2mu 2-cell embryos showed altered gene and isoform expression of thousands of genes enriched in gene ontology terms and biological pathways related to ribosome, RNA transport, spliceosome, and essential zygotic gene activation steps. Alternative splicing was analyzed, showing a significant increase in intron retention in both U2 and U12 intron-containing genes related to cell cycle and mitotic nuclear division. Remarkably, both Zrsr1 and Zrsr2 were required for the conversion of mouse-induced pluripotent stem cells into 2C-like cells. According to our results, Zrsr1 or Zrsr2 are necessary for ZGA and both are indispensable for the conversion of induced pluripotent stem cells into 2C-like cells.
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Affiliation(s)
| | | | | | | | | | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, INIA, Avda. Puerta de Hierro n° 12. Local 10, 28040 Madrid, Spain; (I.G.-R.); (P.R.-I.); (E.P.); (R.F.-G.); (R.L.-B.)
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21
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Gregory LC, Dattani MT. The Molecular Basis of Congenital Hypopituitarism and Related Disorders. J Clin Endocrinol Metab 2020; 105:5614788. [PMID: 31702014 DOI: 10.1210/clinem/dgz184] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 11/07/2019] [Indexed: 12/23/2022]
Abstract
CONTEXT Congenital hypopituitarism (CH) is characterized by the presence of deficiencies in one or more of the 6 anterior pituitary (AP) hormones secreted from the 5 different specialized cell types of the AP. During human embryogenesis, hypothalamo-pituitary (HP) development is controlled by a complex spatio-temporal genetic cascade of transcription factors and signaling molecules within the hypothalamus and Rathke's pouch, the primordium of the AP. EVIDENCE ACQUISITION This mini-review discusses the genes and pathways involved in HP development and how mutations of these give rise to CH. This may present in the neonatal period or later on in childhood and may be associated with craniofacial midline structural abnormalities such as cleft lip/palate, visual impairment due to eye abnormalities such as optic nerve hypoplasia (ONH) and microphthalmia or anophthalmia, or midline forebrain neuroradiological defects including agenesis of the septum pellucidum or corpus callosum or the more severe holoprosencephaly. EVIDENCE SYNTHESIS Mutations give rise to an array of highly variable disorders ranging in severity. There are many known causative genes in HP developmental pathways that are routinely screened in CH patients; however, over the last 5 years this list has rapidly increased due to the identification of variants in new genes and pathways of interest by next-generation sequencing. CONCLUSION The majority of patients with these disorders do not have an identified molecular basis, often making management challenging. This mini-review aims to guide clinicians in making a genetic diagnosis based on patient phenotype, which in turn may impact on clinical management.
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Affiliation(s)
- Louise Cheryl Gregory
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Mehul Tulsidas Dattani
- Genetics and Genomic Medicine Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, United Kingdom
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22
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Beauchamp MC, Alam SS, Kumar S, Jerome-Majewska LA. Spliceosomopathies and neurocristopathies: Two sides of the same coin? Dev Dyn 2020; 249:924-945. [PMID: 32315467 DOI: 10.1002/dvdy.183] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 03/26/2020] [Accepted: 04/15/2020] [Indexed: 12/14/2022] Open
Abstract
Mutations in core components of the spliceosome are responsible for a group of syndromes collectively known as spliceosomopathies. Patients exhibit microcephaly, micrognathia, malar hypoplasia, external ear anomalies, eye anomalies, psychomotor delay, intellectual disability, limb, and heart defects. Craniofacial malformations in these patients are predominantly found in neural crest cells-derived structures of the face and head. Mutations in eight genes SNRPB, RNU4ATAC, SF3B4, PUF60, EFTUD2, TXNL4, EIF4A3, and CWC27 are associated with craniofacial spliceosomopathies. In this review, we provide a brief description of the normal development of the head and the face and an overview of mutations identified in genes associated with craniofacial spliceosomopathies. We also describe a model to explain how and when these mutations are most likely to impact neural crest cells. We speculate that mutations in a subset of core splicing factors lead to disrupted splicing in neural crest cells because these cells have increased sensitivity to inefficient splicing. Hence, disruption in splicing likely activates a cellular stress response that includes increased skipping of regulatory exons in genes such as MDM2 and MDM4, key regulators of P53. This would result in P53-associated death of neural crest cells and consequently craniofacial malformations associated with spliceosomopathies.
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Affiliation(s)
- Marie-Claude Beauchamp
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,McGill University Health Centre at Glen Site, Montreal, Quebec, Canada
| | - Sabrina Shameen Alam
- McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Shruti Kumar
- McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Loydie Anne Jerome-Majewska
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada.,McGill University Health Centre at Glen Site, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
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23
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Baumgartner M, Drake K, Kanadia RN. An Integrated Model of Minor Intron Emergence and Conservation. Front Genet 2019; 10:1113. [PMID: 31798628 PMCID: PMC6865273 DOI: 10.3389/fgene.2019.01113] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022] Open
Abstract
Minor introns constitute <0.5% of the introns in the human genome and have remained an enigma since their discovery. These introns are removed by a distinct splicing complex, the minor spliceosome. Both are ancient, tracing back to the last eukaryotic common ancestor (LECA), which is reflected by minor intron enrichment in specific gene families, such as the mitogen activated-protein kinase kinases, voltage-gated sodium and calcium ion channels, and E2F transcription factors. Most minor introns occur as single introns in genes with predominantly major introns. Due to this organization, minor intron-containing gene (MIG) expression requires the coordinated action of two spliceosomes, which increases the probability of missplicing. Thus, one would expect loss of minor introns via purifying selection. This has resulted in complete minor intron loss in at least nine eukaryotic lineages. However, minor introns are highly conserved in land plants and metazoans, where their importance is underscored by embryonic lethality when the minor spliceosome is inactivated. Conditional inactivation of the minor spliceosome has shown that rapidly dividing progenitor cells are highly sensitive to minor spliceosome loss. Indeed, we found that MIGs were significantly enriched in a screen for genes essential for survival in 341 cycling cell lines. Here, we propose that minor introns inserted randomly into genes in LECA or earlier and were subsequently conserved in genes crucial for cycling cell survival. We hypothesize that the essentiality of MIGs allowed minor introns to endure through the unicellularity of early eukaryotic evolution. Moreover, we identified 59 MIGs that emerged after LECA, and that many of these are essential for cycling cell survival, reinforcing our essentiality model for MIG conservation. This suggests that minor intron emergence is dynamic across eukaryotic evolution, and that minor introns should not be viewed as molecular fossils. We also posit that minor intron splicing was co-opted in multicellular evolution as a regulatory switch for en masse control of MIG expression and the biological processes they regulate. Specifically, this mode of regulation could control cell proliferation and thus body size, an idea supported by domestication syndrome, wherein MIGs are enriched in common candidate animal domestication genes.
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Affiliation(s)
- Marybeth Baumgartner
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States.,Institute of Brain and Cognitive Sciences, University of Connecticut, Mansfield, CT, United States
| | - Kyle Drake
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States
| | - Rahul N Kanadia
- Department of Physiology and Neurobiology, University of Connecticut, Mansfield, CT, United States.,Institute of Systems Genomics, University of Connecticut, Mansfield, CT, United States
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24
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Horiuchi K, Perez-Cerezales S, Papasaikas P, Ramos-Ibeas P, López-Cardona AP, Laguna-Barraza R, Fonseca Balvís N, Pericuesta E, Fernández-González R, Planells B, Viera A, Suja JA, Ross PJ, Alén F, Orio L, Rodriguez de Fonseca F, Pintado B, Valcárcel J, Gutiérrez-Adán A. Impaired Spermatogenesis, Muscle, and Erythrocyte Function in U12 Intron Splicing-Defective Zrsr1 Mutant Mice. Cell Rep 2019; 23:143-155. [PMID: 29617656 DOI: 10.1016/j.celrep.2018.03.028] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/28/2017] [Accepted: 03/08/2018] [Indexed: 11/18/2022] Open
Abstract
The U2AF35-like ZRSR1 has been implicated in the recognition of 3' splice site during spliceosome assembly, but ZRSR1 knockout mice do not show abnormal phenotypes. To analyze ZRSR1 function and its precise role in RNA splicing, we generated ZRSR1 mutant mice containing truncating mutations within its RNA-recognition motif. Homozygous mutant mice exhibited severe defects in erythrocytes, muscle stretch, and spermatogenesis, along with germ cell sloughing and apoptosis, ultimately leading to azoospermia and male sterility. Testis RNA sequencing (RNA-seq) analyses revealed increased intron retention of both U2- and U12-type introns, including U12-type intron events in genes with key functions in spermatogenesis and spermatid development. Affected U2 introns were commonly found flanking U12 introns, suggesting functional cross-talk between the two spliceosomes. The splicing and tissue defects observed in mutant mice attributed to ZRSR1 loss of function suggest a physiological role for this factor in U12 intron splicing.
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Affiliation(s)
- Keiko Horiuchi
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology (RCAST), University of Tokyo, Tokyo 153-8904, Japan
| | - Serafín Perez-Cerezales
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Panagiotis Papasaikas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Priscila Ramos-Ibeas
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | | | - Ricardo Laguna-Barraza
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Noelia Fonseca Balvís
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Eva Pericuesta
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Raul Fernández-González
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Benjamín Planells
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain
| | - Alberto Viera
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Jose Angel Suja
- Unidad de Biología Celular, Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Pablo Juan Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Francisco Alén
- Dpto. Psicobiología, Facultad de Psicología, UCM, Campus de Somosaguas, Madrid, Spain
| | - Laura Orio
- Dpto. Psicobiología, Facultad de Psicología, UCM, Campus de Somosaguas, Madrid, Spain
| | - Fernando Rodriguez de Fonseca
- Dpto. Psicobiología, Facultad de Psicología, UCM, Campus de Somosaguas, Madrid, Spain; UGC Salud Mental, Instituto de Investigación Biomédica de Málaga (IBIMA), Universidad de Málaga-Hospital Universitario Regional de Málaga, Avda. Carlos Haya 82, Pabellón de Gobierno, 29010 Málaga, Spain
| | - Belén Pintado
- Servicio de Transgénicos, CNB-CSIC, UAM, Madrid, Spain
| | - Juan Valcárcel
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain.
| | - Alfonso Gutiérrez-Adán
- Dpto. de Reproducción Animal, INIA, Avda Puerta de Hierro nº 12. Local 10, 28040 Madrid, Spain.
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25
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Cologne A, Benoit-Pilven C, Besson A, Putoux A, Campan-Fournier A, Bober MB, De Die-Smulders CEM, Paulussen ADC, Pinson L, Toutain A, Roifman CM, Leutenegger AL, Mazoyer S, Edery P, Lacroix V. New insights into minor splicing-a transcriptomic analysis of cells derived from TALS patients. RNA (NEW YORK, N.Y.) 2019; 25:1130-1149. [PMID: 31175170 PMCID: PMC6800510 DOI: 10.1261/rna.071423.119] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/28/2019] [Indexed: 06/09/2023]
Abstract
Minor intron splicing plays a central role in human embryonic development and survival. Indeed, biallelic mutations in RNU4ATAC, transcribed into the minor spliceosomal U4atac snRNA, are responsible for three rare autosomal recessive multimalformation disorders named Taybi-Linder (TALS/MOPD1), Roifman (RFMN), and Lowry-Wood (LWS) syndromes, which associate numerous overlapping signs of varying severity. Although RNA-seq experiments have been conducted on a few RFMN patient cells, none have been performed in TALS, and more generally no in-depth transcriptomic analysis of the ∼700 human genes containing a minor (U12-type) intron had been published as yet. We thus sequenced RNA from cells derived from five skin, three amniotic fluid, and one blood biosamples obtained from seven unrelated TALS cases and from age- and sex-matched controls. This allowed us to describe for the first time the mRNA expression and splicing profile of genes containing U12-type introns, in the context of a functional minor spliceosome. Concerning RNU4ATAC-mutated patients, we show that as expected, they display distinct U12-type intron splicing profiles compared to controls, but that rather unexpectedly mRNA expression levels are mostly unchanged. Furthermore, although U12-type intron missplicing concerns most of the expressed U12 genes, the level of U12-type intron retention is surprisingly low in fibroblasts and amniocytes, and much more pronounced in blood cells. Interestingly, we found several occurrences of introns that can be spliced using either U2, U12, or a combination of both types of splice site consensus sequences, with a shift towards splicing using preferentially U2 sites in TALS patients' cells compared to controls.
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Affiliation(s)
- Audric Cologne
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Clara Benoit-Pilven
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Alicia Besson
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Audrey Putoux
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
- Clinical Genetics Unit, Department of Genetics, Hospices Civils de Lyon, F-69500 Bron, France
| | - Amandine Campan-Fournier
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Michael B Bober
- Division of Medical Genetics, Nemours/Alfred I. du Pont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Christine E M De Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Aimee D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Center, 6202 AZ Maastricht, The Netherlands
- School for Oncology and Developmental Biology, GROW, Maastricht University, 6229 ER Maastricht, The Netherlands
| | - Lucile Pinson
- Genetic Department for Rare Diseases and Personalized Medicine, Clinical Division, CHU Montpellier, F-34000 Montpellier, France
| | - Annick Toutain
- Department of Genetics, Tours University Hospital, F-37000 Tours, France
- UMR 1253, iBrain, Tours University, Inserm, F-37000 Tours, France
| | - Chaim M Roifman
- Department of Paediatrics, University of Toronto, Toronto, ON M5G 1X8, Canada
- Division for Immunology and Allergy, Canadian Center for Primary Immunodeficiency, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | | | - Sylvie Mazoyer
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
| | - Patrick Edery
- "Genetics of Neurodevelopment" Team, Lyon Neuroscience Research Centre, UMR5292 CNRS U1028 Inserm, University of Lyon, F-69500 Bron, France
- Clinical Genetics Unit, Department of Genetics, Hospices Civils de Lyon, F-69500 Bron, France
| | - Vincent Lacroix
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, F-69622 Villeurbanne, France
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26
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Olthof AM, Hyatt KC, Kanadia RN. Minor intron splicing revisited: identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns. BMC Genomics 2019; 20:686. [PMID: 31470809 PMCID: PMC6717393 DOI: 10.1186/s12864-019-6046-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Mutations in minor spliceosome components such as U12 snRNA (cerebellar ataxia) and U4atac snRNA (microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)) result in tissue-specific symptoms. Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). The current model of inefficient splicing is thought to apply to the regulation of the ~ 500 MIGs identified in the U12DB. However this database was created more than 10 years ago. Therefore, we first wanted to revisit the classification of minor introns in light of the most recent reference genome. We then sought to address specificity of MIG expression, minor intron retention, and alternative splicing (AS) across mouse and human tissues. RESULTS We employed position-weight matrices to obtain a comprehensive updated list of minor introns, consisting of 722 mouse and 770 human minor introns. These can be found in the Minor Intron DataBase (MIDB). Besides identification of 99% of the minor introns found in the U12DB, we also discovered ~ 150 new MIGs. We then analyzed the RNAseq data from eleven different mouse tissues, which revealed tissue-specific MIG expression and minor intron retention. Additionally, many minor introns were efficiently spliced compared to their flanking major introns. Finally, we identified several novel AS events across minor introns in both mouse and human, which were also tissue-dependent. Bioinformatics analysis revealed that several of the AS events could result in the production of novel tissue-specific proteins. Moreover, like the major introns, we found that these AS events were more prevalent in long minor introns, while retention was favoured in shorter introns. CONCLUSION Here we show that minor intron splicing and AS across minor introns is a highly organised process that might be regulated in coordination with the major spliceosome in a tissue-specific manner. We have provided a framework to further study the impact of the minor spliceosome and the regulation of MIG expression. These findings may shed light on the mechanism underlying tissue-specific phenotypes in diseases associated with minor spliceosome inactivation. MIDB can be accessed at https://midb.pnb.uconn.edu .
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Affiliation(s)
- Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
| | - Katery C. Hyatt
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269 USA
- Institute of Systems Genomics, University of Connecticut, Storrs, CT 06269 USA
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27
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Sex-Dimorphic Behavioral Alterations and Altered Neurogenesis in U12 Intron Splicing-Defective Zrsr1 Mutant Mice. Int J Mol Sci 2019; 20:ijms20143543. [PMID: 31331069 PMCID: PMC6678158 DOI: 10.3390/ijms20143543] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/15/2019] [Accepted: 07/17/2019] [Indexed: 01/10/2023] Open
Abstract
Mutant mice with respect to the splicing factor Zrsr1 present altered spermatogenesis and infertility. To investigate whether Zrsr1 is involved in the homeostatic control that the hypothalamus exerts over reproductive functions, we first analyzed both differential gene and isoform expression and alternative splicing alterations in Zrsr1 mutant (Zrsr1mu) hypothalamus; second, we analyzed the spontaneous and social behavior of Zrsr1mu mice; and third, we analyzed adult cell proliferation and survival in the Zrsr1mu hypothalamus. The Zrsr1mu hypothalamus showed altered expression of genes and isoforms related to the glutathione metabolic process, synaptonemal complex assembly, mRNA transport, and altered splicing events involving the enrichment of U12-type intron retention (IR). Furthermore, increased IR in U12-containing genes related with the prolactin, progesterone, and gonadotropin-releasing hormone (GnRH) reproductive signaling pathway was observed. This was associated with a hyperactive phenotype in both males and females, with an anxious phenotype in females, and with increased social interaction in males, instead of the classical aggressive behavior. In addition, Zrsr1mu females but not males exhibited reduced cell proliferation in both the hypothalamus and the subventricular zone. Overall, these results suggest that Zrsr1 expression and function are relevant to organization of the hypothalamic cell network controlling behavior.
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Planells B, Gómez-Redondo I, Pericuesta E, Lonergan P, Gutiérrez-Adán A. Differential isoform expression and alternative splicing in sex determination in mice. BMC Genomics 2019; 20:202. [PMID: 30871468 PMCID: PMC6419433 DOI: 10.1186/s12864-019-5572-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 02/27/2019] [Indexed: 02/06/2023] Open
Abstract
Background Alternative splicing (AS) may play an important role in gonadal sex determination (GSD) in mammals. The present study was designed to identify differentially expressed isoforms and AS modifications accompanying GSD in mice. Results Using deep RNA-sequencing, we performed a transcriptional analysis of XX and XY gonads during sex determination on embryonic days 11 (E11) and 12 (E12). Analysis of differentially expressed genes (DEG) identified hundreds of genes related to GSD and early sex differentiation that may represent good candidates for sex reversal. Expression at time point E11 in males was significantly enriched in RNA splicing and mRNA processing Gene Ontology terms. Differentially expressed isoform analysis identified hundreds of specific isoforms related to GSD, many of which showed no differences in the DEG analysis. Hundreds of AS events were identified as modified at E11 and E12. Female E11 gonads featured sex-biased upregulation of intron retention (in genes related to regulation of transcription, protein phosphorylation, protein transport and mRNA splicing) and exon skipping (in genes related to chromatin repression) suggesting AS as a post-transcription mechanism that controls sex determination of the bipotential fetal gonad. Conclusion Our data suggests an important role of splicing regulatory mechanisms for sex determination in mice. Electronic supplementary material The online version of this article (10.1186/s12864-019-5572-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamín Planells
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.,School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Isabel Gómez-Redondo
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Eva Pericuesta
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Alfonso Gutiérrez-Adán
- Departamento de Reproducción Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain.
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29
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Bai F, Corll J, Shodja DN, Davenport R, Feng G, Mudunkothge J, Brigolin CJ, Martin F, Spielbauer G, Tseung CW, Siebert AE, Barbazuk WB, Lal S, Settles AM. RNA Binding Motif Protein 48 Is Required for U12 Splicing and Maize Endosperm Differentiation. THE PLANT CELL 2019; 31:715-733. [PMID: 30760564 PMCID: PMC6482629 DOI: 10.1105/tpc.18.00754] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 05/19/2023]
Abstract
The last eukaryotic common ancestor had two classes of introns that are still found in most eukaryotic lineages. Common U2-type and rare U12-type introns are spliced by the major and minor spliceosomes, respectively. Relatively few splicing factors have been shown to be specific to the minor spliceosome. We found that the maize (Zea mays) RNA binding motif protein 48 (RBM48) is a U12 splicing factor that functions to promote cell differentiation and repress cell proliferation. RBM48 is coselected with the U12 splicing factor, zinc finger CCCH-type, RNA binding motif, and Ser/Arg rich 2/Rough endosperm 3 (RGH3). Protein-protein interactions between RBM48, RGH3, and U2 Auxiliary Factor (U2AF) subunits suggest major and minor spliceosome factors required for intron recognition form complexes with RBM48. Human RBM48 interacts with armadillo repeat containing 7 (ARMC7). Maize RBM48 and ARMC7 have a conserved protein-protein interaction. These data predict that RBM48 is likely to function in U12 splicing throughout eukaryotes and that U12 splicing promotes endosperm cell differentiation in maize.
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Affiliation(s)
- Fang Bai
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Jacob Corll
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Donya N Shodja
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Ruth Davenport
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Guanqiao Feng
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Janaki Mudunkothge
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Christian J Brigolin
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - Federico Martin
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Gertraud Spielbauer
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Chi-Wah Tseung
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
| | - Amy E Siebert
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - W Brad Barbazuk
- Department of Biology and Genetics Institute, University of Florida, Gainesville, Florida 32611
| | - Shailesh Lal
- Department of Biological Sciences, Oakland University, Rochester, Michigan 48309
| | - A Mark Settles
- Horticultural Sciences Department, and Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, Florida 32611
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30
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Wai H, Douglas AGL, Baralle D. RNA splicing analysis in genomic medicine. Int J Biochem Cell Biol 2018; 108:61-71. [PMID: 30594648 DOI: 10.1016/j.biocel.2018.12.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 12/03/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
High-throughput next-generation sequencing technologies have led to a rapid increase in the number of sequence variants identified in clinical practice via diagnostic genetic tests. Current bioinformatic analysis pipelines fail to take adequate account of the possible splicing effects of such variants, particularly where variants fall outwith canonical splice site sequences, and consequently the pathogenicity of such variants may often be missed. The regulation of splicing is highly complex and as a result, in silico prediction tools lack sufficient sensitivity and specificity for reliable use. Variants of all kinds can be linked to aberrant splicing in disease and the need for correct identification and diagnosis grows ever more crucial as novel splice-switching antisense oligonucleotide therapies start to enter clinical usage. RT-PCR provides a useful targeted assay of the splicing effects of identified variants, while minigene assays, massive parallel reporter assays and animal models can also be used for more detailed study of a particular splicing system, given enough time and resources. However, RNA-sequencing (RNA-seq) has the potential to be used as a rapid diagnostic tool in genomic medicine. By utilising data science approaches and machine learning, it may prove possible to finally understand and interpret the 'splicing code' and apply this knowledge in human disease diagnostics.
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Affiliation(s)
- Htoo Wai
- Human Development and Health, Faculty of Medicine, University of Southampton, UK
| | - Andrew G L Douglas
- Human Development and Health, Faculty of Medicine, University of Southampton, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, UK; Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
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31
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Doggett K, Williams BB, Markmiller S, Geng FS, Coates J, Mieruszynski S, Ernst M, Thomas T, Heath JK. Early developmental arrest and impaired gastrointestinal homeostasis in U12-dependent splicing-defective Rnpc3-deficient mice. RNA (NEW YORK, N.Y.) 2018; 24:1856-1870. [PMID: 30254136 PMCID: PMC6239176 DOI: 10.1261/rna.068221.118] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 09/20/2018] [Indexed: 05/10/2023]
Abstract
Splicing is an essential step in eukaryotic gene expression. While the majority of introns is excised by the U2-dependent, or major class, spliceosome, the appropriate expression of a very small subset of genes depends on U12-dependent, or minor class, splicing. The U11/U12 65K protein (hereafter 65K), encoded by RNPC3, is one of seven proteins that are unique to the U12-dependent spliceosome, and previous studies including our own have established that it plays a role in plant and vertebrate development. To pinpoint the impact of 65K loss during mammalian development and in adulthood, we generated germline and conditional Rnpc3-deficient mice. Homozygous Rnpc3-/- embryos died prior to blastocyst implantation, whereas Rnpc3+/- mice were born at the expected frequency, achieved sexual maturity, and exhibited a completely normal lifespan. Systemic recombination of conditional Rnpc3 alleles in adult (Rnpc3lox/lox ) mice caused rapid weight loss, leukopenia, and degeneration of the epithelial lining of the entire gastrointestinal tract, the latter due to increased cell death and a reduction in cell proliferation. Accompanying this, we observed a loss of both 65K and the pro-proliferative phospho-ERK1/2 proteins from the stem/progenitor cells at the base of intestinal crypts. RT-PCR analysis of RNA extracted from purified preparations of intestinal epithelial cells with recombined Rnpc3lox alleles revealed increased frequency of U12-type intron retention in all transcripts tested. Our study, using a novel conditional mouse model of Rnpc3 deficiency, establishes that U12-dependent splicing is not only important during development but is indispensable throughout life.
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Affiliation(s)
- Karen Doggett
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Ben B Williams
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Sebastian Markmiller
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia
| | - Fan-Suo Geng
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Janine Coates
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Stephen Mieruszynski
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Matthias Ernst
- Olivia Newton-John Cancer Research Institute and La Trobe University School of Cancer Medicine, Heidelberg, Victoria 3050, Australia
| | - Tim Thomas
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Joan K Heath
- Development and Cancer Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, Victoria 3050, Australia
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Baumgartner M, Olthof AM, Aquino GS, Hyatt KC, Lemoine C, Drake K, Sturrock N, Nguyen N, Al Seesi S, Kanadia RN. Minor spliceosome inactivation causes microcephaly, owing to cell cycle defects and death of self-amplifying radial glial cells. Development 2018; 145:dev.166322. [PMID: 30093551 DOI: 10.1242/dev.166322] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 07/13/2018] [Indexed: 12/13/2022]
Abstract
Mutation in minor spliceosome components is linked to the developmental disorder microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1). Here, we inactivated the minor spliceosome in the developing mouse cortex (pallium) by ablating Rnu11, which encodes the crucial minor spliceosome small nuclear RNA (snRNA) U11. Rnu11 conditional knockout mice were born with microcephaly, which was caused by the death of self-amplifying radial glial cells (RGCs), while intermediate progenitor cells and neurons were produced. RNA sequencing suggested that this cell death was mediated by upregulation of p53 (Trp53 - Mouse Genome Informatics) and DNA damage, which were both observed specifically in U11-null RGCs. Moreover, U11 loss caused elevated minor intron retention in genes regulating the cell cycle, which was consistent with fewer RGCs in S-phase and cytokinesis, alongside prolonged metaphase in RGCs. In all, we found that self-amplifying RGCs are the cell type most sensitive to loss of minor splicing. Together, these findings provide a potential explanation of how disruption of minor splicing might cause microcephaly in MOPD1.
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Affiliation(s)
- Marybeth Baumgartner
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,Connecticut Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT 06269, USA
| | - Anouk M Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Gabriela S Aquino
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Katery C Hyatt
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Christopher Lemoine
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,College of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - Kyle Drake
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Nikita Sturrock
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA.,Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Nhut Nguyen
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA
| | - Sahar Al Seesi
- Computer Science Engineering Department, University of Connecticut, Storrs, CT 06269, USA
| | - Rahul N Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT 06269, USA .,Institute of Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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Guided genetic screen to identify genes essential in the regeneration of hair cells and other tissues. NPJ Regen Med 2018; 3:11. [PMID: 29872546 PMCID: PMC5986822 DOI: 10.1038/s41536-018-0050-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 04/18/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023] Open
Abstract
Regenerative medicine holds great promise for both degenerative diseases and traumatic tissue injury which represent significant challenges to the health care system. Hearing loss, which affects hundreds of millions of people worldwide, is caused primarily by a permanent loss of the mechanosensory receptors of the inner ear known as hair cells. This failure to regenerate hair cells after loss is limited to mammals, while all other non-mammalian vertebrates tested were able to completely regenerate these mechanosensory receptors after injury. To understand the mechanism of hair cell regeneration and its association with regeneration of other tissues, we performed a guided mutagenesis screen using zebrafish lateral line hair cells as a screening platform to identify genes that are essential for hair cell regeneration, and further investigated how genes essential for hair cell regeneration were involved in the regeneration of other tissues. We created genetic mutations either by retroviral insertion or CRISPR/Cas9 approaches, and developed a high-throughput screening pipeline for analyzing hair cell development and regeneration. We screened 254 gene mutations and identified 7 genes specifically affecting hair cell regeneration. These hair cell regeneration genes fell into distinct and somewhat surprising functional categories. By examining the regeneration of caudal fin and liver, we found these hair cell regeneration genes often also affected other types of tissue regeneration. Therefore, our results demonstrate guided screening is an effective approach to discover regeneration candidates, and hair cell regeneration is associated with other tissue regeneration. A study on zebrafish has genetically screened 254 genes and identified 7 genes implicated in the development and regeneration of hair cells and other tissues. Humans and other mammals cannot regrow hair cells—inner-ear sensory receptors that enable hearing—whereas non-mammalian vertebrates, including zebrafish, can regrow these following injury. Researchers from the United States, led by the National Institutes of Health’s Shawn Burgess, screened adult zebrafish for genes active during the regeneration of inner-ear epithelium. The researchers then produced zebrafish without these genes to study their functions. The studies tested 254 genes known to respond during regeneration, and identified seven specifically impacting regeneration. Most of these seven genes also functioned in liver and fin tissue regeneration. Understanding the mechanisms of these genes may enable future research into regenerative therapies in humans.
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34
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Splicing dysfunction and disease: The case of granulopoiesis. Semin Cell Dev Biol 2018; 75:23-39. [DOI: 10.1016/j.semcdb.2017.08.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 08/28/2017] [Accepted: 08/28/2017] [Indexed: 12/20/2022]
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35
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Norppa AJ, Kauppala TM, Heikkinen HA, Verma B, Iwaï H, Frilander MJ. Mutations in the U11/U12-65K protein associated with isolated growth hormone deficiency lead to structural destabilization and impaired binding of U12 snRNA. RNA (NEW YORK, N.Y.) 2018; 24:396-409. [PMID: 29255062 PMCID: PMC5824358 DOI: 10.1261/rna.062844.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/12/2017] [Indexed: 05/09/2023]
Abstract
Mutations in the components of the minor spliceosome underlie several human diseases. A subset of patients with isolated growth hormone deficiency (IGHD) harbors mutations in the RNPC3 gene, which encodes the minor spliceosome-specific U11/U12-65K protein. Although a previous study showed that IGHD patient cells have defects in U12-type intron recognition, the biochemical effects of these mutations on the 65K protein have not been characterized. Here, we show that a proline-to-threonine missense mutation (P474T) and a nonsense mutation (R502X) in the C-terminal RNA recognition motif (C-RRM) of the 65K protein impair the binding of 65K to U12 and U6atac snRNAs. We further show that the nonsense allele is targeted to the nonsense-mediated decay (NMD) pathway, but in an isoform-specific manner, with the nuclear-retained 65K long-3'UTR isoform escaping the NMD pathway. In contrast, the missense P474T mutation leads, in addition to the RNA-binding defect, to a partial defect in the folding of the C-RRM and reduced stability of the full-length protein, thus reducing the formation of U11/U12 di-snRNP complexes. We propose that both the C-RRM folding defect and NMD-mediated decrease in the levels of the U11/U12-65K protein reduce formation of the U12-type intron recognition complex and missplicing of a subset of minor introns leading to pituitary hypoplasia and a subsequent defect in growth hormone secretion.
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Affiliation(s)
- Antto J Norppa
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Tuuli M Kauppala
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Harri A Heikkinen
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Bhupendra Verma
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Hideo Iwaï
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Mikko J Frilander
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
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36
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Minor spliceosome and disease. Semin Cell Dev Biol 2017; 79:103-112. [PMID: 28965864 DOI: 10.1016/j.semcdb.2017.09.036] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 09/21/2017] [Accepted: 09/27/2017] [Indexed: 01/09/2023]
Abstract
The U12-dependent (minor) spliceosome excises a rare group of introns that are characterized by a highly conserved 5' splice site and branch point sequence. Several new congenital or somatic diseases have recently been associated with mutations in components of the minor spliceosome. A common theme in these diseases is the detection of elevated levels of transcripts containing U12-type introns, of which a subset is associated with other splicing defects. Here we review the present understanding of minor spliceosome diseases, particularly those associated with the specific components of the minor spliceosome. We also present a model for interpreting the molecular-level consequences of the different diseases.
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Lei L, Yan SY, Yang R, Chen JY, Li Y, Bu Y, Chang N, Zhou Q, Zhu X, Li CY, Xiong JW. Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors. Nucleic Acids Res 2017; 45:3422-3436. [PMID: 27899647 PMCID: PMC5389467 DOI: 10.1093/nar/gkw1043] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/24/2016] [Indexed: 12/26/2022] Open
Abstract
Haploinsufficiency of EFTUD2 (Elongation Factor Tu GTP Binding Domain Containing 2) is linked to human mandibulofacial dysostosis, Guion-Almeida type (MFDGA), but the underlying cellular and molecular mechanisms remain to be addressed. We report here the isolation, cloning and functional analysis of the mutated eftud2 (snu114) in a novel neuronal mutant fn10a in zebrafish. This mutant displayed abnormal brain development with evident neuronal apoptosis while the development of other organs appeared less affected. Positional cloning revealed a nonsense mutation such that the mutant eftud2 mRNA encoded a truncated Eftud2 protein and was subjected to nonsense-mediated decay. Disruption of eftud2 led to increased apoptosis and mitosis of neural progenitors while it had little effect on differentiated neurons. Further RNA-seq and functional analyses revealed a transcriptome-wide RNA splicing deficiency and a large amount of intron-retaining and exon-skipping transcripts, which resulted in inadequate nonsense-mediated RNA decay and activation of the p53 pathway in fn10a mutants. Therefore, our study has established that eftud2 functions in RNA splicing during neural development and provides a suitable zebrafish model for studying the molecular pathology of the neurological disease MFDGA.
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Affiliation(s)
- Lei Lei
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Shou-Yu Yan
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Ran Yang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Jia-Yu Chen
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Yumei Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Ye Bu
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Nannan Chang
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Qinchao Zhou
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Xiaojun Zhu
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Chuan-Yun Li
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
| | - Jing-Wei Xiong
- Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, and State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100871, China
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Aberrant splicing in maize rough endosperm3 reveals a conserved role for U12 splicing in eukaryotic multicellular development. Proc Natl Acad Sci U S A 2017; 114:E2195-E2204. [PMID: 28242684 PMCID: PMC5358371 DOI: 10.1073/pnas.1616173114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
RNA splicing of U12-type introns functions in human cell differentiation, but it is not known whether this class of introns has a similar role in plants. The maize ROUGH ENDOSPERM3 (RGH3) protein is orthologous to the human splicing factor, ZRSR2. ZRSR2 mutations are associated with myelodysplastic syndrome (MDS) and cause U12 splicing defects. Maize rgh3 mutants have aberrant endosperm cell differentiation and proliferation. We found that most U12-type introns are retained or misspliced in rgh3 Genes affected in rgh3 and ZRSR2 mutants identify cell cycle and protein glycosylation as common pathways disrupted. Transcripts with retained U12-type introns can be found in polysomes, suggesting that splicing efficiency can alter protein isoforms. The rgh3 mutant protein disrupts colocalization with a known ZRSR2-interacting protein, U2AF2. These results indicate conserved function for RGH3/ZRSR2 in U12 splicing and a deeply conserved role for the minor spliceosome to promote cell differentiation from stem cells to terminal fates.
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Abstract
Although the zebrafish was initially developed as a model system to study embryonic development, it has gained increasing attention as an advantageous system to investigate human diseases, including intestinal disorders. Zebrafish embryos develop rapidly, and their digestive system is fully functional and visible by 5days post fertilization. There is a large degree of homology between the intestine of zebrafish and higher vertebrate organisms in terms of its cellular composition and function as both a digestive and immune organ. Furthermore, molecular pathways regulating injury and immune responses are highly conserved. In this chapter, we provide an overview of studies addressing developmental and physiological processes relevant to human intestinal disease. These studies include those related to congenital disorders, host-microbiota interactions, inflammatory diseases, motility disorders, and intestinal cancer. We also highlight the utility of zebrafish to functionally validate candidate genes identified through mutational analyses and genome-wide association studies, and discuss methodologies to investigate the intestinal biology that are unique to zebrafish.
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Affiliation(s)
- X Zhao
- University of Pennsylvania, Philadelphia, PA, United States
| | - M Pack
- University of Pennsylvania, Philadelphia, PA, United States
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40
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Niemelä EH, Verbeeren J, Singha P, Nurmi V, Frilander MJ. Evolutionarily conserved exon definition interactions with U11 snRNP mediate alternative splicing regulation on U11-48K and U11/U12-65K genes. RNA Biol 2016; 12:1256-64. [PMID: 26479860 DOI: 10.1080/15476286.2015.1096489] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Many splicing regulators bind to their own pre-mRNAs to induce alternative splicing that leads to formation of unstable mRNA isoforms. This provides an autoregulatory feedback mechanism that regulates the cellular homeostasis of these factors. We have described such an autoregulatory mechanism for two core protein components, U11-48K and U11/U12-65K, of the U12-dependent spliceosome. This regulatory system uses an atypical splicing enhancer element termed USSE (U11 snRNP-binding splicing enhancer), which contains two U12-type consensus 5' splice sites (5'ss). Evolutionary analysis of the USSE element from a large number of animal and plant species indicate that USSE sequence must be located 25-50 nt downstream from the target 3' splice site (3'ss). Together with functional evidence showing a loss of USSE activity when this distance is reduced and a requirement for RS-domain of U11-35K protein for 3'ss activation, our data suggests that U11 snRNP bound to USSE uses exon definition interactions for regulating alternative splicing. However, unlike standard exon definition where the 5'ss bound by U1 or U11 will be subsequently activated for splicing, the USSE element functions similarly as an exonic splicing enhancer and is involved only in upstream splice site activation but does not function as a splicing donor. Additionally, our evolutionary and functional data suggests that the function of the 5'ss duplication within the USSE elements is to allow binding of two U11/U12 di-snRNPs that stabilize each others' binding through putative mutual interactions.
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Affiliation(s)
- Elina H Niemelä
- a Institute of Biotechnology; University of Helsinki ; Helsinki , Finland
| | - Jens Verbeeren
- a Institute of Biotechnology; University of Helsinki ; Helsinki , Finland
| | - Prosanta Singha
- a Institute of Biotechnology; University of Helsinki ; Helsinki , Finland
| | - Visa Nurmi
- a Institute of Biotechnology; University of Helsinki ; Helsinki , Finland
| | - Mikko J Frilander
- a Institute of Biotechnology; University of Helsinki ; Helsinki , Finland
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41
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Park SJ, Jung HJ, Nguyen Dinh S, Kang H. Structural features important for the U12 snRNA binding and minor spliceosome assembly of Arabidopsis U11/U12-small nuclear ribonucleoproteins. RNA Biol 2016; 13:670-9. [PMID: 27232356 DOI: 10.1080/15476286.2016.1191736] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Although seven proteins unique to U12 intron-specific minor spliceosomes, denoted as U11/U12-65K, -59K, -48K, -35K, -31K, -25K, and -20K, have been identified in humans and the roles of some of them have been demonstrated, the functional role of most of these proteins in plants is not understood. A recent study demonstrated that Arabidopsis U11/U12-65K is essential for U12 intron splicing and normal plant development. However, the structural features and sequence motifs important for 65 K binding to U12 snRNA and other spliceosomal proteins remain unclear. Here, we demonstrated by domain-deletion analysis that the C-terminal region of the 65 K protein bound specifically to the stem-loop III of U12 snRNA, whereas the N-terminal region of the 65 K protein was responsible for interacting with the 59 K protein. Analysis of the interactions between each snRNP protein using yeast two-hybrid analysis and in planta bimolecular fluorescence complementation and luciferase complementation imaging assays demonstrated that the core interactions among the 65 K, 59 K, and 48 K proteins were conserved between plants and animals, and multiple interactions were observed among the U11/U12-snRNP proteins. Taken together, these results reveal that U11/U12-65K is an indispensible component of the minor spliceosome complex by binding to both U11/U12-59K and U12 snRNA, and that multiple interactions among the U11/U12-snRNP proteins are necessary for minor spliceosome assembly.
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Affiliation(s)
- Su Jung Park
- a Department of Plant Biotechnology , College of Agriculture and Life Sciences, Chonnam National University , Yongbong-dong, Buk-gu, Gwangju , South Korea
| | - Hyun Ju Jung
- a Department of Plant Biotechnology , College of Agriculture and Life Sciences, Chonnam National University , Yongbong-dong, Buk-gu, Gwangju , South Korea
| | - Sy Nguyen Dinh
- a Department of Plant Biotechnology , College of Agriculture and Life Sciences, Chonnam National University , Yongbong-dong, Buk-gu, Gwangju , South Korea
| | - Hunseung Kang
- a Department of Plant Biotechnology , College of Agriculture and Life Sciences, Chonnam National University , Yongbong-dong, Buk-gu, Gwangju , South Korea
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42
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Xu T, Kim BM, Kwak KJ, Jung HJ, Kang H. The Arabidopsis homolog of human minor spliceosomal protein U11-48K plays a crucial role in U12 intron splicing and plant development. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:3397-406. [PMID: 27091878 PMCID: PMC4892727 DOI: 10.1093/jxb/erw158] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The minor U12 introns are removed from precursor mRNAs by the U12 intron-specific minor spliceosome. Among the seven ribonucleoproteins unique to the minor spliceosome, denoted as U11/U12-20K, U11/U12-25K, U11/U12-31K, U11/U12-65K, U11-35K, U11-48K, and U11-59K, the roles of only U11/U12-31K and U11/U12-65K have been demonstrated in U12 intron splicing and plant development. Here, the functional role of the Arabidopsis homolog of human U11-48K in U12 intron splicing and the development of Arabidopsis thaliana was examined using transgenic knockdown plants. The u11-48k mutants exhibited several defects in growth and development, such as severely arrested primary inflorescence stems, formation of serrated leaves, production of many rosette leaves after bolting, and delayed senescence. The splicing of most U12 introns analyzed was impaired in the u11-48k mutants. Comparative analysis of the splicing defects and phenotypes among the u11/u12-31k, u11-48k, and u11/12-65k mutants showed that the severity of abnormal development was closely correlated with the degree of impairment in U12 intron splicing. Taken together, these results provide compelling evidence that the Arabidopsis homolog of human U11-48K protein, as well as U11/U12-31K and U11/U12-65K proteins, is necessary for correct splicing of U12 introns and normal plant growth and development.
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Affiliation(s)
- Tao Xu
- College of Life Science, Jiangsu Normal University, Xuzhou 221116, Jiangsu Province, PR China
| | - Bo Mi Kim
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Kyung Jin Kwak
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Hyun Ju Jung
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
| | - Hunseung Kang
- Department of Plant Biotechnology, College of Agriculture and Life Sciences, Chonnam National University, 300 Yongbong-dong, Buk-gu, Gwangju 500-757, South Korea
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43
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Experimental approaches to studying the nature and impact of splicing variation in zebrafish. Methods Cell Biol 2016; 135:259-88. [PMID: 27443930 DOI: 10.1016/bs.mcb.2016.02.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
From a fixed number of genes carried in all cells, organisms create considerable diversity in cellular phenotype through differential regulation of gene expression. One prevalent source of transcriptome diversity is alternative pre-mRNA splicing, which is manifested in many different forms. Zebrafish models of splicing dysfunction due to mutated spliceosome components provide opportunity to link biochemical analyses of spliceosome structure and function with whole organism phenotypic outcomes. Drawing from experience with two zebrafish mutants: cephalophŏnus (a prpf8 mutant, isolated for defects in granulopoiesis) and caliban (a rnpc3 mutant, isolated for defects in digestive organ development), we describe the use of glycerol gradient sedimentation and native gel electrophoresis to resolve components of aberrant splicing complexes. We also describe how RNAseq can be employed to examine relatively rare alternative splicing events including intron retention. Such experimental approaches in zebrafish can promote understanding of how splicing variation and dysfunction contribute to phenotypic diversity and disease pathogenesis.
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44
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Lobert VH, Mouradov D, Heath JK. Focusing the Spotlight on the Zebrafish Intestine to Illuminate Mechanisms of Colorectal Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 916:411-37. [PMID: 27165364 DOI: 10.1007/978-3-319-30654-4_18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Colorectal cancer, encompassing colon and rectal cancer, arises from the epithelial lining of the large bowel. It is most prevalent in Westernised societies and is increasing in frequency as the world becomes more industrialised. Unfortunately, metastatic colorectal cancer is not cured by chemotherapy and the annual number of deaths caused by colorectal cancer, currently 700,000, is expected to rise. Our understanding of the contribution that genetic mutations make to colorectal cancer, although incomplete, is reasonably well advanced. However, it has only recently become widely appreciated that in addition to the ongoing accumulation of genetic mutations, chronic inflammation also plays a critical role in the initiation and progression of this disease. While a robust and tractable genetic model of colorectal cancer in zebrafish, suitable for pre-clinical studies, is not yet available, the identification of genes required for the rapid proliferation of zebrafish intestinal epithelial cells during development has highlighted a number of essential genes that could be targeted to disable colorectal cancer cells. Moreover, appreciation of the utility of zebrafish to study intestinal inflammation is on the rise. In particular, zebrafish provide unique opportunities to investigate the impact of genetic and environmental factors on the integrity of intestinal epithelial barrier function. With currently available tools, the interplay between epigenetic regulators, intestinal injury, microbiota composition and innate immune cell mobilisation can be analysed in exquisite detail. This provides excellent opportunities to define critical events that could potentially be targeted therapeutically. Further into the future, the use of zebrafish larvae as hosts for xenografts of human colorectal cancer tissue, while still in its infancy, holds great promise that zebrafish could one day provide a practical, preclinical personalized medicine platform for the rapid assessment of the metastatic potential and drug-sensitivity of patient-derived cancers.
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Affiliation(s)
- Viola H Lobert
- Development and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia.,Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, Montebello, N-0379, Oslo, Norway
| | - Dmitri Mouradov
- Systems Biology and Personalised Medicine Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia
| | - Joan K Heath
- Development and Cancer Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
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45
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Niemelä EH, Frilander MJ. Regulation of gene expression through inefficient splicing of U12-type introns. RNA Biol 2015; 11:1325-9. [PMID: 25692230 PMCID: PMC4615840 DOI: 10.1080/15476286.2014.996454] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
U12-type introns are a rare class of nuclear introns that are removed by a dedicated U12-dependent spliceosome and are thought to regulate the expression of their target genes owing through their slower splicing reaction. Recent genome-wide studies on the splicing of U12-type introns are now providing new insights on the biological significance of this parallel splicing machinery. The new studies cover multiple different organisms and experimental systems, including human patient cells with mutations in the components of the minor spliceosome, zebrafish with similar mutations and various experimentally manipulated human cells and Arabidopsis plants. Here, we will discuss the potential implications of these studies on the understanding of the mechanism and regulation of the minor spliceosome, as well as their medical implications.
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Affiliation(s)
- Elina H Niemelä
- a Institute of Biotechnology; Genome Biology Research Program ; University of Helsinki ; Helsinki , Finland
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46
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Szabo L, Morey R, Palpant NJ, Wang PL, Afari N, Jiang C, Parast MM, Murry CE, Laurent LC, Salzman J. Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biol 2015; 16:126. [PMID: 26076956 PMCID: PMC4506483 DOI: 10.1186/s13059-015-0690-5] [Citation(s) in RCA: 425] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Accepted: 06/08/2015] [Indexed: 02/06/2023] Open
Abstract
Background The pervasive expression of circular RNA is a recently discovered feature of gene expression in highly diverged eukaryotes, but the functions of most circular RNAs are still unknown. Computational methods to discover and quantify circular RNA are essential. Moreover, discovering biological contexts where circular RNAs are regulated will shed light on potential functional roles they may play. Results We present a new algorithm that increases the sensitivity and specificity of circular RNA detection by discovering and quantifying circular and linear RNA splicing events at both annotated and un-annotated exon boundaries, including intergenic regions of the genome, with high statistical confidence. Unlike approaches that rely on read count and exon homology to determine confidence in prediction of circular RNA expression, our algorithm uses a statistical approach. Using our algorithm, we unveiled striking induction of general and tissue-specific circular RNAs, including in the heart and lung, during human fetal development. We discover regions of the human fetal brain, such as the frontal cortex, with marked enrichment for genes where circular RNA isoforms are dominant. Conclusions The vast majority of circular RNA production occurs at major spliceosome splice sites; however, we find the first examples of developmentally induced circular RNAs processed by the minor spliceosome, and an enriched propensity of minor spliceosome donors to splice into circular RNA at un-annotated, rather than annotated, exons. Together, these results suggest a potentially significant role for circular RNA in human development. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0690-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Linda Szabo
- Stanford Department of Biochemistry and Stanford Cancer Institute, Stanford, CA, USA.
| | - Robert Morey
- UC San Diego Department of Reproductive Medicine, San Diego, CA, USA.
| | - Nathan J Palpant
- Center for Cardiovascular Biology, Institute for Stem Cell and Regenerative Medicine, Departments of Pathology, Bioengineering and Medicine/Cardiology, University of Washington, Seattle, WA, 98109, USA.
| | - Peter L Wang
- Stanford Department of Biochemistry and Stanford Cancer Institute, Stanford, CA, USA.
| | - Nastaran Afari
- UC San Diego Department of Reproductive Medicine, San Diego, CA, USA.
| | - Chuan Jiang
- UC San Diego Department of Reproductive Medicine, San Diego, CA, USA.
| | - Mana M Parast
- UC San Diego Department of Pathology, San Diego, CA, USA.
| | - Charles E Murry
- Center for Cardiovascular Biology, Institute for Stem Cell and Regenerative Medicine, Departments of Pathology, Bioengineering and Medicine/Cardiology, University of Washington, Seattle, WA, 98109, USA.
| | - Louise C Laurent
- UC San Diego Department of Reproductive Medicine, San Diego, CA, USA.
| | - Julia Salzman
- Stanford Department of Biochemistry and Stanford Cancer Institute, Stanford, CA, USA.
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47
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Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome. Nat Commun 2015; 6:6042. [PMID: 25586593 PMCID: PMC4349895 DOI: 10.1038/ncomms7042] [Citation(s) in RCA: 168] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2014] [Accepted: 12/04/2014] [Indexed: 02/07/2023] Open
Abstract
Somatic mutations in the spliceosome gene ZRSR2 — located on the X chromosome — are associated with myelodysplastic syndrome (MDS). ZRSR2 is involved in the recognition of 3΄ splice site during the early stages of spliceosome assembly; however, its precise role in RNA splicing has remained unclear. Here, we characterize ZRSR2 as an essential component of the minor spliceosome (U12-dependent) assembly. shRNA mediated knockdown of ZRSR2 leads to impaired splicing of the U12-type introns, and RNA-Sequencing of MDS bone marrow reveals that loss of ZRSR2 activity causes increased mis-splicing. These splicing defects involve retention of the U12-type introns while splicing of the U2-type introns remain mostly unaffected. ZRSR2 deficient cells also exhibit reduced proliferation potential and distinct alterations in myeloid and erythroid differentiation in vitro. These data identify a specific role for ZRSR2 in RNA splicing and highlight dysregulated splicing of U12-type introns as a characteristic feature of ZRSR2 mutations in MDS.
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48
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Baumgartner M, Lemoine C, Al Seesi S, Karunakaran DKP, Sturrock N, Banday AR, Kilcollins AM, Mandoiu I, Kanadia RN. Minor splicing snRNAs are enriched in the developing mouse CNS and are crucial for survival of differentiating retinal neurons. Dev Neurobiol 2014; 75:895-907. [PMID: 25492806 DOI: 10.1002/dneu.22257] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 11/24/2014] [Accepted: 12/08/2014] [Indexed: 12/21/2022]
Abstract
In eukaryotes, gene expression requires splicing, which starts with the identification of exon-intron boundaries by the small, nuclear RNA (snRNAs) of the spliceosome, aided by associated proteins. In the mammalian genome, <1% of introns lack canonical exon-intron boundary sequences and cannot be spliced by the canonical splicing machinery. These introns are spliced by the minor spliceosome, consisting of unique snRNAs (U11, U12, U4atac, and U6atac). The importance of the minor spliceosome is underscored by the disease microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1), which is caused by mutation in U4atac. Thus, it is important to understand the expression and function of the minor spliceosome and its targets in mammalian development, for which we used the mouse as our model. Here, we report enrichment of the minor snRNAs in the developing head/central nervous system (CNS) between E9.5 and E12.5, along with enrichment of these snRNAs in differentiating retinal neurons. Moreover, dynamic expression kinetics of minor intron-containing genes (MIGs) was observed across retinal development. DAVID analysis of MIGs that were cotranscriptionally upregulated embryonically revealed enrichment for RNA metabolism and cell cycle regulation. In contrast, MIGs that were cotranscriptionally upregulated postnatally revealed enrichment for protein localization/transport, vesicle-mediated transport, and calcium transport. Finally, we used U12 morpholino to inactivate the minor spliceosome in the postnatal retina, which resulted in apoptosis of differentiating retinal neurons. Taken together, our data suggest that the minor spliceosome may have distinct functions in embryonic versus postnatal development. Importantly, we show that the minor spliceosome is crucial for the survival of terminally differentiating retinal neurons.
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Affiliation(s)
- Marybeth Baumgartner
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Christopher Lemoine
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Sahar Al Seesi
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, 06269
| | | | - Nikita Sturrock
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Abdul Rouf Banday
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Ashley M Kilcollins
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
| | - Ion Mandoiu
- Department of Computer Science and Engineering, University of Connecticut, Storrs, Connecticut, 06269
| | - Rahul N Kanadia
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, 06269
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Niemelä EH, Oghabian A, Staals RHJ, Greco D, Pruijn GJM, Frilander MJ. Global analysis of the nuclear processing of transcripts with unspliced U12-type introns by the exosome. Nucleic Acids Res 2014; 42:7358-69. [PMID: 24848017 PMCID: PMC4066798 DOI: 10.1093/nar/gku391] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
U12-type introns are a rare class of introns in the genomes of diverse eukaryotes. In the human genome, they number over 700. A subset of these introns has been shown to be spliced at a slower rate compared to the major U2-type introns. This suggests a rate-limiting regulatory function for the minor spliceosome in the processing of transcripts containing U12-type introns. However, both the generality of slower splicing and the subsequent fate of partially processed pre-mRNAs remained unknown. Here, we present a global analysis of the nuclear retention of transcripts containing U12-type introns and provide evidence for the nuclear decay of such transcripts in human cells. Using SOLiD RNA sequencing technology, we find that, in normal cells, U12-type introns are on average 2-fold more retained than the surrounding U2-type introns. Furthermore, we find that knockdown of RRP41 and DIS3 subunits of the exosome stabilizes an overlapping set of U12-type introns. RRP41 knockdown leads to slower decay kinetics of U12-type introns and globally upregulates the retention of U12-type, but not U2-type, introns. Our results indicate that U12-type introns are spliced less efficiently and are targeted by the exosome. These characteristics support their role in the regulation of cellular mRNA levels.
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Affiliation(s)
- Elina H Niemelä
- Institute of Biotechnology, P.O. Box 56, FI-00014 University of Helsinki, Finland
| | - Ali Oghabian
- Institute of Biotechnology, P.O. Box 56, FI-00014 University of Helsinki, Finland
| | - Raymond H J Staals
- Department of Biomolecular Chemistry, Radboud Institute for Molecular Life Sciences and Institute for Molecules and Materials, Radboud University Nijmegen,The Netherlands
| | - Dario Greco
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Topeliuksenkatu 41 a A, FI-00250 Helsinki, Finland
| | - Ger J M Pruijn
- Department of Biomolecular Chemistry, Radboud Institute for Molecular Life Sciences and Institute for Molecules and Materials, Radboud University Nijmegen,The Netherlands
| | - Mikko J Frilander
- Institute of Biotechnology, P.O. Box 56, FI-00014 University of Helsinki, Finland
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