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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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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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3
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Garcia EL, Steiner RE, Raimer AC, Herring LE, Matera AG, Spring AM. Dysregulation of innate immune signaling in animal models of spinal muscular atrophy. BMC Biol 2024; 22:94. [PMID: 38664795 PMCID: PMC11044505 DOI: 10.1186/s12915-024-01888-z] [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: 10/28/2023] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a devastating neuromuscular disease caused by hypomorphic loss of function in the survival motor neuron (SMN) protein. SMA presents across a broad spectrum of disease severity. Unfortunately, genetic models of intermediate SMA have been difficult to generate in vertebrates and are thus unable to address key aspects of disease etiology. To address these issues, we developed a Drosophila model system that recapitulates the full range of SMA severity, allowing studies of pre-onset biology as well as late-stage disease processes. RESULTS Here, we carried out transcriptomic and proteomic profiling of mild and intermediate Drosophila models of SMA to elucidate molecules and pathways that contribute to the disease. Using this approach, we elaborated a role for the SMN complex in the regulation of innate immune signaling. We find that mutation or tissue-specific depletion of SMN induces hyperactivation of the immune deficiency (IMD) and Toll pathways, leading to overexpression of antimicrobial peptides (AMPs) and ectopic formation of melanotic masses in the absence of an external challenge. Furthermore, the knockdown of downstream targets of these signaling pathways reduced melanotic mass formation caused by SMN loss. Importantly, we identify SMN as a negative regulator of a ubiquitylation complex that includes Traf6, Bendless, and Diap2 and plays a pivotal role in several signaling networks. CONCLUSIONS In alignment with recent research on other neurodegenerative diseases, these findings suggest that hyperactivation of innate immunity contributes to SMA pathology. This work not only provides compelling evidence that hyperactive innate immune signaling is a primary effect of SMN depletion, but it also suggests that the SMN complex plays a regulatory role in this process in vivo. In summary, immune dysfunction in SMA is a consequence of reduced SMN levels and is driven by cellular and molecular mechanisms that are conserved between insects and mammals.
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Affiliation(s)
- Eric L Garcia
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - Rebecca E Steiner
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
- Present Address: Lake, Erie College of Osteopathic Medicine, Bradenton, FL, USA
| | - Amanda C Raimer
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA
- Present Address, Radford University, Radford, VA, USA
| | - Laura E Herring
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, USA
| | - A Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA.
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA.
- RNA Discovery and Lineberger Comprehensive Cancer Centers, University of North Carolina at Chapel Hill, Chapel Hill, 27599, USA.
| | - Ashlyn M Spring
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biology, University of North Carolina at Greensboro, Greensboro, NC, 27402, USA.
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Wang M, Liang AM, Zhou ZZ, Pang TL, Fan YJ, Xu YZ. Deletions of singular U1 snRNA gene significantly interfere with transcription and 3'-end mRNA formation. PLoS Genet 2023; 19:e1011021. [PMID: 37917726 PMCID: PMC10645366 DOI: 10.1371/journal.pgen.1011021] [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: 03/12/2023] [Revised: 11/14/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023] Open
Abstract
Small nuclear RNAs (snRNAs) are structural and functional cores of the spliceosome. In metazoan genomes, each snRNA has multiple copies/variants, up to hundreds in mammals. However, the expressions and functions of each copy/variant in one organism have not been systematically studied. Focus on U1 snRNA genes, we investigated all five copies in Drosophila melanogaster using two series of constructed strains. Analyses of transgenic flies that each have a U1 promoter-driven gfp revealed that U1:21D is the major and ubiquitously expressed copy, and the other four copies have specificities in developmental stages and tissues. Mutant strains that each have a precisely deleted copy of U1-gene exhibited various extents of defects in fly morphology or mobility, especially deletion of U1:82Eb. Interestingly, splicing was changed at limited levels in the deletion strains, while large amounts of differentially-expressed genes and alternative polyadenylation events were identified, showing preferences in the down-regulation of genes with 1-2 introns and selection of proximal sites for 3'-end polyadenylation. In vitro assays suggested that Drosophila U1 variants pulled down fewer SmD2 proteins compared to the canonical U1. This study demonstrates that all five U1-genes in Drosophila have physiological functions in development and play regulatory roles in transcription and 3'-end formation.
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Affiliation(s)
- Mei Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China, University of Chinese Academy of Sciences, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
- Shanghai Institute of Biological Products, Shanghai, China
| | - An-Min Liang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Zhen-Zhen Zhou
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Ting-Lin Pang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China, University of Chinese Academy of Sciences, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei, China
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5
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Faravelli I, Riboldi GM, Rinchetti P, Lotti F. The SMN Complex at the Crossroad between RNA Metabolism and Neurodegeneration. Int J Mol Sci 2023; 24:2247. [PMID: 36768569 PMCID: PMC9917330 DOI: 10.3390/ijms24032247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 01/24/2023] Open
Abstract
In the cell, RNA exists and functions in a complex with RNA binding proteins (RBPs) that regulate each step of the RNA life cycle from transcription to degradation. Central to this regulation is the role of several molecular chaperones that ensure the correct interactions between RNA and proteins, while aiding the biogenesis of large RNA-protein complexes (ribonucleoproteins or RNPs). Accurate formation of RNPs is fundamentally important to cellular development and function, and its impairment often leads to disease. The survival motor neuron (SMN) protein exemplifies this biological paradigm. SMN is part of a multi-protein complex essential for the biogenesis of various RNPs that function in RNA metabolism. Mutations leading to SMN deficiency cause the neurodegenerative disease spinal muscular atrophy (SMA). A fundamental question in SMA biology is how selective motor system dysfunction results from reduced levels of the ubiquitously expressed SMN protein. Recent clarification of the central role of the SMN complex in RNA metabolism and a thorough characterization of animal models of SMA have significantly advanced our knowledge of the molecular basis of the disease. Here we review the expanding role of SMN in the regulation of gene expression through its multiple functions in RNP biogenesis. We discuss developments in our understanding of SMN activity as a molecular chaperone of RNPs and how disruption of SMN-dependent RNA pathways can contribute to the SMA phenotype.
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Affiliation(s)
- Irene Faravelli
- Department of Stem Cell & Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Giulietta M. Riboldi
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
- The Marlene and Paolo Fresco Institute for Parkinson’s and Movement Disorders, NYU Langone Health, New York, NY 10017, USA
| | - Paola Rinchetti
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Francesco Lotti
- Center for Motor Neuron Biology and Diseases, Departments of Pathology & Cell Biology, and Neurology, Columbia University Irving Medical Center, New York, NY 10032, USA
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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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Montañés-Agudo P, Casini S, Aufiero S, Ernault AC, van der Made I, Pinto YM, Remme CA, Creemers EE. Inhibition of minor intron splicing reduces Na+ and Ca2+ channel expression and function in cardiomyocytes. J Cell Sci 2021; 135:273616. [PMID: 34859816 PMCID: PMC8767276 DOI: 10.1242/jcs.259191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/26/2021] [Indexed: 12/04/2022] Open
Abstract
Eukaryotic genomes contain a tiny subset of ‘minor class’ introns with unique sequence elements that require their own splicing machinery. These minor introns are present in certain gene families with specific functions, such as voltage-gated Na+ and voltage-gated Ca2+ channels. Removal of minor introns by the minor spliceosome has been proposed as a post-transcriptional regulatory layer, which remains unexplored in the heart. Here, we investigate whether the minor spliceosome regulates electrophysiological properties of cardiomyocytes by knocking down the essential minor spliceosome small nuclear snRNA component U6atac in neonatal rat ventricular myocytes. Loss of U6atac led to robust minor intron retention within Scn5a and Cacna1c, resulting in reduced protein levels of Nav1.5 and Cav1.2 channels. Functional consequences were studied through patch-clamp analysis, and revealed reduced Na+ and L-type Ca2+ currents after loss of U6atac. In conclusion, minor intron splicing modulates voltage-dependent ion channel expression and function in cardiomyocytes. This may be of particular relevance in situations in which minor splicing activity changes, such as in genetic diseases affecting minor spliceosome components, or in acquired diseases in which minor spliceosome components are dysregulated, such as heart failure. Summary: Knockdown of minor spliceosome component U6atac in cardiomyocytes reveals that expression of the Na+ channel Scn5a and the L-type Ca2+ channel Cacna1c critically depend on minor intron splicing.
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Affiliation(s)
- Pablo Montañés-Agudo
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Casini
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Simona Aufiero
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands.,Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Auriane C Ernault
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Ingeborg van der Made
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Yigal M Pinto
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Carol Ann Remme
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
| | - Esther E Creemers
- Departments of Experimental Cardiology, Biostatistics and Bioinformatics, Amsterdam UMC, location AMC, Amsterdam, The Netherlands
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8
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Zhang B, Ding Z, Li L, Xie LK, Fan YJ, Xu YZ. Two oppositely-charged sf3b1 mutations cause defective development, impaired immune response, and aberrant selection of intronic branch sites in Drosophila. PLoS Genet 2021; 17:e1009861. [PMID: 34723968 PMCID: PMC8559932 DOI: 10.1371/journal.pgen.1009861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
SF3B1 mutations occur in many cancers, and the highly conserved His662 residue is one of the hotspot mutation sites. To address effects on splicing and development, we constructed strains carrying point mutations at the corresponding residue His698 in Drosophila using the CRISPR-Cas9 technique. Two mutations, H698D and H698R, were selected due to their frequent presence in patients and notable opposite charges. Both the sf3b1-H698D and–H698R mutant flies exhibit developmental defects, including less egg-laying, decreased hatching rates, delayed morphogenesis and shorter lifespans. Interestingly, the H698D mutant has decreased resistance to fungal infection, while the H698R mutant shows impaired climbing ability. Consistent with these phenotypes, further analysis of RNA-seq data finds altered expression of immune response genes and changed alternative splicing of muscle and neural-related genes in the two mutants, respectively. Expression of Mef2-RB, an isoform of Mef2 gene that was downregulated due to splicing changes caused by H698R, partly rescues the climbing defects of the sf3b1-H698R mutant. Lariat sequencing reveals that the two sf3b1-H698 mutations cause aberrant selection of multiple intronic branch sites, with the H698R mutant using far upstream branch sites in the changed alternative splicing events. This study provides in vivo evidence from Drosophila that elucidates how these SF3B1 hotspot mutations alter splicing and their consequences in development and in the immune system. In the past decade, one of the important findings in the RNA splicing field has been that somatic SF3B1 mutations widely occur in many cancers. Including R625, H662, K666, K700 and E902, there are five hotspot mutation sites in the highly conserved HEAT repeats of SF3B1. Several kinds of H662 mutations have been found widely in MDS, AML, CLL and breast cancers; however, it remains unclear how these H662 mutations alter splicing and whether they have in vivo effects on development. To address these questions, in this manuscript, we first summarized the H662 mutations in human diseases and constructed two corresponding Drosophila mutant strains, sf3b1-H698D and -H698R using CRISPR-Cas9. Analyses of these two fly strains find that the two oppositely charged Sf3b1-H698 mutants are defective in development. In addition, one mutant has decreased climbing ability, whereas the other mutant has impaired immune response. Further RNA-seq allows us to find responsible genes in each mutant strain, and lariat sequencing reveals that both mutations cause aberrant selection of the intronic branch sites. Our findings provide the first in vivo evidence that Sf3b1 mutations result in defective development, and also reveal a molecular mechanism of these hotspot histidine mutations that enhance the use of cryptic branch sites to alter splicing. Importantly, we demonstrate that the H698R mutant prefers to use far upstream branch sites.
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Affiliation(s)
- Bei Zhang
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Zhan Ding
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Liang Li
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Ling-Kun Xie
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
- * E-mail:
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9
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Pang TL, Ding Z, Liang SB, Li L, Zhang B, Zhang Y, Fan YJ, Xu YZ. Comprehensive Identification and Alternative Splicing of Microexons in Drosophila. Front Genet 2021; 12:642602. [PMID: 33859668 PMCID: PMC8042270 DOI: 10.3389/fgene.2021.642602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/05/2021] [Indexed: 11/29/2022] Open
Abstract
Interrupted exons in the pre-mRNA transcripts are ligated together through RNA splicing, which plays a critical role in the regulation of gene expression. Exons with a length ≤ 30 nt are defined as microexons that are unique in identification. However, microexons, especially those shorter than 8 nt, have not been well studied in many organisms due to difficulties in mapping short segments from sequencing reads. Here, we analyzed mRNA-seq data from a variety of Drosophila samples with a newly developed bioinformatic tool, ce-TopHat. In addition to the Flybase annotated, 465 new microexons were identified. Differentially alternatively spliced (AS) microexons were investigated between the Drosophila tissues (head, body, and gonad) and genders. Most of the AS microexons were found in the head and two AS microexons were identified in the sex-determination pathway gene fruitless.
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Affiliation(s)
- Ting-Lin Pang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Zhan Ding
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Shao-Bo Liang
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Liang Li
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China.,RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Bei Zhang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhang
- University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Wuhan, China
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