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Su Y, Wu J, Chen W, Shan J, Chen D, Zhu G, Ge S, Liu Y. Spliceosomal snRNAs, the Essential Players in pre-mRNA Processing in Eukaryotic Nucleus: From Biogenesis to Functions and Spatiotemporal Characteristics. Adv Biol (Weinh) 2024; 8:e2400006. [PMID: 38797893 DOI: 10.1002/adbi.202400006] [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: 01/03/2024] [Revised: 04/30/2024] [Indexed: 05/29/2024]
Abstract
Spliceosomal small nuclear RNAs (snRNAs) are a fundamental class of non-coding small RNAs abundant in the nucleoplasm of eukaryotic cells, playing a crucial role in splicing precursor messenger RNAs (pre-mRNAs). They are transcribed by DNA-dependent RNA polymerase II (Pol II) or III (Pol III), and undergo subsequent processing and 3' end cleavage to become mature snRNAs. Numerous protein factors are involved in the transcription initiation, elongation, termination, splicing, cellular localization, and terminal modification processes of snRNAs. The transcription and processing of snRNAs are regulated spatiotemporally by various mechanisms, and the homeostatic balance of snRNAs within cells is of great significance for the growth and development of organisms. snRNAs assemble with specific accessory proteins to form small nuclear ribonucleoprotein particles (snRNPs) that are the basal components of spliceosomes responsible for pre-mRNA maturation. This article provides an overview of the biological functions, biosynthesis, terminal structure, and tissue-specific regulation of snRNAs.
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Affiliation(s)
- Yuan Su
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Jiaming Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Wei Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Junling Shan
- Department of basic medicine, Guangxi Medical University of Nursing College, Nanning, Guangxi, 530021, China
| | - Dan Chen
- Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, Guangxi, 530011, China
| | - Guangyu Zhu
- Guangxi Medical University Hospital of Stomatology, Nanning, Guangxi, 530021, China
| | - Shengchao Ge
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
| | - Yunfeng Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, Guangxi, 530004, China
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Kramárek M, Souček P, Réblová K, Grodecká L, Freiberger T. Splicing analysis of STAT3 tandem donor suggests non-canonical binding registers for U1 and U6 snRNAs. Nucleic Acids Res 2024; 52:5959-5974. [PMID: 38426935 PMCID: PMC11162779 DOI: 10.1093/nar/gkae147] [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: 10/10/2022] [Revised: 02/02/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024] Open
Abstract
Tandem donor splice sites (5'ss) are unique regions with at least two GU dinucleotides serving as splicing cleavage sites. The Δ3 tandem 5'ss are a specific subclass of 5'ss separated by 3 nucleotides which can affect protein function by inserting/deleting a single amino acid. One 5'ss is typically preferred, yet factors governing particular 5'ss choice are not fully understood. A highly conserved exon 21 of the STAT3 gene was chosen as a model to study Δ3 tandem 5'ss splicing mechanisms. Based on multiple lines of experimental evidence, endogenous U1 snRNA most likely binds only to the upstream 5'ss. However, the downstream 5'ss is used preferentially, and the splice site choice is not dependent on the exact U1 snRNA binding position. Downstream 5'ss usage was sensitive to exact nucleotide composition and dependent on the presence of downstream regulatory region. The downstream 5'ss usage could be best explained by two novel interactions with endogenous U6 snRNA. U6 snRNA enables the downstream 5'ss usage in STAT3 exon 21 by two mechanisms: (i) binding in a novel non-canonical register and (ii) establishing extended Watson-Crick base pairing with the downstream regulatory region. This study suggests that U6:5'ss interaction is more flexible than previously thought.
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Affiliation(s)
- Michal Kramárek
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
| | - Kamila Réblová
- Centre of Molecular Biology and Genetics, University Hospital and Masaryk University, Brno, Czech Republic
| | - Lucie Kajan Grodecká
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, 656 91 Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 625 00 Brno, Czech Republic
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Wong J, Yellamaty R, Gallante C, Lawrence E, Martelly W, Sharma S. Examining the capacity of human U1 snRNA variants to facilitate pre-mRNA splicing. RNA (NEW YORK, N.Y.) 2024; 30:271-280. [PMID: 38164604 PMCID: PMC10870369 DOI: 10.1261/rna.079892.123] [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: 11/16/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024]
Abstract
The human U1 snRNA is encoded by a multigene family consisting of transcribed variants and defective pseudogenes. Many variant U1 (vU1) snRNAs have been demonstrated to not only be transcribed but also processed by the addition of a trimethylated guanosine cap, packaged into snRNPs, and assembled into spliceosomes; however, their capacity to facilitate pre-mRNA splicing has, so far, not been tested. A recent systematic analysis of the human snRNA genes identified 178 U1 snRNA genes that are present in the genome as either tandem arrays or single genes on multiple chromosomes. Of these, 15 were found to be expressed in human tissues and cell lines, although at significantly low levels from their endogenous loci, <0.001% of the canonical U1 snRNA. In this study, we found that placing the variants in the context of the regulatory elements of the RNU1-1 gene improves the expression of many variants to levels comparable to the canonical U1 snRNA. Application of a previously established HeLa cell-based minigene reporter assay to examine the capacity of the vU1 snRNAs to support pre-mRNA splicing revealed that even though the exogenously expressed variant snRNAs were enriched in the nucleus, only a few had a measurable effect on splicing.
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Affiliation(s)
- Jason Wong
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Ryan Yellamaty
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Christina Gallante
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Ethan Lawrence
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - William Martelly
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona 85004, 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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Gonçalves M, Santos JI, Coutinho MF, Matos L, Alves S. Development of Engineered-U1 snRNA Therapies: Current Status. Int J Mol Sci 2023; 24:14617. [PMID: 37834063 PMCID: PMC10572768 DOI: 10.3390/ijms241914617] [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: 08/17/2023] [Revised: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Splicing of pre-mRNA is a crucial regulatory stage in the pathway of gene expression. The majority of human genes that encode proteins undergo alternative pre-mRNA splicing and mutations that affect splicing are more prevalent than previously thought. Targeting aberrant RNA(s) may thus provide an opportunity to correct faulty splicing and potentially treat numerous genetic disorders. To that purpose, the use of engineered U1 snRNA (either modified U1 snRNAs or exon-specific U1s-ExSpeU1s) has been applied as a potentially therapeutic strategy to correct splicing mutations, particularly those affecting the 5' splice-site (5'ss). Here we review and summarize a vast panoply of studies that used either modified U1 snRNAs or ExSpeU1s to mediate gene therapeutic correction of splicing defects underlying a considerable number of genetic diseases. We also focus on the pre-clinical validation of these therapeutic approaches both in vitro and in vivo, and summarize the main obstacles that need to be overcome to allow for their successful translation to clinic practice in the future.
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Affiliation(s)
- Mariana Gonçalves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Centre for the Research and Technology of Agro-Environmental and Biological Sciences, CITAB, Inov4Agro, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
| | - Juliana Inês Santos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
- Biology Department, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Maria Francisca Coutinho
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Liliana Matos
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
| | - Sandra Alves
- Research and Development Unit, Department of Human Genetics, National Institute of Health Doutor Ricardo Jorge, INSA I.P., Rua Alexandre Herculano, 321, 4000-055 Porto, Portugal; (M.G.); (J.I.S.); (M.F.C.); (L.M.)
- Center for the Study of Animal Science, Institute of Sciences, Technologies and Agro-Environment, CECA-ICETA, University of Porto, Praça Gomes Teixeira, Apartado 55142, 4051-401 Porto, Portugal
- Associate Laboratory for Animal and Veterinary Sciences, AL4AnimalS, Faculty of Veterinary Medicine, University of Lisboa, Avenida da Universidade Técnica, 1300-477 Lisboa, Portugal
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Stott J, Wright T, Holmes J, Wilson J, Griffiths-Jones S, Foster D, Wright B. A systematic review of non-coding RNA genes with differential expression profiles associated with autism spectrum disorders. PLoS One 2023; 18:e0287131. [PMID: 37319303 PMCID: PMC10270643 DOI: 10.1371/journal.pone.0287131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 05/30/2023] [Indexed: 06/17/2023] Open
Abstract
AIMS To identify differential expression of shorter non-coding RNA (ncRNA) genes associated with autism spectrum disorders (ASD). BACKGROUND ncRNA are functional molecules that derive from non-translated DNA sequence. The HUGO Gene Nomenclature Committee (HGNC) have approved ncRNA gene classes with alignment to the reference human genome. One subset is microRNA (miRNA), which are highly conserved, short RNA molecules that regulate gene expression by direct post-transcriptional repression of messenger RNA. Several miRNA genes are implicated in the development and regulation of the nervous system. Expression of miRNA genes in ASD cohorts have been examined by multiple research groups. Other shorter classes of ncRNA have been examined less. A comprehensive systematic review examining expression of shorter ncRNA gene classes in ASD is timely to inform the direction of research. METHODS We extracted data from studies examining ncRNA gene expression in ASD compared with non-ASD controls. We included studies on miRNA, piwi-interacting RNA (piRNA), small NF90 (ILF3) associated RNA (snaR), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), transfer RNA (tRNA), vault RNA (vtRNA) and Y RNA. The following electronic databases were searched: Cochrane Library, EMBASE, PubMed, Web of Science, PsycINFO, ERIC, AMED and CINAHL for papers published from January 2000 to May 2022. Studies were screened by two independent investigators with a third resolving discrepancies. Data was extracted from eligible papers. RESULTS Forty-eight eligible studies were included in our systematic review with the majority examining miRNA gene expression alone. Sixty-four miRNA genes had differential expression in ASD compared to controls as reported in two or more studies, but often in opposing directions. Four miRNA genes had differential expression in the same direction in the same tissue type in at least 3 separate studies. Increased expression was reported in miR-106b-5p, miR-155-5p and miR-146a-5p in blood, post-mortem brain, and across several tissue types, respectively. Decreased expression was reported in miR-328-3p in bloods samples. Seven studies examined differential expression from other classes of ncRNA, including piRNA, snRNA, snoRNA and Y RNA. No individual ncRNA genes were reported in more than one study. Six studies reported differentially expressed snoRNA genes in ASD. A meta-analysis was not possible because of inconsistent methodologies, disparate tissue types examined, and varying forms of data presented. CONCLUSION There is limited but promising evidence associating the expression of certain miRNA genes and ASD, although the studies are of variable methodological quality and the results are largely inconsistent. There is emerging evidence associating differential expression of snoRNA genes in ASD. It is not currently possible to say whether the reports of differential expression in ncRNA may relate to ASD aetiology, a response to shared environmental factors linked to ASD such as sleep and nutrition, other molecular functions, human diversity, or chance findings. To improve our understanding of any potential association, we recommend improved and standardised methodologies and reporting of raw data. Further high-quality research is required to shine a light on possible associations, which may yet yield important information.
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Affiliation(s)
- Jon Stott
- Child Oriented Mental Health Intervention Collaborative (COMIC), University of York in Collaboration with Leeds and York Partnership NHS Foundation Trust, York, United Kingdom
- Tees, Esk & Wear Valleys NHS Foundation Trust, Foss Park Hospital, York, United Kingdom
| | - Thomas Wright
- Manchester Centre for Genomic Medicine, Clinical Genetics Service, Saint Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Jannah Holmes
- Child Oriented Mental Health Intervention Collaborative (COMIC), University of York in Collaboration with Leeds and York Partnership NHS Foundation Trust, York, United Kingdom
- Hull York Medical School, University of York, Heslington, York, United Kingdom
| | - Julie Wilson
- Department of Mathematics, University of York, Heslington, York, United Kingdom
| | - Sam Griffiths-Jones
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom
| | - Deborah Foster
- Tees, Esk & Wear Valleys NHS Foundation Trust, Foss Park Hospital, York, United Kingdom
| | - Barry Wright
- Child Oriented Mental Health Intervention Collaborative (COMIC), University of York in Collaboration with Leeds and York Partnership NHS Foundation Trust, York, United Kingdom
- Hull York Medical School, University of York, Heslington, York, United Kingdom
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Girardini KN, Olthof AM, Kanadia RN. Introns: the "dark matter" of the eukaryotic genome. Front Genet 2023; 14:1150212. [PMID: 37260773 PMCID: PMC10228655 DOI: 10.3389/fgene.2023.1150212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023] Open
Abstract
The emergence of introns was a significant evolutionary leap that is a major distinguishing feature between prokaryotic and eukaryotic genomes. While historically introns were regarded merely as the sequences that are removed to produce spliced transcripts encoding functional products, increasingly data suggests that introns play important roles in the regulation of gene expression. Here, we use an intron-centric lens to review the role of introns in eukaryotic gene expression. First, we focus on intron architecture and how it may influence mechanisms of splicing. Second, we focus on the implications of spliceosomal snRNAs and their variants on intron splicing. Finally, we discuss how the presence of introns and the need to splice them influences transcription regulation. Despite the abundance of introns in the eukaryotic genome and their emerging role regulating gene expression, a lot remains unexplored. Therefore, here we refer to introns as the "dark matter" of the eukaryotic genome and discuss some of the outstanding questions in the field.
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Affiliation(s)
- Kaitlin N. Girardini
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
| | - Anouk M. Olthof
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Rahul N. Kanadia
- Physiology and Neurobiology Department, University of Connecticut, Storrs, CT, United States
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, United States
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Black CS, Whelan TA, Garside EL, MacMillan AM, Fast NM, Rader SD. Spliceosome assembly and regulation: insights from analysis of highly reduced spliceosomes. RNA (NEW YORK, N.Y.) 2023; 29:531-550. [PMID: 36737103 PMCID: PMC10158995 DOI: 10.1261/rna.079273.122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/06/2023] [Indexed: 05/06/2023]
Abstract
Premessenger RNA splicing is catalyzed by the spliceosome, a multimegadalton RNA-protein complex that assembles in a highly regulated process on each intronic substrate. Most studies of splicing and spliceosomes have been carried out in human or S. cerevisiae model systems. There exists, however, a large diversity of spliceosomes, particularly in organisms with reduced genomes, that suggests a means of analyzing the essential elements of spliceosome assembly and regulation. In this review, we characterize changes in spliceosome composition across phyla, describing those that are most frequently observed and highlighting an analysis of the reduced spliceosome of the red alga Cyanidioschyzon merolae We used homology modeling to predict what effect splicing protein loss would have on the spliceosome, based on currently available cryo-EM structures. We observe strongly correlated loss of proteins that function in the same process, for example, in interacting with the U1 snRNP (which is absent in C. merolae), regulation of Brr2, or coupling transcription and splicing. Based on our observations, we predict splicing in C. merolae to be inefficient, inaccurate, and post-transcriptional, consistent with the apparent trend toward its elimination in this lineage. This work highlights the striking flexibility of the splicing pathway and the spliceosome when viewed in the context of eukaryotic diversity.
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Affiliation(s)
- Corbin S Black
- Department of Chemistry and Biochemistry, University of Northern British Columbia, Prince George, British Columbia, Canada V2N 4Z9
- Department of Anatomy and Cell Biology, McGill University, Montréal, Quebec, Canada H3A 0C7
| | - Thomas A Whelan
- Biodiversity Research Center and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Erin L Garside
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Andrew M MacMillan
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7
| | - Naomi M Fast
- Biodiversity Research Center and Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Stephen D Rader
- Department of Chemistry and Biochemistry, University of Northern British Columbia, Prince George, British Columbia, Canada V2N 4Z9
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Rodrigues KS, Petroski LP, Utumi PH, Ferrasa A, Herai RH. IARA: a complete and curated atlas of the biogenesis of spliceosome machinery during RNA splicing. Life Sci Alliance 2023; 6:e202201593. [PMID: 36609432 PMCID: PMC9834665 DOI: 10.26508/lsa.202201593] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/09/2023] Open
Abstract
Splicing is one of the most important post-transcriptional processing systems and is responsible for the generation of transcriptome diversity in all living eukaryotes. Splicing is regulated by the spliceosome machinery, which is responsible for each step of primary RNA processing. However, current molecules and stages involved in RNA splicing are still spread over different studies. Thus, a curated atlas of spliceosome-related molecules and all involved stages during RNA processing can provide all researchers with a reliable resource to better investigate this important mechanism. Here, we present IARA (website access: https://pucpr-bioinformatics.github.io/atlas/), an extensively curated and constantly updated catalog of molecules involved in spliceosome machinery. IARA has a map of the steps involved in the human splicing mechanism, and it allows a detailed overview of the molecules involved throughout the distinct steps of splicing.
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Affiliation(s)
- Kelren S Rodrigues
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Luiz P Petroski
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Paulo H Utumi
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
| | - Adriano Ferrasa
- Informatics Department, Universidade Estadual de Ponta GrossaPonta Grossa, Brazil
| | - Roberto H Herai
- Laboratory of Bioinformatics and Neurogenetics, Graduate Program in Health Sciences (PPGCS), School of Medicine and Life Sciences, Pontifícia Universidade Católica do Paraná, Curitiba, Brazil
- Research Division, Buko Kaesemodel Institute, Curitiba, Brazil
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10
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NeuroLINCS Proteomics: Defining human-derived iPSC proteomes and protein signatures of pluripotency. Sci Data 2023; 10:24. [PMID: 36631473 PMCID: PMC9834231 DOI: 10.1038/s41597-022-01687-7] [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: 11/02/2021] [Accepted: 09/07/2022] [Indexed: 01/13/2023] Open
Abstract
The National Institute of Health (NIH) Library of integrated network-based cellular signatures (LINCS) program is premised on the generation of a publicly available data resource of cell-based biochemical responses or "signatures" to genetic or environmental perturbations. NeuroLINCS uses human inducible pluripotent stem cells (hiPSCs), derived from patients and healthy controls, and differentiated into motor neuron cell cultures. This multi-laboratory effort strives to establish i) robust multi-omic workflows for hiPSC and differentiated neuronal cultures, ii) public annotated data sets and iii) relevant and targetable biological pathways of spinal muscular atrophy (SMA) and amyotrophic lateral sclerosis (ALS). Here, we focus on the proteomics and the quality of the developed workflow of hiPSC lines from 6 individuals, though epigenomics and transcriptomics data are also publicly available. Known and commonly used markers representing 73 proteins were reproducibly quantified with consistent expression levels across all hiPSC lines. Data quality assessments, data levels and metadata of all 6 genetically diverse human iPSCs analysed by DIA-MS are parsable and available as a high-quality resource to the public.
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11
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Sun J, Li X, Hou X, Cao S, Cao W, Zhang Y, Song J, Wang M, Wang H, Yan X, Li Z, Roeder RG, Wang W. Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter. Nat Commun 2022; 13:6871. [PMID: 36369505 PMCID: PMC9652321 DOI: 10.1038/s41467-022-34639-1] [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: 05/27/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022] Open
Abstract
In eukaryotes, small nuclear RNAs (snRNAs) function in many fundamental cellular events such as precursor messenger RNA splicing, gene expression regulation, and ribosomal RNA processing. The snRNA activating protein complex (SNAPc) exclusively recognizes the proximal sequence element (PSE) at snRNA promoters and recruits RNA polymerase II or III to initiate transcription. In view that homozygous gene-knockout of SNAPc core subunits causes mouse embryonic lethality, functions of SNAPc are almost housekeeping. But so far, the structural insight into how SNAPc assembles and regulates snRNA transcription initiation remains unclear. Here we present the cryo-electron microscopy structure of the essential part of human SNAPc in complex with human U6-1 PSE at an overall resolution of 3.49 Å. This structure reveals the three-dimensional features of three conserved subunits (N-terminal domain of SNAP190, SNAP50, and SNAP43) and explains how they are assembled into a stable mini-SNAPc in PSE-binding state with a "wrap-around" mode. We identify three important motifs of SNAP50 that are involved in both major groove and minor groove recognition of PSE, in coordination with the Myb domain of SNAP190. Our findings further elaborate human PSE sequence conservation and compatibility for SNAPc recognition, providing a clear framework of snRNA transcription initiation, especially the U6 system.
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Affiliation(s)
- Jianfeng Sun
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.27255.370000 0004 1761 1174Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.134907.80000 0001 2166 1519Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, 10065 USA
| | - Xue Li
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Xuben Hou
- grid.27255.370000 0004 1761 1174School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Sujian Cao
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Wenjin Cao
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Ye Zhang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Jinyang Song
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Manfu Wang
- grid.512077.6Wuxi Biortus Biosciences Co. Ltd., Jiangyin, 214437 China
| | - Hao Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China
| | - Xiaodong Yan
- grid.512077.6Wuxi Biortus Biosciences Co. Ltd., Jiangyin, 214437 China
| | - Zengpeng Li
- grid.453137.70000 0004 0406 0561Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, 361005 China
| | - Robert G. Roeder
- grid.134907.80000 0001 2166 1519Laboratory of Biochemistry and Molecular Biology, The Rockefeller University, New York, 10065 USA
| | - Wei Wang
- grid.27255.370000 0004 1761 1174Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, 250012 China ,grid.27255.370000 0004 1761 1174Interventional Medicine Department, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250033 China
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12
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Li J, Lim RG, Kaye JA, Dardov V, Coyne AN, Wu J, Milani P, Cheng A, Thompson TG, Ornelas L, Frank A, Adam M, Banuelos MG, Casale M, Cox V, Escalante-Chong R, Daigle JG, Gomez E, Hayes L, Holewenski R, Lei S, Lenail A, Lima L, Mandefro B, Matlock A, Panther L, Patel-Murray NL, Pham J, Ramamoorthy D, Sachs K, Shelley B, Stocksdale J, Trost H, Wilhelm M, Venkatraman V, Wassie BT, Wyman S, Yang S, Van Eyk JE, Lloyd TE, Finkbeiner S, Fraenkel E, Rothstein JD, Sareen D, Svendsen CN, Thompson LM. An integrated multi-omic analysis of iPSC-derived motor neurons from C9ORF72 ALS patients. iScience 2021; 24:103221. [PMID: 34746695 PMCID: PMC8554488 DOI: 10.1016/j.isci.2021.103221] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/29/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Neurodegenerative diseases are challenging for systems biology because of the lack of reliable animal models or patient samples at early disease stages. Induced pluripotent stem cells (iPSCs) could address these challenges. We investigated DNA, RNA, epigenetics, and proteins in iPSC-derived motor neurons from patients with ALS carrying hexanucleotide expansions in C9ORF72. Using integrative computational methods combining all omics datasets, we identified novel and known dysregulated pathways. We used a C9ORF72 Drosophila model to distinguish pathways contributing to disease phenotypes from compensatory ones and confirmed alterations in some pathways in postmortem spinal cord tissue of patients with ALS. A different differentiation protocol was used to derive a separate set of C9ORF72 and control motor neurons. Many individual -omics differed by protocol, but some core dysregulated pathways were consistent. This strategy of analyzing patient-specific neurons provides disease-related outcomes with small numbers of heterogeneous lines and reduces variation from single-omics to elucidate network-based signatures.
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Affiliation(s)
- Jonathan Li
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ryan G. Lim
- UCI MIND, University of California, Irvine, CA 92697, USA
| | - Julia A. Kaye
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Victoria Dardov
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Alyssa N. Coyne
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Pamela Milani
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Andrew Cheng
- Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | | | - Loren Ornelas
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Aaron Frank
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Miriam Adam
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Maria G. Banuelos
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Malcolm Casale
- UCI MIND, University of California, Irvine, CA 92697, USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Veerle Cox
- Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Renan Escalante-Chong
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - J. Gavin Daigle
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Emilda Gomez
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Lindsey Hayes
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Ronald Holewenski
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Susan Lei
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Alex Lenail
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Leandro Lima
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Berhan Mandefro
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Andrea Matlock
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Lindsay Panther
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | | | - Jacqueline Pham
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Divya Ramamoorthy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Karen Sachs
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Brandon Shelley
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Jennifer Stocksdale
- UCI MIND, University of California, Irvine, CA 92697, USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
| | - Hannah Trost
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Mark Wilhelm
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Vidya Venkatraman
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brook T. Wassie
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Stacia Wyman
- Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA 92697, USA
| | - Stephanie Yang
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | | | - Jennifer E. Van Eyk
- Advanced Clinical Biosystems Research Institute, The Barbra Streisand Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Thomas E. Lloyd
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Steven Finkbeiner
- Center for Systems and Therapeutics and the Taube/Koret Center for Neurodegenerative Disease, Gladstone Institutes, University of California, San Francisco, San Francisco, CA 94158, USA
- Departments of Neurology and Physiology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jeffrey D. Rothstein
- Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
- Department of Neurology and Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
- Cellular and Molecular Medicine Program, Johns Hopkins University School of Medicine, Baltimore, MA 212056, USA
| | - Dhruv Sareen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Clive N. Svendsen
- The Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Leslie M. Thompson
- UCI MIND, University of California, Irvine, CA 92697, USA
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
- Department of Neurobiology and Behavior, University of California, Irvine, CA 92697, USA
- Department of Psychiatry and Human Behavior, University of California, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Center, University of California, Irvine, CA 92697, USA
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13
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Mabin JW, Lewis PW, Brow DA, Dvinge H. Human spliceosomal snRNA sequence variants generate variant spliceosomes. RNA (NEW YORK, N.Y.) 2021; 27:1186-1203. [PMID: 34234030 PMCID: PMC8457000 DOI: 10.1261/rna.078768.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/29/2021] [Indexed: 06/02/2023]
Abstract
Human pre-mRNA splicing is primarily catalyzed by the major spliceosome, comprising five small nuclear ribonucleoprotein complexes, U1, U2, U4, U5, and U6 snRNPs, each of which contains the corresponding U-rich snRNA. These snRNAs are encoded by large gene families exhibiting significant sequence variation, but it remains unknown if most human snRNA genes are untranscribed pseudogenes or produce variant snRNAs with the potential to differentially influence splicing. Since gene duplication and variation are powerful mechanisms of evolutionary adaptation, we sought to address this knowledge gap by systematically profiling human U1, U2, U4, and U5 snRNA variant gene transcripts. We identified 55 transcripts that are detectably expressed in human cells, 38 of which incorporate into snRNPs and spliceosomes in 293T cells. All U1 snRNA variants are more than 1000-fold less abundant in spliceosomes than the canonical U1, whereas at least 1% of spliceosomes contain a variant of U2 or U4. In contrast, eight U5 snRNA sequence variants occupy spliceosomes at levels of 1% to 46%. Furthermore, snRNA variants display distinct expression patterns across five human cell lines and adult and fetal tissues. Different RNA degradation rates contribute to the diverse steady state levels of snRNA variants. Our findings suggest that variant spliceosomes containing noncanonical snRNAs may contribute to different tissue- and cell-type-specific alternative splicing patterns.
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Affiliation(s)
- Justin W Mabin
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Peter W Lewis
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - David A Brow
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
| | - Heidi Dvinge
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA
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14
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Saba JA, Liakath-Ali K, Green R, Watt FM. Translational control of stem cell function. Nat Rev Mol Cell Biol 2021; 22:671-690. [PMID: 34272502 DOI: 10.1038/s41580-021-00386-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/22/2022]
Abstract
Stem cells are characterized by their ability to self-renew and differentiate into many different cell types. Research has focused primarily on how these processes are regulated at a transcriptional level. However, recent studies have indicated that stem cell behaviour is strongly coupled to the regulation of protein synthesis by the ribosome. In this Review, we discuss how different translation mechanisms control the function of adult and embryonic stem cells. Stem cells are characterized by low global translation rates despite high levels of ribosome biogenesis. The maintenance of pluripotency, the commitment to a specific cell fate and the switch to cell differentiation depend on the tight regulation of protein synthesis and ribosome biogenesis. Translation regulatory mechanisms that impact on stem cell function include mTOR signalling, ribosome levels, and mRNA and tRNA features and amounts. Understanding these mechanisms important for stem cell self-renewal and differentiation may also guide our understanding of cancer grade and metastasis.
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Affiliation(s)
- James A Saba
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kifayathullah Liakath-Ali
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Fiona M Watt
- King's College London Centre for Stem Cells and Regenerative Medicine, Guy's Hospital, London, UK.
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15
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Sabitha KR, Shetty AK, Upadhya D. Patient-derived iPSC modeling of rare neurodevelopmental disorders: Molecular pathophysiology and prospective therapies. Neurosci Biobehav Rev 2020; 121:201-219. [PMID: 33370574 DOI: 10.1016/j.neubiorev.2020.12.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/12/2022]
Abstract
The pathological alterations that manifest during the early embryonic development due to inherited and acquired factors trigger various neurodevelopmental disorders (NDDs). Besides major NDDs, there are several rare NDDs, exhibiting specific characteristics and varying levels of severity triggered due to genetic and epigenetic anomalies. The rarity of subjects, paucity of neural tissues for detailed analysis, and the unavailability of disease-specific animal models have hampered detailed comprehension of rare NDDs, imposing heightened challenge to the medical and scientific community until a decade ago. The generation of functional neurons and glia through directed differentiation protocols for patient-derived iPSCs, CRISPR/Cas9 technology, and 3D brain organoid models have provided an excellent opportunity and vibrant resource for decoding the etiology of brain development for rare NDDs caused due to monogenic as well as polygenic disorders. The present review identifies cellular and molecular phenotypes demonstrated from patient-derived iPSCs and possible therapeutic opportunities identified for these disorders. New insights to reinforce the existing knowledge of the pathophysiology of these disorders and prospective therapeutic applications are discussed.
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Affiliation(s)
- K R Sabitha
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Ashok K Shetty
- Institute for Regenerative Medicine, Department of Molecular and Cellular Medicine, Texas A&M University College of Medicine, College Station, TX, USA.
| | - Dinesh Upadhya
- Centre for Molecular Neurosciences, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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16
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Adami R, Bottai D. Spinal Muscular Atrophy Modeling and Treatment Advances by Induced Pluripotent Stem Cells Studies. Stem Cell Rev Rep 2020; 15:795-813. [PMID: 31863335 DOI: 10.1007/s12015-019-09910-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spinal Muscular Atrophy (SMA) is a neurodegenerative disease characterized by specific and predominantly lower motor neuron (MN) loss. SMA is the main reason for infant death, while about one in 40 children born is a healthy carrier. SMA is caused by decreased levels of production of a ubiquitously expressed gene: the survival motor neuron (SMN). All SMA patients present mutations of the telomeric SMN1 gene, but many copies of a centromeric, partially functional paralog gene, SMN2, can somewhat compensate for the SMN1 deficiency, scaling inversely with phenotypic harshness. Because the study of neural tissue in and from patients presents too many challenges and is very often not feasible; the use of animal models, such as the mouse, had a pivotal impact in our understanding of SMA pathology but could not portray totally satisfactorily the elaborate regulatory mechanisms that are present in higher animals, particularly in humans. And while recent therapeutic achievements have been substantial, especially for very young infants, some issues should be considered for the treatment of older patients. An alternative way to study SMA, and other neurological pathologies, is the use of induced pluripotent stem cells (iPSCs) derived from patients. In this work, we will present a wide analysis of the uses of iPSCs in SMA pathology, starting from basic science to their possible roles as therapeutic tools.
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Affiliation(s)
- Raffaella Adami
- Department of Health Sciences, University of Milan, via A. di Rudinì 8, 20142, Milan, Italy
| | - Daniele Bottai
- Department of Health Sciences, University of Milan, via A. di Rudinì 8, 20142, Milan, Italy.
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17
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Wu YY, Kuo HC. Functional roles and networks of non-coding RNAs in the pathogenesis of neurodegenerative diseases. J Biomed Sci 2020; 27:49. [PMID: 32264890 PMCID: PMC7140545 DOI: 10.1186/s12929-020-00636-z] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Recent transcriptome analyses have revealed that noncoding RNAs (ncRNAs) are broadly expressed in mammalian cells and abundant in the CNS, with tissue and cell type-specific expression patterns. Moreover, ncRNAs have been found to intricately and dynamically regulate various signaling pathways in neurodegeneration. As such, some antisense transcripts and microRNAs are known to directly affect neurodegeneration in disease contexts. The functions of ncRNAs in pathogenesis are unique for each disorder, as are the pertinent networks of ncRNA/miRNA/mRNA that mediate these functions. Thus, further understanding of ncRNA biogenesis and effects might aid the discovery of diagnostic biomarkers or development of effective therapeutics for neurodegenerative disorders. Here, we review the ncRNAs that have so far been identified in major neurodegenerative disease etiology and the mechanisms that link ncRNAs with disease-specific phenotypes, such as HTT aggregation in HD, α-synuclein in PD, and Aβ plaques and hyperphosphorylated Tau in AD. We also summarize the known lncRNA/miRNA/mRNA networks that participate in neurodegenerative diseases, and we discuss ncRNA-related treatments shown to delay disease onset and prolong lifespan in rodent models.
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Affiliation(s)
- Yi-Ying Wu
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 11529, Taiwan
| | - Hung-Chih Kuo
- Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Sec. 2, Academia Road, Nankang, Taipei, 11529, Taiwan. .,Graduate Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan.
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18
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Seal RL, Chen LL, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA. A guide to naming human non-coding RNA genes. EMBO J 2020; 39:e103777. [PMID: 32090359 PMCID: PMC7073466 DOI: 10.15252/embj.2019103777] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/23/2020] [Accepted: 01/30/2020] [Indexed: 12/15/2022] Open
Abstract
Research on non-coding RNA (ncRNA) is a rapidly expanding field. Providing an official gene symbol and name to ncRNA genes brings order to otherwise potential chaos as it allows unambiguous communication about each gene. The HUGO Gene Nomenclature Committee (HGNC, www.genenames.org) is the only group with the authority to approve symbols for human genes. The HGNC works with specialist advisors for different classes of ncRNA to ensure that ncRNA nomenclature is accurate and informative, where possible. Here, we review each major class of ncRNA that is currently annotated in the human genome and describe how each class is assigned a standardised nomenclature.
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Affiliation(s)
- Ruth L Seal
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
| | - Ling-Ling Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Science, Shanghai, China
| | - Sam Griffiths-Jones
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Todd M Lowe
- Department of Biomolecular Engineering, University of California, Santa Cruz, CA, USA
| | - Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dawn O'Reilly
- Computational Biology and Integrative Genomics Lab, MRC/CRUK Oxford Institute and Department of Oncology, University of Oxford, Oxford, UK
| | - Andrew J Pierce
- Translational Medicine, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia.,Santa Fe Institute, Santa Fe, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Sandra L Wolin
- RNA Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD, USA
| | - Elspeth A Bruford
- Department of Haematology, University of Cambridge School of Clinical Medicine, Cambridge, UK.,European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK
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19
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Watson CN, Belli A, Di Pietro V. Small Non-coding RNAs: New Class of Biomarkers and Potential Therapeutic Targets in Neurodegenerative Disease. Front Genet 2019; 10:364. [PMID: 31080456 PMCID: PMC6497742 DOI: 10.3389/fgene.2019.00364] [Citation(s) in RCA: 89] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/05/2019] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative diseases (NDs) are becoming increasingly prevalent in the world, with an aging population. In the last few decades, due to the devastating nature of these diseases, the research of biomarkers has become crucial to enable adequate treatments and to monitor the progress of disease. Currently, gene mutations, CSF and blood protein markers together with the neuroimaging techniques are the most used diagnostic approaches. However, despite the efforts in the research, conflicting data still exist, highlighting the need to explore new classes of biomarkers, particularly at early stages. Small non-coding RNAs (MicroRNA, Small nuclear RNA, Small nucleolar RNA, tRNA derived small RNA and Piwi-interacting RNA) can be considered a "relatively" new class of molecule that have already proved to be differentially regulated in many NDs, hence they represent a new potential class of biomarkers to be explored. In addition, understanding their involvement in disease development could depict the underlying pathogenesis of particular NDs, so novel treatment methods that act earlier in disease progression can be developed. This review aims to describe the involvement of small non-coding RNAs as biomarkers of NDs and their potential role in future clinical applications.
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Affiliation(s)
- Callum N. Watson
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Antonio Belli
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
| | - Valentina Di Pietro
- Neuroscience and Ophthalmology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Surgical Reconstruction and Microbiology Research Centre, Queen Elizabeth Hospital Birmingham, Birmingham, United Kingdom
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana–Champaign, Urbana, IL, United States
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Schmidt D, Reuter H, Hüttner K, Ruhe L, Rabert F, Seebeck F, Irimia M, Solana J, Bartscherer K. The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea. PLoS Genet 2018; 14:e1007828. [PMID: 30557303 PMCID: PMC6312358 DOI: 10.1371/journal.pgen.1007828] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/31/2018] [Accepted: 11/12/2018] [Indexed: 02/07/2023] Open
Abstract
In multicellular organisms, cell type diversity and fate depend on specific sets of transcript isoforms generated by post-transcriptional RNA processing. Here, we used Schmidtea mediterranea, a flatworm with extraordinary regenerative abilities and a large pool of adult stem cells, as an in vivo model to study the role of Uridyl-rich small nuclear RNAs (UsnRNAs), which participate in multiple RNA processing reactions including splicing, in stem cell regulation. We characterized the planarian UsnRNA repertoire, identified stem cell-enriched variants and obtained strong evidence for an increased rate of UsnRNA 3'-processing in stem cells compared to their differentiated counterparts. Consistently, components of the Integrator complex showed stem cell-enriched expression and their depletion by RNAi disrupted UsnRNA processing resulting in global changes of splicing patterns and reduced processing of histone mRNAs. Interestingly, loss of Integrator complex function disrupted both stem cell maintenance and regeneration of tissues. Our data show that the function of the Integrator complex in UsnRNA 3'-processing is conserved in planarians and essential for maintaining their stem cell pool. We propose that cell type-specific modulation of UsnRNA composition and maturation contributes to in vivo cell fate choices, such as stem cell self-renewal in planarians.
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Affiliation(s)
- David Schmidt
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
- * E-mail: (DS); (KB)
| | - Hanna Reuter
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Katja Hüttner
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Larissa Ruhe
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Franziska Rabert
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Florian Seebeck
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
| | - Manuel Irimia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Solana
- Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Kerstin Bartscherer
- Max Planck Institute for Molecular Biomedicine, Münster, Germany
- Medical Faculty, University of Münster, Münster, Germany
- Hubrecht Institute for Developmental Biology and Stem Cell Research, CT Utrecht, The Netherlands
- * E-mail: (DS); (KB)
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Dvinge H. Regulation of alternative
mRNA
splicing: old players and new perspectives. FEBS Lett 2018; 592:2987-3006. [DOI: 10.1002/1873-3468.13119] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/23/2018] [Accepted: 05/29/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Heidi Dvinge
- Department of Biomolecular Chemistry School of Medicine and Public Health University of Wisconsin‐Madison WI USA
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Abstract
Much evidence is now accumulating that, in addition to their general role in splicing, the components of the core splicing machinery have extensive regulatory potential. In particular, recent evidence has demonstrated that de-regulation of these factors cause the highest extent of alternative splicing changes compared to de-regulation of the classical splicing regulators. This lack of a general inhibition of splicing resonates the differential splicing effects observed in different disease pathologies associated with specific mutations targeting core spliceosomal components. In this review we will summarize what is currently known regarding the involvement of core spliceosomal U-snRNP complexes in perturbed tissue development and human diseases and argue for the existence of a compensatory mechanism enabling cells to cope with drastic perturbations in core splicing components. This system maintains the correct balance of spliceosomal snRNPs through differential expression of variant (v)U-snRNPs.
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Affiliation(s)
- Pilar Vazquez-Arango
- a Nuffield Department of Obstetrics and Gynaecology, Level 3 , Women's Centre, John Radcliffe Hospital , Oxford , England
| | - Dawn O'Reilly
- b Sir William Dunn School of pathology , University of Oxford , South Parks Road, Oxford , England
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Georgomanolis T, Sofiadis K, Papantonis A. Cutting a Long Intron Short: Recursive Splicing and Its Implications. Front Physiol 2016; 7:598. [PMID: 27965595 PMCID: PMC5126111 DOI: 10.3389/fphys.2016.00598] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/16/2016] [Indexed: 11/13/2022] Open
Abstract
Over time eukaryotic genomes have evolved to host genes carrying multiple exons separated by increasingly larger intronic, mostly non-protein-coding, sequences. Initially, little attention was paid to these intronic sequences, as they were considered not to contain regulatory information. However, advances in molecular biology, sequencing, and computational tools uncovered that numerous segments within these genomic elements do contribute to the regulation of gene expression. Introns are differentially removed in a cell type-specific manner to produce a range of alternatively-spliced transcripts, and many span tens to hundreds of kilobases. Recent work in human and fruitfly tissues revealed that long introns are extensively processed cotranscriptionally and in a stepwise manner, before their two flanking exons are spliced together. This process, called "recursive splicing," often involves non-canonical splicing elements positioned deep within introns, and different mechanisms for its deployment have been proposed. Still, the very existence and widespread nature of recursive splicing offers a new regulatory layer in the transcript maturation pathway, which may also have implications in human disease.
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Affiliation(s)
- Theodore Georgomanolis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
| | - Konstantinos Sofiadis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
| | - Argyris Papantonis
- Chromatin Systems Biology Laboratory, Center for Molecular Medicine, University of Cologne Cologne, Germany
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