1
|
Almentina Ramos Shidi F, Cologne A, Delous M, Besson A, Putoux A, Leutenegger AL, Lacroix V, Edery P, Mazoyer S, Bordonné R. Mutations in the non-coding RNU4ATAC gene affect the homeostasis and function of the Integrator complex. Nucleic Acids Res 2023; 51:712-727. [PMID: 36537210 PMCID: PMC9881141 DOI: 10.1093/nar/gkac1182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 11/17/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Various genetic diseases associated with microcephaly and developmental defects are due to pathogenic variants in the U4atac small nuclear RNA (snRNA), a component of the minor spliceosome essential for the removal of U12-type introns from eukaryotic mRNAs. While it has been shown that a few RNU4ATAC mutations result in impaired binding of essential protein components, the molecular defects of the vast majority of variants are still unknown. Here, we used lymphoblastoid cells derived from RNU4ATAC compound heterozygous (g.108_126del;g.111G>A) twin patients with MOPD1 phenotypes to analyze the molecular consequences of the mutations on small nuclear ribonucleoproteins (snRNPs) formation and on splicing. We found that the U4atac108_126del mutant is unstable and that the U4atac111G>A mutant as well as the minor di- and tri-snRNPs are present at reduced levels. Our results also reveal the existence of 3'-extended snRNA transcripts in patients' cells. Moreover, we show that the mutant cells have alterations in splicing of INTS7 and INTS10 minor introns, contain lower levels of the INTS7 and INTS10 proteins and display changes in the assembly of Integrator subunits. Altogether, our results show that compound heterozygous g.108_126del;g.111G>A mutations induce splicing defects and affect the homeostasis and function of the Integrator complex.
Collapse
Affiliation(s)
- Fatimat Almentina Ramos Shidi
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR5535, 34293 Montpellier, France
| | - Audric Cologne
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, 69622 Villeurbanne, France
| | - Marion Delous
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Alicia Besson
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Audrey Putoux
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
- Clinical Genetics Unit, Department of Genetics, Centre de Référence Anomalies du Développement et Syndromes Polymalformatifs, Hospices Civils de Lyon, University Lyon 1, Bron, France
| | | | - Vincent Lacroix
- INRIA Erable, CNRS LBBE UMR 5558, University Lyon 1, University of Lyon, 69622 Villeurbanne, France
| | - Patrick Edery
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
- Clinical Genetics Unit, Department of Genetics, Centre de Référence Anomalies du Développement et Syndromes Polymalformatifs, Hospices Civils de Lyon, University Lyon 1, Bron, France
| | - Sylvie Mazoyer
- Université Claude Bernard Lyon 1, INSERM, CNRS, Centre de Recherche en Neurosciences de Lyon U1028 UMR5292, GENDEV, 69500 Bron, France
| | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR5535, 34293 Montpellier, France
| |
Collapse
|
2
|
Abstract
Spliceosomal snRNPs are complex particles that proceed through a fascinating maturation pathway. Several steps of this pathway are closely linked to nuclear non-membrane structures called Cajal bodies. In this review, I summarize the last 20 y of research in this field. I primarily focus on snRNP biogenesis, specifically on the steps that involve Cajal bodies. I also evaluate the contribution of the Cajal body in snRNP quality control and discuss the role of snRNPs in Cajal body formation.
Collapse
Affiliation(s)
- David Staněk
- a Institute of Molecular Genetics, Czech Academy of Sciences , Prague , Czech Republic
| |
Collapse
|
3
|
Natalizio AH, Matera AG. Identification and characterization of Drosophila Snurportin reveals a role for the import receptor Moleskin/importin-7 in snRNP biogenesis. Mol Biol Cell 2013; 24:2932-42. [PMID: 23885126 PMCID: PMC3771954 DOI: 10.1091/mbc.e13-03-0118] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Previous work established Importin-β and Snurportin1 as the vertebrate snRNP import receptor and adaptor proteins, respectively. This study identifies Drosophila Snurportin and shows that it uses an alternative import receptor, Importin7/Moleskin. Moleskin is required for the stability of other snRNP biogenesis factors. Nuclear import is an essential step in small nuclear ribonucleoprotein (snRNP) biogenesis. Snurportin1 (SPN1), the import adaptor, binds to trimethylguanosine (TMG) caps on spliceosomal small nuclear RNAs. Previous studies indicated that vertebrate snRNP import requires importin-β, the transport receptor that binds directly to SPN1. We identify CG42303/snup as the Drosophila orthologue of human snurportin1 (SNUPN). Of interest, the importin-β binding (IBB) domain of SPN1, which is essential for TMG cap–mediated snRNP import in humans, is not well conserved in flies. Consistent with its lack of an IBB domain, we find that Drosophila SNUP (dSNUP) does not interact with Ketel/importin-β. Fruit fly snRNPs also fail to bind Ketel; however, the importin-7 orthologue Moleskin (Msk) physically associates with both dSNUP and spliceosomal snRNPs and localizes to nuclear Cajal bodies. Strikingly, we find that msk-null mutants are depleted of the snRNP assembly factor, survival motor neuron, and the Cajal body marker, coilin. Consistent with a loss of snRNP import function, long-lived msk larvae show an accumulation of TMG cap signal in the cytoplasm. These data indicate that Ketel/importin-β does not play a significant role in Drosophila snRNP import and demonstrate a crucial function for Msk in snRNP biogenesis.
Collapse
Affiliation(s)
- Amanda Hicks Natalizio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 Departments of Biology, University of North Carolina, Chapel Hill, NC 27599 Departments of Genetics, University of North Carolina, Chapel Hill, NC 27599 Program in Molecular Biology and Biotechnology, University of North Carolina, Chapel Hill, NC 27599 Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599
| | | |
Collapse
|
4
|
Hayduk AJ, Stark MR, Rader SD. In vitro reconstitution of yeast splicing with U4 snRNA reveals multiple roles for the 3' stem-loop. RNA (NEW YORK, N.Y.) 2012; 18:1075-1090. [PMID: 22411955 PMCID: PMC3334694 DOI: 10.1261/rna.031757.111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/26/2012] [Indexed: 05/31/2023]
Abstract
U4 small nuclear RNA (snRNA) plays a fundamental role in the process of premessenger RNA splicing, yet many questions remain regarding the location, interactions, and roles of its functional domains. To address some of these questions, we developed the first in vitro reconstitution system for yeast U4 small nuclear ribonucleoproteins (snRNPs). We used this system to examine the functional domains of U4 by measuring reconstitution of splicing, U4/U6 base-pairing, and triple-snRNP formation. In contrast to previous work in human extracts and Xenopus oocytes, we found that the 3' stem-loop of U4 is necessary for efficient base-pairing with U6. In particular, the loop is sensitive to changes in both length and sequence. Intriguingly, a number of mutations that we tested resulted in more stable interactions with U6 than wild-type U4. Nevertheless, each of these mutants was impaired in its ability to support splicing, indicating that these regions of U4 have functions subsequent to base pair formation with U6. Our data suggest that one such function is likely to be in tri-snRNP formation, when U5 joins the U4/U6 di-snRNP. We have identified two regions, the upper stem of the 3' stem-loop and the central domain, that promote tri-snRNP formation. In addition, the loop of the 3' stem-loop promotes di-snRNP formation, while the central domain and the 3'-terminal domain appear to antagonize di-snRNP formation.
Collapse
Affiliation(s)
- Amy J. Hayduk
- Department of Chemistry, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9 Canada
| | - Martha R. Stark
- Department of Chemistry, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9 Canada
| | - Stephen D. Rader
- Department of Chemistry, University of Northern British Columbia, Prince George, British Columbia, V2N 4Z9 Canada
| |
Collapse
|
5
|
Jacobson MR, Pederson T. A 7-methylguanosine cap commits U3 and U8 small nuclear RNAs to the nucleolar localization pathway. Nucleic Acids Res 1998; 26:756-60. [PMID: 9443967 PMCID: PMC147312 DOI: 10.1093/nar/26.3.756] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
U3 and U8 small nucleolar RNAs (snRNAs) participate in pre-rRNA processing. Like the U1, U2, U4 and U5 major spliceosomal snRNAs, U3 and U8 RNAs are transcribed by RNA polymerase II and their initial 7-methylguanosine (m7G) 5' cap structures subsequently become converted to 2,2,7-trimethylguanosine. However, unlike the polymerase II transcribed spliceosomal snRNAs, which are exported to the cytoplasm for cap hypermethylation, U3 and U8 RNAs undergo cap hypermethylation within the nucleus. Human U3 and U8 RNAs with various cap structures were generated by in vitro transcription, fluorescently labeled and microinjected into nuclei of normal rat kidney (NRK) epithelial cells. When U3 and U8 RNAs containing a m7G cap were microinjected they became extensively localized in nucleoli. U3 and U8 RNAs containing alternative cap structures did not localize in nucleoli nor did U3 or U8 RNAs containing triphosphate 5'-termini. The nucleolar localization of m7G-capped U3 RNA was competed by co-microinjection into the nucleus of a 100-fold molar excess of dinucleotide m7GpppG but not by a 100-fold excess of ApppG dinucleotide. Although it was obviously not possible to assess formation of di- and trimethylguanosine caps on the microinjected U3 and U8 RNAs in these single cell experiments, these results indicate that the initial presence of a m7G cap on U3 and U8 RNAs, most likely together with internal sequence elements, commits these transcripts to the nucleolar localization pathway and point to diverse roles of the m7G cap in the intracellular traffic of various RNAs transcribed by RNA polymerase II.
Collapse
Affiliation(s)
- M R Jacobson
- Cell Biology Group, Worcester Foundation for Biomedical Research, Shrewsbury, MA 01545, USA
| | | |
Collapse
|
6
|
He XP, Bataillé N, Fried HM. Nuclear export of signal recognition particle RNA is a facilitated process that involves the Alu sequence domain. J Cell Sci 1994; 107 ( Pt 4):903-12. [PMID: 7520043 DOI: 10.1242/jcs.107.4.903] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The signal recognition particle is a cytoplasmic RNA-protein complex that mediates translocation of secretory polypeptides into the endoplasmic reticulum. We have used a Xenopus oocyte microinjection assay to determine how signal recognition particle (SRP) RNA is exported from the nucleus. Following nuclear injection, SRP RNA accumulated in the cytoplasm while cytoplasmically injected SRP RNA did not enter the nucleus. Cytoplasmic accumulation of SRP RNA was an apparently facilitated process dependent on limiting trans-acting factors, since nuclear export exhibited saturation kinetics and was completely blocked either at low temperature or by wheat germ agglutinin, a known inhibitor of nuclear pore-mediated transport. At least one target for trans-acting factors that promote nuclear export of SRP RNA appears to be the Alu element of the molecule, since a transcript consisting of only the Alu sequence was exported from the nucleus in a temperature-dependent manner and the Alu transcript competed in the nucleus for transport with intact SRP RNA. Although the identities of trans-acting factors responsible for SRP RNA transport are at present unknown, we suggest that proteins contained within the cytoplasmic form of SRP are candidates. Consistent with this idea were the effects of a mutation in SRP RNA that prevented binding of two known SRP proteins to the Alu sequence.
Collapse
Affiliation(s)
- X P He
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill 27599
| | | | | |
Collapse
|
7
|
Hackl W, Fischer U, Lührmann R. A 69-kD protein that associates reversibly with the Sm core domain of several spliceosomal snRNP species. J Cell Biol 1994; 124:261-72. [PMID: 8294511 PMCID: PMC2119936 DOI: 10.1083/jcb.124.3.261] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The biogenesis of the spliceosomal small nuclear ribonucleoproteins (snRNPs) U1, U2, U4, and U5 involves: (a) migration of the snRNA molecules from the nucleus to the cytoplasm; (b) assembly of a group of common proteins (Sm proteins) and their binding to a region on the snRNAs called the Sm-binding site; and (c) translocation of the RNP back to the nucleus. A first prerequisite for understanding the assembly pathway and nuclear transport of the snRNPs in more detail is the knowledge of all the snRNP proteins that play essential roles in these processes. We have recently observed a previously undetected 69-kD protein in 12S U1 snRNPs isolated from HeLa nuclear extracts under non-denaturing conditions that is clearly distinct from the U1-70K protein. The following evidence indicates that the 69-kD protein is a common, rather than a U1-specific, protein, possibly associating with the snRNP core particles by protein-protein interaction. (a) Antibodies raised against the 69-kD protein, which did not cross-react with any of the Sm proteins B'-G, precipitated not only U1 snRNPs, but also the other spliceosomal snRNPs U2, U4/U6 and U5, albeit to a lower extent. (b) U1, U2, and U5 core RNP particles reconstituted in vitro contain the 69-kD protein. (c) Xenopus laevis oocytes contain an immunologically related homologue of the human 69-kD protein. When U1 snRNA as well as a mutant U1 snRNA, that can bind the Sm core proteins but lacks the capacity to bind the U1-specific proteins 70K, A, and C, were injected into Xenopus oocytes to allow assembly in vivo, they were recognized by antibodies specific against the 69-kD protein in the ooplasm and in the nucleus. The 69-kD protein is under-represented, if present at all, in purified 17S U2 and in 25S [U4/U6.U5] tri-snRNPs, isolated from HeLa nuclear extracts. Our results are consistent with the working hypothesis that this protein may either play a role in the cytoplasmic assembly of the core domain of the snRNPs and/or in the nuclear transport of the snRNPs. After transport of the snRNPs into the nucleus, it may dissociate from the particles as for example in the case of the 17S U2 or the 25S [U4/U6.U5] tri-snRNP, which bind more than 10 different snRNP specific proteins each in the nucleus.
Collapse
Affiliation(s)
- W Hackl
- Institut für Molekularbiologie and Tumorforschung, Philipps Universität Marburg, Federal Republic of Germany
| | | | | |
Collapse
|