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Sarka K, Katzman S, Zahler AM. A role for SNU66 in maintaining 5' splice site identity during spliceosome assembly. RNA (NEW YORK, N.Y.) 2024; 30:695-709. [PMID: 38443114 PMCID: PMC11098459 DOI: 10.1261/rna.079971.124] [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: 01/29/2024] [Accepted: 02/21/2024] [Indexed: 03/07/2024]
Abstract
In spliceosome assembly, the 5' splice site is initially recognized by U1 snRNA. U1 leaves the spliceosome during the assembly process, therefore other factors contribute to the maintenance of 5' splice site identity as it is loaded into the catalytic site. Recent structural data suggest that human tri-snRNP 27K (SNRP27) M141 and SNU66 H734 interact to stabilize the U4/U6 quasi-pseudo knot at the base of the U6 snRNA ACAGAGA box in pre-B complex. Previously, we found that mutations in Caenorhabditis elegans at SNRP-27 M141 promote changes in alternative 5'ss usage. We tested whether the potential interaction between SNRP-27 M141 and SNU-66 H765 (the C. elegans equivalent position to human SNU66 H734) contributes to maintaining 5' splice site identity during spliceosome assembly. We find that SNU-66 H765 mutants promote alternative 5' splice site usage. Many of the alternative 5' splicing events affected by SNU-66(H765G) overlap with those affected SNRP-27(M141T). Double mutants of snrp-27(M141T) and snu-66(H765G) are homozygous lethal. We hypothesize that mutations at either SNRP-27 M141 or SNU-66 H765 allow the spliceosome to load alternative 5' splice sites into the active site. Tests with mutant U1 snRNA and swapped 5' splice sites indicate that the ability of SNRP-27 M141 and SNU-66 H765 mutants to affect a particular 5' splice alternative splicing event is dependent on both the presence of a weaker consensus 5'ss nearby and potentially nearby splicing factor binding sites. Our findings confirm a new role for the C terminus of SNU-66 in maintenance of 5' splice site identity during spliceosome assembly.
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Affiliation(s)
- Kenna Sarka
- Center for Molecular Biology of RNA and Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Sol Katzman
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Alan M Zahler
- Center for Molecular Biology of RNA and Department of Molecular, Cellular and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA
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2
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Beusch I, Madhani HD. Understanding the dynamic design of the spliceosome. Trends Biochem Sci 2024:S0968-0004(24)00078-1. [PMID: 38641465 DOI: 10.1016/j.tibs.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/19/2024] [Indexed: 04/21/2024]
Abstract
The spliceosome catalyzes the splicing of pre-mRNAs. Although the spliceosome evolved from a prokaryotic self-splicing intron and an associated protein, it is a vastly more complex and dynamic ribonucleoprotein (RNP) whose function requires at least eight ATPases and multiple RNA rearrangements. These features afford stepwise opportunities for multiple inspections of the intron substrate, coupled with spliceosome disassembly for substrates that fail inspection. Early work using splicing-defective pre-mRNAs or small nuclear (sn)RNAs in Saccharomyces cerevisiae demonstrated that such checks could occur in catalytically active spliceosomes. We review recent results on pre-mRNA splicing in various systems, including humans, suggesting that earlier steps in spliceosome assembly are also subject to such quality control. The inspection-rejection framework helps explain the dynamic nature of the spliceosome.
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Affiliation(s)
- Irene Beusch
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA.
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Osterhoudt K, Bagno O, Katzman S, Zahler AM. Spliceosomal helicases DDX41/SACY-1 and PRP22/MOG-5 both contribute to proofreading against proximal 3' splice site usage. RNA (NEW YORK, N.Y.) 2024; 30:404-417. [PMID: 38282418 PMCID: PMC10946429 DOI: 10.1261/rna.079888.123] [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: 11/07/2023] [Accepted: 01/12/2024] [Indexed: 01/30/2024]
Abstract
RNA helicases drive necessary rearrangements and ensure fidelity during the pre-mRNA splicing cycle. DEAD-box helicase DDX41 has been linked to human disease and has recently been shown to interact with DEAH-box helicase PRP22 in the spliceosomal C* complex, yet its function in splicing remains unknown. Depletion of DDX41 homolog SACY-1 from somatic cells has been previously shown to lead to changes in alternative 3' splice site (3'ss) usage. Here, we show by transcriptomic analysis of published and novel data sets that SACY-1 perturbation causes a previously unreported pattern in alternative 3' splicing in introns with pairs of 3' splice sites ≤18 nt away from each other. We find that both SACY-1 depletion and the allele sacy-1(G533R) lead to a striking unidirectional increase in the usage of the proximal (upstream) 3'ss. We previously discovered a similar alternative splicing pattern between germline tissue and somatic tissue, in which there is a unidirectional increase in proximal 3'ss usage in the germline for ∼200 events; many of the somatic SACY-1 alternative 3' splicing events overlap with these developmentally regulated events. We generated targeted mutant alleles of the Caenorhabditis elegans homolog of PRP22, mog-5, in the region of MOG-5 that is predicted to interact with SACY-1 based on the human C* structure. These viable alleles, and a mimic of the myelodysplastic syndrome-associated allele DDX41(R525H), all promote the usage of proximal alternative adjacent 3' splice sites. We show that PRP22/MOG-5 and DDX41/SACY-1 have overlapping roles in proofreading the 3'ss.
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Affiliation(s)
- Kenneth Osterhoudt
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Orazio Bagno
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
| | - Sol Katzman
- UCSC Genomics Institute, University of California, Santa Cruz, Santa Cruz, California 95064, USA
| | - Alan M Zahler
- Department of Molecular Cell and Developmental Biology, Center for Molecular Biology of RNA, University of California, Santa Cruz, California 95064, USA
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Ali A, Khatoon A, Shao C, Murtaza B, Tanveer Q, Su Z. Therapeutic potential of natural antisense transcripts and various mechanisms involved for clinical applications and disease prevention. RNA Biol 2024; 21:1-18. [PMID: 38090817 PMCID: PMC10761088 DOI: 10.1080/15476286.2023.2293335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 12/18/2023] Open
Abstract
Antisense transcription, a prevalent occurrence in mammalian genomes, gives rise to natural antisense transcripts (NATs) as RNA molecules. These NATs serve as agents of diverse transcriptional and post-transcriptional regulatory mechanisms, playing crucial roles in various biological processes vital for cell function and immune response. However, when their normal functions are disrupted, they can contribute to human diseases. This comprehensive review aims to establish the molecular foundation linking NATs to the development of disorders like cancer, neurodegenerative conditions, and cardiovascular ailments. Additionally, we evaluate the potential of oligonucleotide-based therapies targeting NATs, presenting both their advantages and limitations, while also highlighting the latest advancements in this promising realm of clinical investigation.Abbreviations: NATs- Natural antisense transcripts, PRC1- Polycomb Repressive Complex 1, PRC2- Polycomb Repressive Complex 2, ADARs- Adenosine deaminases acting on RNA, BDNF-AS- Brain-derived neurotrophic factor antisense transcript, ASOs- Antisense oligonucleotides, SINEUPs- Inverted SINEB2 sequence-mediated upregulating molecules, PTBP1- Polypyrimidine tract binding protein-1, HNRNPK- heterogeneous nuclear ribonucleoprotein K, MAPT-AS1- microtubule-associated protein tau antisense 1, KCNQ1OT- (KCNQ1 opposite strand/antisense transcript 1, ERK- extracellular signal-regulated kinase 1, USP14- ubiquitin-specific protease 14, EGF- Epidermal growth factor, LSD1- Lysine Specific Demethylase 1, ANRIL- Antisense Noncoding RNA in the INK4 Locus, BWS- Beckwith-Wiedemann syndrome, VEGFA- Vascular Endothelial Growth component A.
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Affiliation(s)
- Ashiq Ali
- Department of Histology and Embryology, Shantou University Medical College, Shantou, China
| | - Aisha Khatoon
- Department of Pathology, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Chenran Shao
- Department of Histology and Embryology, Shantou University Medical College, Shantou, China
| | - Bilal Murtaza
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Qaisar Tanveer
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh, UK
| | - Zhongjing Su
- Department of Histology and Embryology, Shantou University Medical College, Shantou, China
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Cartwright-Acar CH, Osterhoudt K, Suzuki JMNGL, Gomez D, Katzman S, Zahler AM. A forward genetic screen in C. elegans identifies conserved residues of spliceosomal proteins PRP8 and SNRNP200/BRR2 with a role in maintaining 5' splice site identity. Nucleic Acids Res 2022; 50:11834-11857. [PMID: 36321655 PMCID: PMC9723624 DOI: 10.1093/nar/gkac991] [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: 11/24/2021] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022] Open
Abstract
The spliceosome undergoes extensive rearrangements as it assembles onto precursor messenger RNAs. In the earliest assembly step, U1snRNA identifies the 5' splice site. However, U1snRNA leaves the spliceosome relatively early in assembly, and 5' splice site identity is subsequently maintained through interactions with U6snRNA, protein factor PRP8, and other components during the rearrangements that build the catalytic site. Using a forward genetic screen in Caenorhabditis elegans, we have identified suppressors of a locomotion defect caused by a 5'ss mutation. Here we report three new suppressor alleles from this screen, two in PRP8 and one in SNRNP200/BRR2. mRNASeq studies of these suppressor strains indicate that they also affect specific native alternative 5'ss, especially for suppressor PRP8 D1549N. A strong suppressor at the unstructured N-terminus of SNRNP200, N18K, indicates a novel role for this region. By examining distinct changes in the splicing of native genes, examining double mutants between suppressors, comparing these new suppressors to previously identified splicing suppressors from yeast, and mapping conserved suppressor residues onto cryoEM structural models of assembling human spliceosomes, we conclude that there are multiple interactions at multiple stages in spliceosome assembly responsible for maintaining the initial 5'ss identified by U1snRNA for entry into the catalytic core.
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Affiliation(s)
- Catiana H Cartwright-Acar
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Kenneth Osterhoudt
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Jessie M N G L Suzuki
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Destiny R Gomez
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Sol Katzman
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA 95060, USA
| | - Alan M Zahler
- Department of MCD Biology and The Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, CA 95060, USA
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Kim JH, Modena MS, Sehgal E, Courney A, Neudorf C, Arribere J. SMG-6 mRNA cleavage stalls ribosomes near premature stop codons in vivo. Nucleic Acids Res 2022; 50:8852-8866. [PMID: 35950494 PMCID: PMC9410879 DOI: 10.1093/nar/gkac681] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/29/2022] [Accepted: 07/26/2022] [Indexed: 12/24/2022] Open
Abstract
Nonsense-mediated mRNA decay (NMD) protects cells from the toxic and potentially dominant effects of truncated proteins. Targeting of mRNAs with early stop codons is mediated by the ribosome and spatiotemporally aligned with translation termination. Previously we identified a novel NMD intermediate: ribosomes stalled on cleaved stop codons, raising the possibility that NMD begins even prior to ribosome removal from the stop codon. Here we show that this intermediate is the result of mRNA cleavage by the endonuclease SMG-6. Our work supports a model in which ribosomes stall secondary to SMG-6 mRNA cleavage in Caenorhabditis elegans and humans, i.e. that the novel NMD intermediate occurs after a prior ribosome elicits NMD. Our genetic analysis of C. elegans' SMG-6 supports a central role for SMG-6 in metazoan NMD, and provides a context for evaluating its function in other metazoans.
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Affiliation(s)
- John H Kim
- Department of MCD Biology, UC Santa Cruz, California, USA
| | | | - Enisha Sehgal
- Department of MCD Biology, UC Santa Cruz, California, USA
| | - Annie Courney
- Department of MCD Biology, UC Santa Cruz, California, USA
| | - Celine W Neudorf
- Department of Biomolecular Engineering, UC Santa Cruz, California, USA
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