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Abstract
Recognition of the intron branch site (BS) by the U2 small nuclear ribonucleoprotein (snRNP) is a critical event during spliceosome assembly. In mammals, BS sequences are poorly conserved, and unambiguous intron recognition cannot be achieved solely through a base-pairing mechanism. We isolated human 17S U2 snRNP and reconstituted in vitro its adenosine 5´-triphosphate (ATP)–dependent remodeling and binding to the pre–messenger RNA substrate. We determined a series of high-resolution (2.0 to 2.2 angstrom) structures providing snapshots of the BS selection process. The substrate-bound U2 snRNP shows that SF3B6 stabilizes the BS:U2 snRNA duplex, which could aid binding of introns with poor sequence complementarity. ATP-dependent remodeling uncoupled from substrate binding captures U2 snRNA in a conformation that competes with BS recognition, providing a selection mechanism based on branch helix stability.
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Affiliation(s)
- Jonas Tholen
- European Molecular Biology Laboratory; 71 Avenue des Martyrs, 38042 Grenoble, France
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences
| | - Michal Razew
- European Molecular Biology Laboratory; 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Felix Weis
- European Molecular Biology Laboratory, Structural and Computational Biology Unit; Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Wojciech P. Galej
- European Molecular Biology Laboratory; 71 Avenue des Martyrs, 38042 Grenoble, France
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52
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Abstract
In Eukarya, immature mRNA transcripts (pre-mRNA) often contain coding sequences, or exons, interleaved by non-coding sequences, or introns. Introns are removed upon splicing, and further regulation of the retained exons leads to alternatively spliced mRNA. The splicing reaction requires the stepwise assembly of the spliceosome, a macromolecular machine composed of small nuclear ribonucleoproteins (snRNPs). This review focuses on the early stage of spliceosome assembly, when U1 snRNP defines each intron 5’-splice site (5ʹss) in the pre-mRNA. We first introduce the splicing reaction and the impact of alternative splicing on gene expression regulation. Thereafter, we extensively discuss splicing descriptors that influence the 5ʹss selection by U1 snRNP, such as sequence determinants, and interactions mediated by U1-specific proteins or U1 small nuclear RNA (U1 snRNA). We also include examples of diseases that affect the 5ʹss selection by U1 snRNP, and discuss recent therapeutic advances that manipulate U1 snRNP 5ʹss selectivity with antisense oligonucleotides and small-molecule splicing switches.
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Affiliation(s)
- Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Cameron D Mackereth
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux, Bordeaux Cedex, France
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53
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Bergfort A, Hilal T, Kuropka B, Ilik İA, Weber G, Aktaş T, Freund C, Wahl MC. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2938-2958. [PMID: 35188580 PMCID: PMC8934646 DOI: 10.1093/nar/gkac087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
Biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and their recycling after splicing require numerous assembly/recycling factors whose modes of action are often poorly understood. The intrinsically disordered TSSC4 protein has been identified as a nuclear-localized U5 snRNP and U4/U6-U5 tri-snRNP assembly/recycling factor, but how TSSC4’s intrinsic disorder supports TSSC4 functions remains unknown. Using diverse interaction assays and cryogenic electron microscopy-based structural analysis, we show that TSSC4 employs four conserved, non-contiguous regions to bind the PRPF8 Jab1/MPN domain and the SNRNP200 helicase at functionally important sites. It thereby inhibits SNRNP200 helicase activity, spatially aligns the proteins, coordinates formation of a U5 sub-module and transiently blocks premature interaction of SNRNP200 with at least three other spliceosomal factors. Guided by the structure, we designed a TSSC4 variant that lacks stable binding to the PRPF8 Jab1/MPN domain or SNRNP200 in vitro. Comparative immunoprecipitation/mass spectrometry from HEK293 nuclear extract revealed distinct interaction profiles of wild type TSSC4 and the variant deficient in PRPF8/SNRNP200 binding with snRNP proteins, other spliceosomal proteins as well as snRNP assembly/recycling factors and chaperones. Our findings elucidate molecular strategies employed by an intrinsically disordered protein to promote snRNP assembly, and suggest multiple TSSC4-dependent stages during snRNP assembly/recycling.
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Affiliation(s)
- Alexandra Bergfort
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
| | - Tarek Hilal
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustr. 6, D-14195 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy, Fabeckstr. 36a, 14195 Berlin, Germany
| | - Benno Kuropka
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Thielallee 63, D-14195, Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Core Facility BioSupraMol, Thielallee 63, D-14195, Berlin, Germany
| | - İbrahim Avşar Ilik
- Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany
| | - Gert Weber
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Str. 15, D-12489 Berlin, Germany
| | - Tuğçe Aktaş
- Max Planck Institute for Molecular Genetics, Ihnestr. 63, D-14195 Berlin, Germany
| | - Christian Freund
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Protein Biochemistry, Thielallee 63, D-14195, Berlin, Germany
| | - Markus C Wahl
- To whom correspondence should be addressed. Tel: +49 30 838 53456; Fax: +49 30 8384 53456;
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54
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Laine P, Rowell WJ, Paulin L, Kujawa S, Raterman D, Mayhew G, Wendt J, Burgess DL, Partonen T, Paunio T, Auvinen P, Ekholm JM. Alu element in the RNA binding motif protein, X-linked 2 (RBMX2) gene found to be linked to bipolar disorder. PLoS One 2021; 16:e0261170. [PMID: 34914762 PMCID: PMC8675739 DOI: 10.1371/journal.pone.0261170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Objective We have used long-read single molecule, real-time (SMRT) sequencing to fully characterize a ~12Mb genomic region on chromosome Xq24-q27, significantly linked to bipolar disorder (BD) in an extended family from a genetic sub-isolate. This family segregates BD in at least four generations with 24 affected individuals. Methods We selected 16 family members for targeted sequencing. The selected individuals either carried the disease haplotype, were non-carriers of the disease haplotype, or served as married-in controls. We designed hybrid capture probes enriching for 5-9Kb fragments spanning the entire 12Mb region that were then sequenced to screen for candidate structural variants (SVs) that could explain the increased risk for BD in this extended family. Results Altogether, 201 variants were detected in the critically linked region. Although most of these represented common variants, three variants emerged that showed near-perfect segregation among all BD type I affected individuals. Two of the SVs were identified in or near genes belonging to the RNA Binding Motif Protein, X-Linked (RBMX) gene family—a 330bp Alu (subfamily AluYa5) deletion in intron 3 of the RBMX2 gene and an intergenic 27bp tandem repeat deletion between the RBMX and G protein-coupled receptor 101 (GPR101) genes. The third SV was a 50bp tandem repeat insertion in intron 1 of the Coagulation Factor IX (F9) gene. Conclusions Among the three genetically linked SVs, additional evidence supported the Alu element deletion in RBMX2 as the leading candidate for contributing directly to the disease development of BD type I in this extended family.
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Affiliation(s)
- Pia Laine
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Lars Paulin
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Steve Kujawa
- Pacific Biosciences, Menlo Park, CA, United States of America
| | - Denise Raterman
- Roche Sequencing Solutions, Madison, WI, United States of America
| | - George Mayhew
- Roche Sequencing Solutions, Madison, WI, United States of America
| | - Jennifer Wendt
- Roche Sequencing Solutions, Madison, WI, United States of America
| | | | - Timo Partonen
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Tiina Paunio
- Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
- Department of Psychiatry, University of Helsinki, Helsinki, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Jenny M. Ekholm
- Pacific Biosciences, Menlo Park, CA, United States of America
- * E-mail:
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55
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Srivastava A, Ambrósio DL, Tasak M, Gosavi U, Günzl A. A distinct complex of PRP19-related and trypanosomatid-specific proteins is required for pre-mRNA splicing in trypanosomes. Nucleic Acids Res 2021; 49:12929-12942. [PMID: 34850936 PMCID: PMC8682746 DOI: 10.1093/nar/gkab1152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/30/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
The pre-mRNA splicing factor PRP19 is recruited into the spliceosome after forming the PRP19/CDC5L complex in humans and the Nineteen complex in yeast. Additionally, ‘PRP19-related’ proteins enter the spliceosome individually or in pre-assemblies that differ in these systems. The protistan family Trypanosomatidae, which harbors parasites such as Trypanosoma brucei, diverged early during evolution from opisthokonts. While introns are rare in these organisms, spliced leader trans splicing is an obligatory step in mRNA maturation. So far, ∼70 proteins have been identified as homologs of human and yeast splicing factors. Moreover, few proteins of unknown function have recurrently co-purified with splicing proteins. Here we silenced the gene of one of these proteins, termed PRC5, and found it to be essential for cell viability and pre-mRNA splicing. Purification of PRC5 combined with sucrose gradient sedimentation revealed a complex of PRC5 with a second trypanosomatid-specific protein, PRC3, and PRP19-related proteins SYF1, SYF3 and ISY1, which we named PRP19-related complex (PRC). Importantly, PRC and the previously described PRP19 complex are distinct from each other because PRC, unlike PRP19, co-precipitates U4 snRNA, which indicates that PRC enters the spliceosome prior to PRP19 and uncovers a unique pre-organization of these proteins in trypanosomes.
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Affiliation(s)
- Ankita Srivastava
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Daniela L Ambrósio
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030-6403, USA.,Departamento de Ciências da Biointeração, Universidade Federal da Bahia, Canela, Salvador, 40231-300, Brazil
| | - Monika Tasak
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Ujwala Gosavi
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
| | - Arthur Günzl
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, 400 Farmington Avenue, Farmington, CT 06030-6403, USA
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56
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Li J, Cai Z, Vaites LP, Shen N, Mitchell DC, Huttlin EL, Paulo JA, Harry BL, Gygi SP. Proteome-wide mapping of short-lived proteins in human cells. Mol Cell 2021; 81:4722-4735.e5. [PMID: 34626566 DOI: 10.1016/j.molcel.2021.09.015] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/11/2021] [Accepted: 09/13/2021] [Indexed: 12/13/2022]
Abstract
Rapid protein degradation enables cells to quickly modulate protein abundance. Dysregulation of short-lived proteins plays essential roles in disease pathogenesis. A focused map of short-lived proteins remains understudied. Cycloheximide, a translational inhibitor, is widely used in targeted studies to measure degradation kinetics for short-lived proteins. Here, we combined cycloheximide chase assays with advanced quantitative proteomics to map short-lived proteins under translational inhibition in four human cell lines. Among 11,747 quantified proteins, we identified 1,017 short-lived proteins (half-lives ≤ 8 h). These short-lived proteins are less abundant, evolutionarily younger, and less thermally stable than other proteins. We quantified 103 proteins with different stabilities among cell lines. We showed that U2OS and HCT116 cells express truncated forms of ATRX and GMDS, respectively, which have lower stability than their full-length counterparts. This study provides a large-scale resource of human short-lived proteins under translational arrest, leading to untapped avenues of protein regulation for therapeutic interventions.
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Affiliation(s)
- Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Zhenying Cai
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | | | - Ning Shen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Dylan C Mitchell
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Brian L Harry
- Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Pathology, University of Colorado, Anschutz Medical Campus, Aurora, CO 80045, USA.
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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57
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Morgan M, Kumar L, Li Y, Baptissart M. Post-transcriptional regulation in spermatogenesis: all RNA pathways lead to healthy sperm. Cell Mol Life Sci 2021; 78:8049-8071. [PMID: 34748024 DOI: 10.1007/s00018-021-04012-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 10/11/2021] [Accepted: 10/25/2021] [Indexed: 01/22/2023]
Abstract
Multiple RNA pathways are required to produce functional sperm. Here, we review RNA post-transcriptional regulation during spermatogenesis with particular emphasis on the role of 3' end modifications. From early studies in the 1970s, it became clear that spermiogenesis transcripts could be stored for days only to be translated at advanced stages of spermatid differentiation. The transition between the translationally repressed and active states was observed to correlate with the shortening of the transcripts' poly(A) tail, establishing a link between RNA 3' end metabolism and male germ cell differentiation. Since then, numerous RNA metabolic pathways have been implicated not only in the progression through spermatogenesis, but also in the maintenance of genomic integrity. Recent studies have characterized the elusive 3' biogenesis of Piwi-interacting RNAs (piRNAs), identified a critical role for messenger RNA (mRNA) 3' uridylation in meiotic progression, established the mechanisms that destabilize transcripts with long 3' untranslated regions (3'UTRs) in post-mitotic cells, and defined the physiological relevance of RNA exonucleases and deadenylases in male germ cells. In this review, we discuss RNA processing in the male germline in the light of the most recent findings. A brief recollection of different RNA-processing events will aid future studies exploring post-transcriptional regulation in spermatogenesis.
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Affiliation(s)
- Marcos Morgan
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA.
| | - Lokesh Kumar
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Yin Li
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
| | - Marine Baptissart
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Durham, NC, 27709, USA
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58
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Bertrand RE, Wang J, Li Y, Cheng X, Wang K, Stoilov P, Chen R. Cwc27, associated with retinal degeneration, functions as a splicing factor in vivo. Hum Mol Genet 2021; 31:1278-1292. [PMID: 34726245 PMCID: PMC9029344 DOI: 10.1093/hmg/ddab319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/14/2022] Open
Abstract
Previous in vitro studies indicate that CWC27 functions as a splicing factor in the Bact spliceosome complex, interacting with CWC22 to form a landing platform for eIF4A3, a core component of the exon junction complex. However, the function of CWC27 as a splicing factor has not been validated in any in vivo systems. CWC27 variants have been shown to cause autosomal recessive retinal degeneration, in both syndromic and non-syndromic forms. The Cwc27K338fs/K338fs mouse model was shown to have significant retinal dysfunction and degeneration by 6 months of age. In this report, we have taken advantage of the Cwc27K338fs/K338fs mouse model to show that Cwc27 is involved in splicing in vivo in the context of the retina. Bulk RNA and single cell RNA-sequencing of the mouse retina showed that there were gene expression and splicing pattern changes, including alternative splice site usage and intron retention. Positive staining for CHOP suggests that ER stress may be activated in response to the splicing pattern changes and is a likely contributor to the disease mechanism. Our results provide the first evidence that CWC27 functions as a splicing factor in an in vivo context. The splicing defects and gene expression changes observed in the Cwc27K338fs/K338fs mouse retina provide insight to the potential disease mechanisms, paving the way for targeted therapeutic development.
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Affiliation(s)
- Renae Elaine Bertrand
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Xuesen Cheng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Peter Stoilov
- Department of Biochemistry, West Virginia University, Morgantown, WV 26506 USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
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59
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Zhang B, Ding Z, Li L, Xie LK, Fan YJ, Xu YZ. Two oppositely-charged sf3b1 mutations cause defective development, impaired immune response, and aberrant selection of intronic branch sites in Drosophila. PLoS Genet 2021; 17:e1009861. [PMID: 34723968 PMCID: PMC8559932 DOI: 10.1371/journal.pgen.1009861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/06/2021] [Indexed: 11/18/2022] Open
Abstract
SF3B1 mutations occur in many cancers, and the highly conserved His662 residue is one of the hotspot mutation sites. To address effects on splicing and development, we constructed strains carrying point mutations at the corresponding residue His698 in Drosophila using the CRISPR-Cas9 technique. Two mutations, H698D and H698R, were selected due to their frequent presence in patients and notable opposite charges. Both the sf3b1-H698D and–H698R mutant flies exhibit developmental defects, including less egg-laying, decreased hatching rates, delayed morphogenesis and shorter lifespans. Interestingly, the H698D mutant has decreased resistance to fungal infection, while the H698R mutant shows impaired climbing ability. Consistent with these phenotypes, further analysis of RNA-seq data finds altered expression of immune response genes and changed alternative splicing of muscle and neural-related genes in the two mutants, respectively. Expression of Mef2-RB, an isoform of Mef2 gene that was downregulated due to splicing changes caused by H698R, partly rescues the climbing defects of the sf3b1-H698R mutant. Lariat sequencing reveals that the two sf3b1-H698 mutations cause aberrant selection of multiple intronic branch sites, with the H698R mutant using far upstream branch sites in the changed alternative splicing events. This study provides in vivo evidence from Drosophila that elucidates how these SF3B1 hotspot mutations alter splicing and their consequences in development and in the immune system. In the past decade, one of the important findings in the RNA splicing field has been that somatic SF3B1 mutations widely occur in many cancers. Including R625, H662, K666, K700 and E902, there are five hotspot mutation sites in the highly conserved HEAT repeats of SF3B1. Several kinds of H662 mutations have been found widely in MDS, AML, CLL and breast cancers; however, it remains unclear how these H662 mutations alter splicing and whether they have in vivo effects on development. To address these questions, in this manuscript, we first summarized the H662 mutations in human diseases and constructed two corresponding Drosophila mutant strains, sf3b1-H698D and -H698R using CRISPR-Cas9. Analyses of these two fly strains find that the two oppositely charged Sf3b1-H698 mutants are defective in development. In addition, one mutant has decreased climbing ability, whereas the other mutant has impaired immune response. Further RNA-seq allows us to find responsible genes in each mutant strain, and lariat sequencing reveals that both mutations cause aberrant selection of the intronic branch sites. Our findings provide the first in vivo evidence that Sf3b1 mutations result in defective development, and also reveal a molecular mechanism of these hotspot histidine mutations that enhance the use of cryptic branch sites to alter splicing. Importantly, we demonstrate that the H698R mutant prefers to use far upstream branch sites.
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Affiliation(s)
- Bei Zhang
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Zhan Ding
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Liang Li
- University of Chinese Academy of Sciences, Beijing, China
- Key Laboratory of Insect Developmental and Evolutionary Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences; Shanghai, China
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Ling-Kun Xie
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Yu-Jie Fan
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
| | - Yong-Zhen Xu
- RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Science, Wuhan University, Hubei, China
- * E-mail:
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60
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Spinello A, Borišek J, Malcovati L, Magistrato A. Investigating the Molecular Mechanism of H3B-8800: A Splicing Modulator Inducing Preferential Lethality in Spliceosome-Mutant Cancers. Int J Mol Sci 2021; 22:ijms222011222. [PMID: 34681880 PMCID: PMC8540225 DOI: 10.3390/ijms222011222] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022] Open
Abstract
The SF3B1 protein, part of the SF3b complex, recognizes the intron branch point sequence of precursor messenger RNA (pre-mRNA), thus contributing to splicing fidelity. SF3B1 is frequently mutated in cancer and is the target of distinct families of splicing modulators (SMs). Among these, H3B-8800 is of particular interest, as it induces preferential lethality in cancer cells bearing the frequent and highly pathogenic K700E SF3B1 mutation. Despite the potential of H3B-8800 to treat myeloid leukemia and other cancer types hallmarked by SF3B1 mutations, the molecular mechanism underlying its preferential lethality towards spliceosome-mutant cancer cells remains elusive. Here, microsecond-long all-atom simulations addressed the binding/dissociation mechanism of H3B-8800 to wild type and K700E SF3B1-containing SF3b (K700ESB3b) complexes at the atomic level, unlocking that the K700E mutation little affects the thermodynamics and kinetic traits of H3B-8800 binding. This supports the hypothesis that the selectivity of H3B-8800 towards mutant cancer cells is unrelated to its preferential targeting of K700ESB3b. Nevertheless, this set of simulations discloses that the K700E mutation and H3B-8800 binding affect the overall SF3b internal motion, which in turn may influence the way SF3b interacts with other spliceosome components. Finally, we unveil the existence of a putative druggable SF3b pocket in the vicinity of K700E that could be harnessed in future rational drug-discovery efforts to specifically target mutant SF3b.
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Affiliation(s)
- Angelo Spinello
- National Research Council of Italy, Institute of Materials Foundry (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy;
| | - Jure Borišek
- National Institute of Chemistry, Theory Department, Hajdrihova 19, 1000 Ljubljana, Slovenia;
| | - Luca Malcovati
- Department of Hematology, IRCCS S. Matteo Hospital Foundation, 27100 Pavia, Italy;
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Alessandra Magistrato
- National Research Council of Italy, Institute of Materials Foundry (CNR-IOM) c/o SISSA, Via Bonomea 265, 34136 Trieste, Italy;
- Correspondence:
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61
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Urabe VK, Stevers M, Ghosh AK, Jurica MS. U2 snRNA structure is influenced by SF3A and SF3B proteins but not by SF3B inhibitors. PLoS One 2021; 16:e0258551. [PMID: 34648557 PMCID: PMC8516221 DOI: 10.1371/journal.pone.0258551] [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: 07/14/2021] [Accepted: 09/29/2021] [Indexed: 11/19/2022] Open
Abstract
U2 snRNP is an essential component of the spliceosome. It is responsible for branch point recognition in the spliceosome A-complex via base-pairing of U2 snRNA with an intron to form the branch helix. Small molecule inhibitors target the SF3B component of the U2 snRNP and interfere with A-complex formation during spliceosome assembly. We previously found that the first SF3B inhibited-complex is less stable than A-complex and hypothesized that SF3B inhibitors interfere with U2 snRNA secondary structure changes required to form the branch helix. Using RNA chemical modifiers, we probed U2 snRNA structure in A-complex and SF3B inhibited splicing complexes. The reactivity pattern for U2 snRNA in the SF3B inhibited-complex is indistinguishable from that of A-complex, suggesting that they have the same secondary structure conformation, including the branch helix. This observation suggests SF3B inhibited-complex instability does not stem from an alternate RNA conformation and instead points to the inhibitors interfering with protein component interactions that normally stabilize U2 snRNP’s association with an intron. In addition, we probed U2 snRNA in the free U2 snRNP in the presence of SF3B inhibitor and again saw no differences. However, increased protection of nucleotides upstream of Stem I in the absence of SF3A and SF3B proteins suggests a change of secondary structure at the very 5′ end of U2 snRNA. Chemical probing of synthetic U2 snRNA in the absence of proteins results in similar protections and predicts a previously uncharacterized extension of Stem I. Because this stem must be disrupted for SF3A and SF3B proteins to stably join the snRNP, the structure has the potential to influence snRNP assembly and recycling after spliceosome disassembly.
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Affiliation(s)
- Veronica K. Urabe
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
| | - Meredith Stevers
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
| | - Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, United States of America
| | - Melissa S. Jurica
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, California, United States of America
- Center for Molecular Biology of RNA, University of California, Santa Cruz, California, United States of America
- * E-mail:
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62
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Riolo G, Cantara S, Ricci C. What's Wrong in a Jump? Prediction and Validation of Splice Site Variants. Methods Protoc 2021; 4:62. [PMID: 34564308 PMCID: PMC8482176 DOI: 10.3390/mps4030062] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 08/27/2021] [Accepted: 09/03/2021] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) is a crucial process to enhance gene expression driving organism development. Interestingly, more than 95% of human genes undergo AS, producing multiple protein isoforms from the same transcript. Any alteration (e.g., nucleotide substitutions, insertions, and deletions) involving consensus splicing regulatory sequences in a specific gene may result in the production of aberrant and not properly working proteins. In this review, we introduce the key steps of splicing mechanism and describe all different types of genomic variants affecting this process (splicing variants in acceptor/donor sites or branch point or polypyrimidine tract, exonic, and deep intronic changes). Then, we provide an updated approach to improve splice variants detection. First, we review the main computational tools, including the recent Machine Learning-based algorithms, for the prediction of splice site variants, in order to characterize how a genomic variant interferes with splicing process. Next, we report the experimental methods to validate the predictive analyses are defined, distinguishing between methods testing RNA (transcriptomics analysis) or proteins (proteomics experiments). For both prediction and validation steps, benefits and weaknesses of each tool/procedure are accurately reported, as well as suggestions on which approaches are more suitable in diagnostic rather than in clinical research.
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Affiliation(s)
| | | | - Claudia Ricci
- Department of Medical, Surgical and Neurological Sciences, University of Siena, 53100 Siena, Italy; (G.R.); (S.C.)
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63
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Ammous Z, Rawlins LE, Jones H, Leslie JS, Wenger O, Scott E, Deline J, Herr T, Evans R, Scheid A, Kennedy J, Chioza BA, Ames RM, Cross HE, Puffenberger EG, Harries L, Baple EL, Crosby AH. A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder. PLoS Genet 2021; 17:e1009803. [PMID: 34570759 PMCID: PMC8496849 DOI: 10.1371/journal.pgen.1009803] [Citation(s) in RCA: 6] [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: 06/14/2021] [Revised: 10/07/2021] [Accepted: 09/02/2021] [Indexed: 12/13/2022] Open
Abstract
SNIP1 (Smad nuclear interacting protein 1) is a widely expressed transcriptional suppressor of the TGF-β signal-transduction pathway which plays a key role in human spliceosome function. Here, we describe extensive genetic studies and clinical findings of a complex inherited neurodevelopmental disorder in 35 individuals associated with a SNIP1 NM_024700.4:c.1097A>G, p.(Glu366Gly) variant, present at high frequency in the Amish community. The cardinal clinical features of the condition include hypotonia, global developmental delay, intellectual disability, seizures, and a characteristic craniofacial appearance. Our gene transcript studies in affected individuals define altered gene expression profiles of a number of molecules with well-defined neurodevelopmental and neuropathological roles, potentially explaining clinical outcomes. Together these data confirm this SNIP1 gene variant as a cause of an autosomal recessive complex neurodevelopmental disorder and provide important insight into the molecular roles of SNIP1, which likely explain the cardinal clinical outcomes in affected individuals, defining potential therapeutic avenues for future research.
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Affiliation(s)
- Zineb Ammous
- The Community Health Clinic, Topeka, Indiana, United States of America
| | - Lettie E. Rawlins
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Hannah Jones
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Joseph S. Leslie
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Olivia Wenger
- New Leaf Center, Clinic for Special Children, Mount Eaton, Ohio, United States of America
| | - Ethan Scott
- New Leaf Center, Clinic for Special Children, Mount Eaton, Ohio, United States of America
| | - Jim Deline
- Center for Special Children, La Farge Medical Center, La Farge, Wisconsin, United States of America
| | - Tom Herr
- Center for Special Children, La Farge Medical Center, La Farge, Wisconsin, United States of America
| | - Rebecca Evans
- The Community Health Clinic, Topeka, Indiana, United States of America
| | - Angela Scheid
- The Community Health Clinic, Topeka, Indiana, United States of America
| | - Joanna Kennedy
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Barry A. Chioza
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Ryan M. Ames
- Biosciences, Geoffrey Pope Building, University of Exeter, Exeter, United Kingdom
| | - Harold E. Cross
- Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
| | | | - Lorna Harries
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
| | - Emma L. Baple
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
- Peninsula Clinical Genetics Service, Royal Devon & Exeter Hospital (Heavitree), Exeter, United Kingdom
| | - Andrew H. Crosby
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Royal Devon & Exeter NHS Foundation Trust, Exeter, United Kingdom
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64
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Therapeutic approaches targeting splicing factor mutations in myelodysplastic syndromes and acute myeloid leukemia. Curr Opin Hematol 2021; 28:73-79. [PMID: 33492002 DOI: 10.1097/moh.0000000000000632] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE OF REVIEW Mutations in components of the spliceosome are the most common acquired lesions in myelodysplastic syndromes (MDS) and are frequently identified in other myeloid malignancies with a high rate of progression to acute myeloid leukemia (AML) including chronic myelomonocytic leukemia and primary myelofibrosis. The only curative option for these disorders remains allogeneic stem-cell transplantation, which is associated with high morbidity and mortality in these patients. The purpose of this review is to highlight the recent therapeutic developments and strategies being pursued for clinical benefit in splicing factor mutant myeloid malignancies. RECENT FINDINGS Cells harboring splicing factor mutations have increased aberrant splicing leading to R-loop formation and cell cycle stalling that create dependencies on Checkpoint kinase 1 (CHK1) activation and canonical splicing maintained by protein arginine methyltransferase activity. Both targeting of the spliceosome and targeting of the downstream consequences of splicing factor mutation expression show promise as selective strategies for the treatment of splicing factor-mutant myeloid malignancies. SUMMARY An improved understanding of the therapeutic vulnerabilities in splicing factor-mutant MDS and AML has led to the development of clinical trials of small molecule inhibitors that target the spliceosome, ataxia telangectasia and Rad3 related (ATR)-CHK1 pathway, and methylation of splicing components.
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65
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Zhang Z, Rigo N, Dybkov O, Fourmann JB, Will CL, Kumar V, Urlaub H, Stark H, Lührmann R. Structural insights into how Prp5 proofreads the pre-mRNA branch site. Nature 2021; 596:296-300. [PMID: 34349264 PMCID: PMC8357632 DOI: 10.1038/s41586-021-03789-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
During the splicing of introns from precursor messenger RNAs (pre-mRNAs), the U2 small nuclear ribonucleoprotein (snRNP) must undergo stable integration into the spliceosomal A complex-a poorly understood, multistep process that is facilitated by the DEAD-box helicase Prp5 (refs. 1-4). During this process, the U2 small nuclear RNA (snRNA) forms an RNA duplex with the pre-mRNA branch site (the U2-BS helix), which is proofread by Prp5 at this stage through an unclear mechanism5. Here, by deleting the branch-site adenosine (BS-A) or mutating the branch-site sequence of an actin pre-mRNA, we stall the assembly of spliceosomes in extracts from the yeast Saccharomyces cerevisiae directly before the A complex is formed. We then determine the three-dimensional structure of this newly identified assembly intermediate by cryo-electron microscopy. Our structure indicates that the U2-BS helix has formed in this pre-A complex, but is not yet clamped by the HEAT domain of the Hsh155 protein (Hsh155HEAT), which exhibits an open conformation. The structure further reveals a large-scale remodelling/repositioning of the U1 and U2 snRNPs during the formation of the A complex that is required to allow subsequent binding of the U4/U6.U5 tri-snRNP, but that this repositioning is blocked in the pre-A complex by the presence of Prp5. Our data suggest that binding of Hsh155HEAT to the bulged BS-A of the U2-BS helix triggers closure of Hsh155HEAT, which in turn destabilizes Prp5 binding. Thus, Prp5 proofreads the branch site indirectly, hindering spliceosome assembly if branch-site mutations prevent the remodelling of Hsh155HEAT. Our data provide structural insights into how a spliceosomal helicase enhances the fidelity of pre-mRNA splicing.
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Affiliation(s)
- Zhenwei Zhang
- Department of Structural Dynamics, MPI for Biophysical Chemistry, Göttingen, Germany
| | - Norbert Rigo
- Cellular Biochemistry, MPI for Biophysical Chemistry, Göttingen, Germany
| | - Olexandr Dybkov
- Cellular Biochemistry, MPI for Biophysical Chemistry, Göttingen, Germany
| | | | - Cindy L Will
- Cellular Biochemistry, MPI for Biophysical Chemistry, Göttingen, Germany
| | - Vinay Kumar
- Cellular Biochemistry, MPI for Biophysical Chemistry, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Göttingen, Germany
- Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Holger Stark
- Department of Structural Dynamics, MPI for Biophysical Chemistry, Göttingen, Germany.
| | - Reinhard Lührmann
- Cellular Biochemistry, MPI for Biophysical Chemistry, Göttingen, Germany.
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66
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Zerkalenkova E, Lebedeva S, Borkovskaia A, Soldatkina O, Plekhanova O, Tsaur G, Maschan M, Maschan A, Novichkova G, Olshanskaya Y. BTK, NUTM2A, and PRPF19 Are Novel KMT2A Partner Genes in Childhood Acute Leukemia. Biomedicines 2021; 9:biomedicines9080924. [PMID: 34440129 PMCID: PMC8391293 DOI: 10.3390/biomedicines9080924] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 01/29/2023] Open
Abstract
Chromosomal rearrangements of the human KMT2A/MLL gene are associated with acute leukemias, especially in infants. KMT2A is rearranged with a big variety of partner genes and in multiple breakpoint locations. Detection of all types of KMT2A rearrangements is an essential part of acute leukemia initial diagnostics and follow-up, as it has a strong impact on the patients’ outcome. Due to their high heterogeneity, KMT2A rearrangements are most effectively uncovered by next-generation sequencing (NGS), which, however, requires a thorough prescreening by cytogenetics. Here, we aimed to characterize uncommon KMT2A rearrangements in childhood acute leukemia by conventional karyotyping, FISH, and targeted NGS on both DNA and RNA level with subsequent validation. As a result of this comprehensive approach, three novel KMT2A rearrangements were discovered: ins(X;11)(q26;q13q25)/KMT2A-BTK, t(10;11)(q22;q23.3)/KMT2A-NUTM2A, and inv(11)(q12.2q23.3)/KMT2A-PRPF19. These novel KMT2A-chimeric genes expand our knowledge of the mechanisms of KMT2A-associated leukemogenesis and allow tracing the dynamics of minimal residual disease in the given patients.
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Affiliation(s)
- Elena Zerkalenkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
- Correspondence:
| | - Svetlana Lebedeva
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Aleksandra Borkovskaia
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Olga Soldatkina
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Olga Plekhanova
- Regional Children Hospital 1, Pediatric Oncology and Hematology Center, Research Institute of Medical Cell Technologies, Ural Federal University Named after the First President of Russia BN Yeltsin, 620149 Ekaterinburg, Russia; (O.P.); (G.T.)
| | - Grigory Tsaur
- Regional Children Hospital 1, Pediatric Oncology and Hematology Center, Research Institute of Medical Cell Technologies, Ural Federal University Named after the First President of Russia BN Yeltsin, 620149 Ekaterinburg, Russia; (O.P.); (G.T.)
| | - Michael Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Aleksey Maschan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Galina Novichkova
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
| | - Yulia Olshanskaya
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, 117997 Moscow, Russia; (S.L.); (A.B.); (O.S.); (M.M.); (A.M.); (G.N.); (Y.O.)
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67
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Alternative splicing of mRNA in colorectal cancer: new strategies for tumor diagnosis and treatment. Cell Death Dis 2021; 12:752. [PMID: 34330892 PMCID: PMC8324868 DOI: 10.1038/s41419-021-04031-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
Alternative splicing (AS) is an important event that contributes to posttranscriptional gene regulation. This process leads to several mature transcript variants with diverse physiological functions. Indeed, disruption of various aspects of this multistep process, such as cis- or trans- factor alteration, promotes the progression of colorectal cancer. Therefore, targeting some specific processes of AS may be an effective therapeutic strategy for treating cancer. Here, we provide an overview of the AS events related to colorectal cancer based on research done in the past 5 years. We focus on the mechanisms and functions of variant products of AS that are relevant to malignant hallmarks, with an emphasis on variants with clinical significance. In addition, novel strategies for exploiting the therapeutic value of AS events are discussed.
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68
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Cretu C, Gee P, Liu X, Agrawal A, Nguyen TV, Ghosh AK, Cook A, Jurica M, Larsen NA, Pena V. Structural basis of intron selection by U2 snRNP in the presence of covalent inhibitors. Nat Commun 2021; 12:4491. [PMID: 34301950 PMCID: PMC8302644 DOI: 10.1038/s41467-021-24741-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/01/2021] [Indexed: 12/27/2022] Open
Abstract
Intron selection during the formation of prespliceosomes is a critical event in pre-mRNA splicing. Chemical modulation of intron selection has emerged as a route for cancer therapy. Splicing modulators alter the splicing patterns in cells by binding to the U2 snRNP (small nuclear ribonucleoprotein)—a complex chaperoning the selection of branch and 3′ splice sites. Here we report crystal structures of the SF3B module of the U2 snRNP in complex with spliceostatin and sudemycin FR901464 analogs, and the cryo-electron microscopy structure of a cross-exon prespliceosome-like complex arrested with spliceostatin A. The structures reveal how modulators inactivate the branch site in a sequence-dependent manner and stall an E-to-A prespliceosome intermediate by covalent coupling to a nucleophilic zinc finger belonging to the SF3B subunit PHF5A. These findings support a mechanism of intron recognition by the U2 snRNP as a toehold-mediated strand invasion and advance an unanticipated drug targeting concept. Chemical modulation of intron selection has emerged as a route for cancer therapy. Here, structures of the U2 snRNP’s SF3B module and of prespliceosome- both in complexes with splicing modulators- provide insight into the mechanisms of intron recognition and branch site inactivation.
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Affiliation(s)
- Constantin Cretu
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK.,Cluster of Excellence Multiscale Bioimaging (MBExC), Universitätsmedizin Göttingen, Göttingen, Germany
| | | | - Xiang Liu
- H3 Biomedicine, Inc, Cambridge, MA, USA
| | | | | | - Arun K Ghosh
- Departments of Chemistry and Medicinal Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Melissa Jurica
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | | | - Vladimir Pena
- Research Group Mechanisms and Regulation of Splicing, The Institute of Cancer Research, London, UK.
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69
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Artemyeva-Isman OV, Porter ACG. U5 snRNA Interactions With Exons Ensure Splicing Precision. Front Genet 2021; 12:676971. [PMID: 34276781 PMCID: PMC8283771 DOI: 10.3389/fgene.2021.676971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 05/12/2021] [Indexed: 11/13/2022] Open
Abstract
Imperfect conservation of human pre-mRNA splice sites is necessary to produce alternative isoforms. This flexibility is combined with the precision of the message reading frame. Apart from intron-termini GU_AG and the branchpoint A, the most conserved are the exon-end guanine and +5G of the intron start. Association between these guanines cannot be explained solely by base-pairing with U1 snRNA in the early spliceosome complex. U6 succeeds U1 and pairs +5G in the pre-catalytic spliceosome, while U5 binds the exon end. Current U5 snRNA reconstructions by CryoEM cannot explain the conservation of the exon-end G. Conversely, human mutation analyses show that guanines of both exon termini can suppress splicing mutations. Our U5 hypothesis explains the mechanism of splicing precision and the role of these conserved guanines in the pre-catalytic spliceosome. We propose: (1) optimal binding register for human exons and U5-the exon junction positioned at U5Loop1 C39|C38; (2) common mechanism for base-pairing of human U5 snRNA with diverse exons and bacterial Ll.LtrB intron with new loci in retrotransposition-guided by base pair geometry; and (3) U5 plays a significant role in specific exon recognition in the pre-catalytic spliceosome. Statistical analyses showed increased U5 Watson-Crick pairs with the 5'exon in the absence of +5G at the intron start. In 5'exon positions -3 and -5, this effect is specific to U5 snRNA rather than U1 snRNA of the early spliceosome. Increased U5 Watson-Crick pairs with 3'exon position +1 coincide with substitutions of the conserved -3C at the intron 3'end. Based on mutation and X-ray evidence, we propose that -3C pairs with U2 G31 juxtaposing the branchpoint and the 3'intron end. The intron-termini pair, formed in the pre-catalytic spliceosome to be ready for transition after branching, and the early involvement of the 3'intron end ensure that the 3'exon contacts U5 in the pre-catalytic complex. We suggest that splicing precision is safeguarded cooperatively by U5, U6, and U2 snRNAs that stabilize the pre-catalytic complex by Watson-Crick base pairing. In addition, our new U5 model explains the splicing effect of exon-start +1G mutations: U5 Watson-Crick pairs with exon +2C/+3G strongly promote exon inclusion. We discuss potential applications for snRNA therapeutics and gene repair by reverse splicing.
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Affiliation(s)
- Olga V Artemyeva-Isman
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Andrew C G Porter
- Gene Targeting Group, Centre for Haematology, Department of Immunology and Inflammation, Faculty of Medicine, Imperial College London, London, United Kingdom
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70
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Cheruiyot A, Li S, Nonavinkere Srivatsan S, Ahmed T, Chen Y, Lemacon DS, Li Y, Yang Z, Wadugu BA, Warner WA, Pruett-Miller SM, Obeng EA, Link DC, He D, Xiao F, Wang X, Bailis JM, Walter MJ, You Z. Nonsense-Mediated RNA Decay Is a Unique Vulnerability of Cancer Cells Harboring SF3B1 or U2AF1 Mutations. Cancer Res 2021; 81:4499-4513. [PMID: 34215620 DOI: 10.1158/0008-5472.can-20-4016] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 05/26/2021] [Accepted: 06/30/2021] [Indexed: 11/16/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is recognized as an RNA surveillance pathway that targets aberrant mRNAs with premature translation termination codons (PTC) for degradation, however, its molecular mechanisms and roles in health and disease remain incompletely understood. In this study, we developed a novel reporter system to accurately measure NMD activity in individual cells. A genome-wide CRISPR-Cas9 knockout screen using this reporter system identified novel NMD-promoting factors, including multiple components of the SF3B complex and other U2 spliceosome factors. Interestingly, cells with mutations in the spliceosome genes SF3B1 and U2AF1, which are commonly found in myelodysplastic syndrome (MDS) and cancers, have overall attenuated NMD activity. Compared with wild-type (WT) cells, SF3B1- and U2AF1-mutant cells were more sensitive to NMD inhibition, a phenotype that is accompanied by elevated DNA replication obstruction, DNA damage, and chromosomal instability. Remarkably, the sensitivity of spliceosome mutant cells to NMD inhibition was rescued by overexpression of RNase H1, which removes R-loops in the genome. Together, these findings shed new light on the functional interplay between NMD and RNA splicing and suggest a novel synthetic lethal strategy for the treatment of MDS and cancers with spliceosome mutations. SIGNIFICANCE: This study has developed a novel NMD reporter system and identified a potential therapeutic approach of targeting the NMD pathway to treat cancer with spliceosome gene mutations.
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Affiliation(s)
- Abigael Cheruiyot
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Shan Li
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Sridhar Nonavinkere Srivatsan
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Tanzir Ahmed
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Yuhao Chen
- Department of Radiation Oncology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Delphine S Lemacon
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Ying Li
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Clinical Biobank, The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Zheng Yang
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.,Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Brian A Wadugu
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Wayne A Warner
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Esther A Obeng
- Molecular Oncology Division, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Daniel C Link
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Dalin He
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an Jiaotong University, Xi'an, China
| | - Fei Xiao
- Clinical Biobank, The Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xiaowei Wang
- Department of Radiation Oncology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | | | - Matthew J Walter
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Washington University School in St. Louis, St. Louis, Missouri
| | - Zhongsheng You
- Department of Cell Biology and Physiology, School of Medicine, Washington University in St. Louis, St. Louis, Missouri.
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Mikolaskova B, Jurcik M, Cipakova I, Selicky T, Jurcik J, Polakova SB, Stupenova E, Dudas A, Sivakova B, Bellova J, Barath P, Aronica L, Gregan J, Cipak L. Identification of Nrl1 Domains Responsible for Interactions with RNA-Processing Factors and Regulation of Nrl1 Function by Phosphorylation. Int J Mol Sci 2021; 22:7011. [PMID: 34209806 PMCID: PMC8268110 DOI: 10.3390/ijms22137011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/15/2021] [Accepted: 06/27/2021] [Indexed: 12/26/2022] Open
Abstract
Pre-mRNA splicing is a key process in the regulation of gene expression. In the fission yeast Schizosaccharomyces pombe, Nrl1 regulates splicing and expression of several genes and non-coding RNAs, and also suppresses the accumulation of R-loops. Here, we report analysis of interactions between Nrl1 and selected RNA-processing proteins and regulation of Nrl1 function by phosphorylation. Bacterial two-hybrid system (BACTH) assays revealed that the N-terminal region of Nrl1 is important for the interaction with ATP-dependent RNA helicase Mtl1 while the C-terminal region of Nrl1 is important for interactions with spliceosome components Ctr1, Ntr2, and Syf3. Consistent with this result, tandem affinity purification showed that Mtl1, but not Ctr1, Ntr2, or Syf3, co-purifies with the N-terminal region of Nrl1. Interestingly, mass-spectrometry analysis revealed that in addition to previously identified phosphorylation sites, Nrl1 is also phosphorylated on serines 86 and 112, and that Nrl1-TAP co-purifies with Cka1, the catalytic subunit of casein kinase 2. In vitro assay showed that Cka1 can phosphorylate bacterially expressed Nrl1 fragments. An analysis of non-phosphorylatable nrl1 mutants revealed defects in gene expression and splicing consistent with the notion that phosphorylation is an important regulator of Nrl1 function. Taken together, our results provide insights into two mechanisms that are involved in the regulation of the spliceosome-associated factor Nrl1, namely domain-specific interactions between Nrl1 and RNA-processing proteins and post-translational modification of Nrl1 by phosphorylation.
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Affiliation(s)
- Barbora Mikolaskova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Matus Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Ingrid Cipakova
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Tomas Selicky
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Jan Jurcik
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
| | - Silvia Bagelova Polakova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia; (S.B.P.); (E.S.)
| | - Erika Stupenova
- Institute of Animal Biochemistry and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05 Bratislava, Slovakia; (S.B.P.); (E.S.)
| | - Andrej Dudas
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Ilkovicova 6, 842 15 Bratislava, Slovakia;
| | - Barbara Sivakova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia; (B.S.); (J.B.); (P.B.)
| | - Jana Bellova
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia; (B.S.); (J.B.); (P.B.)
| | - Peter Barath
- Institute of Chemistry, Slovak Academy of Sciences, Dubravska Cesta 9, 845 38 Bratislava, Slovakia; (B.S.); (J.B.); (P.B.)
- Medirex Group Academy, n.o., Jana Bottu 2, 917 01 Trnava, Slovakia
| | - Lucia Aronica
- Stanford Prevention Research Center, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Juraj Gregan
- Advanced Microscopy Facility, VBCF, Vienna Biocenter (VBC), 1030 Vienna, Austria;
| | - Lubos Cipak
- Cancer Research Institute, Biomedical Research Center, Slovak Academy of Sciences, Dubravska Cesta 9, 845 05 Bratislava, Slovakia; (B.M.); (M.J.); (I.C.); (T.S.); (J.J.)
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72
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Yazhini A, Sandhya S, Srinivasan N. Rewards of divergence in sequences, 3-D structures and dynamics of yeast and human spliceosome SF3b complexes. Curr Res Struct Biol 2021; 3:133-145. [PMID: 35028595 PMCID: PMC8714771 DOI: 10.1016/j.crstbi.2021.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 05/21/2021] [Accepted: 05/26/2021] [Indexed: 12/21/2022] Open
Abstract
The evolution of homologous and functionally equivalent multiprotein assemblies is intriguing considering sequence divergence of constituent proteins. Here, we studied the implications of protein sequence divergence on the structure, dynamics and function of homologous yeast and human SF3b spliceosomal subcomplexes. Human and yeast SF3b comprise of 7 and 6 proteins respectively, with all yeast proteins homologous to their human counterparts at moderate sequence identity. SF3b6, an additional component in the human SF3b, interacts with the N-terminal extension of SF3b1 while the yeast homologue Hsh155 lacks the equivalent region. Through detailed homology studies, we show that SF3b6 is absent not only in yeast but in multiple lineages of eukaryotes implying that it is critical in specific organisms. We probed for the potential role of SF3b6 in the spliceosome assembled form through structural and flexibility analyses. By analysing normal modes derived from anisotropic network models of SF3b1, we demonstrate that when SF3b1 is bound to SF3b6, similarities in the magnitude of residue motions (0.86) and inter-residue correlated motions (0.94) with Hsh155 are significantly higher than when SF3b1 is considered in isolation (0.21 and 0.89 respectively). We observed that SF3b6 promotes functionally relevant 'open-to-close' transition in SF3b1 by enhancing concerted residue motions. Such motions are found to occur in the Hsh155 without SF3b6. The presence of SF3b6 influences motions of 16 residues that interact with U2 snRNA/branchpoint duplex and supports the participation of its interface residues in long-range communication in the SF3b1. These results advocate that SF3b6 potentially acts as an allosteric regulator of SF3b1 for BPS selection and might play a role in alternative splicing. Furthermore, we observe variability in the relative orientation of SF3b4 and in the local structure of three β-propeller domains of SF3b3 with reference to their yeast counterparts. Such differences influence the inter-protein interactions of SF3b between these two organisms. Together, our findings highlight features of SF3b evolution and suggests that the human SF3b may have evolved sophisticated mechanisms to fine tune its molecular function.
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Key Words
- Allostery
- BPS, branch-point sequence
- Bact, activated B spliceosome assembly
- Cryo-EM structure
- Cryo-EM, cryo-electron microscopy
- DOPE, discrete optimized protein energy
- NMA, normal mode analysis
- PDB, protein data bank
- Protein dynamics
- RMSD, root mean square deviation
- RRM, RNA recognition motif
- SF3b complex
- SF3b1
- SF3b1SF3b6−bound, SF3b1 bound to SF3b6
- SF3b1iso, SF3b1 in isolation
- SIP, square inner product
- Spliceosome
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Affiliation(s)
- Arangasamy Yazhini
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
| | - Sankaran Sandhya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka, 560012, India
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73
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Martelly W, Fellows B, Kang P, Vashisht A, Wohlschlegel JA, Sharma S. Synergistic roles for human U1 snRNA stem-loops in pre-mRNA splicing. RNA Biol 2021; 18:2576-2593. [PMID: 34105434 DOI: 10.1080/15476286.2021.1932360] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
During spliceosome assembly, interactions that bring the 5' and 3' ends of an intron in proximity are critical for the production of mature mRNA. Here, we report synergistic roles for the stem-loops 3 (SL3) and 4 (SL4) of the human U1 small nuclear RNA (snRNA) in maintaining the optimal U1 snRNP function, and formation of cross-intron contact with the U2 snRNP. We find that SL3 and SL4 bind distinct spliceosomal proteins and combining a U1 snRNA activity assay with siRNA-mediated knockdown, we demonstrate that SL3 and SL4 act through the RNA helicase UAP56 and the U2 protein SF3A1, respectively. In vitro analysis using UV crosslinking and splicing assays indicated that SL3 likely promotes the SL4-SF3A1 interaction leading to enhancement of A complex formation and pre-mRNA splicing. Overall, these results highlight the vital role of the distinct contacts of SL3 and SL4 in bridging the pre-mRNA bound U1 and U2 snRNPs during the early steps of human spliceosome assembly.
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Affiliation(s)
- William Martelly
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Bernice Fellows
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Paul Kang
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health-Phoenix, University of Arizona, Phoenix, AZ, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - James A Wohlschlegel
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shalini Sharma
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, USA
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74
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A single m 6A modification in U6 snRNA diversifies exon sequence at the 5' splice site. Nat Commun 2021; 12:3244. [PMID: 34050143 PMCID: PMC8163875 DOI: 10.1038/s41467-021-23457-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/29/2021] [Indexed: 11/09/2022] Open
Abstract
N6-methyladenosine (m6A) is a modification that plays pivotal roles in RNA metabolism and function, although its functions in spliceosomal U6 snRNA remain unknown. To elucidate its role, we conduct a large-scale transcriptome analysis of a Schizosaccharomyces pombe strain lacking this modification and found a global change of pre-mRNA splicing. The most significantly impacted introns are enriched for adenosine at the fourth position pairing the m6A in U6 snRNA, and exon sequences weakly recognized by U5 snRNA. This suggests cooperative recognition of 5' splice site by U6 and U5 snRNPs, and also a role of m6A facilitating efficient recognition of the splice sites weakly interacting with U5 snRNA, indicating that U6 snRNA m6A relaxes the 5' exon constraint and allows protein sequence diversity along with explosively increasing number of introns over the course of eukaryotic evolution.
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75
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Lester E, Ooi FK, Bakkar N, Ayers J, Woerman AL, Wheeler J, Bowser R, Carlson GA, Prusiner SB, Parker R. Tau aggregates are RNA-protein assemblies that mislocalize multiple nuclear speckle components. Neuron 2021; 109:1675-1691.e9. [PMID: 33848474 PMCID: PMC8141031 DOI: 10.1016/j.neuron.2021.03.026] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 02/05/2021] [Accepted: 03/18/2021] [Indexed: 12/13/2022]
Abstract
Tau aggregates contribute to neurodegenerative diseases, including frontotemporal dementia and Alzheimer's disease (AD). Although RNA promotes tau aggregation in vitro, whether tau aggregates in cells contain RNA is unknown. We demonstrate, in cell culture and mouse brains, that cytosolic and nuclear tau aggregates contain RNA with enrichment for small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). Nuclear tau aggregates colocalize with and alter the composition, dynamics, and organization of nuclear speckles, membraneless organelles involved in pre-mRNA splicing. Moreover, several nuclear speckle components, including SRRM2, mislocalize to cytosolic tau aggregates in cells, mouse brains, and brains of individuals with AD, frontotemporal dementia (FTD), and corticobasal degeneration (CBD). Consistent with these alterations, we observe that the presence of tau aggregates is sufficient to alter pre-mRNA splicing. This work identifies tau alteration of nuclear speckles as a feature of tau aggregation that may contribute to the pathology of tau aggregates.
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Affiliation(s)
- Evan Lester
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Felicia K Ooi
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Nadine Bakkar
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - Jacob Ayers
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Amanda L Woerman
- Department of Biology and Institute for Applied Life Sciences, University of Massachusetts Amherst, Amherst, MA, USA
| | - Joshua Wheeler
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA; Department of Pathology, Stanford University, Stanford, CA, USA
| | - Robert Bowser
- Department of Neurobiology, Barrow Neurological Institute, Phoenix, AZ, USA
| | - George A Carlson
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Stanley B Prusiner
- Institute for Neurodegenerative Diseases, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Roy Parker
- Department of Biochemistry, University of Colorado, Boulder, CO, USA; Howard Hughes Medical Institute, University of Colorado, Boulder, CO, USA.
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76
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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77
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Bedi K, Magnuson BR, Narayanan I, Paulsen M, Wilson TE, Ljungman M. Co-transcriptional splicing efficiencies differ within genes and between cell types. RNA (NEW YORK, N.Y.) 2021; 27:rna.078662.120. [PMID: 33975916 PMCID: PMC8208053 DOI: 10.1261/rna.078662.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/05/2021] [Indexed: 06/01/2023]
Abstract
Pre-mRNA splicing is carried out by the spliceosome and involves splice site recognition, removal of introns, and ligation of exons. Components of the spliceosome have been shown to interact with the elongating RNA polymerase II (RNAPII) which is thought to allow splicing to occur concurrently with transcription. However, little is known about the regulation and efficiency of co-transcriptional splicing in human cells. In this study, we used Bru-seq and BruChase-seq to determine the co-transcriptional splicing efficiencies of 17,000 introns expressed across 6 human cell lines. We found that less than half of all introns across these 6 cell lines were co-transcriptionally spliced. Splicing efficiencies for individual introns showed variations across cell lines, suggesting that splicing may be regulated in a cell-type specific manner. Moreover, the splicing efficiency of introns varied within genes. The efficiency of co-transcriptional splicing did not correlate with gene length, intron position, splice site strengths, or the intron/neighboring exons GC content. However, we identified binding signals from multiple RNA binding proteins (RBPs) that correlated with splicing efficiency, including core spliceosomal machinery components-such as SF3B4, U2AF1 and U2AF2 showing higher binding signals in poorly spliced introns. In addition, multiple RBPs, such as BUD13, PUM1 and SND1, showed preferential binding in exons that flank introns with high splicing efficiencies. The nascent RNA splicing patterns presented here across multiple cell types add to our understanding of the complexity in RNA splicing, wherein RNA-binding proteins may play important roles in determining splicing outcomes in a cell type- and intron-specific manner.
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78
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Morais P, Adachi H, Yu YT. Spliceosomal snRNA Epitranscriptomics. Front Genet 2021; 12:652129. [PMID: 33737950 PMCID: PMC7960923 DOI: 10.3389/fgene.2021.652129] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
Small nuclear RNAs (snRNAs) are critical components of the spliceosome that catalyze the splicing of pre-mRNA. snRNAs are each complexed with many proteins to form RNA-protein complexes, termed as small nuclear ribonucleoproteins (snRNPs), in the cell nucleus. snRNPs participate in pre-mRNA splicing by recognizing the critical sequence elements present in the introns, thereby forming active spliceosomes. The recognition is achieved primarily by base-pairing interactions (or nucleotide-nucleotide contact) between snRNAs and pre-mRNA. Notably, snRNAs are extensively modified with different RNA modifications, which confer unique properties to the RNAs. Here, we review the current knowledge of the mechanisms and functions of snRNA modifications and their biological relevance in the splicing process.
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Affiliation(s)
| | - Hironori Adachi
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, United States
| | - Yi-Tao Yu
- Department of Biochemistry and Biophysics, Center for RNA Biology, University of Rochester Medical Center, Rochester, NY, United States
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79
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Aki SS, Yura K, Aoyama T, Tsuge T. SAP130 and CSN1 interact and regulate male gametogenesis in Arabidopsis thaliana. JOURNAL OF PLANT RESEARCH 2021; 134:279-289. [PMID: 33555481 DOI: 10.1007/s10265-021-01260-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
COP9 signalosome (CSN) is a nuclear complex composed of eight distinct subunits that governs vast developmental processes in Arabidopsis thaliana (L.) Heynh. The null alleles of csn mutants display pleiotropic phenotypes that result in seedling lethality. To date, several partially complemented transgenic plants, expressing the particular CSN subunit in its corresponding null mutant allele, were utilized to bypass seedling lethality and investigate CSN regulation at later stages of development. One such transgenic plant corresponding to CSN1 subunit, fus6/CSN1-3-4, accumulates wild-type level of CSN1 and displays normal plant architecture at vegetative stage. Here we show through histological analyses that fus6/CSN1-3-4 plants display impairment of pollen development at the bicellular stage. This defect is identical to that observed in RNAi plants of SAP130, encoding a subunit of the multiprotein splicing factor SF3b. We further dissected the previously reported interaction between CSN1 and SAP130, to reveal that approximately 100 amino-acid residues located at the N-terminal end of CSN1 (CSN1NN) were essential for this interaction. In silico structure modeling demonstrated that CSN1NN could swing out towards SAP130 to dock onto its Helical Insertion protruding from the structure. These results support our model that CSN1 embeds itself within CSN protein complex through its C-terminal half and reaches out to targets through its N-terminal portion of the protein. Taken together, this is the first report to document the identical loss-of-function phenotypes of CSN1 and SAP130 during male gametogenesis. Thus, we propose that SAP130 and CSN1 coordinately regulate development of male reproductive organs.
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Affiliation(s)
- Shiori S Aki
- Molecular Biology Laboratory, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192, Japan
| | - Kei Yura
- School of Advanced Science and Engineering, Waseda University, 513 Tsurumaki, Waseda, Shinjuku, Tokyo, 162-0041, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
- Center for Interdisciplinary AI and Data Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo, Tokyo, 112-8610, Japan
| | - Takashi Aoyama
- Molecular Biology Laboratory, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Tomohiko Tsuge
- Molecular Biology Laboratory, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan.
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80
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De Bortoli F, Espinosa S, Zhao R. DEAH-Box RNA Helicases in Pre-mRNA Splicing. Trends Biochem Sci 2021; 46:225-238. [PMID: 33272784 PMCID: PMC8112905 DOI: 10.1016/j.tibs.2020.10.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 10/04/2020] [Accepted: 10/26/2020] [Indexed: 11/25/2022]
Abstract
In eukaryotic cells, pre-mRNA splicing is catalyzed by the spliceosome, a highly dynamic molecular machinery that undergoes dramatic conformational and compositional rearrangements throughout the splicing cycle. These crucial rearrangements are largely driven by eight DExD/H-box RNA helicases. Interestingly, the four helicases participating in the late stages of splicing are all DEAH-box helicases that share structural similarities. This review aims to provide an overview of the structure and function of these DEAH-box helicases, including new information provided by recent cryo-electron microscopy structures of the spliceosomal complexes.
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Affiliation(s)
- Francesca De Bortoli
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Sara Espinosa
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Rui Zhao
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
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81
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Etibor TA, Yamauchi Y, Amorim MJ. Liquid Biomolecular Condensates and Viral Lifecycles: Review and Perspectives. Viruses 2021; 13:366. [PMID: 33669141 PMCID: PMC7996568 DOI: 10.3390/v13030366] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/16/2021] [Accepted: 02/20/2021] [Indexed: 02/06/2023] Open
Abstract
Viruses are highly dependent on the host they infect. Their dependence triggers processes of virus-host co-adaptation, enabling viruses to explore host resources whilst escaping immunity. Scientists have tackled viral-host interplay at differing levels of complexity-in individual hosts, organs, tissues and cells-and seminal studies advanced our understanding about viral lifecycles, intra- or inter-species transmission, and means to control infections. Recently, it emerged as important to address the physical properties of the materials in biological systems; membrane-bound organelles are only one of many ways to separate molecules from the cellular milieu. By achieving a type of compartmentalization lacking membranes known as biomolecular condensates, biological systems developed alternative mechanisms of controlling reactions. The identification that many biological condensates display liquid properties led to the proposal that liquid-liquid phase separation (LLPS) drives their formation. The concept of LLPS is a paradigm shift in cellular structure and organization. There is an unprecedented momentum to revisit long-standing questions in virology and to explore novel antiviral strategies. In the first part of this review, we focus on the state-of-the-art about biomolecular condensates. In the second part, we capture what is known about RNA virus-phase biology and discuss future perspectives of this emerging field in virology.
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Affiliation(s)
- Temitope Akhigbe Etibor
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, University of Bristol, Bristol BS8 1TL, UK;
| | - Maria João Amorim
- Cell Biology of Viral Infection Lab, Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal;
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82
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Goenka A, Tiek D, Song X, Huang T, Hu B, Cheng SY. The Many Facets of Therapy Resistance and Tumor Recurrence in Glioblastoma. Cells 2021; 10:cells10030484. [PMID: 33668200 PMCID: PMC7995978 DOI: 10.3390/cells10030484] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/19/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is the most lethal type of primary brain cancer. Standard care using chemo- and radio-therapy modestly increases the overall survival of patients; however, recurrence is inevitable, due to treatment resistance and lack of response to targeted therapies. GBM therapy resistance has been attributed to several extrinsic and intrinsic factors which affect the dynamics of tumor evolution and physiology thus creating clinical challenges. Tumor-intrinsic factors such as tumor heterogeneity, hypermutation, altered metabolomics and oncologically activated alternative splicing pathways change the tumor landscape to facilitate therapy failure and tumor progression. Moreover, tumor-extrinsic factors such as hypoxia and an immune-suppressive tumor microenvironment (TME) are the chief causes of immunotherapy failure in GBM. Amid the success of immunotherapy in other cancers, GBM has occurred as a model of resistance, thus focusing current efforts on not only alleviating the immunotolerance but also evading the escape mechanisms of tumor cells to therapy, caused by inter- and intra-tumoral heterogeneity. Here we review the various mechanisms of therapy resistance in GBM, caused by the continuously evolving tumor dynamics as well as the complex TME, which cumulatively contribute to GBM malignancy and therapy failure; in an attempt to understand and identify effective therapies for recurrent GBM.
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Affiliation(s)
| | | | | | | | | | - Shi-Yuan Cheng
- Correspondence: ; Tel.: +1-312-503-3043; Fax: +1-312-503-5603
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83
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Donsbach P, Klostermeier D. Regulation of RNA helicase activity: principles and examples. Biol Chem 2021; 402:529-559. [PMID: 33583161 DOI: 10.1515/hsz-2020-0362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/29/2021] [Indexed: 12/16/2022]
Abstract
RNA helicases are a ubiquitous class of enzymes involved in virtually all processes of RNA metabolism, from transcription, mRNA splicing and export, mRNA translation and RNA transport to RNA degradation. Although ATP-dependent unwinding of RNA duplexes is their hallmark reaction, not all helicases catalyze unwinding in vitro, and some in vivo functions do not depend on duplex unwinding. RNA helicases are divided into different families that share a common helicase core with a set of helicase signature motives. The core provides the active site for ATP hydrolysis, a binding site for non-sequence-specific interaction with RNA, and in many cases a basal unwinding activity. Its activity is often regulated by flanking domains, by interaction partners, or by self-association. In this review, we summarize the regulatory mechanisms that modulate the activities of the helicase core. Case studies on selected helicases with functions in translation, splicing, and RNA sensing illustrate the various modes and layers of regulation in time and space that harness the helicase core for a wide spectrum of cellular tasks.
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Affiliation(s)
- Pascal Donsbach
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Münster, Corrensstrasse 30, D-48149Münster, Germany
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84
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Wood KA, Eadsforth MA, Newman WG, O'Keefe RT. The Role of the U5 snRNP in Genetic Disorders and Cancer. Front Genet 2021; 12:636620. [PMID: 33584830 PMCID: PMC7876476 DOI: 10.3389/fgene.2021.636620] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Pre-mRNA splicing is performed by the spliceosome, a dynamic macromolecular complex consisting of five small uridine-rich ribonucleoprotein complexes (the U1, U2, U4, U5, and U6 snRNPs) and numerous auxiliary splicing factors. A plethora of human disorders are caused by genetic variants affecting the function and/or expression of splicing factors, including the core snRNP proteins. Variants in the genes encoding proteins of the U5 snRNP cause two distinct and tissue-specific human disease phenotypes – variants in PRPF6, PRPF8, and SNRP200 are associated with retinitis pigmentosa (RP), while variants in EFTUD2 and TXNL4A cause the craniofacial disorders mandibulofacial dysostosis Guion-Almeida type (MFDGA) and Burn-McKeown syndrome (BMKS), respectively. Furthermore, recurrent somatic mutations or changes in the expression levels of a number of U5 snRNP proteins (PRPF6, PRPF8, EFTUD2, DDX23, and SNRNP40) have been associated with human cancers. How and why variants in ubiquitously expressed spliceosome proteins required for pre-mRNA splicing in all human cells result in tissue-restricted disease phenotypes is not clear. Additionally, why variants in different, yet interacting, proteins making up the same core spliceosome snRNP result in completely distinct disease outcomes – RP, craniofacial defects or cancer – is unclear. In this review, we define the roles of different U5 snRNP proteins in RP, craniofacial disorders and cancer, including how disease-associated genetic variants affect pre-mRNA splicing and the proposed disease mechanisms. We then propose potential hypotheses for how U5 snRNP variants cause tissue specificity resulting in the restricted and distinct human disorders.
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Affiliation(s)
- Katherine A Wood
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Megan A Eadsforth
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - William G Newman
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom.,Manchester Centre for Genomic Medicine, Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
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85
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Bai R, Wan R, Wang L, Xu K, Zhang Q, Lei J, Shi Y. Structure of the activated human minor spliceosome. Science 2021; 371:science.abg0879. [PMID: 33509932 DOI: 10.1126/science.abg0879] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/18/2021] [Indexed: 12/31/2022]
Abstract
The minor spliceosome mediates splicing of the rare but essential U12-type precursor messenger RNA. Here, we report the atomic features of the activated human minor spliceosome determined by cryo-electron microscopy at 2.9-angstrom resolution. The 5' splice site and branch point sequence of the U12-type intron are recognized by the U6atac and U12 small nuclear RNAs (snRNAs), respectively. Five newly identified proteins stabilize the conformation of the catalytic center: The zinc finger protein SCNM1 functionally mimics the SF3a complex of the major spliceosome, the RBM48-ARMC7 complex binds the γ-monomethyl phosphate cap at the 5' end of U6atac snRNA, the U-box protein PPIL2 coordinates loop I of U5 snRNA and stabilizes U5 small nuclear ribonucleoprotein (snRNP), and CRIPT stabilizes U12 snRNP. Our study provides a framework for the mechanistic understanding of the function of the human minor spliceosome.
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Affiliation(s)
- Rui Bai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Ruixue Wan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Lin Wang
- Beijing Advanced Innovation Center for Structural Biology and Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kui Xu
- Beijing Advanced Innovation Center for Structural Biology and Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Zhang
- Beijing Advanced Innovation Center for Structural Biology and Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology and Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Xihu District, Hangzhou 310024, Zhejiang Province, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Beijing Advanced Innovation Center for Structural Biology and Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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86
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Larsen NA. The SF3b Complex is an Integral Component of the Spliceosome and Targeted by Natural Product-Based Inhibitors. Subcell Biochem 2021; 96:409-432. [PMID: 33252738 DOI: 10.1007/978-3-030-58971-4_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
In this chapter, the essential role of the SF3b multi-protein complex will be discussed in the context of the overall spliceosome. SF3b is critical during spliceosome assembly for recognition of the branch point (BP) adenosine and, by de facto, selection of the 3' splice site. This complex is highly dynamic, undergoing significant conformational changes upon loading of the branch duplex RNA and in its relative positioning during spliceosomal remodeling from the A, pre-B, B, Bact and B* complexes. Ultimately, during the spliceosome activation phase, SF3b must be displaced to unmask the branch point adenosine for the first splicing reaction to occur. In certain cancers, such as the hematological malignancies CML, CLL and MDS, the SF3b subunit SF3B1 is frequently mutated. Recent studies suggest these mutations lead to inappropriate branch point selection and mis-splicing events that appear to be drivers of disease. Finally, the SF3b complex is the target for at least three different classes of natural product-based inhibitors. These inhibitors bind in the BP adenosine-binding pocket and demonstrate a pre-mRNA competitive mechanism of action resulting in either intron retention or exon skipping. These compounds are extremely useful as chemical probes to isolate and characterize early stages of spliceosome assembly. They are also being explored preclinically and clinically as possible agents for hematological cancers.
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87
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Elcheva IA, Spiegelman VS. The Role of cis- and trans-Acting RNA Regulatory Elements in Leukemia. Cancers (Basel) 2020; 12:E3854. [PMID: 33419342 PMCID: PMC7766907 DOI: 10.3390/cancers12123854] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 02/06/2023] Open
Abstract
RNA molecules are a source of phenotypic diversity and an operating system that connects multiple genetic and metabolic processes in the cell. A dysregulated RNA network is a common feature of cancer. Aberrant expression of long non-coding RNA (lncRNA), micro RNA (miRNA), and circular RNA (circRNA) in tumors compared to their normal counterparts, as well as the recurrent mutations in functional regulatory cis-acting RNA motifs have emerged as biomarkers of disease development and progression, opening avenues for the design of novel therapeutic approaches. This review looks at the progress, challenges and future prospects of targeting cis-acting and trans-acting RNA elements for leukemia diagnosis and treatment.
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Affiliation(s)
- Irina A. Elcheva
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
| | - Vladimir S. Spiegelman
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, P.O. Box 850, MC H085, 500 University Drive, Hershey, PA 17033-0850, USA
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88
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Bai R, Wan R, Yan C, Jia Q, Lei J, Shi Y. Mechanism of spliceosome remodeling by the ATPase/helicase Prp2 and its coactivator Spp2. Science 2020; 371:science.abe8863. [PMID: 33243853 DOI: 10.1126/science.abe8863] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/04/2020] [Indexed: 01/01/2023]
Abstract
Spliceosome remodeling, executed by conserved adenosine triphosphatase (ATPase)/helicases including Prp2, enables precursor messenger RNA (pre-mRNA) splicing. However, the structural basis for the function of the ATPase/helicases remains poorly understood. Here, we report atomic structures of Prp2 in isolation, Prp2 complexed with its coactivator Spp2, and Prp2-loaded activated spliceosome and the results of structure-guided biochemical analysis. Prp2 weakly associates with the spliceosome and cannot function without Spp2, which stably associates with Prp2 and anchors on the spliceosome, thus tethering Prp2 to the activated spliceosome and allowing Prp2 to function. Pre-mRNA is loaded into a featured channel between the N and C halves of Prp2, where Leu536 from the N half and Arg844 from the C half prevent backward sliding of pre-mRNA toward its 5'-end. Adenosine 5'-triphosphate binding and hydrolysis trigger interdomain movement in Prp2, which drives unidirectional stepwise translocation of pre-mRNA toward its 3'-end. These conserved mechanisms explain the coupling of spliceosome remodeling to pre-mRNA splicing.
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Affiliation(s)
- Rui Bai
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China.,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Ruixue Wan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China
| | - Chuangye Yan
- Beijing Advanced Innovation Center for Structural Biology and Advanced Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Jia
- Beijing Advanced Innovation Center for Structural Biology and Advanced Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jianlin Lei
- Beijing Advanced Innovation Center for Structural Biology and Advanced Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yigong Shi
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, Zhejiang Province, China. .,Westlake Laboratory of Life Sciences and Biomedicine, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Xihu District, Hangzhou 310024, Zhejiang Province, China.,Beijing Advanced Innovation Center for Structural Biology and Advanced Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
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89
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Townsend C, Leelaram MN, Agafonov DE, Dybkov O, Will CL, Bertram K, Urlaub H, Kastner B, Stark H, Lührmann R. Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Science 2020; 370:science.abc3753. [PMID: 33243851 DOI: 10.1126/science.abc3753] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/23/2020] [Indexed: 01/02/2023]
Abstract
Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-Bact complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature Bact complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA.
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Affiliation(s)
- Cole Townsend
- Department of Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Majety N Leelaram
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Dmitry E Agafonov
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Olexandr Dybkov
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Cindy L Will
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Karl Bertram
- Department of Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, D-37075 Göttingen, Germany
| | - Berthold Kastner
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
| | - Holger Stark
- Department of Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
| | - Reinhard Lührmann
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, D-37077 Göttingen, Germany.
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90
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Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly. Neuron 2020; 109:241-256.e9. [PMID: 33220177 DOI: 10.1016/j.neuron.2020.10.035] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 09/17/2020] [Accepted: 10/30/2020] [Indexed: 12/23/2022]
Abstract
Autosomal-recessive cerebellar hypoplasia and ataxia constitute a group of heterogeneous brain disorders caused by disruption of several fundamental cellular processes. Here, we identified 10 families showing a neurodegenerative condition involving pontocerebellar hypoplasia with microcephaly (PCHM). Patients harbored biallelic mutations in genes encoding the spliceosome components Peptidyl-Prolyl Isomerase Like-1 (PPIL1) or Pre-RNA Processing-17 (PRP17). Mouse knockouts of either gene were lethal in early embryogenesis, whereas PPIL1 patient mutation knockin mice showed neuron-specific apoptosis. Loss of either protein affected splicing integrity, predominantly affecting short and high GC-content introns and genes involved in brain disorders. PPIL1 and PRP17 form an active isomerase-substrate interaction, but we found that isomerase activity is not critical for function. Thus, we establish disrupted splicing integrity and "major spliceosome-opathies" as a new mechanism underlying PCHM and neurodegeneration and uncover a non-enzymatic function of a spliceosomal proline isomerase.
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91
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Dou Y, Kalmykova S, Pashkova M, Oghbaie M, Jiang H, Molloy KR, Chait BT, Rout MP, Fenyö D, Jensen TH, Altukhov I, LaCava J. Affinity proteomic dissection of the human nuclear cap-binding complex interactome. Nucleic Acids Res 2020; 48:10456-10469. [PMID: 32960270 PMCID: PMC7544204 DOI: 10.1093/nar/gkaa743] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
A 5′,7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed due to its participation in RNA-fate decisions via interactions with RNA productive factors as well as with adapters of the degradative RNA exosome. A novel cap-binding protein, NCBP3, was recently proposed to form an alternative CBC together with NCBP1, and to interact with the canonical CBC along with the protein SRRT. The theme of post-transcriptional RNA fate, and how it relates to co-transcriptional ribonucleoprotein assembly, is abundant with complicated, ambiguous, and likely incomplete models. In an effort to clarify the compositions of NCBP1-, 2- and 3-related macromolecular assemblies, we have applied an affinity capture-based interactome screen where the experimental design and data processing have been modified to quantitatively identify interactome differences between targets under a range of experimental conditions. This study generated a comprehensive view of NCBP-protein interactions in the ribonucleoprotein context and demonstrates the potential of our approach to benefit the interpretation of complex biological pathways.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Maria Pashkova
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mehrnoosh Oghbaie
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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92
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Bertram K, El Ayoubi L, Dybkov O, Agafonov DE, Will CL, Hartmuth K, Urlaub H, Kastner B, Stark H, Lührmann R. Structural Insights into the Roles of Metazoan-Specific Splicing Factors in the Human Step 1 Spliceosome. Mol Cell 2020; 80:127-139.e6. [PMID: 33007253 DOI: 10.1016/j.molcel.2020.09.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 09/08/2020] [Accepted: 09/09/2020] [Indexed: 11/17/2022]
Abstract
Human spliceosomes contain numerous proteins absent in yeast, whose functions remain largely unknown. Here we report a 3D cryo-EM structure of the human spliceosomal C complex at 3.4 Å core resolution and 4.5-5.7 Å at its periphery, and aided by protein crosslinking we determine its molecular architecture. Our structure provides additional insights into the spliceosome's architecture between the catalytic steps of splicing, and how proteins aid formation of the spliceosome's catalytically active RNP (ribonucleoprotein) conformation. It reveals the spatial organization of the metazoan-specific proteins PPWD1, WDR70, FRG1, and CIR1 in human C complexes, indicating they stabilize functionally important protein domains and RNA structures rearranged/repositioned during the Bact to C transition. Structural comparisons with human Bact, C∗, and P complexes reveal an intricate cascade of RNP rearrangements during splicing catalysis, with intermediate RNP conformations not found in yeast, and additionally elucidate the structural basis for the sequential recruitment of metazoan-specific spliceosomal proteins.
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Affiliation(s)
- Karl Bertram
- Department of Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Leyla El Ayoubi
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Olexandr Dybkov
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Dmitry E Agafonov
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Cindy L Will
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Klaus Hartmuth
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany; Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany
| | - Berthold Kastner
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Holger Stark
- Department of Structural Dynamics, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Reinhard Lührmann
- Cellular Biochemistry, MPI for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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93
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Francies FZ, Marima R, Hull R, Molefi T, Dlamini Z. Genomics and splicing events of type II endometrial cancers in the black population: racial disparity, socioeconomic and geographical differences. Am J Cancer Res 2020; 10:3061-3082. [PMID: 33163258 PMCID: PMC7642673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023] Open
Abstract
Endometrial cancer, also known as uterine cancer, is the most common gynaecological malignancy with burgeoning incidence and mortality rates globally. Racial disparity, socioeconomic and geographical differences are important determinants of endometrial cancer incidence and mortality. Endometrial cancer is mainly categorised as type I and type II. Although less prevalent, type II is the most aggressive form of the disease and typically diagnosed at a late stage, contributing to higher mortality. Black women are at higher risk of developing aggressive, type II disease. Type I tumours are related to higher levels of circulating estrogen with lower-grade tumours that have a good prognosis and frequently related to PTEN mutations. In comparison, type II tumours are estrogen-independent, typically have poor prognosis and associated with the p53, HER2, PPP2R1A, FBXW7 and PIK3R1 mutations. The risk of developing type II malignancy is higher in women with Lynch syndrome as a result of mutations in the MMR gene family. Genetic modifications contribute to aberrant alternative splicing events that are related to tumour development, progression and resistance to therapy. Alternative splicing events are rapidly emerging as potential biomarkers and therapeutic targets. Type II endometrial cancer lacks targeted therapy and biomarkers for novel therapeutic strategies. Recent advances have illustrated a number of molecular targets that are currently explored for the treatment of advanced, late-stage endometrial cancer. The aim of this review is to outline 1) the epidemiology of type II endometrial cancer in black women, 2) discuss the correlated risk factors that contribute to the development of type II endometrial cancer and 3) the associated molecular mechanisms and genetic factors underlying the disease, and 4) aberrant splicing events and biomarkers with therapeutic potential as novel drug targets.
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Affiliation(s)
- Flavia Zita Francies
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health SciencesHatfield 0028, South Africa
| | - Rahaba Marima
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health SciencesHatfield 0028, South Africa
| | - Rodney Hull
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health SciencesHatfield 0028, South Africa
| | - Thulo Molefi
- Department of Medical Oncology, University of Pretoria, Faculty of Health SciencesHatfield 0028, South Africa
| | - Zodwa Dlamini
- SAMRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health SciencesHatfield 0028, South Africa
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94
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Abstract
Objective Alternative splicing can generate various structural and functional protein isoforms. Recently, accumulating evidence shows a relationship between alternative splicing and cancer. Cancer is a complex and chronic disease that involves malignant transformation. In this review, we consider alternative splicing events in relation to the hallmarks of cancer cells, and discuss current therapies to treat cancer-related to alternative splicing. Data sources Data cited in this article are from the PubMed and Embase database, primarily focusing on research published from 2000 to 2018. Study selection Articles were selected with the search terms “alternative splicing,” “cancer cell,” “tumor microenvironment,” and “therapy.” Results Alternative splicing plays an important role in tumorigenesis, development, and escape from cell death. Taking this trait of cancer cells into consideration will allow more definite diagnoses of cancer, and allow the development of more effective medicines to intervene in cancer that could focus on controlling alternative splicing or competitively binding to the final products. Conclusions Alternative splicing is common in cancer cells. Consideration of alternative splicing may allow different strategies for cancer therapy or the identification of novel biomarkers for cancer diagnosis.
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95
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Borchardt EK, Martinez NM, Gilbert WV. Regulation and Function of RNA Pseudouridylation in Human Cells. Annu Rev Genet 2020; 54:309-336. [PMID: 32870730 DOI: 10.1146/annurev-genet-112618-043830] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in pseudouridine detection reveal a complex pseudouridine landscape that includes messenger RNA and diverse classes of noncoding RNA in human cells. The known molecular functions of pseudouridine, which include stabilizing RNA conformations and destabilizing interactions with varied RNA-binding proteins, suggest that RNA pseudouridylation could have widespread effects on RNA metabolism and gene expression. Here, we emphasize how much remains to be learned about the RNA targets of human pseudouridine synthases, their basis for recognizing distinct RNA sequences, and the mechanisms responsible for regulated RNA pseudouridylation. We also examine the roles of noncoding RNA pseudouridylation in splicing and translation and point out the potential effects of mRNA pseudouridylation on protein production, including in the context of therapeutic mRNAs.
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Affiliation(s)
- Erin K Borchardt
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Nicole M Martinez
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
| | - Wendy V Gilbert
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, Yale University, New Haven, Connecticut 06520, USA; , ,
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96
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Busetto V, Barbosa I, Basquin J, Marquenet É, Hocq R, Hennion M, Paternina JA, Namane A, Conti E, Bensaude O, Le Hir H. Structural and functional insights into CWC27/CWC22 heterodimer linking the exon junction complex to spliceosomes. Nucleic Acids Res 2020; 48:5670-5683. [PMID: 32329775 PMCID: PMC7261170 DOI: 10.1093/nar/gkaa267] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/01/2020] [Accepted: 04/22/2020] [Indexed: 11/22/2022] Open
Abstract
Human CWC27 is an uncharacterized splicing factor and mutations in its gene are linked to retinal degeneration and other developmental defects. We identify the splicing factor CWC22 as the major CWC27 partner. Both CWC27 and CWC22 are present in published Bact spliceosome structures, but no interacting domains are visible. Here, the structure of a CWC27/CWC22 heterodimer bound to the exon junction complex (EJC) core component eIF4A3 is solved at 3Å-resolution. According to spliceosomal structures, the EJC is recruited in the C complex, once CWC27 has left. Our 3D structure of the eIF4A3/CWC22/CWC27 complex is compatible with the Bact spliceosome structure but not with that of the C complex, where a CWC27 loop would clash with the EJC core subunit Y14. A CWC27/CWC22 building block might thus form an intermediate landing platform for eIF4A3 onto the Bact complex prior to its conversion into C complex. Knock-down of either CWC27 or CWC22 in immortalized retinal pigment epithelial cells affects numerous common genes, indicating that these proteins cooperate, targeting the same pathways. As the most up-regulated genes encode factors involved in inflammation, our findings suggest a possible link to the retinal degeneration associated with CWC27 deficiencies.
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Affiliation(s)
- Virginia Busetto
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Isabelle Barbosa
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Jérôme Basquin
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | - Émelie Marquenet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Rémi Hocq
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Magali Hennion
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Janio Antonio Paternina
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Abdelkader Namane
- Génétique des Interactions Macromoléculaires, Genomes and Genetics Department, Institut Pasteur, 25-28 rue du docteur Roux 75015 Paris, France
| | - Elena Conti
- Department of Structural Cell Biology, MPI of Biochemistry, Munich, Germany
| | - Olivier Bensaude
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
| | - Hervé Le Hir
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, PSL Research University, 46 rue d'Ulm, 75005 Paris, France
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97
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Slane D, Lee CH, Kolb M, Dent C, Miao Y, Franz-Wachtel M, Lau S, Maček B, Balasubramanian S, Bayer M, Jürgens G. The integral spliceosomal component CWC15 is required for development in Arabidopsis. Sci Rep 2020; 10:13336. [PMID: 32770129 PMCID: PMC7415139 DOI: 10.1038/s41598-020-70324-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Efficient mRNA splicing is a prerequisite for protein biosynthesis and the eukaryotic splicing machinery is evolutionarily conserved among species of various phyla. At its catalytic core resides the activated splicing complex Bact consisting of the three small nuclear ribonucleoprotein complexes (snRNPs) U2, U5 and U6 and the so-called NineTeen complex (NTC) which is important for spliceosomal activation. CWC15 is an integral part of the NTC in humans and it is associated with the NTC in other species. Here we show the ubiquitous expression and developmental importance of the Arabidopsis ortholog of yeast CWC15. CWC15 associates with core components of the Arabidopsis NTC and its loss leads to inefficient splicing. Consistent with the central role of CWC15 in RNA splicing, cwc15 mutants are embryo lethal and additionally display strong defects in the female haploid phase. Interestingly, the haploid male gametophyte or pollen in Arabidopsis, on the other hand, can cope without functional CWC15, suggesting that developing pollen might be more tolerant to CWC15-mediated defects in splicing than either embryo or female gametophyte.
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Affiliation(s)
- Daniel Slane
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Cameron H Lee
- Howard Hughes Medical Institute, Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Martina Kolb
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Craig Dent
- School of Biological Sciences, Monash University, Clayton Campus, Clayton, VIC, 3800, Australia
| | - Yingjing Miao
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Mirita Franz-Wachtel
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | - Steffen Lau
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Boris Maček
- Proteome Center Tübingen, University of Tübingen, Auf der Morgenstelle 15, 72076, Tübingen, Germany
| | | | - Martin Bayer
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany
| | - Gerd Jürgens
- Max Planck Institute for Developmental Biology, Cell Biology, 72076, Tübingen, Germany.
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98
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Fica SM. Cryo-EM snapshots of the human spliceosome reveal structural adaptions for splicing regulation. Curr Opin Struct Biol 2020; 65:139-148. [PMID: 32717639 DOI: 10.1016/j.sbi.2020.06.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/19/2020] [Accepted: 06/21/2020] [Indexed: 12/28/2022]
Abstract
Introns are excised from pre-messenger RNAs by the spliceosome, which produces mRNAs with continuous protein-coding information. In humans, most pre-mRNAs undergo alternative splicing to expand proteomic diversity. Cryo-electron microscopy (cryo-EM) structures of the yeast spliceosome elucidated how proteins stabilize and remodel an RNA-based active site to effect splicing catalysis. More recent cryo-EM snapshots of the human spliceosome reveal a complex protein scaffold and provide insights into the role of specific human proteins in modulating spliceosome activation, splice site positioning, and the ATPase-mediated dynamics of the active site. The emerging molecular picture highlights how, compared to its yeast counterpart, the human spliceosome has coopted additional protein factors to allow increased plasticity of splice site recognition and remodeling, and potentially to regulate alternative splicing.
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Affiliation(s)
- Sebastian M Fica
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, United Kingdom.
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99
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Two distinct nucleic acid binding surfaces of Cdc5 regulate development. Biochem J 2020; 476:3355-3368. [PMID: 31652438 DOI: 10.1042/bcj20190502] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 11/17/2022]
Abstract
Cell division cycle 5 (Cdc5) is a highly conserved nucleic acid binding protein among eukaryotes and plays critical roles in development. Cdc5 can simultaneously bind to DNA and RNA by its N-terminal DNA-binding domain (DBD), but molecular mechanisms describing its nucleic acid recognition and the regulation of development through its nucleic acid binding remain unclear. Herein, we present a crystal structure of the N-terminal DBD of MoCdc5 (MoCdc5-DBD) from the rice blast fungus Magnaporthe oryzae. Residue K100 of MoCdc5 is on the periphery of a positively charged groove that is formed by K42, K45, R47, and N92 and is evolutionally conserved. Mutation of K100 significantly reduces the affinity of MoCdc5-DBD to a Cdc5-binding element but not to a conventional myeloblastosis (Myb) domain-binding element, suggesting that K100 is a key residue of the high binding affinity to Cdc5-binding element. Another conserved residue (R31) is located close to the U6 RNA in the structure of the spliceosome, and its mutation dramatically reduces the binding capacity of MoCdc5-DBD for U6 RNA. Importantly, mutations in these key residues, including R31, K42, and K100 in AtCDC5, an Arabidopsis thaliana ortholog of MoCdc5, greatly impair the functions of AtCDC5, resulting in pleiotropic development defects and reduced levels of primary microRNA transcripts. Taken together, our findings suggest that Cdc5-DBD binds nucleic acids with two distinct binding surfaces, one for DNA and another for RNA, which together contribute to establishing the regulation mechanism of Cdc5 on development through nucleic acid binding.
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100
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Arribere JA, Kuroyanagi H, Hundley HA. mRNA Editing, Processing and Quality Control in Caenorhabditis elegans. Genetics 2020; 215:531-568. [PMID: 32632025 PMCID: PMC7337075 DOI: 10.1534/genetics.119.301807] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 05/03/2020] [Indexed: 02/06/2023] Open
Abstract
While DNA serves as the blueprint of life, the distinct functions of each cell are determined by the dynamic expression of genes from the static genome. The amount and specific sequences of RNAs expressed in a given cell involves a number of regulated processes including RNA synthesis (transcription), processing, splicing, modification, polyadenylation, stability, translation, and degradation. As errors during mRNA production can create gene products that are deleterious to the organism, quality control mechanisms exist to survey and remove errors in mRNA expression and processing. Here, we will provide an overview of mRNA processing and quality control mechanisms that occur in Caenorhabditis elegans, with a focus on those that occur on protein-coding genes after transcription initiation. In addition, we will describe the genetic and technical approaches that have allowed studies in C. elegans to reveal important mechanistic insight into these processes.
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Affiliation(s)
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan, and
| | - Heather A Hundley
- Medical Sciences Program, Indiana University School of Medicine-Bloomington, Indiana 47405
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