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Abrhámová K, Groušlová M, Valentová A, Hao X, Liu B, Převorovský M, Gahura O, Půta F, Sunnerhagen P, Folk P. Truncating the spliceosomal 'rope protein' Prp45 results in Htz1 dependent phenotypes. RNA Biol 2024; 21:1-17. [PMID: 38711165 PMCID: PMC11085953 DOI: 10.1080/15476286.2024.2348896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/24/2024] [Indexed: 05/08/2024] Open
Abstract
Spliceosome assembly contributes an important but incompletely understood aspect of splicing regulation. Prp45 is a yeast splicing factor which runs as an extended fold through the spliceosome, and which may be important for bringing its components together. We performed a whole genome analysis of the genetic interaction network of the truncated allele of PRP45 (prp45(1-169)) using synthetic genetic array technology and found chromatin remodellers and modifiers as an enriched category. In agreement with related studies, H2A.Z-encoding HTZ1, and the components of SWR1, INO80, and SAGA complexes represented prominent interactors, with htz1 conferring the strongest growth defect. Because the truncation of Prp45 disproportionately affected low copy number transcripts of intron-containing genes, we prepared strains carrying intronless versions of SRB2, VPS75, or HRB1, the most affected cases with transcription-related function. Intron removal from SRB2, but not from the other genes, partly repaired some but not all the growth phenotypes identified in the genetic screen. The interaction of prp45(1-169) and htz1Δ was detectable even in cells with SRB2 intron deleted (srb2Δi). The less truncated variant, prp45(1-330), had a synthetic growth defect with htz1Δ at 16°C, which also persisted in the srb2Δi background. Moreover, htz1Δ enhanced prp45(1-330) dependent pre-mRNA hyper-accumulation of both high and low efficiency splicers, genes ECM33 and COF1, respectively. We conclude that while the expression defects of low expression intron-containing genes contribute to the genetic interactome of prp45(1-169), the genetic interactions between prp45 and htz1 alleles demonstrate the sensitivity of spliceosome assembly, delayed in prp45(1-169), to the chromatin environment.
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Affiliation(s)
- Kateřina Abrhámová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Martina Groušlová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Anna Valentová
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Xinxin Hao
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Martin Převorovský
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Ondřej Gahura
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - František Půta
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Petr Folk
- Department of Cell Biology, Faculty of Science, Charles University, Praha, Czech Republic
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Wang C, Xu L, Du C, Yun H, Wang K, Liu H, Ye M, Fan J, Zhou Y, Cheng H. CDK11 requires a critical activator SAP30BP to regulate pre-mRNA splicing. EMBO J 2023; 42:e114051. [PMID: 38059508 PMCID: PMC10711644 DOI: 10.15252/embj.2023114051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 12/08/2023] Open
Abstract
CDK11 is an emerging druggable target for cancer therapy due to its prevalent roles in phosphorylating critical transcription and splicing factors and in facilitating cell cycle progression in cancer cells. Like other cyclin-dependent kinases, CDK11 requires its cognate cyclin, cyclin L1 or cyclin L2, for activation. However, little is known about how CDK11 activities might be modulated by other regulators. In this study, we show that CDK11 forms a tight complex with cyclins L1/L2 and SAP30BP, the latter of which is a poorly characterized factor. Acute degradation of SAP30BP mirrors that of CDK11 in causing widespread and strong defects in pre-mRNA splicing. Furthermore, we demonstrate that SAP30BP facilitates CDK11 kinase activities in vitro and in vivo, through ensuring the stabilities and the assembly of cyclins L1/L2 with CDK11. Together, these findings uncover SAP30BP as a critical CDK11 activator that regulates global pre-mRNA splicing.
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Affiliation(s)
- Changshou Wang
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Lin Xu
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Chen Du
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina§
| | - Hao Yun
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Hui Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical PhysicsChinese Academy of SciencesDalianChina
| | - Jing Fan
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell HomeostasisWuhan UniversityWuhanChina§
| | - Hong Cheng
- Key Laboratory of RNA Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell ScienceChinese Academy of Sciences, University of Chinese Academy of SciencesShanghaiChina
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouChina
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3
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Khan M, Hou S, Chen M, Lei H. Mechanisms of RNA export and nuclear retention. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1755. [PMID: 35978483 DOI: 10.1002/wrna.1755] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/21/2022] [Accepted: 07/06/2022] [Indexed: 05/13/2023]
Abstract
With the identification of huge amount of noncoding RNAs in recent years, the concept of RNA localization has extended from traditional mRNA export to RNA export of mRNA and ncRNA as well as nuclear retention of ncRNA. This review aims to summarize the recent findings from studies on the mechanisms of export of different RNAs and nuclear retention of some lncRNAs in higher eukaryotes, with a focus on splicing-dependent TREX recruitment for the export of spliced mRNA and the sequence-dependent mechanism of mRNA export in the absence of splicing. In addition, evidence to support the involvement of m6 A modification in RNA export with the coordination between the methylase complex and TREX complex as well as sequence-dependent nuclear retention of lncRNA is recapitulated. Finally, a model of sequence-dependent RNA localization is proposed along with the many questions that remain to be answered. This article is categorized under: RNA Export and Localization > RNA Localization RNA Export and Localization > Nuclear Export/Import.
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Affiliation(s)
- Misbah Khan
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Shuai Hou
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Mo Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Haixin Lei
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
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4
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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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5
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Caizzi L, Monteiro-Martins S, Schwalb B, Lysakovskaia K, Schmitzova J, Sawicka A, Chen Y, Lidschreiber M, Cramer P. Efficient RNA polymerase II pause release requires U2 snRNP function. Mol Cell 2021; 81:1920-1934.e9. [PMID: 33689748 DOI: 10.1016/j.molcel.2021.02.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 01/07/2021] [Accepted: 02/10/2021] [Indexed: 12/21/2022]
Abstract
Transcription by RNA polymerase II (Pol II) is coupled to pre-mRNA splicing, but the underlying mechanisms remain poorly understood. Co-transcriptional splicing requires assembly of a functional spliceosome on nascent pre-mRNA, but whether and how this influences Pol II transcription remains unclear. Here we show that inhibition of pre-mRNA branch site recognition by the spliceosome component U2 snRNP leads to a widespread and strong decrease in new RNA synthesis from human genes. Multiomics analysis reveals that inhibition of U2 snRNP function increases the duration of Pol II pausing in the promoter-proximal region, impairs recruitment of the pause release factor P-TEFb, and reduces Pol II elongation velocity at the beginning of genes. Our results indicate that efficient release of paused Pol II into active transcription elongation requires the formation of functional spliceosomes and that eukaryotic mRNA biogenesis relies on positive feedback from the splicing machinery to the transcription machinery.
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Affiliation(s)
- Livia Caizzi
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Sara Monteiro-Martins
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Kseniia Lysakovskaia
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jana Schmitzova
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Anna Sawicka
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Ying Chen
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.
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6
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Matsumoto K, Okamoto K, Okabe S, Fujii R, Ueda K, Ohashi K, Seimiya H. G-quadruplex-forming nucleic acids interact with splicing factor 3B subunit 2 and suppress innate immune gene expression. Genes Cells 2021; 26:65-82. [PMID: 33290632 PMCID: PMC7898707 DOI: 10.1111/gtc.12824] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/20/2020] [Accepted: 12/03/2020] [Indexed: 12/16/2022]
Abstract
G‐quadruplex (G4), a non‐canonical higher‐order structure formed by guanine‐rich nucleic acid sequences, affects various genetic events in cis, including replication, transcription and translation. Whereas up‐regulation of innate immune/interferon‐stimulated genes (ISGs) is implicated in cancer progression, G4‐forming oligonucleotides that mimic telomeric repeat‐containing RNA suppress ISG induction in three‐dimensional (3D) culture of cancer cells. However, it is unclear how G4 suppresses ISG expression in trans. In this study, we found that G4 binding to splicing factor 3B subunit 2 (SF3B2) down‐regulated STAT1 phosphorylation and ISG expression in 3D‐cultured cancer cells. Liquid chromatography‐tandem mass spectrometry analysis identified SF3B2 as a G4‐binding protein. Either G4‐forming oligonucleotides or SF3B2 knockdown suppressed ISG induction, whereas Phen‐DC3, a G4‐stabilizing compound, reversed the inhibitory effect of G4‐forming oligonucleotides on ISG induction. Phen‐DC3 inhibited SF3B2 binding to G4 in vitro. SF3B2‐mediated ISG induction appeared to occur independently of RNA splicing because SF3B2 knockdown did not affect pre‐mRNA splicing under the experimental conditions, and pharmacological inhibition of splicing by pladienolide B did not repress ISG induction. These observations suggest that G4 disrupts the ability of SF3B2 to induce ISGs in cancer. We propose a new mode for gene regulation, which employs G4 as an inhibitory trans‐element.
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Affiliation(s)
- Kyoko Matsumoto
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
| | - Keiji Okamoto
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Sachiko Okabe
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Risa Fujii
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Kenichi Ohashi
- Department of Pathology, Graduate School of Medicine, Yokohama City University, Yokohama, Japan.,Department of Human Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan.,Department of Pathology, Graduate School of Medicine, Yokohama City University, Yokohama, Japan
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7
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Abstract
While the processing of mRNA is essential for gene expression, recent findings have highlighted that RNA processing is systematically altered in cancer. Mutations in RNA splicing factor genes and the shortening of 3' untranslated regions are widely observed. Moreover, evidence is accumulating that other types of RNAs, including circular RNAs, can contribute to tumorigenesis. In this Review, we highlight how altered processing or activity of coding and non-coding RNAs contributes to cancer. We introduce the regulation of gene expression by coding and non-coding RNA and discuss both established roles (microRNAs and long non-coding RNAs) and emerging roles (selective mRNA processing and circular RNAs) for RNAs, highlighting the potential mechanisms by which these RNA subtypes contribute to cancer. The widespread alteration of coding and non-coding RNA demonstrates that altered RNA biogenesis contributes to multiple hallmarks of cancer.
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Affiliation(s)
- Gregory J Goodall
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia.
- Department of Medicine, University of Adelaide, Adelaide, SA, Australia.
- School of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia.
| | - Vihandha O Wickramasinghe
- RNA Biology and Cancer Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia.
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8
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Wang Y, Li J, Wan QX, Zhao Q, Wang KX, Zha XF. Spliceosomal Protein Gene BmSPX Regulates Reproductive Organ Development in Bombyx mori. Int J Mol Sci 2020; 21:ijms21072579. [PMID: 32276369 PMCID: PMC7177926 DOI: 10.3390/ijms21072579] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/03/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023] Open
Abstract
Sex determination and differentiation are nearly universal to all eukaryotic organisms, encompassing diverse systems and mechanisms. Here, we identified a spliceosomal protein gene BmSPX involved in sex determination of the lepidopeteran insect, Bombyx mori. In a transgenic silkworm line that overexpressed the BmSPX gene, transgenic silkworm males exhibited differences in their external genitalia compared to wild-type males, but normal internal genitalia. Additionally, transgenic silkworm females exhibited a developmental disorder of the reproductive organs. Upregulation of BmSPX significantly increased the expression levels of sex-determining genes (BmMasc and BmIMP) and reduced the female-type splice isoform of Bmdsx, which is a key switch gene downstream of the sex-determination pathway. Additionally, co-immunoprecipitation assays confirmed an interaction between the BmSPX protein and BmPSI, an upstream regulatory factor of Bmdsx. Quantitative real-time PCR showed that BmSPX over-expression upregulated the expression of the Hox gene abdominal-B (Adb-B), which is required for specification of the posterior abdomen, external genitalia, and gonads of insects, as well as the genes in the Receptor Tyrosine Kinase (RTK) signaling pathway. In conclusion, our study suggested the involvement of BmSPX, identified as a novel regulatory factor, in the sex-determination pathway and regulation of reproductive organ development in silkworms.
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Affiliation(s)
- Yao Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Science, Fudan University, Shanghai 200438, China
| | - Juan Li
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
| | - Qiu-Xing Wan
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
| | - Qin Zhao
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
| | - Kai-Xuan Wang
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
| | - Xing-Fu Zha
- State Key Laboratory of Silkworm Genome Biology, Biological Science Research Center, Southwest University, Beibei, Chongqing 400715, China; (Y.W.); (J.L.); (Q.-X.W.); (Q.Z.); (K.-X.W.)
- Chongqing Key Laboratory of Sericultural Science, Southwest University, Chongqing 400715, China
- Chongqing Engineering and Technology Research Center for Novel Silk Materials, Southwest University, Chongqing 400715, China
- Correspondence: ; Tel.: +86-23-68251573; Fax: +86-23-68251128
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9
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Sun C. The SF3b complex: splicing and beyond. Cell Mol Life Sci 2020; 77:3583-3595. [PMID: 32140746 PMCID: PMC7452928 DOI: 10.1007/s00018-020-03493-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/13/2020] [Accepted: 02/20/2020] [Indexed: 12/17/2022]
Abstract
The SF3b complex is an intrinsic component of the functional U2 small nuclear ribonucleoprotein (snRNP). As U2 snRNP enters nuclear pre-mRNA splicing, SF3b plays key roles in recognizing the branch point sequence (BPS) and facilitating spliceosome assembly and activation. Since the discovery of SF3b, substantial progress has been made in elucidating its molecular mechanism during splicing. In addition, numerous recent studies indicate that SF3b and its components are engaged in various molecular and cellular events that are beyond the canonical role in splicing. This review summarizes the current knowledge on the SF3b complex and highlights its multiple roles in splicing and beyond.
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Affiliation(s)
- Chengfu Sun
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, 610500, China.
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10
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Into the basket and beyond: the journey of mRNA through the nuclear pore complex. Biochem J 2020; 477:23-44. [DOI: 10.1042/bcj20190132] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 11/28/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023]
Abstract
The genetic information encoded in nuclear mRNA destined to reach the cytoplasm requires the interaction of the mRNA molecule with the nuclear pore complex (NPC) for the process of mRNA export. Numerous proteins have important roles in the transport of mRNA out of the nucleus. The NPC embedded in the nuclear envelope is the port of exit for mRNA and is composed of ∼30 unique proteins, nucleoporins, forming the distinct structures of the nuclear basket, the pore channel and cytoplasmic filaments. Together, they serve as a rather stationary complex engaged in mRNA export, while a variety of soluble protein factors dynamically assemble on the mRNA and mediate the interactions of the mRNA with the NPC. mRNA export factors are recruited to and dissociate from the mRNA at the site of transcription on the gene, during the journey through the nucleoplasm and at the nuclear pore at the final stages of export. In this review, we present the current knowledge derived from biochemical, molecular, structural and imaging studies, to develop a high-resolution picture of the many events that culminate in the successful passage of the mRNA out of the nucleus.
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van der Feltz C, Hoskins AA. Structural and functional modularity of the U2 snRNP in pre-mRNA splicing. Crit Rev Biochem Mol Biol 2019; 54:443-465. [PMID: 31744343 DOI: 10.1080/10409238.2019.1691497] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The U2 small nuclear ribonucleoprotein (snRNP) is an essential component of the spliceosome, the cellular machine responsible for removing introns from precursor mRNAs (pre-mRNAs) in all eukaryotes. U2 is an extraordinarily dynamic splicing factor and the most frequently mutated in cancers. Cryo-electron microscopy (cryo-EM) has transformed our structural and functional understanding of the role of U2 in splicing. In this review, we synthesize these and other data with respect to a view of U2 as an assembly of interconnected functional modules. These modules are organized by the U2 small nuclear RNA (snRNA) for roles in spliceosome assembly, intron substrate recognition, and protein scaffolding. We describe new discoveries regarding the structure of U2 components and how the snRNP undergoes numerous conformational and compositional changes during splicing. We specifically highlight large scale movements of U2 modules as the spliceosome creates and rearranges its active site. U2 serves as a compelling example for how cellular machines can exploit the modular organization and structural plasticity of an RNP.
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Affiliation(s)
| | - Aaron A Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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12
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Shin J, Cheng H, Tian B. New means to an end: mRNA export activity impacts alternative polyadenylation. Transcription 2019; 10:207-211. [PMID: 31474181 DOI: 10.1080/21541264.2019.1658557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Gene expression involves multiple co- and post-transcriptional processes that have been increasingly found intertwined. A recent work by our groups (Chen et al. Mol Cell, 2019) indicates that expression of alternative polyadenylation isoforms in mammalian cells can be controlled by nuclear export activities. This regulation has distinct impacts on genes having different sizes and nucleotide contents, and involves RNA polymerase II distribution toward the 3' end of genes. This work raises a number of intriguing questions concerning how 3' end processing and nuclear export are integrated and how their regulation feeds back to transcription.
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Affiliation(s)
- Jihae Shin
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
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