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Beusch I, Barraud P, Moursy A, Cléry A, Allain FHT. Tandem hnRNP A1 RNA recognition motifs act in concert to repress the splicing of survival motor neuron exon 7. eLife 2017. [PMID: 28650318 PMCID: PMC5503513 DOI: 10.7554/elife.25736] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
HnRNP A1 regulates many alternative splicing events by the recognition of splicing silencer elements. Here, we provide the solution structures of its two RNA recognition motifs (RRMs) in complex with short RNA. In addition, we show by NMR that both RRMs of hnRNP A1 can bind simultaneously to a single bipartite motif of the human intronic splicing silencer ISS-N1, which controls survival of motor neuron exon 7 splicing. RRM2 binds to the upstream motif and RRM1 to the downstream motif. Combining the insights from the structure with in cell splicing assays we show that the architecture and organization of the two RRMs is essential to hnRNP A1 function. The disruption of the inter-RRM interaction or the loss of RNA binding capacity of either RRM impairs splicing repression by hnRNP A1. Furthermore, both binding sites within the ISS-N1 are important for splicing repression and their contributions are cumulative rather than synergistic. DOI:http://dx.doi.org/10.7554/eLife.25736.001
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Affiliation(s)
- Irene Beusch
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Pierre Barraud
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.,Laboratoire de cristallographie et RMN biologiques, UMR 8015, CNRS, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Laboratoire d'expression génétique microbienne, UMR 8261, CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de biologie physico-chimique, Paris, France
| | - Ahmed Moursy
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
| | - Frédéric Hai-Trieu Allain
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland
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52
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Hammarskjold ML, Rekosh D. SR proteins: To shuttle or not to shuttle, that is the question. J Cell Biol 2017; 216:1875-1877. [PMID: 28600433 PMCID: PMC5496630 DOI: 10.1083/jcb.201705009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Hammarskjold and Rekosh preview new results from the Müller-McNicoll laboratory suggesting that the differentiation state modulates SR protein nucleocytoplasmic shuttling and function. Serine- and arginine-rich proteins play important roles in splicing, nuclear export, and translation. In this issue, Botti et al. (2017. J. Cell Biol. https://doi.org/10.1083/jcb.201610051) show that SRSF2 and SRSF5, previously thought to be nuclear, shuttle with messenger RNA to the cytoplasm in pluripotent P19 cells, but not in differentiated cells.
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Affiliation(s)
- Marie-Louise Hammarskjold
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA .,Department of Microbiology, University of Venda, Thohoyandou, South Africa
| | - David Rekosh
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA.,Department of Microbiology, University of Venda, Thohoyandou, South Africa
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53
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Fernandez N, Cordiner RA, Young RS, Hug N, Macias S, Cáceres JF. Genetic variation and RNA structure regulate microRNA biogenesis. Nat Commun 2017; 8:15114. [PMID: 28466845 PMCID: PMC5418625 DOI: 10.1038/ncomms15114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 03/01/2017] [Indexed: 12/20/2022] Open
Abstract
MiRNA biogenesis is highly regulated at the post-transcriptional level; however, the role of sequence and secondary RNA structure in this process has not been extensively studied. A single G to A substitution present in the terminal loop of pri-mir-30c-1 in breast and gastric cancer patients had been previously described to result in increased levels of mature miRNA. Here, we report that this genetic variant directly affects Drosha-mediated processing of pri-mir-30c-1 in vitro and in cultured cells. Structural analysis of this variant revealed an altered RNA structure that facilitates the interaction with SRSF3, an SR protein family member that promotes pri-miRNA processing. Our results are compatible with a model whereby a genetic variant in pri-mir-30c-1 leads to a secondary RNA structure rearrangement that facilitates binding of SRSF3 resulting in increased levels of miR-30c. These data highlight that primary sequence determinants and RNA structure are key regulators of miRNA biogenesis.
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Affiliation(s)
- Noemi Fernandez
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Ross A. Cordiner
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Robert S. Young
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Nele Hug
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sara Macias
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Javier F. Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Genome Regulation Section, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
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54
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Hu M, Wang R, Li X, Fan M, Lin J, Zhen J, Chen L, Lv Z. LncRNA MALAT1 is dysregulated in diabetic nephropathy and involved in high glucose-induced podocyte injury via its interplay with β-catenin. J Cell Mol Med 2017; 21:2732-2747. [PMID: 28444861 PMCID: PMC5661111 DOI: 10.1111/jcmm.13189] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/09/2017] [Indexed: 12/17/2022] Open
Abstract
Metastasis associated lung adenocarcinoma transcript 1(MALAT1) is a long non-coding RNA, broadly expressed in mammalian tissues including kidney and up-regulated in a variety of cancer cells. To date, its functions in podocytes are largely unknown. β-catenin is a key mediator in the canonical and non-canonical Wnt signalling pathway; its aberrant expression promotes podocyte malfunction and albuminuria, and contributes to kidney fibrosis. In this study, we found that MALAT1 levels were increased in kidney cortices from C57BL/6 mice with streptozocin (STZ)-induced diabetic nephropathy, and dynamically regulated in cultured mouse podocytes stimulated with high glucose, which showed a trend from rise to decline. The decline of MALAT1 levels was accompanied with β-catenin translocation to the nuclei and enhanced expression of serine/arginine splicing factor 1 (SRSF1), a MALAT1 RNA-binding protein. Further we showed early interference with MALAT1 siRNA partially restored podocytes function and prohibited β-catenin nuclear accumulation and SRSF1 overexpression. Intriguingly, we showed that β-catenin was involved in MALAT1 transcription by binding to the promotor region of MALAT1; β-catenin knock-down also decreased MALAT1 levels, suggesting a novel feedback regulation between MALAT1 and β-catenin. Notably, β-catenin deletion had limited effects on SRSF1 expression, demonstrating β-catenin might serve as a downstream signal of SRSF1. These findings provided evidence for a pivotal role of MALAT1 in diabetic nephropathy and high glucose-induced podocyte damage.
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Affiliation(s)
- Mengsi Hu
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Rong Wang
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Xiaobing Li
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, China
| | - Minghua Fan
- Department of Obstetrics and Gynecology, The Second Hospital of Shandong University, Jinan, China
| | - Jiangong Lin
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
| | - Junhui Zhen
- Department of Pathology, School of Medicine, Shandong University, Jinan, China
| | - Liqun Chen
- Department of Nephrology, First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhimei Lv
- Department of Nephrology, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, China
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55
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Kawaguchi Y, Nariki H, Kawamoto N, Kanehiro Y, Miyazaki S, Suzuki M, Magari M, Tokumitsu H, Kanayama N. SRSF1-3 contributes to diversification of the immunoglobulin variable region gene by promoting accumulation of AID in the nucleus. Biochem Biophys Res Commun 2017; 485:261-266. [DOI: 10.1016/j.bbrc.2017.02.097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 02/19/2017] [Indexed: 01/06/2023]
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56
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Yan Q, Xia X, Sun Z, Fang Y. Depletion of Arabidopsis SC35 and SC35-like serine/arginine-rich proteins affects the transcription and splicing of a subset of genes. PLoS Genet 2017; 13:e1006663. [PMID: 28273088 PMCID: PMC5362245 DOI: 10.1371/journal.pgen.1006663] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2016] [Revised: 03/22/2017] [Accepted: 02/28/2017] [Indexed: 12/23/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are important splicing factors which play significant roles in spliceosome assembly and splicing regulation. However, little is known regarding their biological functions in plants. Here, we analyzed the phenotypes of mutants upon depleting different subfamilies of Arabidopsis SR proteins. We found that loss of the functions of SC35 and SC35-like (SCL) proteins cause pleiotropic changes in plant morphology and development, including serrated leaves, late flowering, shorter roots and abnormal silique phyllotaxy. Using RNA-seq, we found that SC35 and SCL proteins play roles in the pre-mRNA splicing. Motif analysis revealed that SC35 and SCL proteins preferentially bind to a specific RNA sequence containing the AGAAGA motif. In addition, the transcriptions of a subset of genes are affected by the deletion of SC35 and SCL proteins which interact with NRPB4, a specific subunit of RNA polymerase II. The splicing of FLOWERING LOCUS C (FLC) intron1 and transcription of FLC were significantly regulated by SC35 and SCL proteins to control Arabidopsis flowering. Therefore, our findings provide mechanistic insight into the functions of plant SC35 and SCL proteins in the regulation of splicing and transcription in a direct or indirect manner to maintain the proper expression of genes and development. SR proteins were identified to be important splicing factors. This work generated mutants of different subfamilies of the classic Arabidopsis SR proteins. Genetic analysis revealed that loss of the function of SC35/SCL proteins influences the plant development. This study revealed SC35/SCL proteins regulate alternative splicing, preferentially bind a specific RNA motif, interact with NRPB4, and affect the transcription of a subset of genes. This study further revealed that SC35/SCL proteins control flowering by regulating the splicing and transcription of FLC. These results shed light on the functions of SR proteins in plants.
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Affiliation(s)
- Qingqing Yan
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Xi Xia
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Zhenfei Sun
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
| | - Yuda Fang
- National key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, China
- * E-mail:
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57
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Rodor J, Pan Q, Blencowe BJ, Eyras E, Cáceres JF. The RNA-binding profile of Acinus, a peripheral component of the exon junction complex, reveals its role in splicing regulation. RNA (NEW YORK, N.Y.) 2016; 22:1411-26. [PMID: 27365209 PMCID: PMC4986896 DOI: 10.1261/rna.057158.116] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 05/24/2016] [Indexed: 05/21/2023]
Abstract
Acinus (apoptotic chromatin condensation inducer in the nucleus) is an RNA-binding protein (RBP) originally identified for its role in apoptosis. It was later found to be an auxiliary component of the exon junction complex (EJC), which is deposited at exon junctions as a consequence of pre-mRNA splicing. To uncover the cellular functions of Acinus and investigate its role in splicing, we mapped its endogenous RNA targets using the cross-linking immunoprecipitation protocol (iCLIP). We observed that Acinus binds to pre-mRNAs, associating specifically to a subset of suboptimal introns, but also to spliced mRNAs. We also confirmed the presence of Acinus as a peripheral factor of the EJC. RNA-seq was used to investigate changes in gene expression and alternative splicing following siRNA-mediated depletion of Acinus in HeLa cells. This analysis revealed that Acinus is preferentially required for the inclusion of specific alternative cassette exons and also controls the faithful splicing of a subset of introns. Moreover, a large number of splicing changes can be related to Acinus binding, suggesting a direct role of Acinus in exon and intron definition. In particular, Acinus regulates the splicing of DFFA/ICAD transcript, a major regulator of DNA fragmentation. Globally, the genome-wide identification of RNA targets of Acinus revealed its role in splicing regulation as well as its involvement in other cellular pathways, including cell cycle progression. Altogether, this study uncovers new cellular functions of an RBP transiently associated with the EJC.
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Affiliation(s)
- Julie Rodor
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Qun Pan
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin J Blencowe
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Eduardo Eyras
- Universitat Pompeu Fabra, E08003, Barcelona, Spain Catalan Institution for Research and Advanced Studies (ICREA), E08010 Barcelona, Spain
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
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58
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Skrdlant L, Stark JM, Lin RJ. Myelodysplasia-associated mutations in serine/arginine-rich splicing factor SRSF2 lead to alternative splicing of CDC25C. BMC Mol Biol 2016; 17:18. [PMID: 27552991 PMCID: PMC4994158 DOI: 10.1186/s12867-016-0071-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 08/16/2016] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Serine-arginine rich splicing factor 2 (SRSF2) is a protein known for its role in RNA splicing and genome stability. It has been recently discovered that SRSF2, along with other splicing regulators, is frequently mutated in patients with myelodysplastic syndrome (MDS). The most common MDS mutations in SRSF2 occur at proline 95; the mutant proteins are shown to have different RNA binding preferences, which may contribute to splicing changes detected in mutant cells. However, the influence of these SRSF2 MDS-associated mutations on specific splicing events remains poorly understood. RESULTS A tetracycline-inducible TF-1 erythroleukemia cell line was transduced with retroviruses to create cell lines expressing HA-tagged wildtype SRSF2, SRSF2 with proline 95 point mutations found in MDS, or SRSF2 with a deletion of one of the four major domains of the protein. Effects of these mutants on apoptosis and specific alternative splicing events were evaluated. Cells were also treated with DNA damaging drugs for comparison. MDS-related P95 point mutants of SRSF2 were expressed and phosphorylated at similar levels as wildtype SRSF2. However, cells expressing mutant SRSF2 exhibited higher levels of apoptosis than cells expressing wildtype SRSF2. Regarding alternative splicing events, in nearly all examined cases, SRSF2 P95 mutants acted in a similar fashion as the wildtype SRSF2. However, cells expressing SRSF2 P95 mutants had a percent increase in the C5 spliced isoform of cell division cycle 25C (CDC25C). The same alternative splicing of CDC25C was detected by treating cells with DNA damaging drugs, such as cisplatin, camptothecin, and trichostatin A at appropriate dosage. However, unlike DNA damaging drugs, SRSF2 P95 mutants did not activate the Ataxia telangiectasia mutated (ATM) pathway. CONCLUSION SRSF2 P95 mutants lead to alternative splicing of CDC25C in a manner that is not dependent on the DNA damage response.
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Affiliation(s)
- Lindsey Skrdlant
- Department of Molecular and Cellular Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
| | - Jeremy M. Stark
- Department of Cancer Genetics and Epigenetics, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
| | - Ren-Jang Lin
- Department of Molecular and Cellular Biology, Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA 91010 USA
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59
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Bruun GH, Doktor TK, Borch-Jensen J, Masuda A, Krainer AR, Ohno K, Andresen BS. Global identification of hnRNP A1 binding sites for SSO-based splicing modulation. BMC Biol 2016; 14:54. [PMID: 27380775 PMCID: PMC4932749 DOI: 10.1186/s12915-016-0279-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 06/23/2016] [Indexed: 01/14/2023] Open
Abstract
Background Many pathogenic genetic variants have been shown to disrupt mRNA splicing. Besides splice mutations in the well-conserved splice sites, mutations in splicing regulatory elements (SREs) may deregulate splicing and cause disease. A promising therapeutic approach is to compensate for this deregulation by blocking other SREs with splice-switching oligonucleotides (SSOs). However, the location and sequence of most SREs are not well known. Results Here, we used individual-nucleotide resolution crosslinking immunoprecipitation (iCLIP) to establish an in vivo binding map for the key splicing regulatory factor hnRNP A1 and to generate an hnRNP A1 consensus binding motif. We find that hnRNP A1 binding in proximal introns may be important for repressing exons. We show that inclusion of the alternative cassette exon 3 in SKA2 can be significantly increased by SSO-based treatment which blocks an iCLIP-identified hnRNP A1 binding site immediately downstream of the 5’ splice site. Because pseudoexons are well suited as models for constitutive exons which have been inactivated by pathogenic mutations in SREs, we used a pseudoexon in MTRR as a model and showed that an iCLIP-identified hnRNP A1 binding site downstream of the 5′ splice site can be blocked by SSOs to activate the exon. Conclusions The hnRNP A1 binding map can be used to identify potential targets for SSO-based therapy. Moreover, together with the hnRNP A1 consensus binding motif, the binding map may be used to predict whether disease-associated mutations and SNPs affect hnRNP A1 binding and eventually mRNA splicing. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0279-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Gitte H Bruun
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Jonas Borch-Jensen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Akio Masuda
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY, 11724, USA
| | - Kinji Ohno
- Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark.
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60
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Stankovic N, Schloesser M, Joris M, Sauvage E, Hanikenne M, Motte P. Dynamic Distribution and Interaction of the Arabidopsis SRSF1 Subfamily Splicing Factors. PLANT PHYSIOLOGY 2016; 170:1000-13. [PMID: 26697894 PMCID: PMC4734559 DOI: 10.1104/pp.15.01338] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 12/19/2015] [Indexed: 05/19/2023]
Abstract
Ser/Arg-rich (SR) proteins are essential nucleus-localized splicing factors. Our prior studies showed that Arabidopsis (Arabidopsis thaliana) RSZ22, a homolog of the human SRSF7 SR factor, exits the nucleus through two pathways, either dependent or independent on the XPO1 receptor. Here, we examined the expression profiles and shuttling dynamics of the Arabidopsis SRSF1 subfamily (SR30, SR34, SR34a, and SR34b) under control of their endogenous promoter in Arabidopsis and in transient expression assay. Due to its rapid nucleocytoplasmic shuttling and high expression level in transient assay, we analyzed the multiple determinants that regulate the localization and shuttling dynamics of SR34. By site-directed mutagenesis of SR34 RNA-binding sequences and Arg/Ser-rich (RS) domain, we further show that functional RRM1 or RRM2 are dispensable for the exclusive protein nuclear localization and speckle-like distribution. However, mutations of both RRMs induced aggregation of the protein whereas mutation in the RS domain decreased the stability of the protein and suppressed its nuclear accumulation. Furthermore, the RNA-binding motif mutants are defective for their export through the XPO1 (CRM1/Exportin-1) receptor pathway, but retain nucleocytoplasmic mobility. We performed a yeast two hybrid screen with SR34 as bait and discovered SR45 as a new interactor. SR45 is an unusual SR splicing factor bearing two RS domains. These interactions were confirmed in planta by FLIM-FRET and BiFC and the roles of SR34 domains in protein-protein interactions were further studied. Altogether, our report extends our understanding of shuttling dynamics of Arabidopsis SR splicing factors.
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Affiliation(s)
- Nancy Stankovic
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Marie Schloesser
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Marine Joris
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Eric Sauvage
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Marc Hanikenne
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
| | - Patrick Motte
- Laboratory of Functional Genomics and Plant Molecular Imaging (N.S., M.S., M.J., M.H., P.M.), Laboratory of Macromolecular Crystallography (E.S.), PhytoSYSTEMS (M.H., P.M.), Centre for Protein Engineering (CIP; N.S., M.S., M.J., E.S., M.H., P.M.), Department of Life Sciences, and Centre for Assistance in Technology of Microscopy (CATM; P.M.), University of Liège, B-4000 Liège, Belgium
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61
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Kim CH, Kim YD, Choi EK, Kim HR, Na BR, Im SH, Jun CD. Nuclear Speckle-related Protein 70 Binds to Serine/Arginine-rich Splicing Factors 1 and 2 via an Arginine/Serine-like Region and Counteracts Their Alternative Splicing Activity. J Biol Chem 2016; 291:6169-81. [PMID: 26797131 DOI: 10.1074/jbc.m115.689414] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 11/06/2022] Open
Abstract
Nuclear speckles are subnuclear storage sites containing pre-mRNA splicing machinery. Proteins assembled in nuclear speckles are known to modulate transcription and pre-mRNA processing. We have previously identified nuclear speckle-related protein 70 (NSrp70) as a novel serine/arginine (SR)-related protein that co-localizes with classical SR proteins such as serine/arginine-rich splicing factor 1 (SRSF1 or ASF/SF2) and SRSF2 (SC35). NSrp70 mediates alternative splice site selection, targeting several pre-mRNAs, including CD44 exon v5. Here we demonstrated that NSrp70 interacts physically with two SR proteins, SRSF1 and SRSF2, and reverses their splicing activity in terms of CD44 exon v5 as exon exclusion. The NSrp70 RS-like region was subdivided into three areas. Deletion of the first arginine/serine-rich-like region (RS1) completely abrogated binding to the SR proteins and to target mRNA and also failed to induce splicing of CD44 exon v5, suggesting that RS1 is critical for NSrp70 functioning. Interestingly, RS1 deletion also resulted in the loss of NSrp70 and SR protein speckle positioning, implying a potential scaffolding role for NSrp70 in nuclear speckles. NSrp70 contains an N-terminal coiled-coil domain that is critical not only for self-oligomerization but also for splicing activity. Consistently, deletion of the coiled-coil domain resulted in indefinite formation of nuclear speckles. Collectively, these results demonstrate that NSrp70 acts as a new molecular counterpart for alternative splicing of target RNA, counteracting SRSF1 and SRSF2 splicing activity.
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Affiliation(s)
- Chang-Hyun Kim
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Young-Dae Kim
- the Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, 125 Gwahak-ro, Yuseng-gu, Daejeon 3414, Korea, and
| | - Eun-Kyung Choi
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Hye-Ran Kim
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Bo-Ra Na
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea
| | - Sin-Hyeog Im
- the Academy of Immunology and Microbiology, Institute for Basic Science, and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Chang-Duk Jun
- From the School of Life Sciences, Immune Synapse Research Center, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea,
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Craigie M, Regan P, Otalora YL, Sariyer IK. Molecular interplay between T-Antigen and splicing factor, arginine/serine-rich 1 (SRSF1) controls JC virus gene expression in glial cells. Virol J 2015; 12:196. [PMID: 26596376 PMCID: PMC4657255 DOI: 10.1186/s12985-015-0426-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/15/2015] [Indexed: 01/12/2023] Open
Abstract
Background Human polyomavirus JCV is the etiologic agent of progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease characterized by lytic infection of glial cells in the central nervous system. PML is seen primarily in immunosuppressed patients and is mainly classified as an AIDS-defining disease. In addition to structural capsid proteins, JCV encodes multiple regulatory proteins, including T-antigen and agnoprotein, which are required for functional lytic infection. Previous studies have suggested that molecular interaction between viral proteins and host factors play an important role in reactivation of JCV and progression of the viral life cycle in glial cells. Recently, serine/arginine rich splicing factor 1 (SRSF1), a cellular alternative splicing factor, was identified as a strong negative regulator of JCV in glial cells. SRSF1 inhibits JCV gene expression and viral replication by directly interacting with viral promoter sequences. Here, we have investigated possible impact of JCV regulatory proteins, T-antigen and agnoprotein, on SRSF1-mediated suppression of JCV gene expression in glial cells. Results Reporter gene analysis has suggested that T-antigen rescues viral transcriptional suppression mediated by SRSF1. Further analyses have revealed that T-antigen promotes viral gene expression by suppressing SRSF1 gene transcription in glial cells. A subsequent ChIP analysis revealed that T-antigen associates with the promoter region of SRSF1 to induce the transcriptional suppression. Conclusions These findings have revealed a molecular interplay between cellular SRSF1 and viral T-antigen in controlling JCV gene expression, and may suggest a novel mechanism of JCV reactivation in patients who are at risk of developing PML.
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Affiliation(s)
- Michael Craigie
- Department of Neuroscience, Center for Neurovirology, Temple University Lewis Katz School of Medicine, 3500 North Broad Street, 7th Floor, Philadelphia, PA, 19140, USA.
| | - Patrick Regan
- Department of Neuroscience, Center for Neurovirology, Temple University Lewis Katz School of Medicine, 3500 North Broad Street, 7th Floor, Philadelphia, PA, 19140, USA.
| | - Yolanda-Lopez Otalora
- Department of Neuroscience, Center for Neurovirology, Temple University Lewis Katz School of Medicine, 3500 North Broad Street, 7th Floor, Philadelphia, PA, 19140, USA.
| | - Ilker Kudret Sariyer
- Department of Neuroscience, Center for Neurovirology, Temple University Lewis Katz School of Medicine, 3500 North Broad Street, 7th Floor, Philadelphia, PA, 19140, USA.
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McCuaig RD, Dunn J, Li J, Masch A, Knaute T, Schutkowski M, Zerweck J, Rao S. PKC-Theta is a Novel SC35 Splicing Factor Regulator in Response to T Cell Activation. Front Immunol 2015; 6:562. [PMID: 26594212 PMCID: PMC4633479 DOI: 10.3389/fimmu.2015.00562] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/21/2015] [Indexed: 11/13/2022] Open
Abstract
Alternative splicing of nuclear pre-mRNA is essential for generating protein diversity and regulating gene expression. While many immunologically relevant genes undergo alternative splicing, the role of regulated splicing in T cell immune responses is largely unexplored, and the signaling pathways and splicing factors that regulate alternative splicing in T cells are poorly defined. Here, we show using a combination of Jurkat T cells, human primary T cells, and ex vivo naïve and effector virus-specific T cells isolated after influenza A virus infection that SC35 phosphorylation is induced in response to stimulatory signals. We show that SC35 colocalizes with RNA polymerase II in activated T cells and spatially overlaps with H3K27ac and H3K4me3, which mark transcriptionally active genes. Interestingly, SC35 remains coupled to the active histone marks in the absence of continuing stimulatory signals. We show for the first time that nuclear PKC-θ co-exists with SC35 in the context of the chromatin template and is a key regulator of SC35 in T cells, directly phosphorylating SC35 peptide residues at RNA recognition motif and RS domains. Collectively, our findings suggest that nuclear PKC-θ is a novel regulator of the key splicing factor SC35 in T cells.
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Affiliation(s)
- Robert Duncan McCuaig
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Maths, University of Canberra , Canberra, ACT , Australia
| | - Jennifer Dunn
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Maths, University of Canberra , Canberra, ACT , Australia
| | - Jasmine Li
- Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, University of Melbourne , Melbourne, VIC , Australia
| | - Antonia Masch
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University , Halle , Germany
| | | | - Mike Schutkowski
- Department of Enzymology, Institute of Biochemistry and Biotechnology, Martin-Luther-University , Halle , Germany
| | | | - Sudha Rao
- Discipline of Biomedical Sciences, Faculty of Education, Science, Technology and Maths, University of Canberra , Canberra, ACT , Australia
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Suchanek AL, Salati LM. Construction and evaluation of an adenoviral vector for the liver-specific expression of the serine/arginine-rich splicing factor, SRSF3. Plasmid 2015; 82:1-9. [PMID: 26241824 DOI: 10.1016/j.plasmid.2015.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 07/24/2015] [Accepted: 07/27/2015] [Indexed: 01/09/2023]
Abstract
Serine/arginine-rich splicing factor-3 (SRSF3), alternatively known as SRp20, is a member of the highly-conserved SR protein family of mRNA splicing factors. SRSF3 generally functions as an enhancer of mRNA splicing by binding to transcripts in a sequence-specific manner to both recruit and stabilize the binding of spliceosomal components to the mRNA. In liver, expression of SRSF3 is relatively low and its activity is increased in response to insulin and feeding a high carbohydrate diet. We sought to over-express SRSF3 in primary rat hepatocytes to identify regulatory targets. A standard adenoviral shuttle vector system containing an epitope-tagged SRSF3 under the transcriptional control of the CMV promoter could not be used to produce infectious adenoviral particles. SRSF3 over-expression in the packaging cell line prevented the production of infectious adenovirus particles by interfering with the viral splicing program. To circumvent this issue, SRSF3 expression from the shuttle vector was blocked by placing its expression under the control of the liver-specific albumin promoter. In this system, the FLAG-SRSF3 transgene is only expressed in the target cells (hepatocytes) but not in the packaging cell line. An additional benefit of the albumin promoter is that expression of the transgene does not require the addition of hormones or antibiotics to drive SRSF3 expression in the hepatocytes. Robust expression of FLAG-SRSF3 protein is detected in both HepG2 cells and primary rat hepatocytes infected with adenovirus prepared from this new shuttle vector. Furthermore, abundances of several known and suspected mRNA targets of SRSF3 action are increased in response to over-expression using this virus. This report details the construction of the albumin promoter-driven adenoviral shuttle vector, termed pmAlbAd5-FLAG.SRSF3, that can be used to generate functional adenovirus to express FLAG-SRSF3 specifically in liver. This vector would be suitable for over-expression of other splicing factors that could inhibit virus production. In addition, this vector would allow only liver-specific expression of other cargo genes when used in a whole-animal paradigm.
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Affiliation(s)
- Amanda L Suchanek
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV 26506, United States
| | - Lisa M Salati
- Department of Biochemistry, West Virginia University School of Medicine, Morgantown, WV 26506, United States.
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Posttranscriptional Regulation of Splicing Factor SRSF1 and Its Role in Cancer Cell Biology. BIOMED RESEARCH INTERNATIONAL 2015; 2015:287048. [PMID: 26273603 PMCID: PMC4529898 DOI: 10.1155/2015/287048] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 12/16/2014] [Indexed: 01/23/2023]
Abstract
Over the past decade, alternative splicing has been progressively recognized as a major mechanism regulating gene expression patterns in different tissues and disease states through the generation of multiple mRNAs from the same gene transcript. This process requires the joining of selected exons or usage of different pairs of splice sites and is regulated by gene-specific combinations of RNA-binding proteins. One archetypical splicing regulator is SRSF1, for which we review the molecular mechanisms and posttranscriptional modifications involved in its life cycle. These include alternative splicing of SRSF1 itself, regulatory protein phosphorylation events, and the role of nuclear versus cytoplasmic SRSF1 localization. In addition, we resume current knowledge on deregulated SRSF1 expression in tumors and describe SRSF1-regulated alternative transcripts with functional consequences for cancer cell biology at different stages of tumor development.
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Regulation of CD44E by DARPP-32-dependent activation of SRp20 splicing factor in gastric tumorigenesis. Oncogene 2015; 35:1847-56. [PMID: 26119931 PMCID: PMC4486340 DOI: 10.1038/onc.2015.250] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 05/11/2015] [Accepted: 05/22/2015] [Indexed: 12/19/2022]
Abstract
Objective CD44E is a frequently overexpressed variant of CD44 in gastric cancer. Mechanisms that regulate CD44 splicing and expression in gastric cancer remain unknown. Herein, we investigated the role of DARPP-32 (dopamine and cAMP-regulated phosphoprotein, Mr 32000) in promoting tumor growth through regulation of CD44 splicing. Design Quantitative luciferase reporter, quantitative real-time RT-PCR (qRT-PCR), Western blot, co-immunoprecipitation, ubiquitination, and tumor xenograft experiments were performed. Results Western blot and qRT-PCR results indicated that knockdown of endogenous DARPP-32 markedly reduces expression of CD44 V8-V10 (CD44E). Using a quantitative splicing luciferase reporter system, we detected a significant increase in the reporter activity following DARPP-32 overexpression (p < 0.001). Conversely, knocking down endogenous DARPP-32 significantly attenuated the splicing activity (p < 0.001). Further experiments showed that DARPP-32 regulates the expression of SRp20 splicing factor and co-exists with it in the same protein complex. Inhibition of alternative splicing with digitoxin followed by immunoprecipitation and immunoblotting indicated that DARPP-32 plays an important role in regulating SRp20 protein stability. The knockdown of endogenous DARPP-32 confirmed that DARPP-32 regulates the SRp20-dependent CD44E splicing. Using tumor xenograft mouse model, knocking down endogenous DARPP-32 markedly reduced SRp20 and CD44E protein levels with a decreased tumor growth. The reconstitution of SRp20 expression in these cells rescued tumor growth. In addition, we also demonstrated frequent co-overexpression and positive correlation of DARPP-32, SRp20 and CD44E expression levels in human gastric primary tumors. Conclusion Our novel findings establish for the first time the role of DARPP-32 in regulating splicing factors in gastric cancer cells. The DARPP-32–SRp20 axis plays a key role in regulating the CD44E splice variant that promotes gastric tumorigenesis.
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Wang F, Wendling KS, Soprano KJ, Soprano DR. The SAP motif and C-terminal RS- and RD/E-rich region influences the sub-nuclear localization of Acinus isoforms. J Cell Biochem 2015; 115:2165-74. [PMID: 25079509 DOI: 10.1002/jcb.24893] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 07/25/2014] [Indexed: 11/06/2022]
Abstract
Acinus has been reported to function in apoptosis, RNA processing and regulation of gene transcription including RA-dependent transcription. There are three different isoforms of Acinus termed Acinus-L, Acinus-S', and Acinus-S. The isoforms of Acinus differ in their N-terminus while the C-terminus is consistent in all isoforms. The sub-nuclear localization of Acinus-L and Acinus-S' was determined using fluorescence microscopy. Acinus-S' colocalizes with SC35 in nuclear speckles while Acinus-L localizes diffusely throughout the nucleoplasm. RA treatment has little effect on the sub-nuclear localization of Acinus-L and Acinus-S'. The domains/regions necessary for the distinct sub-nuclear localization of Acinus-L and Acinus-S' were identified. The speckled sub-nuclear localization of Acinus-S' is dependent on its C-terminal RS- and RD/E-rich region but is independent of the phosphorylation status of Ser-453 and Ser-604 within this region. The unique N-terminal SAP motif of Acinus-L is responsible for its diffuse localization in the nucleus. Moreover, the sub-nuclear localization of Acinus isoforms is affected by each other, which is determined by the combinatorial effect of the more potent SAP motif of Acinus-L and the C-terminal RS- and RD/E-rich region in all Acinus isoforms. The C-terminal RS- and RD/E-rich region of Acinus mediates the colocalization of Acinus isoforms as well as with its interacting protein RNPS1. In conclusion, the SAP motif is responsible for the difference in the nuclear localization between Acinus-L and Acinus-S'. This difference in the nuclear localization of Acinus-S' and Acinus-L may suggest that these two isoforms have different functional roles.
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Affiliation(s)
- Fang Wang
- Department of Biochemistry, Temple University School of Medicine, Philadelphia, Pennsylvania, 19140
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Abstract
Efficient transcription of the HIV-1 genome is regulated by Tat, which recruits P-TEFb from the 7SK small nuclear ribonucleoprotein (snRNP) and other nucleoplasmic complexes to phosphorylate RNA polymerase II and other factors associated with the transcription complex. Although Tat activity is dependent on its binding to the viral TAR sequence, little is known about the cellular factors that might also assemble onto this region of the viral transcript. Here, we report that the splicing factor SRSF1 (SF2/ASF) and Tat recognize overlapping sequences within TAR and the 7SK RNA. SRSF1 expression can inhibit Tat transactivation by directly competing for its binding to TAR. Additionally, we provide evidence that SRSF1 can increase the basal level of viral transcription in the absence of Tat. We propose that SRSF1 activates transcription in the early stages of viral infection by recruiting P-TEFb to TAR from the 7SK snRNP. Whereas in the later stages, Tat substitutes for SRSF1 by promoting release of the stalled polymerase and more efficient transcriptional elongation.
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Affiliation(s)
- Sean Paz
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA
| | | | - Massimo Caputi
- Charles E. Schmidt College of Medicine, Florida Atlantic University, 777 Glades Rd, Boca Raton, FL 33431, USA
- To whom correspondence should be addressed. Tel: +1 5612970627;
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Eshar S, Altenhofen L, Rabner A, Ross P, Fastman Y, Mandel-Gutfreund Y, Karni R, Llinás M, Dzikowski R. PfSR1 controls alternative splicing and steady-state RNA levels in Plasmodium falciparum through preferential recognition of specific RNA motifs. Mol Microbiol 2015; 96:1283-97. [PMID: 25807998 DOI: 10.1111/mmi.13007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2015] [Indexed: 11/28/2022]
Abstract
Plasmodium species have evolved complex biology to adapt to different hosts and changing environments throughout their life cycle. Remarkably, these adaptations are achieved by a relatively small genome. One way by which the parasite expands its proteome is through alternative splicing (AS). We recently identified PfSR1 as a bona fide Ser/Arg-rich (SR) protein that shuttles between the nucleus and cytoplasm and regulates AS in Plasmodium falciparum. Here we show that PfSR1 is localized adjacent to the Nuclear Pore Complex (NPC) clusters in the nucleus of early stage parasites. To identify the endogenous RNA targets of PfSR1, we adapted an inducible overexpression system for tagged PfSR1 and performed RNA immunoprecipitation followed by microarray analysis (RIP-chip) to recover and identify the endogenous RNA targets that bind PfSR1. Bioinformatic analysis of these RNAs revealed common sequence motifs potentially recognized by PfSR1. RNA-EMSAs show that PfSR1 preferentially binds RNA molecules containing these motifs. Interestingly, we find that PfSR1 not only regulates AS but also the steady-state levels of mRNAs containing these motifs in vivo.
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Affiliation(s)
- Shiri Eshar
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Lindsey Altenhofen
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.,Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Alona Rabner
- Department of Biology, Israel Institute of Technology-Technion, Haifa, Israel
| | - Phil Ross
- Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Yair Fastman
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | | | - Rotem Karni
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
| | - Manuel Llinás
- Department of Molecular Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA.,Department of Biochemistry and Molecular Biology, Department of Chemistry and Center for Malaria Research, Pennsylvania State University, State College, PA, 16802, USA
| | - Ron Dzikowski
- Department of Microbiology and Molecular Genetics, The Kuvin Center for the Study of Infectious and Tropical Diseases, The Institute for Medical Research Israel-Canada, The Hebrew University - Hadassah Medical School, Jerusalem, Israel
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SRSF1 RNA Recognition Motifs Are Strong Inhibitors of HIV-1 Replication. J Virol 2015; 89:6275-86. [PMID: 25855733 DOI: 10.1128/jvi.00693-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 03/27/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED Replication of the integrated HIV-1 genome is tightly regulated by a series of cellular factors. In previous work we showed that transactivation of the HIV-1 promoter is regulated by the cellular splicing factor SRSF1. Here we report that SRSF1 can downregulate the replication of B, C, and D subtype viruses by >200-fold in a cell culture system. We show that viral transcription and splicing are inhibited by SRSF1 expression. Furthermore, SRSF1 deletion mutants containing the protein RNA-binding domains but not the arginine serine-rich activator domain can downregulate viral replication by >2,000-fold with minimal impact on cell viability and apoptosis. These data suggest a therapeutic potential for SRSF1 and its RNA-binding domains. IMPORTANCE Most drugs utilized to treat the HIV-1 infection are based on compounds that directly target proteins encoded by the virus. However, given the high viral mutation rate, the appearance of novel drug-resistant viral strains is common. Thus, there is a need for novel therapeutics with diverse mechanisms of action. In this study, we show that the cellular protein SRSF1 is a strong inhibitor of viral replication. Furthermore, expression of the SRSF1 RNA-binding domains alone can inhibit viral replication by >2,000-fold in multiple viral strains without impacting cell viability. Given the strong antiviral properties of this protein, the RNA-binding domains, and the minimal effects observed on cell metabolism, further studies are warranted to assess the therapeutic potential of peptides derived from these sequences.
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Balanced splicing at the Tat-specific HIV-1 3'ss A3 is critical for HIV-1 replication. Retrovirology 2015; 12:29. [PMID: 25889056 PMCID: PMC4422144 DOI: 10.1186/s12977-015-0154-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 02/26/2015] [Indexed: 11/12/2022] Open
Abstract
Background The viral regulatory protein Tat is essential for establishing a productive transcription from the 5′-LTR promoter during the early phase of viral gene expression. Formation of the Tat-encoding mRNAs requires splicing at the viral 3′ss A3, which has previously been shown to be both negatively and positively regulated by the downstream splicing regulatory elements (SREs) ESS2p and ESE2/ESS2. However, using the novel RESCUE-type computational HEXplorer algorithm, we were recently able to identify another splicing enhancer (ESE5807-5838, henceforth referred to as ESEtat) located between ESS2p and ESE2/ESS2. Here we show that ESEtat has a great impact on viral tat-mRNA splicing and that it is fundamental for regulated 3′ss A3 usage. Results Mutational inactivation or locked nucleic acid (LNA)-directed masking of the ESEtat sequence in the context of a replication-competent virus was associated with a failure (i) to activate viral 3′ss A3 and (ii) to accumulate Tat-encoding mRNA species. Consequently, due to insufficient amounts of Tat protein efficient viral replication was drastically impaired. RNA in vitro binding assays revealed SRSF2 and SRSF6 as candidate splicing factors acting through ESEtat and ESE2 for 3′ss A3 activation. This notion was supported by coexpression experiments, in which wild-type, but not ESEtat-negative provirus responded to higher levels of SRSF2 and SRSF6 proteins with higher levels of tat-mRNA splicing. Remarkably, we could also find that SRSF6 overexpression established an antiviral state within provirus-transfected cells, efficiently blocking virus particle production. For the anti-HIV-1 activity the arginine-serine (RS)-rich domain of the splicing factor was dispensable. Conclusions Based on our results, we propose that splicing at 3′ss A3 is dependent on binding of the enhancing SR proteins SRSF2 and SRSF6 to the ESEtat and ESE2 sequence. Mutational inactivation or interference specifically with ESEtat activity by LNA-directed masking seem to account for an early stage defect in viral gene expression, probably by cutting off the supply line of Tat that HIV needs to efficiently transcribe its genome.
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Palusa SG, Reddy ASN. Differential recruitment of splice variants from SR pre-mRNAs to polysomes during development and in response to stresses. PLANT & CELL PHYSIOLOGY 2015; 56:421-7. [PMID: 25637375 DOI: 10.1093/pcp/pcv010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We have previously shown that precursor mRNAs (pre-mRNAs) of serine/arginine-rich (SR) proteins are extensively alternatively spliced to generate approximately 100 distinct splice variants from 14 SR genes and that the splicing pattern of SR pre-mRNAs changes in different organs and in response to abiotic stresses. About half of the splice variants are potential targets of nonsense-mediated decay (NMD) and 25 splice forms were confirmed to be real NMD targets. However, it is not known whether (i) all splice variants are recruited to polysomes for translation; (ii) there is a preferential recruitment of specific splice isoforms to polysomes; and (iii) there is a differential recruitment of splice variants during development and in response to stresses. To address these questions, we analyzed the association of SR splice variants with polysomes from seedlings, different organs and seedlings exposed to heat and cold stress. In seedlings, about one-third of the splice variants (22 out of 72) are not recruited to polysomes. Among those associated with polysomes, the functional isoforms that code for full-length proteins and some candidate putative and confirmed NMD targets were identified. There was preferential recruitment of some splice forms over others. Predominant recruitment of functional isoforms along with a few NMD candidates was found in different organs. Furthermore, we observed differential recruitment of isoforms in different organs. Heat and cold stress enhanced or reduced recruitment of specific splice variants. Our studies reveal differential recruitment of SR splice variants to polysomes under normal conditions, during development and in response to stresses.
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Affiliation(s)
- Saiprasad Goud Palusa
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Anireddy S N Reddy
- Department of Biology, Program in Molecular Plant Biology, Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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Yearim A, Gelfman S, Shayevitch R, Melcer S, Glaich O, Mallm JP, Nissim-Rafinia M, Cohen AHS, Rippe K, Meshorer E, Ast G. HP1 is involved in regulating the global impact of DNA methylation on alternative splicing. Cell Rep 2015; 10:1122-34. [PMID: 25704815 DOI: 10.1016/j.celrep.2015.01.038] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 12/03/2014] [Accepted: 01/15/2015] [Indexed: 01/07/2023] Open
Abstract
The global impact of DNA methylation on alternative splicing is largely unknown. Using a genome-wide approach in wild-type and methylation-deficient embryonic stem cells, we found that DNA methylation can either enhance or silence exon recognition and affects the splicing of more than 20% of alternative exons. These exons are characterized by distinct genetic and epigenetic signatures. Alternative splicing regulation of a subset of these exons can be explained by heterochromatin protein 1 (HP1), which silences or enhances exon recognition in a position-dependent manner. We constructed an experimental system using site-specific targeting of a methylated/unmethylated gene and demonstrate a direct causal relationship between DNA methylation and alternative splicing. HP1 regulates this gene's alternative splicing in a methylation-dependent manner by recruiting splicing factors to its methylated form. Our results demonstrate DNA methylation's significant global influence on mRNA splicing and identify a specific mechanism of splicing regulation mediated by HP1.
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Affiliation(s)
- Ahuvi Yearim
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Sahar Gelfman
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel; Center for Human Genome Variation, Duke University School of Medicine, Durham, NC 27708, USA
| | - Ronna Shayevitch
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Shai Melcer
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra (Givat Ram) Campus, Jerusalem 91904, Israel
| | - Ohad Glaich
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Jan-Philipp Mallm
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Malka Nissim-Rafinia
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra (Givat Ram) Campus, Jerusalem 91904, Israel
| | - Ayelet-Hashahar S Cohen
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra (Givat Ram) Campus, Jerusalem 91904, Israel
| | - Karsten Rippe
- Deutsches Krebsforschungszentrum (DKFZ) and BioQuant, Research Group Genome Organization & Function, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Eran Meshorer
- Department of Genetics, Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra (Givat Ram) Campus, Jerusalem 91904, Israel.
| | - Gil Ast
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel-Aviv University, Ramat Aviv 69978, Israel.
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Wee CD, Havens MA, Jodelka FM, Hastings ML. Targeting SR proteins improves SMN expression in spinal muscular atrophy cells. PLoS One 2014; 9:e115205. [PMID: 25506695 PMCID: PMC4266657 DOI: 10.1371/journal.pone.0115205] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 11/19/2014] [Indexed: 12/19/2022] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common inherited causes of pediatric mortality. SMA is caused by deletions or mutations in the survival of motor neuron 1 (SMN1) gene, which results in SMN protein deficiency. Humans have a centromeric copy of the survival of motor neuron gene, SMN2, which is nearly identical to SMN1. However, SMN2 cannot compensate for the loss of SMN1 because SMN2 has a single-nucleotide difference in exon 7, which negatively affects splicing of the exon. As a result, most mRNA produced from SMN2 lacks exon 7. SMN2 mRNA lacking exon 7 encodes a truncated protein with reduced functionality. Improving SMN2 exon 7 inclusion is a goal of many SMA therapeutic strategies. The identification of regulators of exon 7 inclusion may provide additional therapeutic targets or improve the design of existing strategies. Although a number of regulators of exon 7 inclusion have been identified, the function of most splicing proteins in exon 7 inclusion is unknown. Here, we test the role of SR proteins and hnRNP proteins in SMN2 exon 7 inclusion. Knockdown and overexpression studies reveal that SRSF1, SRSF2, SRSF3, SRSF4, SRSF5, SRSF6, SRSF7, SRSF11, hnRNPA1/B1 and hnRNP U can inhibit exon 7 inclusion. Depletion of two of the most potent inhibitors of exon 7 inclusion, SRSF2 or SRSF3, in cell lines derived from SMA patients, increased SMN2 exon 7 inclusion and SMN protein. Our results identify novel regulators of SMN2 exon 7 inclusion, revealing potential targets for SMA therapeutics.
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Affiliation(s)
- Claribel D. Wee
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Mallory A. Havens
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Francine M. Jodelka
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
| | - Michelle L. Hastings
- Department of Cell Biology and Anatomy, The Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, Illinois, United States of America
- * E-mail:
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75
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Majerciak V, Lu M, Li X, Zheng ZM. Attenuation of the suppressive activity of cellular splicing factor SRSF3 by Kaposi sarcoma-associated herpesvirus ORF57 protein is required for RNA splicing. RNA (NEW YORK, N.Y.) 2014; 20:1747-1758. [PMID: 25234929 PMCID: PMC4201827 DOI: 10.1261/rna.045500.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 08/04/2014] [Indexed: 05/29/2023]
Abstract
Kaposi sarcoma-associated herpesvirus (KSHV) ORF57 is a multifunctional post-transcriptional regulator essential for viral gene expression during KSHV lytic infection. ORF57 requires interactions with various cellular proteins for its function. Here, we identified serine/arginine-rich splicing factor 3 (SRSF3, formerly known as SRp20) as a cellular cofactor involved in ORF57-mediated splicing of KSHV K8β RNA. In the absence of ORF57, SRSF3 binds to a suboptimal K8β intron and inhibits K8β splicing. Knockdown of SRSF3 promotes K8β splicing, mimicking the effect of ORF57. The N-terminal half of ORF57 binds to the RNA recognition motif of SRSF3, which prevents SRSF3 from associating with the K8β intron RNA and therefore attenuates the suppressive effect of SRSF3 on K8β splicing. ORF57 also promotes splicing of heterologous non-KSHV transcripts that are negatively regulated by SRSF3, indicating that the effect of ORF57 on SRSF3 activity is independent of RNA target. SPEN proteins, previously identified as ORF57-interacting partners, suppress ORF57 splicing activity by displacing ORF57 from SRSF3-RNA complexes. In summary, we have identified modulation of SRSF3 activity as the molecular mechanism by which ORF57 promotes RNA splicing.
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Affiliation(s)
- Vladimir Majerciak
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Mathew Lu
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Xiaofan Li
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, USA
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76
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Regulation of gene expression programmes by serine–arginine rich splicing factors. Semin Cell Dev Biol 2014; 32:11-21. [DOI: 10.1016/j.semcdb.2014.03.011] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 03/11/2014] [Indexed: 12/21/2022]
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77
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Du C, Ma X, Meruvu S, Hugendubler L, Mueller E. The adipogenic transcriptional cofactor ZNF638 interacts with splicing regulators and influences alternative splicing. J Lipid Res 2014; 55:1886-96. [PMID: 25024404 DOI: 10.1194/jlr.m047555] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Increasing evidence indicates that transcription and alternative splicing are coordinated processes; however, our knowledge of specific factors implicated in both functions during the process of adipocyte differentiation is limited. We have previously demonstrated that the zinc finger protein ZNF638 plays a role as a transcriptional coregulator of adipocyte differentiation via induction of PPARγ in cooperation with CCAAT/enhancer binding proteins (C/EBPs). Here we provide new evidence that ZNF638 is localized in nuclear bodies enriched with splicing factors, and through biochemical purification of ZNF638's interacting proteins in adipocytes and mass spectrometry analysis, we show that ZNF638 interacts with splicing regulators. Functional analysis of the effects of ectopic ZNF638 expression on a minigene reporter demonstrated that ZNF638 is sufficient to promote alternative splicing, a function enhanced through its recruitment to the minigene promoter at C/EBP responsive elements via C/EBP proteins. Structure-function analysis revealed that the arginine/serine-rich motif and the C-terminal zinc finger domain required for speckle localization are necessary for the adipocyte differentiation function of ZNF638 and for the regulation of the levels of alternatively spliced isoforms of lipin1 and nuclear receptor co-repressor 1. Overall, our data demonstrate that ZNF638 participates in splicing decisions and that it may control adipogenesis through regulation of the relative amounts of differentiation-specific isoforms.
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Affiliation(s)
- Chen Du
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Xinran Ma
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sunitha Meruvu
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Lynne Hugendubler
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Elisabetta Mueller
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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78
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Kulshreshtha V, Ayalew LE, Islam A, Tikoo SK. Conserved arginines of bovine adenovirus-3 33K protein are important for transportin-3 mediated transport and virus replication. PLoS One 2014; 9:e101216. [PMID: 25019945 PMCID: PMC4096500 DOI: 10.1371/journal.pone.0101216] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 06/04/2014] [Indexed: 01/14/2023] Open
Abstract
The L6 region of bovine adenovirus (BAdV)-3 encodes a spliced protein designated 33K. The 33K specific sera detected five major proteins and three minor proteins in transfected or virus infected cells, which could arise by internal initiation of translation and alternative splicing. The 33K protein is predominantly localized to the nucleus of BAdV-3 infected cells. The 33K nuclear transport utilizes both classical importin-α/-β and importin-β dependent nuclear import pathways and preferentially binds to importin-α5 and transportin-3 receptors, respectively. Analysis of mutant 33K proteins demonstrated that amino acids 201–240 of the conserved C-terminus of 33K containing RS repeat are required for nuclear localization and, binding to both importin-α5 and transportin-3 receptors. Interestingly, the arginine residues of conserved RS repeat are required for binding to transportin-3 receptor but not to importin-α5 receptor. Moreover, mutation of arginines residues of RS repeat proved lethal for production of progeny virus. Our results suggest that arginines of RS repeat are required for efficient nuclear transport of 33K mediated by transportin-3, which appears to be essential for replication and production of infectious virion.
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Affiliation(s)
- Vikas Kulshreshtha
- VIDO-InterVac, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Lisanework E. Ayalew
- VIDO-InterVac, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Azharul Islam
- VIDO-InterVac, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Suresh K. Tikoo
- VIDO-InterVac, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Vaccinology & Immunotherapeutics Program, School of Public Health, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail:
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79
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Abstract
This review summarizes the current understanding of the role of nuclear bodies in regulating gene expression. The compartmentalization of cellular processes, such as ribosome biogenesis, RNA processing, cellular response to stress, transcription, modification and assembly of spliceosomal snRNPs, histone gene synthesis and nuclear RNA retention, has significant implications for gene regulation. These functional nuclear domains include the nucleolus, nuclear speckle, nuclear stress body, transcription factory, Cajal body, Gemini of Cajal body, histone locus body and paraspeckle. We herein review the roles of nuclear bodies in regulating gene expression and their relation to human health and disease.
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Affiliation(s)
| | - Cornelius F. Boerkoel
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-604-875-2157; Fax: +1-604-875-2376
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80
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Das S, Krainer AR. Emerging functions of SRSF1, splicing factor and oncoprotein, in RNA metabolism and cancer. Mol Cancer Res 2014; 12:1195-204. [PMID: 24807918 DOI: 10.1158/1541-7786.mcr-14-0131] [Citation(s) in RCA: 194] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Serine/Arginine Splicing Factor 1 (SRSF1) is the archetype member of the SR protein family of splicing regulators. Since its discovery over two decades ago, SRSF1 has been repeatedly surprising and intriguing investigators by the plethora of complex biologic pathways it regulates. These include several key aspects of mRNA metabolism, such as mRNA splicing, stability, and translation, as well as other mRNA-independent processes, such as miRNA processing, protein sumoylation, and the nucleolar stress response. In this review, the structural features of SRSF1 are discussed as they relate to the intricate mechanism of splicing and the multiplicity of functions it performs. Similarly, a list of relevant alternatively spliced transcripts and SRSF1 interacting proteins is provided. Finally, emphasis is given to the deleterious consequences of overexpression of the SRSF1 proto-oncogene in human cancers, and the complex mechanisms and pathways underlying SRSF1-mediated transformation. The accumulated knowledge about SRSF1 provides critical insight into the integral role it plays in maintaining cellular homeostasis and suggests new targets for anticancer therapy. Mol Cancer Res; 12(9); 1195-204. ©2014 AACR.
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Affiliation(s)
- Shipra Das
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
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81
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Maslon MM, Heras SR, Bellora N, Eyras E, Cáceres JF. The translational landscape of the splicing factor SRSF1 and its role in mitosis. eLife 2014; 3:e02028. [PMID: 24842991 PMCID: PMC4027812 DOI: 10.7554/elife.02028] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 04/21/2014] [Indexed: 12/19/2022] Open
Abstract
The shuttling Serine/Arginine rich (SR) protein SRSF1 (previously known as SF2/ASF) is a splicing regulator that also activates translation in the cytoplasm. In order to dissect the gene network that is translationally regulated by SRSF1, we performed a high-throughput deep sequencing analysis of polysomal fractions in cells overexpressing SRSF1. We identified approximately 1,500 mRNAs that are translational targets of SRSF1. These include mRNAs encoding proteins involved in cell cycle regulation, such as spindle, kinetochore and M phase proteins, which are essential for accurate chromosome segregation. Indeed, we show that translational activity of SRSF1 is required for normal mitotic progression. Furthermore, we found that mRNAs that display alternative splicing changes upon SRSF1 overexpression are also its translational targets; strongly suggesting that SRSF1 couples pre-mRNA splicing and translation. These data provide insights on the complex role of SRSF1 in the control of gene expression at multiple levels and its implications in cancer.
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Affiliation(s)
- Magdalena M Maslon
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sara R Heras
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, Spain
| | - Nicolas Bellora
- Computational Genomics Group, Universitat Pompeu Fabra, Barcelona, Spain
| | - Eduardo Eyras
- Computational Genomics Group, Universitat Pompeu Fabra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Javier F Cáceres
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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82
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Identification of a BRCA1-mRNA splicing complex required for efficient DNA repair and maintenance of genomic stability. Mol Cell 2014; 54:445-59. [PMID: 24746700 PMCID: PMC4017265 DOI: 10.1016/j.molcel.2014.03.021] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 12/21/2013] [Accepted: 02/14/2014] [Indexed: 12/30/2022]
Abstract
Mutations within BRCA1 predispose carriers to a high risk of breast and ovarian cancers. BRCA1 functions to maintain genomic stability through the assembly of multiple protein complexes involved in DNA repair, cell-cycle arrest, and transcriptional regulation. Here, we report the identification of a DNA damage-induced BRCA1 protein complex containing BCLAF1 and other key components of the mRNA-splicing machinery. In response to DNA damage, this complex regulates pre-mRNA splicing of a number of genes involved in DNA damage signaling and repair, thereby promoting the stability of these transcripts/proteins. Further, we show that abrogation of this complex results in sensitivity to DNA damage, defective DNA repair, and genomic instability. Interestingly, mutations in a number of proteins found within this complex have been identified in numerous cancer types. These data suggest that regulation of splicing by the BRCA1-mRNA splicing complex plays an important role in the cellular response to DNA damage.
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83
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Gonçalves V, Henriques A, Pereira J, Neves Costa A, Moyer MP, Moita LF, Gama-Carvalho M, Matos P, Jordan P. Phosphorylation of SRSF1 by SRPK1 regulates alternative splicing of tumor-related Rac1b in colorectal cells. RNA (NEW YORK, N.Y.) 2014; 20:474-82. [PMID: 24550521 PMCID: PMC3964909 DOI: 10.1261/rna.041376.113] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 01/07/2014] [Indexed: 05/28/2023]
Abstract
The premessenger RNA of the majority of human genes can generate various transcripts through alternative splicing, and different tissues or disease states show specific patterns of splicing variants. These patterns depend on the relative concentrations of the splicing factors present in the cell nucleus, either as a consequence of their expression levels or of post-translational modifications, such as protein phosphorylation, which are determined by signal transduction pathways. Here, we analyzed the contribution of protein kinases to the regulation of alternative splicing variant Rac1b that is overexpressed in certain tumor types. In colorectal cells, we found that depletion of AKT2, AKT3, GSK3β, and SRPK1 significantly decreased endogenous Rac1b levels. Although knockdown of AKT2 and AKT3 affected only Rac1b protein levels suggesting a post-splicing effect, the depletion of GSK3β or SRPK1 decreased Rac1b alternative splicing, an effect mediated through changes in splicing factor SRSF1. In particular, the knockdown of SRPK1 or inhibition of its catalytic activity reduced phosphorylation and subsequent translocation of SRSF1 to the nucleus, limiting its availability to promote the inclusion of alternative exon 3b into the Rac1 pre-mRNA. Altogether, the data identify SRSF1 as a prime regulator of Rac1b expression in colorectal cells and provide further mechanistic insight into how the regulation of alternative splicing events by protein kinases can contribute to sustain tumor cell survival.
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Affiliation(s)
- Vânia Gonçalves
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Andreia Henriques
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Joana Pereira
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Ana Neves Costa
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | | | - Luís Ferreira Moita
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisboa, Portugal
| | - Margarida Gama-Carvalho
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Paulo Matos
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Peter Jordan
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- BioFIG–Centre for Biodiversity, Functional and Integrative Genomics, University of Lisbon, 1749-016 Lisbon, Portugal
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84
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Qian W, Liu F. Regulation of alternative splicing of tau exon 10. Neurosci Bull 2014; 30:367-77. [PMID: 24627328 DOI: 10.1007/s12264-013-1411-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 01/03/2014] [Indexed: 12/22/2022] Open
Abstract
The neuronal microtubule-associated protein tau is abnormally hyperphosphorylated and aggregated into neurofibrillary tangles in the brains of individuals with Alzheimer's disease and related neurodegenerative disorders. The adult human brain expresses six isoforms of tau generated by alternative splicing of exons 2, 3, and 10 of its pre-mRNA. Exon 10 encodes the second microtubule-binding repeat of tau. Its alternative splicing produces tau isoforms with either three or four microtubule-binding repeats, termed 3R-tau and 4Rtau. In the normal adult human brain, the level of 3R-tau is approximately equal to that of 4R-tau. Several silent and intronic mutations of the tau gene associated with FTDP-17T (frontotemporal dementia with Parkinsonism linked to chromosome 17 and specifically characterized by tau pathology) only disrupt exon 10 splicing, but do not influence the primary sequence of the tau protein. Thus, abnormal exon 10 splicing is sufficient to cause neurodegeneration and dementia. Here, we review the regulation of tau exon 10 splicing by cis-elements and trans-factors and summarize all the mutations associated with FTDP-17T and related tauopathies. The findings suggest that correction of exon 10 splicing may be a potential target for tau exon 10 splicing-related tauopathies.
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Affiliation(s)
- Wei Qian
- Department of Biochemistry and Molecular Biology, School of Medicine, Nantong University, Nantong, 226001, China
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85
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Kano S, Nishida K, Kurebe H, Nishiyama C, Kita K, Akaike Y, Kajita K, Kurokawa K, Masuda K, Kuwano Y, Tanahashi T, Rokutan K. Oxidative stress-inducible truncated serine/arginine-rich splicing factor 3 regulates interleukin-8 production in human colon cancer cells. Am J Physiol Cell Physiol 2014; 306:C250-62. [DOI: 10.1152/ajpcell.00091.2013] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Serine/arginine-rich splicing factor 3 (SRSF3) is a member of the SR protein family and plays wide-ranging roles in gene expression. The human SRSF3 gene generates two alternative splice transcripts, a major mRNA isoform ( SRSF3-FL) encoding functional full-length protein and a premature termination codon (PTC)-containing isoform ( SRSF3-PTC). The latter is degraded through nonsense-mediated mRNA decay (NMD). Treatment of a human colon cancer cell line (HCT116) with 100 μM sodium arsenite increased SRSF3-PTC mRNA levels without changing SRSF3-FL mRNA levels. A chemiluminescence-based NMD reporter assay system demonstrated that arsenite treatment inhibited NMD activity and increased SRSF3-PTC mRNA levels in the cytoplasm, facilitating translation of a truncated SRSF3 protein (SRSF3-TR) from SRSF3-PTC mRNA. SRSF3-TR lacked two-thirds of the Arg/Ser-rich (RS) domain whose phosphorylation state is known to be crucial for subcellular distribution. SRSF3-FL was localized in the nucleus, while overexpressed SRSF3-TR was diffusely distributed in the cytoplasm and the nucleus. A part of SRSF3-TR was also associated with stress granules in the cytoplasm. Interestingly, treatment of HCT116 cells with a small interference RNA specifically targeting SRSF3-PTC mRNA significantly attenuated arsenite-stimulated induction of c-JUN protein, its binding activity to the AP-1 binding site (−126 to 120 bp) in the interleukin (IL)-8 gene promoter, and AP-1 promoter activity, resulting in significant reduction of arsenite-stimulated IL-8 production. Our results suggest that SRSF3-TR may function as a positive regulator of oxidative stress-initiated inflammatory responses in colon cancer cells.
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Affiliation(s)
- Shizuka Kano
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Kensei Nishida
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Hiroyuki Kurebe
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Chihiro Nishiyama
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Kentaro Kita
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Yoko Akaike
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Keisuke Kajita
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Ken Kurokawa
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Kiyoshi Masuda
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Yuki Kuwano
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Toshihito Tanahashi
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - Kazuhito Rokutan
- Department of Stress Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
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86
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Burgute BD, Peche VS, Steckelberg AL, Glöckner G, Gaßen B, Gehring NH, Noegel AA. NKAP is a novel RS-related protein that interacts with RNA and RNA binding proteins. Nucleic Acids Res 2013; 42:3177-93. [PMID: 24353314 PMCID: PMC3950704 DOI: 10.1093/nar/gkt1311] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
NKAP is a highly conserved protein with roles in transcriptional repression, T-cell development, maturation and acquisition of functional competency and maintenance and survival of adult hematopoietic stem cells. Here we report the novel role of NKAP in splicing. With NKAP-specific antibodies we found that NKAP localizes to nuclear speckles. NKAP has an RS motif at the N-terminus followed by a highly basic domain and a DUF 926 domain at the C-terminal region. Deletion analysis showed that the basic domain is important for speckle localization. In pull-down experiments, we identified RNA-binding proteins, RNA helicases and splicing factors as interaction partners of NKAP, among them FUS/TLS. The FUS/TLS–NKAP interaction takes place through the RS domain of NKAP and the RGG1 and RGG3 domains of FUS/TLS. We analyzed the ability of NKAP to interact with RNA using in vitro splicing assays and found that NKAP bound both spliced messenger RNA (mRNA) and unspliced pre-mRNA. Genome-wide analysis using crosslinking and immunoprecipitation-seq revealed NKAP association with U1, U4 and U5 small nuclear RNA, and we also demonstrated that knockdown of NKAP led to an increase in pre-mRNA percentage. Our results reveal NKAP as nuclear speckle protein with roles in RNA splicing and processing.
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Affiliation(s)
- Bhagyashri D Burgute
- Institute of Biochemistry I, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), 50931 Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany, Institute of Genetics, University of Cologne, 50931 Cologne, Germany and Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301, 12587 Berlin, Germany
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87
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Follo MY, Faenza I, Piazzi M, Blalock WL, Manzoli L, McCubrey JA, Cocco L. Nuclear PI-PLCβ1: an appraisal on targets and pathology. Adv Biol Regul 2013; 54:2-11. [PMID: 24296032 DOI: 10.1016/j.jbior.2013.11.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 11/08/2013] [Indexed: 11/16/2022]
Abstract
Lipid signalling molecules are essential components of the processes that allow one extracellular signal to be transferred inside the nucleus, where specific lipid second messengers elicit reactions capable of regulating gene transcription, DNA replication or repair and DNA cleavage, eventually resulting in cell growth, differentiation, apoptosis or many other cell functions. Nuclear inositides are independently regulated, suggesting that the nucleus constitutes a functionally distinct compartment of inositol lipids metabolism. Indeed, nuclear inositol lipids themselves can modulate nuclear processes, such as transcription and pre-mRNA splicing, growth, proliferation, cell cycle regulation and differentiation. Nuclear PI-PLCβ1 is a key molecule for nuclear inositide signalling, where it plays a role in cell cycle progression, proliferation and differentiation. Here we review the targets and possible involvement of nuclear PI-PLCβ1 in human physiology and pathology.
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Affiliation(s)
- Matilde Y Follo
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
| | - Irene Faenza
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Manuela Piazzi
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - William L Blalock
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Genetica Molecolare and SC Laboratorio di Biologia Cellulare Muscoloscheletrica, IOR, Bologna, Italy
| | - Lucia Manzoli
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Lucio Cocco
- Department of Biomedical and Neuromotor Sciences, Cellular Signalling Laboratory, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
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88
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Cléry A, Sinha R, Anczuków O, Corrionero A, Moursy A, Daubner GM, Valcárcel J, Krainer AR, Allain FHT. Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition. Proc Natl Acad Sci U S A 2013; 110:E2802-11. [PMID: 23836656 PMCID: PMC3725064 DOI: 10.1073/pnas.1303445110] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Serine/arginine (SR) proteins, one of the major families of alternative-splicing regulators in Eukarya, have two types of RNA-recognition motifs (RRMs): a canonical RRM and a pseudo-RRM. Although pseudo-RRMs are crucial for activity of SR proteins, their mode of action was unknown. By solving the structure of the human SRSF1 pseudo-RRM bound to RNA, we discovered a very unusual and sequence-specific RNA-binding mode that is centered on one α-helix and does not involve the β-sheet surface, which typically mediates RNA binding by RRMs. Remarkably, this mode of binding is conserved in all pseudo-RRMs tested. Furthermore, the isolated pseudo-RRM is sufficient to regulate splicing of about half of the SRSF1 target genes tested, and the bound α-helix is a pivotal element for this function. Our results strongly suggest that SR proteins with a pseudo-RRM frequently regulate splicing by competing with, rather than recruiting, spliceosome components, using solely this unusual RRM.
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Affiliation(s)
- Antoine Cléry
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Rahul Sinha
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Olga Anczuków
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | - Anna Corrionero
- Institució Catalana de Recerca i Estudis Avançats, Universitat Pompeu Fabra 08003 Barcelona, Spain; and
- Centre de Regulació Genòmica, 08003 Barcelona, Spain
| | - Ahmed Moursy
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Gerrit M. Daubner
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
| | - Juan Valcárcel
- Institució Catalana de Recerca i Estudis Avançats, Universitat Pompeu Fabra 08003 Barcelona, Spain; and
- Centre de Regulació Genòmica, 08003 Barcelona, Spain
| | | | - Frédéric H.-T. Allain
- Institute for Molecular Biology and Biophysics, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland
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89
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Identification of nuclear retention domains in the RBM20 protein. FEBS Lett 2013; 587:2989-95. [PMID: 23886709 DOI: 10.1016/j.febslet.2013.07.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/07/2013] [Accepted: 07/15/2013] [Indexed: 11/21/2022]
Abstract
RBM20 is a nuclear protein which regulates alternative splicing of expressed genes that have a key role in cardiac function. By cloning the human and mouse RBM20 cDNA, producing expressing vectors for truncated proteins, and comparing their sub-cellular distribution in transfected cells, we have identified the sequences necessary for RBM20 full nuclear retention. The region overlaps an RNA binding motif and a serine-arginine domain. The sequence is conserved in many species but belongs only to RBM20 orthologs. The RMB20 tissue specificity, together with the properties of its nuclear localization determinant, demonstrates a specific evolutionary selection of post-transcriptional regulation factors.
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90
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Shimoni-Sebag A, Lebenthal-Loinger I, Zender L, Karni R. RRM1 domain of the splicing oncoprotein SRSF1 is required for MEK1-MAPK-ERK activation and cellular transformation. Carcinogenesis 2013; 34:2498-504. [PMID: 23843040 DOI: 10.1093/carcin/bgt247] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing regulators have emerged as new players in cancer development, modulating the activities of many tumor suppressors and oncogenes and regulating the signaling pathways. However, little is known about the mechanisms by which these oncogenic splicing factors lead to cellular transformation. We have shown previously that the splicing factor serine and arginine splicing factor 1 (SRSF1; SF2/ASF) is a proto-oncogene, which is amplified in breast cancer and transforms immortal cells when overexpressed. In this study, we performed a structure-function analysis of SRSF1 and found that the RNA recognition motif 1 (RRM1) domain is required for its oncogenic activity. Deletion of RRM1 eliminated the splicing activity of SRSF1 on some of its endogenous targets. Moreover, we found that SRSF1 elevates the expression of B-Raf and activates the mitogen-activated protein kinase kinase (MEK) extracellular signal-regulated kinase (ERK) pathway and that RRM1 is required for this activation as well. B-Raf-MEK-ERK activation by SRSF1 contributes to transformation as pharmacological inhibition of MEK1 inhibits SRSF1-mediated transformation. In conclusion, RRM1 of SRSF1 is both required (and when tethered to the RS domain) also sufficient to activate the Raf-MEK-ERK pathway and to promote cellular transformation.
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Affiliation(s)
- Ariel Shimoni-Sebag
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Ein Karem, Jerusalem 91120, Israel and
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91
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Cao LJ, Zhao MM, Liu C, Dong HJ, Li WC, Ren HY. LlSR28 is involved in pollen germination by affecting filamentous actin dynamics. MOLECULAR PLANT 2013; 6:1163-1175. [PMID: 23741063 DOI: 10.1093/mp/sst097] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Alternative splicing plays important roles in gene regulation and contributes to protein complexity. Previous studies suggest that alternative splicing exists in members of the villin/gelsolin/fragmin superfamily. In this study, a serine/argine-rich (SR) protein cDNA with 28 kDa protein (LlSR28) was isolated from a lily (Lilium longiflorum) expression library. Protein domain analysis showed that LlSR28 had similar structures to Arabidopsis SR45 (AtSR45), and LlSR28 could complement the phenotype of loss of AtSR45 function. Therefore, overexpression of LlSR28 and AtSR45 mutant (atsr45-1) were used in the following experiments. Overexpression of LlSR28 in Arabidopsis completely inhibited pollen germination. In contrast, the pollen germination of atsr45-1 was earlier than that of wild-type. In addition, pollen of atsr45-1 contained less F-actin at the corresponding hydration stage during pollen germination compared to that of wild-type. Alternative splicing analysis showed that Arabidopsis villin1 (AtVLN1) transcript encoding the full-length protein was increased, and that encoding the truncated protein was decreased in atst45-1. Moreover, the mRNA expression level of other actin-binding proteins (ABPs) abundant in Arabidopsis pollen was also changed in atsr45-1. In conclusion, we hypothesize that LlSR28 alters F-actin dynamics probably through its alternative splicing activities to affect directly or indirectly the alternative splicing of AtVLN1 and the expression of different ABPs, which then affects the pollen germination.
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Affiliation(s)
- Li-Juan Cao
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Science, Beijing Normal University, Beijing 100875, China
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92
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Fu Y, Huang B, Shi Z, Han J, Wang Y, Huangfu J, Wu W. SRSF1 and SRSF9 RNA binding proteins promote Wnt signalling-mediated tumorigenesis by enhancing β-catenin biosynthesis. EMBO Mol Med 2013; 5:737-50. [PMID: 23592547 PMCID: PMC3662316 DOI: 10.1002/emmm.201202218] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Revised: 02/08/2013] [Accepted: 03/06/2013] [Indexed: 12/21/2022] Open
Abstract
Wnt/β-catenin signalling is widely implicated in embryogenesis, tissue homeostasis and tumorigenesis. The key event in Wnt signalling activation is β-catenin accumulation, which is controlled by both its production and degradation. However, much more emphasis has been placed on the understanding of its degradation. Here, we show that the synthesis of β-catenin protein, which requires a group of serine/arginine-rich splicing factors (SRSF), also contributes to its tumorigenic activity. Overexpression of SRSF1 and SRSF9 promote β-catenin accumulation via the recruitment of β-catenin mRNA and by enhancing its translation in an mTOR-dependent manner. We further demonstrate that, like SRSF1, SRSF9 is also an oncogene, and is frequently overexpressed in multiple types of human tumours. Finally, our results suggest that promoting degradation and blocking production of β-catenin synergistically reduce β-catenin levels under pathological conditions and that a combinational therapy could be a promising approach for the treatment of cancer patients.
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Affiliation(s)
- Yu Fu
- Protein Science Laboratory of the Ministry of Education, School of Life Sciences, Tsinghua University, Beijing, China
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93
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Kim Y, Kong M, Lee C. Association of intronic sequence variant in the gene encoding spleen tyrosine kinase with susceptibility to vascular dementia. World J Biol Psychiatry 2013; 14:220-6. [PMID: 23480133 DOI: 10.3109/15622975.2011.559272] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
OBJECTIVES This study was aimed to identify a novel strong candidate gene for the susceptibility to vascular dementia (VaD) with comprehensive evidences. METHODS A preliminary genome-wide association study (GWAS) was conducted to identify nucleotide sequence variants susceptible to VaD. Literature-based analysis and network analysis were conducted to single out the best candidate gene, and its association was thoroughly examined over its whole sequences. Functions of the most probable variant were predicted by in silico alternative splicing analysis and evaluated by minigene assay. RESULTS The GWAS showed the most significant variant in spleen tyrosine kinase (SYK) gene. This concurred with the suggestions from both literature-based analysis and network analysis. Further association analysis over the whole SYK gene revealed that rs290227 in intron 8 was the most significant (P = 7.38 × 10(-11)). The subsequent in silico analysis showed that the intronic variant played potential roles in alternative splicing by skipping exon 8 or by truncating exon 9. It was validated by in vivo minigene assay that the G allele of rs290227 induced the delayed splicing. CONCLUSIONS We suggested a novel association of the VaD susceptibility with an intronic variant of rs290227 in the SYK gene. Its Gallele could render mature transcripts inappropriately by intron retention and thus lead to a genetic risk for VaD.
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Affiliation(s)
- Younyoung Kim
- Department of Bioinformatics and Life Science, Soongsil University, Seoul, Korea
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94
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Roca X, Krainer AR, Eperon IC. Pick one, but be quick: 5' splice sites and the problems of too many choices. Genes Dev 2013; 27:129-44. [PMID: 23348838 DOI: 10.1101/gad.209759.112] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Splice site selection is fundamental to pre-mRNA splicing and the expansion of genomic coding potential. 5' Splice sites (5'ss) are the critical elements at the 5' end of introns and are extremely diverse, as thousands of different sequences act as bona fide 5'ss in the human transcriptome. Most 5'ss are recognized by base-pairing with the 5' end of the U1 small nuclear RNA (snRNA). Here we review the history of research on 5'ss selection, highlighting the difficulties of establishing how base-pairing strength determines splicing outcomes. We also discuss recent work demonstrating that U1 snRNA:5'ss helices can accommodate noncanonical registers such as bulged duplexes. In addition, we describe the mechanisms by which other snRNAs, regulatory proteins, splicing enhancers, and the relative positions of alternative 5'ss contribute to selection. Moreover, we discuss mechanisms by which the recognition of numerous candidate 5'ss might lead to selection of a single 5'ss and propose that protein complexes propagate along the exon, thereby changing its physical behavior so as to affect 5'ss selection.
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Affiliation(s)
- Xavier Roca
- School of Biological Sciences, Division of Molecular Genetics and Cell Biology, Nanyang Technological University, Singapore.
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95
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Choudhury NR, de Lima Alves F, de Andrés-Aguayo L, Graf T, Cáceres JF, Rappsilber J, Michlewski G. Tissue-specific control of brain-enriched miR-7 biogenesis. Genes Dev 2013; 27:24-38. [PMID: 23307866 DOI: 10.1101/gad.199190.112] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
MicroRNA (miRNA) biogenesis is a highly regulated process in eukaryotic cells. Several mature miRNAs exhibit a tissue-specific pattern of expression without an apparent tissue-specific pattern for their corresponding primary transcripts. This discrepancy is suggestive of post-transcriptional regulation of miRNA abundance. Here, we demonstrate that the brain-enriched expression of miR-7, which is processed from the ubiquitous hnRNP K pre-mRNA transcript, is achieved by inhibition of its biogenesis in nonbrain cells in both human and mouse systems. Using stable isotope labeling by amino acids in cell culture (SILAC) mass spectrometry combined with RNase-assisted RNA pull-down, we identified Musashi homolog 2 (MSI2) and Hu antigen R (HuR) proteins as inhibitors of miR-7 processing in nonneural cells. This is achieved through HuR-mediated binding of MSI2 to the conserved terminal loop of pri-miR-7. Footprinting and electrophoretic gel mobility shift analysis (EMSA) provide further evidence for a direct interaction between pri-miR-7-1 and the HuR/MSI2 complex, resulting in stabilization of the pri-miR-7-1 structure. We also confirmed the physiological relevance of this inhibitory mechanism in a neuronal differentiation system using human SH-SY5Y cells. Finally, we show elevated levels of miR-7 in selected tissues from MSI2 knockout (KO) mice without apparent changes in the abundance of the pri-miR-7 transcript. Altogether, our data provide the first insight into the regulation of brain-enriched miRNA processing by defined tissue-specific factors.
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Affiliation(s)
- Nila Roy Choudhury
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, United Kingdom
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96
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Li SJ, Qi Y, Zhao JJ, Li Y, Liu XY, Chen XH, Xu P. Characterization of nuclear localization signals (NLSs) and function of NLSs and phosphorylation of serine residues in subcellular and subnuclear localization of transformer-2β (Tra2β). J Biol Chem 2013; 288:8898-909. [PMID: 23396973 DOI: 10.1074/jbc.m113.456715] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The serine/arginine-rich (SR) proteins are one type of major actors in regulation of pre-mRNA splicing. Their functions are closely related to the intracellular spatial organization. The RS domain and phosphorylation status of SR proteins are two critical factors in determining the subcellular distribution. Mammalian Transformer-2β (Tra2β) protein, a member of SR proteins, is known to play multiple important roles in development and diseases. In the present study, we characterized the subcellular and subnuclear localization of Tra2β protein and its related mechanisms. The results demonstrated that in the brain the nuclear and cytoplasmic localization of Tra2β were correlated with its phosphorylation status. Using deletional mutation analysis, we showed that the nuclear localization of Tra2β was determined by multiple nuclear localization signals (NLSs) in the RS domains. The point-mutation analysis disclosed that phosphorylation of serine residues in the NLSs inhibited the function of NLS in directing Tra2β to the nucleus. In addition, we identified at least two nuclear speckle localization signals within the RS1 domain, but not in the RS2 domain. The nuclear speckle localization signals determined the localization of RS1 domain-contained proteins to the nuclear speckle. The function of the signals did not depend on the presence of serine residues. The results provide new insight into the mechanisms by which the subcellular and subnuclear localization of Tra2β proteins are regulated.
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Affiliation(s)
- Shu-Jing Li
- Laboratory of Genomic Physiology, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China
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97
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Lin-Moshier Y, Sebastian PJ, Higgins L, Sampson ND, Hewitt JE, Marchant JS. Re-evaluation of the role of calcium homeostasis endoplasmic reticulum protein (CHERP) in cellular calcium signaling. J Biol Chem 2013; 288:355-67. [PMID: 23148228 PMCID: PMC3537033 DOI: 10.1074/jbc.m112.405761] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/31/2012] [Indexed: 11/06/2022] Open
Abstract
Changes in cytoplasmic Ca(2+) concentration, resulting from activation of intracellular Ca(2+) channels within the endoplasmic reticulum, regulate several aspects of cellular growth and differentiation. Ca(2+) homeostasis endoplasmic reticulum protein (CHERP) is a ubiquitously expressed protein that has been proposed as a regulator of both major families of endoplasmic reticulum Ca(2+) channels, inositol 1,4,5-trisphosphate receptors (IP(3)Rs) and ryanodine receptors (RyRs), with resulting effects on mitotic cycling. However, the manner by which CHERP regulates intracellular Ca(2+) channels to impact cellular growth is unknown. Here, we challenge previous findings that CHERP acts as a direct cytoplasmic regulator of IP(3)Rs and RyRs and propose that CHERP acts in the nucleus to impact cellular proliferation by regulating the function of the U2 snRNA spliceosomal complex. The previously reported effects of CHERP on cellular growth therefore are likely indirect effects of altered spliceosomal function, consistent with prior data showing that loss of function of U2 snRNP components can interfere with cell growth and induce cell cycle arrest.
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Affiliation(s)
| | | | - LeeAnn Higgins
- Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, Minnesota 55455 and
| | - Natalie D. Sampson
- the School of Biology, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
| | - Jane E. Hewitt
- the School of Biology, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, United Kingdom
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98
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Sugaya K, Ishihara Y, Sugaya K, Inoue S. Characterization of the role of Smu1 in nuclear localization of splicing factors in the mammalian temperature-sensitive mutant. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajmb.2013.31005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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99
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Schor IE, Llères D, Risso GJ, Pawellek A, Ule J, Lamond AI, Kornblihtt AR. Perturbation of chromatin structure globally affects localization and recruitment of splicing factors. PLoS One 2012; 7:e48084. [PMID: 23152763 PMCID: PMC3495951 DOI: 10.1371/journal.pone.0048084] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Accepted: 09/19/2012] [Indexed: 12/02/2022] Open
Abstract
Chromatin structure is an important factor in the functional coupling between transcription and mRNA processing, not only by regulating alternative splicing events, but also by contributing to exon recognition during constitutive splicing. We observed that depolarization of neuroblastoma cell membrane potential, which triggers general histone acetylation and regulates alternative splicing, causes a concentration of SR proteins in nuclear speckles. This prompted us to analyze the effect of chromatin structure on splicing factor distribution and dynamics. Here, we show that induction of histone hyper-acetylation results in the accumulation in speckles of multiple splicing factors in different cell types. In addition, a similar effect is observed after depletion of the heterochromatic protein HP1α, associated with repressive chromatin. We used advanced imaging approaches to analyze in detail both the structural organization of the speckle compartment and nuclear distribution of splicing factors, as well as studying direct interactions between splicing factors and their association with chromatin in vivo. The results support a model where perturbation of normal chromatin structure decreases the recruitment efficiency of splicing factors to nascent RNAs, thus causing their accumulation in speckles, which buffer the amount of free molecules in the nucleoplasm. To test this, we analyzed the recruitment of the general splicing factor U2AF65 to nascent RNAs by iCLIP technique, as a way to monitor early spliceosome assembly. We demonstrate that indeed histone hyper-acetylation decreases recruitment of U2AF65 to bulk 3′ splice sites, coincident with the change in its localization. In addition, prior to the maximum accumulation in speckles, ∼20% of genes already show a tendency to decreased binding, while U2AF65 seems to increase its binding to the speckle-located ncRNA MALAT1. All together, the combined imaging and biochemical approaches support a model where chromatin structure is essential for efficient co-transcriptional recruitment of general and regulatory splicing factors to pre-mRNA.
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Affiliation(s)
- Ignacio E. Schor
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - David Llères
- Dundee Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Guillermo J. Risso
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Andrea Pawellek
- Dundee Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Jernej Ule
- Laboratory of Molecular Biology, Medical Research Council, Cambridge, England, United Kingdom
| | - Angus I. Lamond
- Dundee Centre for Gene Regulation and Expression, University of Dundee, Dundee, Scotland, United Kingdom
| | - Alberto R. Kornblihtt
- Laboratorio de Fisiología y Biología Molecular, Departamento de Fisiología, Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias, Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
- * E-mail:
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100
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Elinav H, Wu Y, Coskun A, Hryckiewicz K, Kemler I, Hu Y, Rogers H, Hao B, Ben Mamoun C, Poeschla E, Sutton R. Human CRM1 augments production of infectious human and feline immunodeficiency viruses from murine cells. J Virol 2012; 86:12053-68. [PMID: 22933280 PMCID: PMC3486471 DOI: 10.1128/jvi.01970-12] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 08/18/2012] [Indexed: 11/20/2022] Open
Abstract
Productive replication of human immunodeficiency virus type 1 (HIV-1) occurs efficiently only in humans. The posttranscriptional stages of the HIV-1 life cycle proceed poorly in mouse cells, with a resulting defect in viral assembly and release. Previous work has shown that the presence of human chromosome 2 increases HIV-1 production in mouse cells. Recent studies have shown that human chromosome region maintenance 1 (hCRM1) stimulates Gag release from rodent cells. Here we report that expressions of hCRM1 in murine cells resulted in marked increases in the production of infectious HIV-1 and feline immunodeficiency virus (FIV). HIV-1 production was also increased by hSRp40, and a combination of hCRM1 and hSRp40 resulted in a more-than-additive effect on HIV-1 release. In contrast, the overexpression of mouse CRM1 (mCRM1) minimally affected HIV-1 and FIV production and did not antagonize hCRM1. In the presence of hCRM1 there were large increases in the amounts of released capsid, which paralleled the increases in the infectious titers. Consistent with this finding, the ratios of unspliced to spliced HIV-1 mRNAs in mouse cells expressing hCRM1 and SRp40 became similar to those of human cells. Furthermore, imaging of intron-containing FIV RNA showed that hCRM1 increased RNA export to the cytoplasm.By testing chimeras between mCRM1 and hCRM1 and comparing those sequences to feline CRM1, we mapped the functional domain to HEAT (Huntingtin, elongation factor 3, protein phosphatase 2A, and the yeast kinase TOR1) repeats 4A to 9A and a triple point mutant in repeat 9A, which showed a loss of function. Structural analysis suggested that this region of hCRM1 may serve as a binding site for viral or cellular factors to facilitate lentiviral RNA nuclear export.
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Affiliation(s)
- Hila Elinav
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Yuanfei Wu
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Ayse Coskun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Katarzyna Hryckiewicz
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Iris Kemler
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Yani Hu
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Hilary Rogers
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Bing Hao
- Department of Molecular, Microbial and Structural Biology, University of Connecticut Health Center, Farmington, Connecticut, USA
| | - Choukri Ben Mamoun
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Eric Poeschla
- Department of Molecular Medicine, Mayo Clinic College of Medicine, Rochester, Minnesota, USA
| | - Richard Sutton
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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