1
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De Silva N, Lehman N, Fargason T, Paul T, Zhang Z, Zhang J. Unearthing a novel function of SRSF1 in binding and unfolding of RNA G-quadruplexes. Nucleic Acids Res 2024; 52:4676-4690. [PMID: 38567732 PMCID: PMC11077049 DOI: 10.1093/nar/gkae213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
SRSF1 governs splicing of over 1500 mRNA transcripts. SRSF1 contains two RNA-recognition motifs (RRMs) and a C-terminal Arg/Ser-rich region (RS). It has been thought that SRSF1 RRMs exclusively recognize single-stranded exonic splicing enhancers, while RS lacks RNA-binding specificity. With our success in solving the insolubility problem of SRSF1, we can explore the unknown RNA-binding landscape of SRSF1. We find that SRSF1 RS prefers purine over pyrimidine. Moreover, SRSF1 binds to the G-quadruplex (GQ) from the ARPC2 mRNA, with both RRMs and RS being crucial. Our binding assays show that the traditional RNA-binding sites on the RRM tandem and the Arg in RS are responsible for GQ binding. Interestingly, our FRET and circular dichroism data reveal that SRSF1 unfolds the ARPC2 GQ, with RS leading unfolding and RRMs aiding. Our saturation transfer difference NMR results discover that Arg residues in SRSF1 RS interact with the guanine base but not other nucleobases, underscoring the uniqueness of the Arg/guanine interaction. Our luciferase assays confirm that SRSF1 can alleviate the inhibitory effect of GQ on gene expression in the cell. Given the prevalence of RNA GQ and SR proteins, our findings unveil unexplored SR protein functions with broad implications in RNA splicing and translation.
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Affiliation(s)
- Naiduwadura Ivon Upekala De Silva
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL 35294-1240, USA
| | - Nathan Lehman
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL 35294-1240, USA
| | - Talia Fargason
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL 35294-1240, USA
| | - Trenton Paul
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL 35294-1240, USA
| | - Zihan Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL 35294-1240, USA
| | - Jun Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL 35294-1240, USA
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2
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Forman TE, Sajek MP, Larson ED, Mukherjee N, Fantauzzo KA. PDGFRα signaling regulates Srsf3 transcript binding to affect PI3K signaling and endosomal trafficking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.03.587975. [PMID: 38617350 PMCID: PMC11014628 DOI: 10.1101/2024.04.03.587975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Signaling through the platelet-derived growth factor receptor alpha (PDGFRa) plays a critical role in craniofacial development, as mutations in PDGFRA are associated with cleft lip/palate in humans and Pdgfra mutant mouse models display varying degrees of facial clefting. Phosphatidylinositol 3-kinase (PI3K)/Akt is the primary effector of PDGFRα signaling during skeletal development in the mouse. We previously demonstrated that Akt phosphorylates the RNA-binding protein serine/arginine-rich splicing factor 3 (Srsf3) downstream of PI3K-mediated PDGFRa signaling in mouse embryonic palatal mesenchyme (MEPM) cells, leading to its nuclear translocation. We further showed that ablation of Srsf3 in the murine neural crest lineage results in severe midline facial clefting, due to defects in proliferation and survival of cranial neural crest cells, and widespread alternative RNA splicing (AS) changes. Here, we sought to determine the molecular mechanisms by which Srsf3 activity is regulated downstream of PDGFRa signaling to control AS of transcripts necessary for craniofacial development. We demonstrated via enhanced UV-crosslinking and immunoprecipitation (eCLIP) of MEPM cells that PDGF-AA stimulation leads to preferential binding of Srsf3 to exons and loss of binding to canonical Srsf3 CA-rich motifs. Through the analysis of complementary RNA-seq data, we showed that Srsf3 activity results in the preferential inclusion of exons with increased GC content and lower intron to exon length ratio. Moreover, we found that the subset of transcripts that are bound by Srsf3 and undergo AS upon PDGFRα signaling commonly encode regulators of PI3K signaling and early endosomal trafficking. Functional validation studies further confirmed that Srsf3 activity downstream of PDGFRα signaling leads to retention of the receptor in early endosomes and increases in downstream PI3K-mediated Akt signaling. Taken together, our findings reveal that growth factor-mediated phosphorylation of an RNA-binding protein underlies gene expression regulation necessary for mammalian craniofacial development.
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Affiliation(s)
- Thomas E. Forman
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Marcin P. Sajek
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Eric D. Larson
- Department of Otolaryngology – Head and Neck Surgery, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- Basic and Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Neelanjan Mukherjee
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Katherine A. Fantauzzo
- Department of Craniofacial Biology, School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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3
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Sudhakar SRN, Khan SN, Clark A, Hendrickson-Rebizant T, Patel S, Lakowski TM, Davie JR. Protein arginine methyltransferase 1, a major regulator of biological processes. Biochem Cell Biol 2024; 102:106-126. [PMID: 37922507 DOI: 10.1139/bcb-2023-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) is a major type I arginine methyltransferase that catalyzes the formation of monomethyl and asymmetric dimethylarginine in protein substrates. It was first identified to asymmetrically methylate histone H4 at the third arginine residue forming the H4R3me2a active histone mark. However, several protein substrates are now identified as being methylated by PRMT1. As a result of its association with diverse classes of substrates, PRMT1 regulates several biological processes like chromatin dynamics, transcription, RNA processing, and signal transduction. The review provides an overview of PRMT1 structure, biochemical features, specificity, regulation, and role in cellular functions. We discuss the genomic distribution of PRMT1 and its association with tRNA genes. Further, we explore the different substrates of PRMT1 involved in splicing. In the end, we discuss the proteins that interact with PRMT1 and their downstream effects in diseased states.
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Affiliation(s)
- Sadhana R N Sudhakar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Shahper N Khan
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ariel Clark
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | | | - Shrinal Patel
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ted M Lakowski
- College of Pharmacy Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
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4
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Granados AA, Kanrar N, Elowitz MB. Combinatorial expression motifs in signaling pathways. CELL GENOMICS 2024; 4:100463. [PMID: 38216284 PMCID: PMC10794782 DOI: 10.1016/j.xgen.2023.100463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/02/2023] [Accepted: 11/15/2023] [Indexed: 01/14/2024]
Abstract
In animal cells, molecular pathways often comprise families of variant components, such as ligands or receptors. These pathway components are differentially expressed by different cell types, potentially tailoring pathway function to cell context. However, it has remained unclear how pathway expression profiles are distributed across cell types and whether similar profiles can occur in dissimilar cell types. Here, using single-cell gene expression datasets, we identified pathway expression motifs, defined as recurrent expression profiles that are broadly distributed across diverse cell types. Motifs appeared in core pathways, including TGF-β, Notch, Wnt, and the SRSF splice factors, and involved combinatorial co-expression of multiple components. Motif usage was weakly correlated between pathways in adult cell types and during dynamic developmental transitions. Together, these results suggest a mosaic view of cell type organization, in which different cell types operate many of the same pathways in distinct modes.
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Affiliation(s)
- Alejandro A Granados
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Nivedita Kanrar
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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5
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De Silva NIU, Lehman N, Fargason T, Paul T, Zhang Z, Zhang J. Unearthing SRSF1's Novel Function in Binding and Unfolding of RNA G-Quadruplexes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.563137. [PMID: 37961538 PMCID: PMC10634998 DOI: 10.1101/2023.10.30.563137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
SRSF1 governs splicing of over 1,500 mRNA transcripts. SRSF1 contains two RNA-recognition motifs (RRMs) and a C-terminal Arg/Ser-rich region (RS). It has been thought that SRSF1 RRMs exclusively recognize single-stranded exonic splicing enhancers, while RS lacks RNA-binding specificity. With our success in solving the insolubility problem of SRSF1, we can explore the unknown RNA-binding landscape of SRSF1. We find that SRSF1 RS prefers purine over pyrimidine. Moreover, SRSF1 binds to the G-quadruplex (GQ) from the ARPC2 mRNA, with both RRMs and RS being crucial. Our binding assays show that the traditional RNA-binding sites on the RRM tandem and the Arg in RS are responsible for GQ binding. Interestingly, our FRET and circular dichroism data reveal that SRSF1 unfolds the ARPC2 GQ, with RS leading unfolding and RRMs aiding. Our saturation transfer difference NMR results discover that Arg residues in SRSF1 RS interact with the guanine base but other nucleobases, underscoring the uniqueness of the Arg/guanine interaction. Our luciferase assays confirm that SRSF1 can alleviate the inhibitory effect of GQ on gene expression in the cell. Given the prevalence of RNA GQ and SR proteins, our findings unveil unexplored SR protein functions with broad implications in RNA splicing and translation.
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Affiliation(s)
- Naiduwadura Ivon Upekala De Silva
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Nathan Lehman
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Talia Fargason
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Trenton Paul
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Zihan Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
| | - Jun Zhang
- Department of Chemistry, College of Arts and Sciences, University of Alabama at Birmingham, CH266, 901 14th Street South, Birmingham, AL, 35294-1240, USA
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6
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Saccone G. A history of the genetic and molecular identification of genes and their functions controlling insect sex determination. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 151:103873. [PMID: 36400424 DOI: 10.1016/j.ibmb.2022.103873] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
The genetics of the sex determination regulatory cascade in Drosophila melanogaster has a fascinating history, interlinked with the foundation of the Genetics discipline itself. The discovery that alternative splicing rather than differential transcription is the molecular mechanism underlying the upstream control of sex differences in the Drosophila model system was surprising. This notion is now fully integrated into the scientific canon, appearing in many genetics textbooks and online education resources. In the last three decades, it was a key reference point for starting evolutionary studies in other insect species by using homology-based approaches. This review will introduce a very brief history of Drosophila genetics. It will describe the genetic and molecular approaches applied for the identifying and cloning key genes involved in sex determination in Drosophila and in many other insect species. These comparative analyses led to supporting the idea that sex-determining pathways have evolved mainly by recruiting different upstream signals/genes while maintaining widely conserved intermediate and downstream regulatory genes. The review also provides examples of the link between technological advances and research achievements, to stimulate reflections on how science is produced. It aims to hopefully strengthen the related historical and conceptual knowledge of general readers of other disciplines and of younger geneticists, often focused on the latest technical-molecular approaches.
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Affiliation(s)
- Giuseppe Saccone
- Department of Biology, University of Naples Federico II, Via Cinthia 26, 80126, Naples, Italy.
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7
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Shenasa H, Movassat M, Forouzmand E, Hertel KJ. Allosteric regulation of U1 snRNP by splicing regulatory proteins controls spliceosomal assembly. RNA (NEW YORK, N.Y.) 2020; 26:1389-1399. [PMID: 32522889 PMCID: PMC7491332 DOI: 10.1261/rna.075135.120] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/02/2020] [Indexed: 06/01/2023]
Abstract
Alternative splicing is responsible for much of the transcriptomic and proteomic diversity observed in eukaryotes and involves combinatorial regulation by many cis-acting elements and trans-acting factors. SR and hnRNP splicing regulatory proteins often have opposing effects on splicing efficiency depending on where they bind the pre-mRNA relative to the splice site. Position-dependent splicing repression occurs at spliceosomal E-complex, suggesting that U1 snRNP binds but cannot facilitate higher order spliceosomal assembly. To test the hypothesis that the structure of U1 snRNA changes during activation or repression, we developed a method to structure-probe native U1 snRNP in enriched conformations that mimic activated or repressed spliceosomal E-complexes. While the core of U1 snRNA is highly structured, the 5' end of U1 snRNA shows different SHAPE reactivities and psoralen crosslinking efficiencies depending on where splicing regulatory elements are located relative to the 5' splice site. A motif within the 5' splice site binding region of U1 snRNA is more reactive toward SHAPE electrophiles when repressors are bound, suggesting U1 snRNA is bound, but less base-paired. These observations demonstrate that splicing regulators modulate splice site selection allosterically.
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Affiliation(s)
- Hossein Shenasa
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, USA
| | - Maliheh Movassat
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, USA
| | - Elmira Forouzmand
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, USA
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, USA
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8
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Park S, Brugiolo M, Akerman M, Das S, Urbanski L, Geier A, Kesarwani AK, Fan M, Leclair N, Lin KT, Hu L, Hua I, George J, Muthuswamy SK, Krainer AR, Anczuków O. Differential Functions of Splicing Factors in Mammary Transformation and Breast Cancer Metastasis. Cell Rep 2019; 29:2672-2688.e7. [PMID: 31775037 PMCID: PMC6936330 DOI: 10.1016/j.celrep.2019.10.110] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/09/2019] [Accepted: 10/28/2019] [Indexed: 12/28/2022] Open
Abstract
Misregulation of alternative splicing is a hallmark of human tumors, yet to what extent and how it contributes to malignancy are only beginning to be unraveled. Here, we define which members of the splicing factor SR and SR-like families contribute to breast cancer and uncover differences and redundancies in their targets and biological functions. We identify splicing factors frequently altered in human breast tumors and assay their oncogenic functions using breast organoid models. We demonstrate that not all splicing factors affect mammary tumorigenesis in MCF-10A cells. Specifically, the upregulation of SRSF4, SRSF6, or TRA2β disrupts acinar morphogenesis and promotes cell proliferation and invasion in MCF-10A cells. By characterizing the targets of these oncogenic splicing factors, we identify shared spliced isoforms associated with well-established cancer hallmarks. Finally, we demonstrate that TRA2β is regulated by the MYC oncogene, plays a role in metastasis maintenance in vivo, and its levels correlate with breast cancer patient survival.
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Affiliation(s)
- SungHee Park
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,These authors contributed equally
| | - Mattia Brugiolo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,These authors contributed equally
| | - Martin Akerman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Envisagenics Inc., New York, NY, USA,These authors contributed equally
| | - Shipra Das
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,These authors contributed equally
| | - Laura Urbanski
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | | | | | - Martin Fan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Nathan Leclair
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Graduate Program in Genetics and Development, UConn Health, Farmington, CT, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Leo Hu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ian Hua
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Joshy George
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA,Institute for Systems Genomics, UConn Health, Farmington, CT, USA
| | - Senthil K. Muthuswamy
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Departments of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Adrian R. Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA,Correspondence: (O.A.), (A.R.K.)
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA; Institute for Systems Genomics, UConn Health, Farmington, CT, USA; Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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9
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Comiskey DF, Montes M, Khurshid S, Singh RK, Chandler DS. SRSF2 Regulation of MDM2 Reveals Splicing as a Therapeutic Vulnerability of the p53 Pathway. Mol Cancer Res 2019; 18:194-203. [PMID: 31662450 DOI: 10.1158/1541-7786.mcr-19-0541] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 09/06/2019] [Accepted: 10/25/2019] [Indexed: 11/16/2022]
Abstract
MDM2 is an oncogene and critical negative regulator of tumor suppressor p53. Genotoxic stress causes alternative splicing of MDM2 transcripts, which leads to alterations in p53 activity and contributes to tumorigenesis. MDM2-ALT1 is one of the alternatively spliced transcripts predominantly produced in response to genotoxic stress, and is comprised of terminal coding exons 3 and 12. Previously, we found that SRSF1 induces MDM2-ALT1 by promoting MDM2 exon 11 skipping. Here we report that splicing regulator SRSF2 antagonizes the regulation of SRSF1 by facilitating the inclusion of exon 11 through binding at two conserved exonic splicing enhancers. Overexpression of SRSF2 reduced the generation of MDM2-ALT1 under genotoxic stress, whereas SRSF2 knockdown induced the expression of MDM2-ALT1 in the absence of genotoxic stress. Blocking the exon 11 SRSF2-binding sites using oligonucleotides promoted MDM2-ALT1 splicing and induced p53 protein expression, and apoptosis in p53 wild-type cells. The regulation of MDM2 splicing by SRSF2 is also conserved in mice, as mutation of one SRSF2-binding site in Mdm2 exon 11, using CRISPR-Cas9, increased the expression of the MDM2-ALT1 homolog Mdm2-MS2. IMPLICATIONS: Taken together, the data indicate that modulating MDM2 splicing may be a useful tool for fine-tuning p53 activity in response to genotoxic stress.
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Affiliation(s)
- Daniel F Comiskey
- Department of Pediatrics, The Ohio State University, Columbus, Ohio.,Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Center for RNA Biology, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Matías Montes
- Department of Pediatrics, The Ohio State University, Columbus, Ohio.,Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Center for RNA Biology, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Safiya Khurshid
- Department of Pediatrics, The Ohio State University, Columbus, Ohio.,Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Center for RNA Biology, Wexner Medical Center, The Ohio State University, Columbus, Ohio
| | - Ravi K Singh
- Department of Pediatrics, The Ohio State University, Columbus, Ohio.,Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Center for RNA Biology, Wexner Medical Center, The Ohio State University, Columbus, Ohio.,Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Dawn S Chandler
- Department of Pediatrics, The Ohio State University, Columbus, Ohio. .,Center for Childhood Cancer, The Research Institute at Nationwide Children's Hospital, Columbus, Ohio.,Center for RNA Biology, Wexner Medical Center, The Ohio State University, Columbus, Ohio
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10
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Shenasa H, Hertel KJ. Combinatorial regulation of alternative splicing. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194392. [PMID: 31276857 DOI: 10.1016/j.bbagrm.2019.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 12/23/2022]
Abstract
The generation of protein coding mRNAs from pre-mRNA is a fundamental biological process that is required for gene expression. Alternative pre-mRNA splicing is responsible for much of the transcriptomic and proteomic diversity observed in higher order eukaryotes. Aberrations that disrupt regular alternative splicing patterns are known to cause human diseases, including various cancers. Alternative splicing is a combinatorial process, meaning many factors affect which two splice sites are ligated together. The features that dictate exon inclusion are comprised of splice site strength, intron-exon architecture, RNA secondary structure, splicing regulatory elements, promoter use and transcription speed by RNA polymerase and the presence of post-transcriptional nucleotide modifications. A comprehensive view of all of the factors that influence alternative splicing decisions is necessary to predict splicing outcomes and to understand the molecular basis of disease. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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Affiliation(s)
- Hossein Shenasa
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, United States of America
| | - Klemens J Hertel
- Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697, United States of America.
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11
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Bose D, D V, Shetty M, J K, Kutty AVM. Identification of intronic-splice site mutations in GATA4 gene in Indian patients with congenital heart disease. Mutat Res 2017; 803-805:26-34. [PMID: 28843068 DOI: 10.1016/j.mrfmmm.2017.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/01/2017] [Accepted: 08/08/2017] [Indexed: 12/19/2022]
Abstract
Congenital Heart Disease (CHD) is the most common birth defect among congenital anomalies that arise before birth. GATA4 transcription factor plays an important role in foetal heart development. Mutational analysis of GATA4 gene in CHD patients revealed five known heterozygous mutations (p.T355S, p.S377G, p.V380M, p.P394T and p.D425N) identified in exons 5 and 6 regions and fifteen intronic variants in the non-coding regions (g.76885T>C/Y,g.76937G>S, g.78343G>R, g.83073T>Y, g.83271C>A/M, g.83318G>K, g.83415G>R, g.83502A>C/M, g.84991G>R, g.85294C>Y, g.85342C>T/Y, g.86268A>R, g.87409G>A/R, g.87725T>Y, g.87813A>T/W). In silico analysis of these intronic variants identified two potential branch point mutations (g.83271C>A/M, g.86268A>R) and predicted effects of these on intronic splice sites as enhancer and silencer motifs. This study attempts to correlate the pattern of intronic variants of GATA4 gene which might provide new insights to unravel the possible molecular etiology of CHD.
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Affiliation(s)
- Divya Bose
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, Karnataka, India
| | - Vaigundan D
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, Karnataka, India
| | - Mitesh Shetty
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, Karnataka, India
| | - Krishnappa J
- Department of Pediatrics, Sri Devaraj Urs Medical College, R. L. Jalappa Hospital and Research Centre, Tamaka, Kolar, Karnataka, India
| | - A V M Kutty
- Division of Genomics, Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Tamaka, Kolar, Karnataka, India.
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12
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Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M. Cellular differentiation state modulates the mRNA export activity of SR proteins. J Cell Biol 2017; 216:1993-2009. [PMID: 28592444 PMCID: PMC5496613 DOI: 10.1083/jcb.201610051] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 03/22/2017] [Accepted: 04/24/2017] [Indexed: 01/22/2023] Open
Abstract
SR proteins connect nuclear pre-mRNA processing to mRNA export and translation. Botti et al. develop a quantitative nucleocytoplasmic shuttling assay and show that SR proteins are differentially modified and active in differentiated and pluripotent cells. SR proteins function in nuclear pre-mRNA processing, mRNA export, and translation. To investigate their cellular dynamics, we developed a quantitative assay, which detects differences in nucleocytoplasmic shuttling among seven canonical SR protein family members. As expected, SRSF2 and SRSF5 shuttle poorly in HeLa cells but surprisingly display considerable shuttling in pluripotent murine P19 cells. Combining individual-resolution cross-linking and immunoprecipitation (iCLIP) and mass spectrometry, we show that elevated arginine methylation of SRSF5 and lower phosphorylation levels of cobound SRSF2 enhance shuttling of SRSF5 in P19 cells by modulating protein–protein and protein–RNA interactions. Moreover, SRSF5 is bound to pluripotency-specific transcripts such as Lin28a and Pou5f1/Oct4 in the cytoplasm. SRSF5 depletion reduces and overexpression increases their cytoplasmic mRNA levels, suggesting that enhanced mRNA export by SRSF5 is required for the expression of pluripotency factors. Remarkably, neural differentiation of P19 cells leads to dramatically reduced SRSF5 shuttling. Our findings indicate that posttranslational modification of SR proteins underlies the regulation of their mRNA export activities and distinguishes pluripotent from differentiated cells.
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Affiliation(s)
- Valentina Botti
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - François McNicoll
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Michaela C Steiner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Florian M Richter
- Functional Proteomics Group, Institute for Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anfisa Solovyeva
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marius Wegener
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Oliver D Schwich
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany.,Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Ilka Wittig
- Functional Proteomics Group, Institute for Biochemistry I, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karla M Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Michaela Müller-McNicoll
- Cluster of Excellence Macromolecular Complexes, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
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13
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Shi X, Castandet B, Germain A, Hanson MR, Bentolila S. ORRM5, an RNA recognition motif-containing protein, has a unique effect on mitochondrial RNA editing. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:2833-2847. [PMID: 28549172 PMCID: PMC5853588 DOI: 10.1093/jxb/erx139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/30/2017] [Indexed: 05/02/2023]
Abstract
Plants have an RNA editing mechanism that prevents deleterious organelle mutations from resulting in impaired proteins. A typical flowering plant modifies about 40 cytidines in chloroplast transcripts and many hundreds of cytidines in mitochondrial transcripts. The plant editosome, the molecular machinery responsible for this process, contains members of several protein families, including the organelle RNA recognition motif (ORRM)-containing family. ORRM1 and ORRM6 are chloroplast editing factors, while ORRM2, ORRM3, and ORRM4 are mitochondrial editing factors. Here we report the identification of organelle RRM protein 5 (ORRM5) as a mitochondrial editing factor with a unique mode of action. Unlike other ORRM editing factors, the absence of ORRM5 in orrm5 mutant plants results in an increase of the editing extent in 14% of the mitochondrial sites surveyed. The orrm5 mutant also exhibits a reduced splicing efficiency of the first nad5 intron and slower growth and delayed flowering time. ORRM5 contains an RNA recognition motif (RRM) and a glycine-rich domain at the C terminus. The RRM provides the editing activity of ORRM5 and is able to complement the splicing but not the morphological defects.
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Affiliation(s)
- Xiaowen Shi
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | | | - Arnaud Germain
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Stéphane Bentolila
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Correspondence:
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14
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Ponnuraj K, Saravanan KM. Dihedral angle preferences of DNA and RNA binding amino acid residues in proteins. Int J Biol Macromol 2017; 97:434-439. [PMID: 28099891 DOI: 10.1016/j.ijbiomac.2017.01.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/12/2017] [Accepted: 01/13/2017] [Indexed: 11/30/2022]
Abstract
A protein can interact with DNA or RNA molecules to perform various cellular processes. Identifying or analyzing DNA/RNA binding site amino acid residues is important to understand molecular recognition process. It is quite possible to accurately model DNA/RNA binding amino acid residues in experimental protein-DNA/RNA complex by using the electron density map whereas, locating/modeling the binding site amino acid residues in the predicted three dimensional structures of DNA/RNA binding proteins is still a difficult task. Considering the above facts, in the present work, we have carried out a comprehensive analysis of dihedral angle preferences of DNA and RNA binding site amino acid residues by using a classical Ramachandran map. We have computed backbone dihedral angles of non-DNA/RNA binding residues and used as control dataset to make a comparative study. The dihedral angle preference of DNA and RNA binding site residues of twenty amino acid type is presented. Our analysis clearly revealed that the dihedral angles (φ, ψ) of DNA/RNA binding amino acid residues prefer to occupy (-89° to -60°, -59° to -30°) bins. The results presented in this paper will help to model/locate DNA/RNA binding amino acid residues with better accuracy.
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Affiliation(s)
- Karthe Ponnuraj
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India
| | - Konda Mani Saravanan
- Centre of Advanced Study in Crystallography & Biophysics, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India.
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15
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Abstract
Serine and arginine-rich (SR) proteins are RNA-binding proteins (RBPs) known as constitutive and alternative splicing regulators. As splicing is linked to transcriptional and post-transcriptional steps, SR proteins are implicated in the regulation of multiple aspects of the gene expression program. Recent global analyses of SR-RNA interaction maps have advanced our understanding of SR-regulated gene expression. Diverse SR proteins play partially overlapping but distinct roles in transcription-coupled splicing and mRNA processing in the nucleus. In addition, shuttling SR proteins act as adaptors for mRNA export and as regulators for translation in the cytoplasm. This mini-review will summarize the roles of SR proteins as RNA binders, regulators, and connectors from transcription in the nucleus to translation in the cytoplasm.
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Affiliation(s)
- Sunjoo Jeong
- Department of Bioconvergent Science and Technology, Dankook University, Yongin 16890,
Korea
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16
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He Y, Balasubramanian M, Humphreys N, Waruiru C, Brauner M, Kohlhase J, O'Reilly R, Has C. Intronic ITGA3 Mutation Impacts Splicing Regulation and Causes Interstitial Lung Disease, Nephrotic Syndrome, and Epidermolysis Bullosa. J Invest Dermatol 2016; 136:1056-1059. [PMID: 26854491 DOI: 10.1016/j.jid.2015.11.031] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/07/2015] [Accepted: 11/16/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Yinghong He
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | | | | | | | | | - Ruth O'Reilly
- Sheffield Children's NHS Foundation Trust, Sheffield, UK
| | - Cristina Has
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany.
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17
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Expression of SRPK1 in gliomas and its role in glioma cell lines viability. Tumour Biol 2016; 37:8699-707. [PMID: 26738865 DOI: 10.1007/s13277-015-4738-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/22/2015] [Indexed: 12/30/2022] Open
Abstract
Among factors regulating the splicing of major importance is serine/arginine protein kinase 1 (SRPK1) that phosphorylates SR splicing factors. SRPK1 is expressed in the mammalian central nervous system in a region- and neuron-specific manner. Based on previous observations that glial cells are practically devoid of SRPK1 and reports showing aberrant expression of SRPK1 in numerous tumors, but with conflicting roles, this study aims to investigate the expression of SRPK1 in glioma and its influence on tumor cell biological features. As shown by immunohistochemical analysis, malignant glioma cells express SRPK1 in glioblastomas with significant association between SRPK1 expression and patients' survival. SRPK1 expression was also significantly upregulated at the messenger RNA (mRNA) and protein level in glioma cell lines. Small interfering RNA-mediated downregulation of SRPK1 had little effect on cell viability, while it slightly enhanced the sensitivity of cells to killing by cisplatin. These results support the idea that at least in vitro, the effect of SRPK1 knockdown on the viability of glioma cell lines is rather limited, while the in vivo effects could be attributed to the modulation of angiogenesis by SRPK1.
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18
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Shilo A, Siegfried Z, Karni R. The role of splicing factors in deregulation of alternative splicing during oncogenesis and tumor progression. Mol Cell Oncol 2015; 2:e970955. [PMID: 27308389 PMCID: PMC4905244 DOI: 10.4161/23723548.2014.970955] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/13/2014] [Accepted: 09/15/2014] [Indexed: 04/18/2023]
Abstract
In past decades, cancer research has focused on genetic alterations that are detected in malignant tissues and contribute to the initiation and progression of cancer. These changes include mutations, copy number variations, and translocations. However, it is becoming increasingly clear that epigenetic changes, including alternative splicing, play a major role in cancer development and progression. There are relatively few studies on the contribution of alternative splicing and the splicing factors that regulate this process to cancer development and progression. Recently, multiple studies have revealed altered splicing patterns in cancers and several splicing factors were found to contribute to tumor development. Studies using high-throughput genomic analysis have identified mutations in components of the core splicing machinery and in splicing factors in several cancers. In this review, we will highlight new findings on the role of alternative splicing and its regulators in cancer initiation and progression, in addition to novel approaches to correct oncogenic splicing.
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Affiliation(s)
- Asaf Shilo
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
- Correspondence to: Rotem Karni;
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19
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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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20
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Male-specific phosphorylated SR proteins in adult flies of the Mediterranean fruitfly Ceratitis capitata. BMC Genet 2014; 15 Suppl 2:S6. [PMID: 25472723 PMCID: PMC4255826 DOI: 10.1186/1471-2156-15-s2-s6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Alternative splicing is a widely used mechanism of gene regulation in sex determination pathways of Insects. In species from orders as distant as Diptera, Hymenoptera and Coleoptera, female differentiation relies on the activities of conserved splicing regulators, TRA and TRA-2, promoting female-specific expression of the global effector doublesex (dsx). Less understood is to what extent post-translational modifications of splicing regulators plays a role in this pathway. In Drosophila melanogaster phosphorylation of TRA, TRA-2 and the general RBP1 factor by the LAMMER kinase doa (darkener of apricot) is required for proper female sex determination. To explore whether this is a general feature of the pathway we examined sex-specific differences in phosphorylation levels of SR splicing factors in the dipteran species D. melanogaster, Ceratitis capitata (Medfly) and Musca domestica (Housefly). We found a distinct and reproducible pattern of male-specific phosphorylation on protein extracts enriched for SR proteins in C. capitata suggesting that differential phosphorylation may also contribute to the regulation of sex-specific splicing in the Medfly.
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21
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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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22
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Roberts JM, Ennajdaoui H, Edmondson C, Wirth B, Sanford J, Chen B. Splicing factor TRA2B is required for neural progenitor survival. J Comp Neurol 2014; 522:372-92. [PMID: 23818142 PMCID: PMC3855887 DOI: 10.1002/cne.23405] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/20/2013] [Accepted: 06/21/2013] [Indexed: 01/08/2023]
Abstract
Alternative splicing of pre-mRNAs can rapidly regulate the expression of large groups of proteins. The RNA binding protein TRA2B (SFRS10) plays well-established roles in developmentally regulated alternative splicing during Drosophila sexual differentiation. TRA2B is also essential for mammalian embryogenesis and is implicated in numerous human diseases. Precise regulation of alternative splicing is critical to the development and function of the central nervous system; however, the requirements for specific splicing factors in neurogenesis are poorly understood. This study focuses on the role of TRA2B in mammalian brain development. We show that, during murine cortical neurogenesis, TRA2B is expressed in both neural progenitors and cortical projection neurons. Using cortex-specific Tra2b mutant mice, we show that TRA2B depletion results in apoptosis of the neural progenitor cells as well as disorganization of the cortical plate. Thus, TRA2B is essential for proper development of the cerebral cortex.
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Affiliation(s)
- Jacqueline M Roberts
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Hanane Ennajdaoui
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Carina Edmondson
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Brunhilde Wirth
- Institute of Human Genetics, Institute for Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne 50931, Germany
| | - Jeremy Sanford
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
| | - Bin Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, CA 95064, USA
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23
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Discovering transcription and splicing networks in myelodysplastic syndromes. PLoS One 2013; 8:e79118. [PMID: 24244432 PMCID: PMC3828332 DOI: 10.1371/journal.pone.0079118] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 09/17/2013] [Indexed: 11/19/2022] Open
Abstract
More and more transcription factors and their motifs have been reported and linked to specific gene expression levels. However, focusing only on transcription is not sufficient for mechanism research. Most genes, especially in eukaryotes, are alternatively spliced to different isoforms. Some of these isoforms increase the biodiversity of proteins. From this viewpoint, transcription and splicing are two of important mechanisms to modulate expression levels of isoforms. To integrate these two kinds of regulation, we built a linear regression model to select a subset of transcription factors and splicing factors for each co-expressed isoforms using least-angle regression approach. Then, we applied this method to investigate the mechanism of myelodysplastic syndromes (MDS), a precursor lesion of acute myeloid leukemia. Results suggested that expression levels of most isoforms were regulated by a set of selected regulatory factors. Some of the detected factors, such as EGR1 and STAT family, are highly correlated with progression of MDS. We discovered that the splicing factor SRSF11 experienced alternative splicing switch, and in turn induced different amino acid sequences between MDS and controls. This splicing switch causes two different splicing mechanisms. Polymerase Chain Reaction experiments also confirmed that one of its isoforms was over-expressed in MDS. We analyzed the regulatory networks constructed from the co-expressed isoforms and their regulatory factors in MDS. Many of these networks were enriched in the herpes simplex infection pathway which involves many splicing factors, and pathways in cancers and acute or chronic myeloid leukemia.
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24
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Expression of Tra2 β in Cancer Cells as a Potential Contributory Factor to Neoplasia and Metastasis. Int J Cell Biol 2013; 2013:843781. [PMID: 23935626 PMCID: PMC3723085 DOI: 10.1155/2013/843781] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/09/2013] [Indexed: 01/17/2023] Open
Abstract
The splicing regulator proteins SRSF1 (also known as ASF/SF2) and SRSF3 (also known as SRP20) belong to the SR family of proteins and can be upregulated in cancer. The SRSF1 gene itself is amplified in some cancer cells, and cancer-associated changes in the expression of MYC also increase SRSF1 gene expression. Increased concentrations of SRSF1 protein promote prooncogenic splicing patterns of a number of key regulators of cell growth. Here, we review the evidence that upregulation of the SR-related Tra2β protein might have a similar role in cancer cells. The TRA2B gene encoding Tra2β is amplified in particular tumours including those of the lung, ovary, cervix, stomach, head, and neck. Both TRA2B RNA and Tra2β protein levels are upregulated in breast, cervical, ovarian, and colon cancer, and Tra2β expression is associated with cancer cell survival. The TRA2B gene is a transcriptional target of the protooncogene ETS-1 which might cause higher levels of expression in some cancer cells which express this transcription factor. Known Tra2β splicing targets have important roles in cancer cells, where they affect metastasis, proliferation, and cell survival. Tra2β protein is also known to interact directly with the RBMY protein which is implicated in liver cancer.
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25
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RRP1B is a metastasis modifier that regulates the expression of alternative mRNA isoforms through interactions with SRSF1. Oncogene 2013; 33:1818-27. [PMID: 23604122 PMCID: PMC3925194 DOI: 10.1038/onc.2013.133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 02/14/2013] [Accepted: 02/28/2013] [Indexed: 12/22/2022]
Abstract
RRP1B (ribosomal RNA processing 1 homolog B) was first identified as a metastasis susceptibility gene in breast cancer through its ability to modulate gene expression in a manner that can be used to accurately predict prognosis in breast cancer. However, the mechanism(s) by which RRP1B modulates gene expression is currently unclear. Many RRP1B binding candidates are involved in alternative splicing, a mechanism of gene expression regulation that is increasingly recognized to be involved in cancer progression and metastasis. One such target is SRSF1 (SF2/ASF), an essential splicing regulator that also functions as an oncoprotein. Earlier studies demonstrated that splicing and transcription occur concurrently and are coupled processes. Given that RRP1B regulates transcriptional activity, we hypothesized that RRP1B also regulates the expression of alternative mRNA isoforms through its interaction with SRSF1. Interaction between RRP1B and SRSF1 was verified by co-immunoprecipitation and co-immunofluorescence. Treatment of cells with transcriptional inhibitors significantly increased this interaction, demonstrating that the association of these two proteins is transcriptionally regulated. To assess the role of RRP1B in the regulation of alternative isoform expression, RNA-seq data were generated from control and Rrp1b-knockdown cells. Knockdown of Rrp1b induced a significant change in isoform expression in over 600 genes compared to control cell lines. This was verified by qRT-PCR using isoform-specific primers. Pathway enrichment analyses identified cell cycle and checkpoint regulation to be those most affected by Rrp1b knockdown. These data suggest that RRP1B suppresses metastatic progression by altering the transcriptome through its interaction with splicing regulators such as SRSF1.
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26
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Wong RW, Balachandran A, Ostrowski MA, Cochrane A. Digoxin suppresses HIV-1 replication by altering viral RNA processing. PLoS Pathog 2013; 9:e1003241. [PMID: 23555254 PMCID: PMC3610647 DOI: 10.1371/journal.ppat.1003241] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/24/2013] [Indexed: 11/18/2022] Open
Abstract
To develop new approaches to control HIV-1 replication, we examined the capacity of recently described small molecular modulators of RNA splicing for their effects on viral RNA metabolism. Of the drugs tested, digoxin was found to induce a dramatic inhibition of HIV-1 structural protein synthesis, a response due, in part, to reduced accumulation of the corresponding viral mRNAs. In addition, digoxin altered viral RNA splice site use, resulting in loss of the essential viral factor Rev. Digoxin induced changes in activity of the CLK family of SR protein kinases and modification of several SR proteins, including SRp20 and Tra2β, which could account for the effects observed. Consistent with this hypothesis, overexpression of SRp20 elicited changes in HIV-1 RNA processing similar to those observed with digoxin. Importantly, digoxin was also highly active against clinical strains of HIV-1 in vitro, validating this novel approach to treatment of this infection.
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Affiliation(s)
- Raymond W. Wong
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | | | | | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- * E-mail:
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27
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Regulation of splicing by SR proteins and SR protein-specific kinases. Chromosoma 2013; 122:191-207. [PMID: 23525660 DOI: 10.1007/s00412-013-0407-z] [Citation(s) in RCA: 312] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 03/04/2013] [Accepted: 03/06/2013] [Indexed: 12/21/2022]
Abstract
Genomic sequencing reveals similar but limited numbers of protein-coding genes in different genomes, which begs the question of how organismal diversities are generated. Alternative pre-mRNA splicing, a widespread phenomenon in higher eukaryotic genomes, is thought to provide a mechanism to increase the complexity of the proteome and introduce additional layers for regulating gene expression in different cell types and during development. Among a large number of factors implicated in the splicing regulation are the SR protein family of splicing factors and SR protein-specific kinases. Here, we summarize the rules for SR proteins to function as splicing regulators, which depend on where they bind in exons versus intronic regions, on alternative exons versus flanking competing exons, and on cooperative as well as competitive binding between different SR protein family members on many of those locations. We review the importance of cycles of SR protein phosphorylation/dephosphorylation in the splicing reaction with emphasis on the recent molecular insight into the role of SR protein phosphorylation in early steps of spliceosome assembly. Finally, we highlight recent discoveries of SR protein-specific kinases in transducing growth signals to regulate alternative splicing in the nucleus and the connection of both SR proteins and SR protein kinases to human diseases, particularly cancer.
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Sikora D, Zhang D, Bojic T, Beeharry Y, Tanara A, Pelchat M. Identification of a binding site for ASF/SF2 on an RNA fragment derived from the hepatitis delta virus genome. PLoS One 2013; 8:e54832. [PMID: 23349975 PMCID: PMC3548785 DOI: 10.1371/journal.pone.0054832] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 12/19/2012] [Indexed: 02/07/2023] Open
Abstract
The hepatitis delta virus (HDV) is a small (∼1700 nucleotides) RNA pathogen which encodes only one open reading frame. Consequently, HDV is dependent on host proteins to replicate its RNA genome. Recently, we reported that ASF/SF2 binds directly and specifically to an HDV-derived RNA fragment which has RNA polymerase II promoter activity. Here, we localized the binding site of ASF/SF2 on the HDV RNA fragment by performing binding experiments using purified recombinant ASF/SF2 combined with deletion analysis and site-directed mutagenesis. In addition, we investigated the requirement of ASF/SF2 for HDV RNA replication using RNAi-mediated knock-down of ASF/SF2 in 293 cells replicating HDV RNA. Overall, our results indicate that ASF/SF2 binds to a purine-rich region distant from both the previously published initiation site of HDV mRNA transcription and binding site of RNAP II, and suggest that this protein is not involved in HDV replication in the cellular system used.
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Affiliation(s)
- Dorota Sikora
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Dajiang Zhang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Teodora Bojic
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Yasnee Beeharry
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Ali Tanara
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
| | - Martin Pelchat
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, Canada
- * E-mail:
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Sen S, Jumaa H, Webster NJG. Splicing factor SRSF3 is crucial for hepatocyte differentiation and metabolic function. Nat Commun 2013; 4:1336. [PMID: 23299886 PMCID: PMC4314219 DOI: 10.1038/ncomms2342] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 11/28/2012] [Indexed: 12/23/2022] Open
Abstract
SR family RNA binding proteins regulate splicing of nascent RNAs in vitro but their physiological role in vivo is largely unexplored, as genetic deletion of many SR protein genes results in embryonic lethality. Here we show that SRSF3HKO mice carrying a hepatocyte-specific deletion of Srsf3 (homologous to human SRSF3/SRp20) have a disrupted hepatic architecture and show pre- and postnatal growth retardation. SRSF3HKO mice exhibit impaired hepatocyte maturation with alterations in glucose and lipid homeostasis characterized by reduced glycogen storage, fasting hypoglycemia, increased insulin sensitivity and reduced cholesterol synthesis. We identify various splicing alterations in the SRSF3HKO liver that explain the in vivo phenotype. In particular, loss of SRSF3 causes aberrant splicing of Hnf1α, Ern1, Hmgcs1, Dhcr7 and Scap genes, which are critical regulators of glucose and lipid metabolism. Our study provides the first evidence for a SRSF3-driven genetic programme required for morphological and functional differentiation of hepatocytes that may have relevance for human liver disease and metabolic dysregulation.
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Affiliation(s)
- Supriya Sen
- Medical Research Service, VA San Diego Healthcare System, 3350 La Jolla Village Drive, San Diego, California 92161, USA
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Pradeepa MM, Sutherland HG, Ule J, Grimes GR, Bickmore WA. Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet 2012; 8:e1002717. [PMID: 22615581 PMCID: PMC3355077 DOI: 10.1371/journal.pgen.1002717] [Citation(s) in RCA: 257] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2011] [Accepted: 04/02/2012] [Indexed: 12/25/2022] Open
Abstract
Increasing evidence suggests that chromatin modifications have important roles in modulating constitutive or alternative splicing. Here we demonstrate that the PWWP domain of the chromatin-associated protein Psip1/Ledgf can specifically recognize tri-methylated H3K36 and that, like this histone modification, the Psip1 short (p52) isoform is enriched at active genes. We show that the p52, but not the long (p75), isoform of Psip1 co-localizes and interacts with Srsf1 and other proteins involved in mRNA processing. The level of H3K36me3 associated Srsf1 is reduced in Psip1 mutant cells and alternative splicing of specific genes is affected. Moreover, we show altered Srsf1 distribution around the alternatively spliced exons of these genes in Psip1 null cells. We propose that Psip1/p52, through its binding to both chromatin and splicing factors, might act to modulate splicing.
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Affiliation(s)
- Madapura M. Pradeepa
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Heidi G. Sutherland
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Jernej Ule
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Graeme R. Grimes
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
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Hallgren O, Malmström J, Malmström L, Andersson-Sjöland A, Wildt M, Tufvesson E, Juhasz P, Marko-Varga G, Westergren-Thorsson G. Splicosomal and serine and arginine-rich splicing factors as targets for TGF-β. FIBROGENESIS & TISSUE REPAIR 2012; 5:6. [PMID: 22541002 PMCID: PMC3472233 DOI: 10.1186/1755-1536-5-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Accepted: 04/28/2012] [Indexed: 11/29/2022]
Abstract
Background Transforming growth factor-β1 (TGF-β1) is a potent regulator of cell growth and differentiation. TGF-β1 has been shown to be a key player in tissue remodeling processes in a number of disease states by inducing expression of extracellular matrix proteins. In this study a quantitative proteomic analysis was undertaken to investigate if TGF-β1 contributes to tissue remodeling by mediating mRNA splicing and production of alternative isoforms of proteins. Methodology/Principal findings The expression of proteins involved in mRNA splicing from TGF-β1-stimulated lung fibroblasts was compared to non-stimulated cells by employing isotope coded affinity tag (ICATTM) reagent labeling and tandem mass spectrometry. A total of 1733 proteins were identified and quantified with a relative standard deviation of 11% +/− 8 from enriched nuclear fractions. Seventy-six of these proteins were associated with mRNA splicing, including 22 proteins involved in splice site selection. In addition, TGF-β1 was observed to alter the relative expression of splicing proteins that may be important for alternative splicing of fibronectin. Specifically, TGF-β1 significantly induced expression of SRp20, and reduced the expression of SRp30C, which has been suggested to be a prerequisite for generation of alternatively spliced fibronectin. The induction of SRp20 was further confirmed by western blot and immunofluorescence. Conclusions The results show that TGF-β1 induces the expression of proteins involved in mRNA splicing and RNA processing in human lung fibroblasts. This may have an impact on the production of alternative isoforms of matrix proteins and can therefore be an important factor in tissue remodeling and disease progression.
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Affiliation(s)
- Oskar Hallgren
- Department of Experimental Medical Science, Lund University, Lund, Sweden.
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Li M, Kannian P, Yin H, Kesic M, Green PL. Human T lymphotropic virus type 1 regulatory and accessory gene transcript expression and export are not rex dependent. AIDS Res Hum Retroviruses 2012; 28:405-10. [PMID: 21819218 DOI: 10.1089/aid.2011.0130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Human T lymphotropic virus type 1 (HTLV-1) requires regulated gene expression from unspliced and alternatively spliced transcripts for efficient replication and persistence. HTLV-1 Rex is known to facilitate cytoplasmic export of unspliced, gag/pol and incompletely spliced env mRNAs, but its contribution to the expression of other viral transcripts has not been experimentally assessed. In this study, we utilized HTLV-1 proviral clones, cellular fractionation, and real-time reverse transcriptase PCR to determine the role of Rex on the expression and export of all viral mRNAs. Our results indicate that the steady-state levels of the different viral mRNAs are modulated by Rex, which we attribute to a redistribution of completely spliced mRNAs toward incompletely spliced mRNAs. Furthermore, we confirmed the positive effect of Rex on the unspliced gag/pol mRNA and singly spliced env mRNA, resulting in increased cytoplasmic expression. However, the cytoplasmic export of the alternatively spliced HTLV-1 mRNAs encoding the accessory proteins and the antisense Hbz mRNA are independent of direct Rex regulation. This is consistent with the conclusion that viral mRNAs that contain the cis-acting repressive sequence (CRS) and/or a fully functional splice donor site require a Rex/RxRE interaction for efficient cytoplasmic expression.
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Affiliation(s)
- Min Li
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Priya Kannian
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Han Yin
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Matthew Kesic
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
| | - Patrick L. Green
- Center for Retrovirus Research, The Ohio State University, Columbus, Ohio
- Department of Veterinary Biosciences, The Ohio State University, Columbus, Ohio
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, Ohio
- Comprehensive Cancer Center and Solove Research Institute, The Ohio State University, Columbus, Ohio
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Mytilinaios DG, Tsamis KI, Nikolakaki E, Giannakouros T. Distribution of SRPK1 in human brain. J Chem Neuroanat 2011; 43:20-7. [PMID: 22019390 DOI: 10.1016/j.jchemneu.2011.10.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 10/08/2011] [Accepted: 10/08/2011] [Indexed: 10/16/2022]
Abstract
Extensive alternative splicing is observed in the mammalian nervous system providing for protein diversity and specificity to accomplish the complex neuronal functions. Mechanisms underlying neuron specific splicing are not yet well understood. Among the factors regulating splicing of major importance are serine/arginine protein kinases (SRPKs) that phosphorylate SR splicing factors. SRPK1 is known to be expressed in the mammalian central nervous system. The present immunohistochemical study reveals a region- and neuron-specific localization of SRPK1 in human brain. The potential involvement of the kinase in the regulation of alternative splicing of various neuronal proteins is discussed.
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Affiliation(s)
- D G Mytilinaios
- Laboratory of Neuropathology, 1st Department of Neurology, School of Medicine, Aristotle University, 54636 Thessaloniki, Greece
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Giannakouros T, Nikolakaki E, Mylonis I, Georgatsou E. Serine-arginine protein kinases: a small protein kinase family with a large cellular presence. FEBS J 2011; 278:570-86. [DOI: 10.1111/j.1742-4658.2010.07987.x] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Miura K, Fujibuchi W, Sasaki I. Alternative pre-mRNA splicing in digestive tract malignancy. Cancer Sci 2010; 102:309-16. [PMID: 21134075 DOI: 10.1111/j.1349-7006.2010.01797.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alternative precursor messenger RNA (pre-mRNA) splicing plays an important role in the generation of functional diversity of the genome. The process of pre-mRNA splicing is regulated by cis- and trans-elements, and their deregulations result in aberrantly spliced individual variants and aberrant expression profiles. Accumulating evidence has revealed that aberrant splicing contributes to a number of diseases including human neoplasms. It is well known that germ line mutations in the cis-element of tumor suppressor genes such as mismatch repair (MMR) genes, the adenomatous polyposis coli (APC) gene and the E-cadherin (CDH1) gene are involved in Lynch syndrome, familial adenomatous polyposis and hereditary diffuse gastric cancer, respectively. In addition, somatic mutations in cis-elements also play a role in tumorigenesis. These genetic alterations including nonsense, missense or silent mutations in cis-elements led to aberrant transcripts by exon skipping, retention of the intron or introduction of a new splice site. The majority of erroneous transcripts with a premature termination codon are eliminated through nonsense-mediated mRNA decay. However, it is difficult to accurately predict the resulting transcripts with current in silico strategies. Correct interpretation of genetic alterations and the investigation of aberrant transcripts are crucial for genetic diagnosis of hereditary diseases and elucidation of the molecular characteristics of neoplasms from a clinical point of view. In this review we summarize the current knowledge of the regulatory mechanism underlying alternative pre-mRNA splicing and aberrant splicing, with particular focus on digestive tract malignancies.
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Affiliation(s)
- Koh Miura
- Department of Surgery, Tohoku University Graduate School of Medicine, Sendai Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Tokyo, Japan.
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Global analysis reveals SRp20- and SRp75-specific mRNPs in cycling and neural cells. Nat Struct Mol Biol 2010; 17:962-70. [PMID: 20639886 DOI: 10.1038/nsmb.1862] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 05/26/2010] [Indexed: 01/17/2023]
Abstract
Members of the SR protein family of RNA-binding proteins have numerous roles in mRNA metabolism, from transcription to translation. To understand how SR proteins coordinate gene regulation, comprehensive knowledge of endogenous mRNA targets is needed. Here we establish physiological expression of GFP-tagged SR proteins from stable transgenes. Using the GFP tag for immunopurification of mRNPs, mRNA targets of SRp20 and SRp75 were identified in cycling and neurally induced P19 cells. Genome-wide analysis showed that SRp20 and SRp75 associate with hundreds of distinct, functionally related groups of transcripts that change in response to neural differentiation. Knockdown of either SRp20 or SRp75 led to up- or downregulation of specific transcripts, including identified targets, and rescue by the GFP-tagged SR proteins proved their functionality. Thus, SR proteins contribute to the execution of gene-expression programs through their association with distinct endogenous mRNAs.
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Kattah NH, Kattah MG, Utz PJ. The U1-snRNP complex: structural properties relating to autoimmune pathogenesis in rheumatic diseases. Immunol Rev 2010; 233:126-45. [PMID: 20192997 PMCID: PMC3074261 DOI: 10.1111/j.0105-2896.2009.00863.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The U1 small nuclear ribonucleoprotein particle (snRNP) is a target of autoreactive B cells and T cells in several rheumatic diseases including systemic lupus erythematosus (SLE) and mixed connective tissue disease (MCTD). We propose that inherent structural properties of this autoantigen complex, including common RNA-binding motifs, B and T-cell epitopes, and a unique stimulatory RNA molecule, underlie its susceptibility as a target of the autoimmune response. Immune mechanisms that may contribute to overall U1-snRNP immunogenicity include epitope spreading through B and T-cell interactions, apoptosis-induced modifications, and toll-like receptor (TLR) activation through stimulation by U1-snRNA. We conclude that understanding the interactions between U1-snRNP and the immune system will provide insights into why certain patients develop anti-U1-snRNP autoimmunity, and more importantly how to effectively target therapies against this autoimmune response.
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Affiliation(s)
- Nicole H Kattah
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
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Calarco JA, Superina S, O'Hanlon D, Gabut M, Raj B, Pan Q, Skalska U, Clarke L, Gelinas D, van der Kooy D, Zhen M, Ciruna B, Blencowe BJ. Regulation of vertebrate nervous system alternative splicing and development by an SR-related protein. Cell 2009; 138:898-910. [PMID: 19737518 DOI: 10.1016/j.cell.2009.06.012] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 03/11/2009] [Accepted: 06/01/2009] [Indexed: 01/02/2023]
Abstract
Alternative splicing is a key process underlying the evolution of increased proteomic and functional complexity and is especially prevalent in the mammalian nervous system. However, the factors and mechanisms governing nervous system-specific alternative splicing are not well understood. Through a genome-wide computational and expression profiling strategy, we have identified a tissue- and vertebrate-restricted Ser/Arg (SR) repeat splicing factor, the neural-specific SR-related protein of 100 kDa (nSR100). We show that nSR100 regulates an extensive network of brain-specific alternative exons enriched in genes that function in neural cell differentiation. nSR100 acts by increasing the levels of the neural/brain-enriched polypyrimidine tract binding protein and by interacting with its target transcripts. Disruption of nSR100 prevents neural cell differentiation in cell culture and in the developing zebrafish. Our results thus reveal a critical neural-specific alternative splicing regulator, the evolution of which has contributed to increased complexity in the vertebrate nervous system.
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Affiliation(s)
- John A Calarco
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
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Abstract
The SR protein family comprises a number of phylogenetically conserved and structurally related proteins with a characteristic domain rich in arginine and serine residues, known as the RS domain. They play significant roles in constitutive pre-mRNA splicing and are also important regulators of alternative splicing. In addition they participate in post-splicing activities, such as mRNA nuclear export, nonsense-mediated mRNA decay and mRNA translation. These wide-ranging roles of SR proteins highlight their importance as pivotal regulators of mRNA metabolism, and if these functions are disrupted, developmental defects or disease may result. Furthermore, animal models have shown a highly specific, non-redundant role for individual SR proteins in the regulation of developmental processes. Here, we will review the current literature to demonstrate how SR proteins are emerging as one of the master regulators of gene expression.
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Thakur A, Bollig A, Wu J, Liao DJ. Gene expression profiles in primary pancreatic tumors and metastatic lesions of Ela-c-myc transgenic mice. Mol Cancer 2008; 7:11. [PMID: 18218118 PMCID: PMC2259361 DOI: 10.1186/1476-4598-7-11] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2007] [Accepted: 01/24/2008] [Indexed: 12/20/2022] Open
Abstract
Background Pancreatic carcinoma usually is a fatal disease with no cure, mainly due to its invasion and metastasis prior to diagnosis. We analyzed the gene expression profiles of paired primary pancreatic tumors and metastatic lesions from Ela-c-myc transgenic mice in order to identify genes that may be involved in the pancreatic cancer progression. Differentially expressed selected genes were verified by semi-quantitative and quantitative RT-PCR. To further evaluate the relevance of some of the selected differentially expressed genes, we investigated their expression pattern in human pancreatic cancer cell lines with high and low metastatic potentials. Results Data indicate that genes involved in posttranscriptional regulation were a major functional category of upregulated genes in both primary pancreatic tumors (PT) and liver metastatic lesions (LM) compared to normal pancreas (NP). In particular, differential expression for splicing factors, RNA binding/pre-mRNA processing factors and spliceosome related genes were observed, indicating that RNA processing and editing related events may play critical roles in pancreatic tumor development and progression. High expression of insulin growth factor binding protein-1 (Igfbp1) and Serine proteinase inhibitor A1 (Serpina1), and low levels or absence of Wt1 gene expression were exclusive to liver metastatic lesion samples. Conclusion We identified Igfbp1, Serpina1 and Wt1 genes that are likely to be clinically useful biomarkers for prognostic or therapeutic purposes in metastatic pancreatic cancer, particularly in pancreatic cancer where c-Myc is overexpressed.
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Affiliation(s)
- Archana Thakur
- Department of Pathology, Karmanos Cancer Institute, Wayne State University School of Medicine, 110 E, Warren Ave,, Detroit, Michigan 48201, USA.
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Jing P, Jin Q, Wu J, Zhang XJ. GSK3beta mediates the induced expression of synaptic acetylcholinesterase during apoptosis. J Neurochem 2007; 104:409-19. [PMID: 17949411 DOI: 10.1111/j.1471-4159.2007.04975.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Besides its role in terminating acetylcholine-mediated neurotransmission, acetylcholinesterase (AChE) is found to be expressed and participate in the process of apoptosis in various cell types. However, the mechanisms underlying AChE up-regulation in neuronal cells remain elusive. Herein we demonstrated that glycogen synthase kinase-3beta (GSK3beta) mediates induced AChE-S expression during apoptosis. In this study, A23187 and thapsigargin (TG) were employed to induce apoptosis in neuroendocrine PC12 cells. The results showed that exposure of PC12 cells to A23187 and TG up-regulated AChE activity significantly. The same treatment also led to activation of GSK3beta. Two different inhibitors of GSK3beta (lithium and GSK3beta-specific inhibitor VIII) could block A23187- or TG-induced up-regulation of AChE activity, AChE-S mRNA level and protein expression. However, lithium could not inhibit the induction of AChE-R mRNA and protein under similar conditions. Taken together, our results show that GSK3beta is specifically involved in the induction of AChE-S expression in PC12 cells during apoptosis.
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Affiliation(s)
- Peng Jing
- Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai, China
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Patwardhan P, Miller WT. Processive phosphorylation: mechanism and biological importance. Cell Signal 2007; 19:2218-26. [PMID: 17644338 PMCID: PMC2034209 DOI: 10.1016/j.cellsig.2007.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2007] [Revised: 05/31/2007] [Accepted: 06/12/2007] [Indexed: 01/13/2023]
Abstract
Recent proteomic data indicate that a majority of the phosphorylated proteins in a eucaryotic cell contain multiple sites of phosphorylation. In many signaling events, a single kinase phosphorylates multiple sites on a target protein. Processive phosphorylation occurs when a protein kinase binds once to a substrate and phosphorylates all of the available sites before dissociating. In this review, we discuss examples of processive phosphorylation by serine/threonine kinases and tyrosine kinases. We describe current experimental approaches for distinguishing processive from non-processive phosphorylation. Finally, we contrast the biological situations that are suited to regulation by processive and non-processive phosphorylation.
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Affiliation(s)
- Parag Patwardhan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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Lin S, Fu XD. SR proteins and related factors in alternative splicing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2007; 623:107-22. [PMID: 18380343 DOI: 10.1007/978-0-387-77374-2_7] [Citation(s) in RCA: 165] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
SR proteins are a family of RNA binding proteins that contain a signature RS domain enriched with serine/arginine repeats. The RS domain is also found in many other proteins, which are collectively referred to as SR-related proteins. Several prototypical SR proteins are essential splicing factors, but the majority of RS domain-containing factors are characterized by their ability to alter splice site selection in vitro or in transfected cells. SR proteins and SR-related proteins are generally believed to modulate splice site selection via RNA recognition motif-mediated binding to exonic splicing enhancers and RS domain-mediated protein-protein and protein-RNA interactions during spliceosome assembly. However, the biological function of individual RS domain-containing splicing regulators is complex because of redundant as well as competitive functions, context-dependent effects and regulation by cotranscriptional and post-translational events. This chapter will focus on our current mechanistic understanding of alternative splicing regulation by SR proteins and SR-related proteins and will discuss some of the questions that remain to be addressed in future research.
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Affiliation(s)
- Shengrong Lin
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA
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Singh OP, Visa N, Wieslander L, Daneholt B. A specific SR protein binds preferentially to the secretory protein gene transcripts in salivary glands of Chironomus tentans. Chromosoma 2006; 115:449-58. [PMID: 16858590 DOI: 10.1007/s00412-006-0073-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Revised: 05/20/2006] [Accepted: 05/22/2006] [Indexed: 11/26/2022]
Abstract
The members of the serine-arginine (SR) family of proteins play multiple roles in posttranscriptional gene expression. Initially considered as essential splicing factors confined to the nucleus and regulating constitutive and alternative splicing, SR proteins are now known to shuttle between the nucleus and the cytoplasm and to be involved in mRNA biogenesis, transport, and translation. In Chironomus tentans, hrp45 is an SR protein structurally similar to the Drosophila SRp55/B52 SR protein. We have studied how hrp45, hrp36 [a heterogenous nuclear ribonucleoprotein (hnRNP) protein], and small nuclear RNP (snRNP) proteins are distributed in the transcriptionally active loci of polytene chromosomes in C. tentans. Immunofluorescence visualization of the proteins in double-labeling experiments revealed that hrp45 preferentially associates with a small number of puffs. On the other hand, hrp36 and snRNP proteins were found distributed in a large number of loci with little quantitative difference. Remarkably, hrp45-labeled loci coincide with the sites of transcription of premessenger RNPs of secretory protein (sp) genes. Because the labeling was found sensitive to RNase A treatment, we conclude that the SR protein hrp45 preferentially binds to sp gene transcripts in salivary gland cells. The preferential association of a specific SR protein with a particular type of gene transcripts reflects substrate-specific function(s) of an SR protein, in vivo. The possible roles that hrp45 might be playing in speedy and efficient processing of sp gene transcripts are discussed.
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Affiliation(s)
- Om Prakash Singh
- Department of Cell and Molecular Biology, Medical Nobel Institute, Karolinska Institutet, Stockholm, 171 77, Sweden
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45
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Cochrane AW, McNally MT, Mouland AJ. The retrovirus RNA trafficking granule: from birth to maturity. Retrovirology 2006; 3:18. [PMID: 16545126 PMCID: PMC1475878 DOI: 10.1186/1742-4690-3-18] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Accepted: 03/17/2006] [Indexed: 11/10/2022] Open
Abstract
Post-transcriptional events in the life of an RNA including RNA processing, transport, translation and metabolism are characterized by the regulated assembly of multiple ribonucleoprotein (RNP) complexes. At each of these steps, there is the engagement and disengagement of RNA-binding proteins until the RNA reaches its final destination. For retroviral genomic RNA, the final destination is the capsid. Numerous studies have provided crucial information about these processes and serve as the basis for studies on the intracellular fate of retroviral RNA. Retroviral RNAs are like cellular mRNAs but their processing is more tightly regulated by multiple cis-acting sequences and the activities of many trans-acting proteins. This review describes the viral and cellular partners that retroviral RNA encounters during its maturation that begins in the nucleus, focusing on important events including splicing, 3' end-processing, RNA trafficking from the nucleus to the cytoplasm and finally, mechanisms that lead to its compartmentalization into progeny virions.
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Affiliation(s)
- Alan W Cochrane
- Department of Medical Genetics and Microbiology, University of Toronto, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Mark T McNally
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, 53226, USA
| | - Andrew J Mouland
- HIV-1 RNA Trafficking Laboratory, Lady Davis Institute for Medical Research-Sir Mortimer B. Davis Jewish General Hospital and McGill University, 3755 Côte-Ste-Catherine Road, H3T 1E2, Canada
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Li-Korotky HS, Hebda PA, Kelly LA, Lo CY, Dohar JE. Identification of a pre-mRNA splicing factor, arginine/serine-rich 3 (Sfrs3), and its co-expression with fibronectin in fetal and postnatal rabbit airway mucosal and skin wounds. Biochim Biophys Acta Mol Basis Dis 2006; 1762:34-45. [PMID: 16168628 DOI: 10.1016/j.bbadis.2005.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 06/28/2005] [Accepted: 08/09/2005] [Indexed: 10/25/2022]
Abstract
Fibronectin (FN) is a multi-functional, adhesion protein and involved in multi-steps of the wound healing process. Strong evidence suggests that FN protein diversity is controlled by alternative RNA splicing; a coordinated transcription and RNA processing that is development-, age-, and tissue/cell type-regulated. We previously demonstrated that fetal rabbit airway mucosal healing is regenerative and scarless. Expression, regulation, and biological function of the FN gene and various spliced forms in this model are unknown. Airway and skin incisional wounds were made in fetal (gestation days 21-23), weanling (4-6 weeks) and adult (>6 months) rabbits. Non-wounded and wounded tissues were collected at 12 h (all age groups), 24 h and 48 h (weanling only) post-wounding. Expression profiles were obtained using mRNA differential display and cDNAs of interest were cloned, sequenced and validated by real-time PCR. Here, we report two rabbit cDNAs that showed similar expression patterns after wounding. One encodes a rabbit fibronectin gene, Fn1, and another shares a high sequence homology to a human pre-mRNA splicing factor, arginine/serine-rich 3 (Sfrs3), coding for a RNA binding protein, SRp20. Both Fn1 and Sfrs3 mRNAs were suppressed in fetal wounds but induced in postnatal wounds 12 h post-wounding. The increased levels of both Fn1 and Sfrs3 transcripts were sustained up to 48 h in weanling airway mucosal wounds. The augmentations of the two genes in postnatal airway mucosal wounds were more prominent than that in skin wounds, indicating that the involvement of Sfrs3 and Fn1 genes in postnatal airway mucosal wounds is tissue-specific. Literature provides evidence that SRp20 is indeed involved in the alternative splicing of FN and that the embryonic FN variants reappear during adult wound healing. A connection between the enhanced molecular activity of Sfrs3 and the regulation of the FN gene expression through alternative splicing during the early events of postnatal airway mucosal wound repair was proposed.
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Affiliation(s)
- Ha-Sheng Li-Korotky
- Division of Pediatric Otolaryngology, Children's Hospital of Pittsburgh, Pittsburgh, PA 15213, USA.
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Soret J, Gabut M, Tazi J. SR Proteins as Potential Targets for Therapy. ALTERNATIVE SPLICING AND DISEASE 2006; 44:65-87. [PMID: 17076265 DOI: 10.1007/978-3-540-34449-0_4] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Serine- and arginine-rich (SR) proteins constitute a highly conserved family of pre-mRNA splicing factors that play key roles in the regulation of splice site selection, and thereby in the control of alternative splicing processes. In addition to conserved sequences at the splice junctions, splice site selection also depends upon different sets of auxiliary cis regulatory elements known as exonic and intronic splicing enhancers (ESEs and ISEs) or exonic and intronic silencers (ESSs and ISSs). Specific binding of SR proteins to their cognate splicing enhancers as well as binding of splicing repressor to silencer sequences serve to enhance or inhibit recognition of weak splice sites by the splicing machinery. Given that the vast majority of human genes contain introns and that most pre-mRNAs containing multiple exons undergo alternative splicing, mutations disrupting or creating such auxiliary elements can result in aberrant splicing events at the origin of various human diseases. In the past few years, numerous studies have reported several approaches allowing correction of such aberrant splicing events by targeting either the mutated sequences or the splicing regulators whose binding is affected by the mutation. The aim of the present review is to highlight the different means by which it is possible to modulate the activity of SR splicing factors and to bring out those holding the greatest promises for the development of therapeutic treatments.
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Affiliation(s)
- Johann Soret
- Institut de Génétique Moléculaire de Montpellier, UMR 5535, IFR 122, Centre National de Recherche Scientifique, 1919, route de Mende, 34293 Montpellier, France
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Isshiki M, Tsumoto A, Shimamoto K. The serine/arginine-rich protein family in rice plays important roles in constitutive and alternative splicing of pre-mRNA. THE PLANT CELL 2006; 18:146-58. [PMID: 16339852 PMCID: PMC1323490 DOI: 10.1105/tpc.105.037069] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Ser/Arg-rich (SR) proteins play important roles in the constitutive and alternative splicing of pre-mRNA. We isolated 20 rice (Oryza sativa) genes encoding SR proteins, of which six contain plant-specific characteristics. To determine whether SR proteins modulate splicing efficiency and alternative splicing of pre-mRNA in rice, we used transient assays in rice protoplasts by cotransformation of SR protein genes with the rice Waxy(b) (Wx(b))-beta-glucuronidase fusion gene. The results showed that plant-specific RSp29 and RSZp23, an SR protein homologous to human 9G8, enhanced splicing and altered the alternative 5' splice sites of Wx(b) intron 1. The resulting splicing pattern was unique to each SR protein; RSp29 stimulated splicing at the distal site, and RSZp23 enhanced splicing at the proximal site. Results of domain-swapping experiments between plant-specific RSp29 and SCL26, which is a homolog of human SC35, showed the importance of RNA recognition motif 1 and the Arg/Ser-rich (RS) domain for the enhancement of splicing efficiencies. Overexpression of plant-specific RSZ36 and SRp33b, a homolog of human ASF/SF2, in transgenic rice changed the alternative splicing patterns of their own pre-mRNAs and those of other SR proteins. These results show that SR proteins play important roles in constitutive and alternative splicing of rice pre-mRNA.
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Affiliation(s)
- Masayuki Isshiki
- Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Ikoma, Japan
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Wilusz JE, Devanney SC, Caputi M. Chimeric peptide nucleic acid compounds modulate splicing of the bcl-x gene in vitro and in vivo. Nucleic Acids Res 2005; 33:6547-54. [PMID: 16299354 PMCID: PMC1289079 DOI: 10.1093/nar/gki960] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Alternative splicing of the bcl-x gene generates two transcripts: the anti-apoptotic bcl-xL isoform and the pro-apoptotic bcl-xS isoform. The ratio between the two isoforms is a key factor in development and in cancer progression. Here, we show that a short antisense chimeric peptide nucleic acid (PNA) oligonucleotide conjugated to a polypeptide containing eight Ser-Arg repeats (SR)8 can modulate splicing of bcl-x both in vitro and in vivo and induces apoptosis in HeLa cells. The PNA-SR oligo was targeted to a region of bcl-x that does not contain splicing regulatory sequences and was able to override the complex network of splicing enhancers and silencers that regulates the ratio between the two bcl-x isoforms. Thus, PNA-SR oligos are powerful tools that can potentially modulate splice site choice in endogenous genes independent of the presence of other splicing regulatory mechanisms on the target gene.
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Affiliation(s)
| | - Sean C. Devanney
- Biomedical Science Department, Florida Atlantic UniversityBoca Raton, FL 33431, USA
| | - Massimo Caputi
- Biomedical Science Department, Florida Atlantic UniversityBoca Raton, FL 33431, USA
- To whom correspondence should be addressed. Tel: +1 561 297 0627; Fax: +1 561 297 2221;
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Ngo JCK, Chakrabarti S, Ding JH, Velazquez-Dones A, Nolen B, Aubol BE, Adams JA, Fu XD, Ghosh G. Interplay between SRPK and Clk/Sty Kinases in Phosphorylation of the Splicing Factor ASF/SF2 Is Regulated by a Docking Motif in ASF/SF2. Mol Cell 2005; 20:77-89. [PMID: 16209947 DOI: 10.1016/j.molcel.2005.08.025] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2005] [Revised: 08/12/2005] [Accepted: 08/24/2005] [Indexed: 10/25/2022]
Abstract
The arginine-serine (RS)-rich domain of the SR protein ASF/SF2 is phosphorylated by SR protein kinases (SRPKs) and Clk/Sty kinases. However, the mode of phosphorylation by these kinases and their coordination in the biological regulation of ASF/SF2 is unknown. Here, we report the crystal structure of an active fragment of human SRPK1 bound to a peptide derived from an SR protein. This structure led us to identify a docking motif in ASF/SF2. We find that this docking motif restricts phosphorylation of ASF/SF2 by SRPK1 to the N-terminal part of the RS domain - a property essential for its assembly into nuclear speckles. We further show that Clk/Sty causes release of ASF/SF2 from speckles by phosphorylating the C-terminal part of its RS domain. These results suggest that the docking motif of ASF/SF2 is a key regulatory element for sequential phosphorylation by SRPK1 and Clk/Sty and, thus, is essential for its subcellular localization.
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Affiliation(s)
- Jacky Chi Ki Ngo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
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