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Kwiecien K, Majewski P, Bak M, Brzoza P, Godlewska U, Skulimowska I, Cichy J, Kwitniewski M. Alternative splicing is not a key source of chemerin isoforms diversity. Mol Biol Rep 2023; 50:2521-2529. [PMID: 36609751 PMCID: PMC10011272 DOI: 10.1007/s11033-022-08174-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 12/02/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Chemerin is a chemoattractant protein with adipokine and antimicrobial properties encoded by the retinoic acid receptor responder 2 (RARRES2) gene. Chemerin bioactivity largely depends on carboxyl-terminal proteolytic processing that generates chemerin isoforms with different chemotactic, regulatory, and antimicrobial potentials. While these mechanisms are relatively well known, the role of alternative splicing in generating isoform diversity remains obscure. METHODS AND RESULTS Using rapid amplification of cDNA ends (RACE) PCR, we determined RARRES2 transcript variants present in mouse and human tissues and identified novel transcript variant 4 of mouse Rarres2 encoding mChem153K. Moreover, analyses of real-time quantitative PCR (RT-qPCR) and publicly-available next-generation RNA sequencing (RNA-seq) datasets showed that different alternatively spliced variants of mouse Rarres2 are present in mouse tissues and their expression patterns were unaffected by inflammatory and infectious stimuli except brown adipose tissue. However, only one transcript variant of human RARRES2 was present in liver and adipose tissue. CONCLUSION Our findings indicate a limited role for alternative splicing in generating chemerin isoform diversity under all tested conditions.
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Affiliation(s)
- Kamila Kwiecien
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Pawel Majewski
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Maciej Bak
- Department of Mathematics, City, University of London, EC1V 0HB, London, United Kingdom
| | - Piotr Brzoza
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Urszula Godlewska
- Laboratory of Host-Microbiota Interactions, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093, Warsaw, Poland
| | - Izabella Skulimowska
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Joanna Cichy
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Mateusz Kwitniewski
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland.
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Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023; 14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.
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Affiliation(s)
- Jeru Manoj Manuel
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Inès Khatir
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada,Quebec Network for Research on Protein Function Structure and Engineering, PROTEO, Québec, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,*Correspondence: Benoit Laurent,
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Lee ES, Smith HW, Wolf EJ, Guvenek A, Wang YE, Emili A, Tian B, Palazzo AF. ZFC3H1 and U1-70K promote the nuclear retention of mRNAs with 5' splice site motifs within nuclear speckles. RNA (NEW YORK, N.Y.) 2022; 28:878-894. [PMID: 35351812 PMCID: PMC9074902 DOI: 10.1261/rna.079104.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/12/2022] [Indexed: 05/22/2023]
Abstract
Quality control of mRNA represents an important regulatory mechanism for gene expression in eukaryotes. One component of this quality control is the nuclear retention and decay of misprocessed RNAs. Previously, we demonstrated that mature mRNAs containing a 5' splice site (5'SS) motif, which is typically found in misprocessed RNAs such as intronic polyadenylated (IPA) transcripts, are nuclear retained and degraded. Using high-throughput sequencing of cellular fractions, we now demonstrate that IPA transcripts require the zinc finger protein ZFC3H1 for their nuclear retention and degradation. Using reporter mRNAs, we demonstrate that ZFC3H1 promotes the nuclear retention of mRNAs with intact 5'SS motifs by sequestering them into nuclear speckles. Furthermore, we find that U1-70K, a component of the spliceosomal U1 snRNP, is also required for the nuclear retention of these reporter mRNAs and likely functions in the same pathway as ZFC3H1. Finally, we show that the disassembly of nuclear speckles impairs the nuclear retention of reporter mRNAs with 5'SS motifs. Our results highlight a splicing independent role of U1 snRNP and indicate that it works in conjunction with ZFC3H1 in preventing the nuclear export of misprocessed mRNAs by sequestering them into nuclear speckles.
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Affiliation(s)
- Eliza S Lee
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Harrison W Smith
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Eric J Wolf
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
| | - Aysegul Guvenek
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
| | - Yifan E Wang
- Department of Biochemistry, University of Toronto, Ontario M5S 1A8, Canada
| | - Andrew Emili
- Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada
- Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Bin Tian
- Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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4
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Plotz G, Lopez-Garcia LA, Brieger A, Zeuzem S, Biondi RM. Alternative AKT2 splicing produces protein lacking the hydrophobic motif regulatory region. PLoS One 2020; 15:e0242819. [PMID: 33253205 PMCID: PMC7703976 DOI: 10.1371/journal.pone.0242819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/09/2020] [Indexed: 12/20/2022] Open
Abstract
Three AKT serine/threonine kinase isoforms (AKT1/AKT2/AKT3) mediate proliferation, metabolism, differentiation and anti-apoptotic signals. AKT isoforms are activated downstream of PI3-kinase and also by PI3-kinase independent mechanisms. Mutations in the lipid phosphatase PTEN and PI3-kinase that increase PIP3 levels increase AKT signaling in a large proportion of human cancers. AKT and other AGC kinases possess a regulatory mechanism that relies on a conserved hydrophobic motif (HM) C-terminal to the catalytic core. In AKT, the HM is contiguous to the serine 473 and two other newly discovered (serine 477 and tyrosine 479) regulatory phosphorylation sites. In AKT genes, this regulatory HM region is encoded in the final exon. We identified a splice variant of AKT2 (AKT2-13a), which contains an alternative final exon and lacks the HM regulatory site. We validated the presence of mRNA for this AKT2-13a splice variant in different tissues, and the presence of AKT2-13a protein in extracts from HEK293 cells. When overexpressed in HEK293 cells, AKT2-13a is phosphorylated at the activation loop and at the zipper/turn motif phosphorylation sites but has reduced specific activity. Analysis of the human transcriptome corresponding to other AGC kinases revealed that all three AKT isoforms express alternative transcripts lacking the HM regulatory motif, which was not the case for SGK1-3, S6K1-2, and classical, novel and atypical PKC isoforms. The transcripts of splice variants of Akt1-3 excluding the HM regulatory region could lead to expression of deregulated forms of AKT.
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Affiliation(s)
- Guido Plotz
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Laura A Lopez-Garcia
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angela Brieger
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Stefan Zeuzem
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany
| | - Ricardo M Biondi
- Biomedizinisches Forschungslabor, Medizinische Klinik 1, Universitätsklinik Frankfurt, Frankfurt, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.,Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA)-CONICET-Partner Institute of the Max Planck Society, Buenos Aires, Argentina
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Lee BR, Rengaraj D, Choi HJ, Han JY. A novel F-box domain containing cyclin F like gene is required for maintaining the genome stability and survival of chicken primordial germ cells. FASEB J 2019; 34:1001-1017. [PMID: 31914591 DOI: 10.1096/fj.201901294r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/25/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
The stability and survival of germ cells are controlled by the germline-specific genes, however, such genes are less known in the avian species. Using a microarray-based the National Center for Biotechnology Information Gene Expression Omnibus dataset, we found an unigene (Gga.9721) that upregulated in the chicken primordial germ cells (PGCs). The unigene showed 97% identities with an uncharacterized chicken cyclin F like gene. The predicted chicken cyclin F like gene was further characterized through expression and regulation in the chicken PGCs. The sequence analysis revealed that the gene shows identities with cyclin F gene and contains an F-box domain. The expression of chicken cyclin F like was detected specifically in the gonads, PGCs, and germline cells. The knockdown of cyclin F like gene resulted in DNA damage and apoptosis in the PGCs. The genes related to stemness and germness were downregulated, whereas, genes related to apoptosis and DNA damage response were increased in the PGCs after the knockdown of chicken cyclin F like. We further observed that the Nanog homeobox controlled the transcriptional activity of chicken cyclin F like gene in PGCs. Collectively, the chicken cyclin F like gene, which is not reported in any other species, is required for maintaining the genome stability of germ cells.
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Affiliation(s)
- Bo Ram Lee
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.,Animal Biotechnology Division, National Institute of Animal Science, Rural Development Administration, Wanju-gun, Korea
| | - Deivendran Rengaraj
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Hee Jung Choi
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
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Boldinova EO, Khairullin RF, Makarova AV, Zharkov DO. Isoforms of Base Excision Repair Enzymes Produced by Alternative Splicing. Int J Mol Sci 2019; 20:ijms20133279. [PMID: 31277343 PMCID: PMC6651865 DOI: 10.3390/ijms20133279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 06/29/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023] Open
Abstract
Transcripts of many enzymes involved in base excision repair (BER) undergo extensive alternative splicing, but functions of the corresponding alternative splice variants remain largely unexplored. In this review, we cover the studies describing the common alternatively spliced isoforms and disease-associated variants of DNA glycosylases, AP-endonuclease 1, and DNA polymerase beta. We also discuss the roles of alternative splicing in the regulation of their expression, catalytic activities, and intracellular transport.
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Affiliation(s)
| | - Rafil F Khairullin
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, 9 Parizhskoy Kommuny Str., 420012 Kazan, Russia
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., 123182 Moscow, Russia.
| | - Dmitry O Zharkov
- Novosibirsk State University, 1 Pirogova St., 630090 Novosibirsk, Russia.
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia.
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