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Wang Y, Chembazhi UV, Yee D, Chen S, Ji J, Wang Y, Nguyen KL, Lin P, Ratti A, Hess R, Qiao H, Ko C, Yang J, Kalsotra A, Mei W. PTBP1 mediates Sertoli cell actin cytoskeleton organization by regulating alternative splicing of actin regulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598725. [PMID: 38915624 PMCID: PMC11195235 DOI: 10.1101/2024.06.12.598725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Spermatogenesis is a biological process within the testis that produces haploid spermatozoa for the continuity of species. Sertoli cells are somatic cells in the seminiferous epithelium that orchestrate spermatogenesis. Cyclic reorganization of Sertoli cell actin cytoskeleton is vital for spermatogenesis, but the underlying mechanism remains largely unclear. Here, we report that RNA-binding protein PTBP1 controls Sertoli cell actin cytoskeleton reorganization by programming alternative splicing of actin cytoskeleton regulators. This splicing control enables ectoplasmic specializations, the actin-based adhesion junctions, to maintain the blood-testis barrier and support spermatid transport and transformation. Particularly, we show that PTBP1 promotes actin bundle formation by repressing the inclusion of exon 14 of Tnik, a kinase present at the ectoplasmic specialization. Our results thus reveal a novel mechanism wherein Sertoli cell actin cytoskeleton dynamics is controlled post-transcriptionally by utilizing functionally distinct isoforms of actin regulatory proteins, and PTBP1 is a critical regulatory factor in generating such isoforms.
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Affiliation(s)
- Yuexi Wang
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
- These authors contributed equally to the work
| | - Ullas Valiya Chembazhi
- Department of Biochemistry, The School of Molecular and Cellular Biology, College of Liberal Arts & Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Current address: Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- These authors contributed equally to the work
| | - Danielle Yee
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Current address: University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sijie Chen
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jie Ji
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Current address: Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yujie Wang
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Current address: College of Arts and Science, Vanderbilt University, Nashville, TN, USA
| | - Ka Lam Nguyen
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - PoChing Lin
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Antonia Ratti
- Department of Medical Biotechnology and Translational Medicine, Universita degli studi di Milano, Via Fratelli Cervi 93, 20090, Segrate, Milan, Italy
| | - Rex Hess
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Huanyu Qiao
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - CheMyong Ko
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jing Yang
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Auinash Kalsotra
- Department of Biochemistry, The School of Molecular and Cellular Biology, College of Liberal Arts & Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutrition Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Wenyan Mei
- Department of Comparative Biosciences, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Division of Nutrition Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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2
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Sato J, Satoh Y, Yamamoto T, Watanabe T, Matsubara S, Satake H, Kimura AP. PTBP2 binds to a testis-specific long noncoding RNA, Tesra, and activates transcription of the Prss42/Tessp-2 gene. Gene 2024; 893:147907. [PMID: 37858745 DOI: 10.1016/j.gene.2023.147907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 09/22/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023]
Abstract
Long noncoding RNAs (lncRNAs) have recently been proved to be functional in the testis. Tesra, a testis-specific lncRNA, was suggested to activate the transcription of Prss42/Tessp-2, a gene that is involved in meiotic progression, in mouse spermatocytes. To reveal the molecular mechanism underlying the activation, we searched for Tesra-binding proteins by a Ribotrap assay followed by LC-MS/MS analysis and identified polypyrimidine tract binding protein 2 (PTBP2) as a candidate. Analysis of public RNA-seq data and our qRT-PCR results indicated that Ptbp2 mRNA showed an expression pattern similar to the expression patterns of Tesra and Prss42/Tessp-2 during testis development. Moreover, PTBP2 was found to be associated with Tesra in testicular germ cells by RNA immunoprecipitation. To evaluate the effect of PTBP2 on the Prss42/Tessp-2 promoter, we established an in vitro reporter gene assay system in which Tesra expression could be induced by the Tet-on system and thereby Prss42/Tessp-2 promoter activity could be increased. In this system, the Prss42/Tessp-2 promoter activity was significantly decreased by the knockdown of PTBP2. These results suggest that PTBP2 contributes to Prss42/Tessp-2 transcriptional activation by Tesra in spermatocytes. The finding provides a precious example of a molecular mechanism of testis lncRNA functioning in spermatogenesis.
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Affiliation(s)
- Josei Sato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Yui Satoh
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takehiro Yamamoto
- Department of Biochemistry, School of Medicine, Keio University, Tokyo, Japan
| | - Takehiro Watanabe
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Shin Matsubara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Atsushi P Kimura
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan; Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan.
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3
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Chen XD, Liu HL, Li S, Hu KB, Wu QY, Liao P, Wang HY, Long ZY, Lu XM, Wang YT. The latest role of nerve-specific splicing factor PTBP1 in the transdifferentiation of glial cells into neurons. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1740. [PMID: 35574699 DOI: 10.1002/wrna.1740] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/16/2022] [Accepted: 04/21/2022] [Indexed: 11/07/2022]
Abstract
Central nervous system injury diseases can cause the loss of many neurons, and it is difficult to regenerate. The field of regenerative medicine believes that supplementing the missing neurons may be an ideal method for nerve injury repair. Recent studies have found that down-regulation of polypyrimidine tract binding protein 1 (PTBP1) expression can make glial cells transdifferentiate into different types of neurons, which is expected to be an alternative therapy to restore neuronal function. This article summarized the research progress on the structure and biological function of the PTBP family, the mutual regulation of PTBP1 and PTBP2, their role in neurogenesis, and the latest research progress in targeting PTBP1 to mediate the transdifferentiation of glial cells into neurons, which may provide some new strategies and new ideas for the future treatment of central nervous system injury and neurodegenerative diseases. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Xing-Dong Chen
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China.,State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Hui-Lin Liu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Sen Li
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Kai-Bin Hu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Qing-Yun Wu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Ping Liao
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Hai-Yan Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Zai-Yun Long
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiu-Min Lu
- College of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, China
| | - Yong-Tang Wang
- State Key Laboratory of Trauma, Burns and Combined Injury, Daping Hospital, Army Medical University, Chongqing, China
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4
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Liu W, Zhao Y, Liu X, Zhang X, Ding J, Li Y, Tian Y, Wang H, Liu W, Lu Z. A Novel Meiosis-Related lncRNA, Rbakdn, Contributes to Spermatogenesis by Stabilizing Ptbp2. Front Genet 2021; 12:752495. [PMID: 34707642 PMCID: PMC8542969 DOI: 10.3389/fgene.2021.752495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/23/2021] [Indexed: 01/18/2023] Open
Abstract
Spermatocyte meiosis is the cornerstone of mammalian production. Thousands of long noncoding RNAs (lncRNAs) have been reported to be functional in various cellular processes, but the function of lncRNAs in meiosis remains largely unknown. Here, we profiled lncRNAs in spermatocytes at stage I of meiosis and identified a testis-specific lncRNA, Rbakdn, as a vital regulator of meiosis. Rbakdn is dynamically expressed during meiosis I, and Rbakdn knockdown inhibits meiosis in vitro. Furthermore, Rbakdn knockdown in testes in mice by intratesticular injection disturbs meiosis, reduces testicular volume, and increases apoptosis of spermatocytes, resulting in vacuolation of the seminiferous tubules. Rbakdn can bind to Ptbp2, an RNA-binding protein that is important in the regulation of the alternative splicing of many genes in spermatogenesis. Rbakdn knockdown leads to a decrease in Ptbp2 through the ubiquitination degradation pathway, indicating that Rbakdn maintains the stability of Ptbp2. In conclusion, our study identified an lncRNA, Rbakdn, with a crucial role in meiosis.
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Affiliation(s)
- Wensheng Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yinan Zhao
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Xiaohua Liu
- NHC Key Laboratory of Male Reproduction and Genetics, Family Planning Research Institute of Guangdong Province, Guangzhou, China
| | - Xiaoya Zhang
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Jiancheng Ding
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yang Li
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Yingpu Tian
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, China
| | - Wen Liu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
| | - Zhongxian Lu
- State Key Laboratory of Cellular Stress Biology, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, China.,Fujian Provincial Key Laboratory of Innovative Drug Target Research, School of Pharmaceutical Sciences, Xiamen University, Xiamen, China
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5
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Song H, Wang L, Chen D, Li F. The Function of Pre-mRNA Alternative Splicing in Mammal Spermatogenesis. Int J Biol Sci 2020; 16:38-48. [PMID: 31892844 PMCID: PMC6930371 DOI: 10.7150/ijbs.34422] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/20/2019] [Indexed: 01/05/2023] Open
Abstract
Alternative pre-mRNA splicing plays important roles in co-transcriptional and post-transcriptional regulation of gene expression functioned during many developmental processes, such as spermatogenesis. The studies focusing on alternative splicing on spermatogenesis supported the notion that the development of testis is regulated by a higher level of alternative splicing than other tissues. Here, we aim to review the mechanisms underlying alternative splicing, particularly the splicing variants functioned in the process of spermatogenesis and the male infertility. There are five points regarding the alternative splicing including ⅰ) a brief introduction of alternative pre-mRNA splicing; ⅱ) the alternative splicing events in spermatogenesis-associated genes enriched in different stages of spermatogenesis; ⅲ) the mechanisms of alternative splicing regulation, such as splicing factors and m6A demethylation; ⅳ) the splice site recognition and alternative splicing, including the production and degradation of abnormal transcripts caused by gene variations and nonsense-mediated mRNA decay, respectively; ⅴ) abnormal alternative splicing correlated with male infertility. Taking together, this review highlights the impacts of alternative splicing and splicing variants in mammal spermatogenesis and provides new insights of the potential application of the alternative splicing into the therapy of male infertility.
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Affiliation(s)
- Huibin Song
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ling Wang
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Dake Chen
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Fenge Li
- Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs & Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, PR China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, PR China
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6
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Hale BJ, Fernandez RF, Kim SQ, Diaz VD, Jackson SN, Liu L, Brenna JT, Hermann BP, Geyer CB, Ellis JM. Acyl-CoA synthetase 6 enriches seminiferous tubules with the ω-3 fatty acid docosahexaenoic acid and is required for male fertility in the mouse. J Biol Chem 2019; 294:14394-14405. [PMID: 31399511 PMCID: PMC6768642 DOI: 10.1074/jbc.ra119.009972] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/01/2019] [Indexed: 12/31/2022] Open
Abstract
Docosahexaenoic acid (DHA) is an ω-3 dietary-derived polyunsaturated fatty acid of marine origin enriched in testes and necessary for normal fertility, yet the mechanisms regulating the enrichment of DHA in the testes remain unclear. Long-chain ACSL6 (acyl-CoA synthetase isoform 6) activates fatty acids for cellular anabolic and catabolic metabolism by ligating a CoA to a fatty acid, is highly expressed in testes, and has high preference for DHA. Here, we investigated the role of ACSL6 for DHA enrichment in the testes and its requirement for male fertility. Acsl6-/- males were severely subfertile with smaller testes, reduced cauda epididymal sperm counts, germ cell loss, and disorganization of the seminiferous epithelium. Total fatty acid profiling of Acsl6-/- testes revealed reduced DHA and increased ω-6 arachidonic acid, a fatty acid profile also reflected in phospholipid composition. Strikingly, lipid imaging demonstrated spatial redistribution of phospholipids in Acsl6-/- testes. Arachidonic acid-containing phospholipids were predominantly interstitial in control testes but diffusely localized across Acsl6-/- testes. In control testes, DHA-containing phospholipids were predominantly within seminiferous tubules, which contain Sertoli cells and spermatogenic cells but relocalized to the interstitium in Acsl6-/- testes. Taken together, these data demonstrate that ACSL6 is an initial driving force for germ cell DHA enrichment and is required for normal spermatogenesis and male fertility.
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Affiliation(s)
- Benjamin J Hale
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27834
| | - Regina F Fernandez
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27834
| | - Sora Q Kim
- Department of Nutrition Science, Purdue University, West Lafayette, Indiana 47907
| | - Victoria D Diaz
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249
| | - Shelley N Jackson
- National Institute on Drug Abuse, Intramural Research Program, Structural Biology Core, Baltimore, Maryland 21224
| | - Lei Liu
- Departments of Pediatrics, Chemistry, and Nutrition, Dell Pediatric Research Institute, University of Texas at Austin, Austin, Texas 78723
- Department of Veterinary Sciences, Hunan Agricultural University, Changsha 410128, China
| | - J Thomas Brenna
- Departments of Pediatrics, Chemistry, and Nutrition, Dell Pediatric Research Institute, University of Texas at Austin, Austin, Texas 78723
| | - Brian P Hermann
- Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249
| | - Christopher B Geyer
- Department of Anatomy and Cell Biology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27834
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina 27834
| | - Jessica M Ellis
- Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina 27834
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina 27834
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7
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Jeong DE, Heo S, Han JH, Lee EY, Kulkarni RN, Kim W. Glucose Controls the Expression of Polypyrimidine Tract-Binding Protein 1 via the Insulin Receptor Signaling Pathway in Pancreatic β Cells. Mol Cells 2018; 41:909-916. [PMID: 30165730 PMCID: PMC6199568 DOI: 10.14348/molcells.2018.0147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/06/2018] [Accepted: 08/09/2018] [Indexed: 01/04/2023] Open
Abstract
In pancreatic β cells, glucose stimulates the biosynthesis of insulin at transcriptional and post-transcriptional levels. The RNA-binding protein, polypyrimidine tract-binding protein 1 (PTBP1), also named hnRNP I, acts as a critical mediator of insulin biosynthesis through binding to the pyrimidine-rich region in the 3'-untranslated region (UTR) of insulin mRNA. However, the underlying mechanism that regulates its expression in β cells is unclear. Here, we report that glucose induces the expression of PTBP1 via the insulin receptor (IR) signaling pathway in β cells. PTBP1 is present in β cells of both mouse and monkey, where its levels are increased by glucose and insulin, but not by insulin-like growth factor 1. PTBP1 levels in immortalized β cells established from wild-type (βIRWT) mice are higher than levels in β cells established from IR-null (βIRKO) mice, and ectopic re-expression of IR-WT in βIRKO cells restored PTBP1 levels. However, PTBP1 levels were not altered in βIRKO cells transfected with IR-3YA, in which the Tyr1158/1162/1163 residues are substituted with Ala. Consistently, treatment with glucose or insulin elevated PTBP1 levels in βIRWT cells, but not in βIRKO cells. In addition, silencing Akt significantly lowered PTBP1 levels. Thus, our results identify insulin as a pivotal mediator of glucose-induced PTBP1 expression in pancreatic β cells.
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Affiliation(s)
- Da Eun Jeong
- Department of Molecular Science and Technology, Ajou University, Suwon 16499,
Korea
| | - Sungeun Heo
- Department of Molecular Science and Technology, Ajou University, Suwon 16499,
Korea
| | - Ji Hye Han
- Department of Molecular Science and Technology, Ajou University, Suwon 16499,
Korea
| | - Eun-young Lee
- Department of Molecular Science and Technology, Ajou University, Suwon 16499,
Korea
| | - Rohit N. Kulkarni
- Department of Islet Cell and Regenerative Biology, Joslin Diabetes Center and Department of Medicine, Harvard Medical School, and Harvard Stem Cell Institute, Boston, MA 02215,
USA
| | - Wook Kim
- Department of Molecular Science and Technology, Ajou University, Suwon 16499,
Korea
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8
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RNA processing in the male germline: Mechanisms and implications for fertility. Semin Cell Dev Biol 2018; 79:80-91. [DOI: 10.1016/j.semcdb.2017.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/04/2017] [Accepted: 10/09/2017] [Indexed: 12/22/2022]
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9
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MacDonald CC, Grozdanov PN. Nonsense in the testis: multiple roles for nonsense-mediated decay revealed in male reproduction. Biol Reprod 2018; 96:939-947. [PMID: 28444146 PMCID: PMC5803779 DOI: 10.1093/biolre/iox033] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/20/2017] [Indexed: 01/23/2023] Open
Abstract
Nonsense-mediated mRNA decay, or NMD, is a quality control mechanism that identifies cytoplasmic mRNAs containing translational termination (stop) codons in specific contexts—either premature termination codons or unusually long 3΄ untranslated regions (UTRs)—and targets them for degradation. In recent studies, researchers in different labs have knocked out important genes involved in NMD, the up-frameshift genes Upf2 and Upf3a, and one component of chromatoid bodies, the Tudor domain-containing protein Tdrd6, and examined the consequences for spermatogenesis. Disruption of Upf2 during early stages of spermatogenesis resulted in disappearance of nearly all spermatogenic cells through loss of NMD. However, disruption of Upf2 during postmeiotic stages resulted in decreased long 3΄ UTR-mediated NMD but no interruption of exon junction-associated NMD. This difference in NMD targeting is possibly due to increased expression of Upf3a in postmeiotic germ cells that antagonizes the functions of Upf3b and somehow favors long 3΄ UTR-mediated NMD. Tying these all together, loss of Tdrd6, a structural component of the germ cell-specific cytoplasmic structures called chromatoid bodies, also resulted in loss of long 3΄ UTR-mediated NMD by interfering with UPF1/UPF2 interactions, delocalizing UPF1, and destroying chromatoid body integrity. These results suggest that chromatoid bodies play a specialized role in modulating the NMD machinery in postmeiotic spermatids.
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Affiliation(s)
- Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
- Correspondence: Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, 3601 4th Street, Lubbock, TX 79430-6540, USA. Tel: +1-806-743-2524; Fax: +1-806-743-2990; E-mail:
| | - Petar N. Grozdanov
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, Texas
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10
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Conservation of polypyrimidine tract binding proteins and their putative target RNAs in several storage root crops. BMC Genomics 2018; 19:124. [PMID: 29415650 PMCID: PMC5803842 DOI: 10.1186/s12864-018-4502-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/28/2018] [Indexed: 11/21/2022] Open
Abstract
Background Polypyrimidine-tract binding proteins (PTBs) are ubiquitous RNA-binding proteins in plants and animals that play diverse role in RNA metabolic processes. PTB proteins bind to target RNAs through motifs rich in cytosine/uracil residues to fine-tune transcript metabolism. Among tuber and root crops, potato has been widely studied to understand the mobile signals that activate tuber development. Potato PTBs, designated as StPTB1 and StPTB6, function in a long-distance transport system by binding to specific mRNAs (StBEL5 and POTH1) to stabilize them and facilitate their movement from leaf to stolon, the site of tuber induction, where they activate tuber and root growth. Storage tubers and root crops are important sustenance food crops grown throughout the world. Despite the availability of genome sequence for sweet potato, cassava, carrot and sugar beet, the molecular mechanism of root-derived storage organ development remains completely unexplored. Considering the pivotal role of PTBs and their target RNAs in potato storage organ development, we propose that a similar mechanism may be prevalent in storage root crops as well. Results Through a bioinformatics survey utilizing available genome databases, we identify the orthologues of potato PTB proteins and two phloem-mobile RNAs, StBEL5 and POTH1, in five storage root crops - sweet potato, cassava, carrot, radish and sugar beet. Like potato, PTB1/6 type proteins from these storage root crops contain four conserved RNA Recognition Motifs (characteristic of RNA-binding PTBs) in their protein sequences. Further, 3´ UTR (untranslated region) analysis of BEL5 and POTH1 orthologues revealed the presence of several cytosine/uracil motifs, similar to those present in potato StBEL5 and POTH1 RNAs. Using RT-qPCR assays, we verified the presence of these related transcripts in leaf and root tissues of these five storage root crops. Similar to potato, BEL5-, PTB1/6- and POTH1-like orthologue RNAs from the aforementioned storage root crops exhibited differential accumulation patterns in leaf and storage root tissues. Conclusions Our results suggest that the PTB1/6-like orthologues and their putative targets, BEL5- and POTH1-like mRNAs, from storage root crops could interact physically, similar to that in potato, and potentially, could function as key molecular signals controlling storage organ development in root crops. Electronic supplementary material The online version of this article (10.1186/s12864-018-4502-7) contains supplementary material, which is available to authorized users.
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11
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Dou X, Gao J, Gao P, Tang D, Peng D, Mao J, Huang Z, Chen P, Chen H, Ke S, Liang C, Zhang X. Association between RNA-binding protein Ptbp2 and germ cell injury in an experimentally-induced unilateral cryptorchidism murine model. PLoS One 2017; 12:e0186654. [PMID: 29045475 PMCID: PMC5646856 DOI: 10.1371/journal.pone.0186654] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 10/03/2017] [Indexed: 01/06/2023] Open
Abstract
RNA binding protein polypyrimidine tract binding protein 2 (Ptbp2) as a key alternative splicing regulator for male germ cell development is well established. However, its expression levels and role in cryptorchidism testes tissues has not been explored. Additionally, the molecular mechanism of heat stress impacts the correct proliferation and differentiation of germ cells is unclear. To investigate whether changes in Ptbp2 expression are correlated with heat stress-induced germ cell injury in testicular tissue, we used a murine model of intraperitoneal cryptorchidism with surgical operation. Here we present compelling evidence that germ cells are severely damaged in mice with unilateral cryptorchidism, with non-obstructive azoospermia. And the Ptbp2 and Pgk2 mRNA levels were significantly decreased in parallel, leading us to conclude that the negative correlation between Ptbp2 levels and germ cell injury in unilateral cryptorchidism murine model. We hypothesize that Ptbp2 is susceptible to heat stress and its disruption has resulted in stability decline of germ cell transcripts Pgk2 mRNA, which consequently lead to germ cell injury in cryptorchidism testes. Thus, we confirm that Ptbp2 is an essential factor in heat stress-induced sperm cell injury and non-obstructive azoospermia.
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Affiliation(s)
- Xianming Dou
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jingjing Gao
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Pan Gao
- Department of Urology, the Second Affiliated Hospital of Wannan Medical College, Wuhu, Anhui, China
| | - Dongdong Tang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Dangwei Peng
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Jun Mao
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhenyu Huang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Peng Chen
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - He Chen
- Department of Laboratory, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Shengwei Ke
- Department of Cell and Developmental Biology, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Chaozhao Liang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xiansheng Zhang
- Department of Urology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- * E-mail:
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12
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Hannigan MM, Zagore LL, Licatalosi DD. Ptbp2 Controls an Alternative Splicing Network Required for Cell Communication during Spermatogenesis. Cell Rep 2017; 19:2598-2612. [PMID: 28636946 PMCID: PMC5543815 DOI: 10.1016/j.celrep.2017.05.089] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 05/04/2017] [Accepted: 05/25/2017] [Indexed: 01/12/2023] Open
Abstract
Alternative splicing has essential roles in development. Remarkably, spermatogenic cells express more alternatively spliced RNAs compared to most whole tissues; however, regulation of these RNAs remains unclear. Here, we characterize the alternative splicing landscape during spermatogenesis and reveal an essential function for the RNA-binding protein Ptbp2 in this highly regulated developmental program. We found that Ptbp2 controls a network of genes involved in cell adhesion, migration, and polarity, suggesting that splicing regulation by Ptbp2 is critical for germ cell communication with Sertoli cells (multifunctional somatic cells necessary for spermatogenesis). Indeed, Ptbp2 ablation in germ cells resulted in disorganization of the filamentous actin (F-actin) cytoskeleton in Sertoli cells, indicating that alternative splicing regulation is necessary for cellular crosstalk during germ cell development. Collectively, the data delineate an alternative splicing regulatory network essential for spermatogenesis, the splicing factor that controls it, and its biological importance in germ-Sertoli communication.
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Affiliation(s)
- Molly M Hannigan
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Leah L Zagore
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Donny D Licatalosi
- Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.
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13
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Song WY, Meng H, Wang XG, Jin HX, Yao GD, Shi SL, Wu L, Zhang XY, Sun YP. Reduced microRNA-188-3p expression contributes to apoptosis of spermatogenic cells in patients with azoospermia. Cell Prolif 2016; 50. [PMID: 27868267 DOI: 10.1111/cpr.12297] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 08/24/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND AND AIMS Human mutL homologl (MLH1) works coordinately in sequential steps to initiate repair of DNA mismatches, and aberrant MLH1 expression is related to spermatogenetic malfunction. In the present study, MLH1 expression in patients with azoospermia was investigated, and moderating effects of miR-188-3p on MLH1 expression and spermatogenesis were identified. METHODS Testicular tissues from 16 patients with obstructive azoospermia (OA) and non-obstructive azoospermia (NOA), and tissues of eight healthy patients were collected. Real-time PCR, Western blotting and immunohistochemical staining were used to detect MLH1 expression. Chromatin immunoprecipitation assay and luciferase reporter assay were performed to evaluate histone acetylation level of miR-188-3p and relationships between miR-188-3p and MLH1. RESULTS Testicular MLH1 expression at mRNA and protein levels was significantly increased, while miR-188-3p expression was lower in patients with OA and NOA than that in controls. Reduced histone acetylation level of miR-188-3p promoter was observed in patients with azoospermia. Overexpression/inhibition of HDAC1, but not HDAC2, contributed to the significant reduction/increase of miR-188-3p expression. miR-188-3p targeted 3' UTR of MLH1 and regulated MLH1 expression. miR-188-3p inhibitor led to elevation of apoptotic level of spermatogenic cells in mice, while this effect was reversed by si-MLH1. CONCLUSION Down-regulation of miR-188-3p by reducing histone acetylation up-regulated MLH1 expression and contributed to promotion of apoptosis in spermatogenic cells, in patients with azoospermia.
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Affiliation(s)
- Wen-Yan Song
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hui Meng
- Pathology Department, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xue-Gai Wang
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hai-Xia Jin
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Gui-Dong Yao
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sen-Lin Shi
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Liang Wu
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiang-Yang Zhang
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying-Pu Sun
- Reproductive Medicine Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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14
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Abstract
Splicing can be epigenetically regulated and involved in cellular differentiation in somatic cells, but the interplay of epigenetic factors and the splicing machinery during spermatogenesis remains unclear. To study these interactions in vivo, we generated a germline deletion of MORF-related gene on chromosome 15 (MRG15), a multifunctional chromatin organizer that binds to methylated histone H3 lysine 36 (H3K36) in introns of transcriptionally active genes and has been implicated in regulation of histone acetylation, homology-directed DNA repair, and alternative splicing in somatic cells. Conditional KO (cKO) males lacking MRG15 in the germline are sterile secondary to spermatogenic arrest at the round spermatid stage. There were no significant alterations in meiotic division and histone acetylation. Specific mRNA sequences disappeared from 66 germ cell-expressed genes in the absence of MRG15, and specific intronic sequences were retained in mRNAs of 4 genes in the MRG15 cKO testes. In particular, introns were retained in mRNAs encoding the transition proteins that replace histones during sperm chromatin condensation. In round spermatids, MRG15 colocalizes with splicing factors PTBP1 and PTBP2 at H3K36me3 sites between the exons and single intron of transition nuclear protein 2 (Tnp2). Thus, our results reveal that MRG15 is essential for pre-mRNA splicing during spermatogenesis and that epigenetic regulation of pre-mRNA splicing by histone modification could be useful to understand not only spermatogenesis but also, epigenetic disorders underlying male infertile patients.
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Duan X, Zhang W, Huang J, Hao L, Wang S, Wang A, Meng D, Zhang Q, Chen Q, Li T. PbWoxT1 mRNA from pear (Pyrus betulaefolia) undergoes long-distance transport assisted by a polypyrimidine tract binding protein. THE NEW PHYTOLOGIST 2016; 210:511-24. [PMID: 26661583 DOI: 10.1111/nph.13793] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/25/2015] [Indexed: 05/23/2023]
Abstract
Little is known about the mechanisms by which mRNAs are transported over long distances in the phloem between the rootstock and the scion in grafted woody plants. We identified an mRNA in the pear variety 'Du Li' (Pyrus betulaefolia) that was shown to be transportable in the phloem. It contains a WUSCHEL-RELATED HOMEOBOX (WOX) domain and was therefore named Wox Transport 1 (PbWoxT1). A 548-bp fragment of PbWoxT1 is critical in long-distance transport. PbWoxT1 is rich in CUCU polypyrimidine domains and its mRNAs interact with a polypyrimidine tract binding protein, PbPTB3. Furthermore, the expression of PbWoxT1 significantly increased in the stems of wild-type (WT) tobacco grafted onto the rootstocks of PbWoxT1 or PbPTB3 co-overexpressing lines, but this was not the case in WT plants grafted onto PbWoxT1 overexpressing rootstocks, suggesting that PbPTB3 mediates PbWoxT1 mRNA long-distance transport. We provide novel information that adds a new mechanism with which to explain the noncell-autonomous manner of WOX gene function, which enriches our understanding of how WOX genes work in fruit trees and other species.
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Affiliation(s)
- Xuwei Duan
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Wenna Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Jing Huang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Li Hao
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Shengnan Wang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Aide Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Dong Meng
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Qiulei Zhang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Qiuju Chen
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing, 100193, China
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Lin JC, Lu YH, Liu YR, Lin YJ. RBM4a-regulated splicing cascade modulates the differentiation and metabolic activities of brown adipocytes. Sci Rep 2016; 6:20665. [PMID: 26857472 PMCID: PMC4746625 DOI: 10.1038/srep20665] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/11/2016] [Indexed: 12/11/2022] Open
Abstract
RNA-binding motif protein 4a (RBM4a) reportedly reprograms splicing profiles of the insulin receptor (IR) and myocyte enhancer factor 2C (MEF2C) genes, facilitating the differentiation of brown adipocytes. Using an RNA-sequencing analysis, we first compared the gene expressing profiles between wild-type and RBM4a−/− brown adipocytes. The ablation of RBM4a led to increases in the PTBP1, PTBP2 (nPTB), and Nova1 proteins, whereas elevated RBM4a reduced the expression of PTBP1 and PTBP2 proteins in brown adipocytes through an alternative splicing-coupled nonsense-mediated decay mechanism. Subsequently, RBM4a indirectly shortened the half-life of the Nova1 transcript which was comparatively stable in the presence of PTBP2. RBM4a diminished the influence of PTBP2 in adipogenic development by reprogramming the splicing profiles of the FGFR2 and PKM genes. These results constitute a mechanistic understanding of the RBM4a-modulated splicing cascade during the brown adipogenesis.
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Affiliation(s)
- Jung-Chun Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yi-Han Lu
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Yun-Ru Liu
- Joint Biobank, Office of Human Research, Taipei Medical University, Taipei, Taiwan
| | - Ying-Ju Lin
- School of Chinese Medicine, China Medical University, Taichung, Taiwan
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Licatalosi DD. Roles of RNA-binding Proteins and Post-transcriptional Regulation in Driving Male Germ Cell Development in the Mouse. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 907:123-51. [PMID: 27256385 DOI: 10.1007/978-3-319-29073-7_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tissue development and homeostasis are dependent on highly regulated gene expression programs in which cell-specific combinations of regulatory factors determine which genes are expressed and the post-transcriptional fate of the resulting RNA transcripts. Post-transcriptional regulation of gene expression by RNA-binding proteins has critical roles in tissue development-allowing individual genes to generate multiple RNA and protein products, and the timing, location, and abundance of protein synthesis to be finely controlled. Extensive post-transcriptional regulation occurs during mammalian gametogenesis, including high levels of alternative mRNA expression, stage-specific expression of mRNA variants, broad translational repression, and stage-specific activation of mRNA translation. In this chapter, an overview of the roles of RNA-binding proteins and the importance of post-transcriptional regulation in male germ cell development in the mouse is presented.
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Affiliation(s)
- Donny D Licatalosi
- Center for RNA Molecular Biology, Case Western Reserve University, Cleveland, OH, 44106, USA.
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18
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Cho SK, Sharma P, Butler NM, Kang IH, Shah S, Rao AG, Hannapel DJ. Polypyrimidine tract-binding proteins of potato mediate tuberization through an interaction with StBEL5 RNA. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:6835-47. [PMID: 26283046 PMCID: PMC4623692 DOI: 10.1093/jxb/erv389] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Polypyrimidine tract-binding (PTB) proteins are a family of RNA-binding proteins that function in a wide range of RNA metabolic processes by binding to motifs rich in uracils and cytosines. A PTB protein of pumpkin was identified as the core protein of an RNA-protein complex that trafficks RNA. The biological function of the PTB-RNA complex, however, has not been demonstrated. In potato, six PTB proteins have been identified, and two, designated StPTB1 and StPTB6, are similar to the phloem-mobile pumpkin type. RNA binding assays confirmed the interaction of StPTB1 and StPTB6 with discrete pyrimidine-rich sequences of the 3'-untranslated regions of the phloem-mobile mRNA, StBEL5. The promoter of StPTB1 was active in companion cells of phloem in both stem and petioles. Expression of both types was evident in phloem cells of roots and in stolons during tuber formation. RNA accumulation of both PTB proteins was induced by short days in leaves in correlation with enhanced accumulation of StBEL5 RNA. StPTB suppression lines exhibited reduced tuber yields and decreased StBEL5 RNA accumulation, whereas StPTB overexpression lines displayed an increase in tuber production correlated with the enhanced production in stolons of steady-state levels of StBEL5 transcripts and RNA of key tuber identity genes. In StPTB overexpression lines, both the stability and long-distance transport of StBEL5 transcripts were enhanced, whereas in suppression lines stability and transport decreased. Using a transgenic approach, it is shown that the StPTB family of RNA-binding proteins regulate specific stages of development through an interaction with phloem-mobile transcripts of StBEL5.
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Affiliation(s)
- Sung Ki Cho
- Plant Biology Major, Iowa State University, Ames, IA 50011-1100, USA
| | - Pooja Sharma
- Plant Biology Major, Iowa State University, Ames, IA 50011-1100, USA
| | | | - Il-Ho Kang
- Plant Biology Major, Iowa State University, Ames, IA 50011-1100, USA
| | - Shweta Shah
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - A Gururaj Rao
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - David J Hannapel
- Plant Biology Major, Iowa State University, Ames, IA 50011-1100, USA
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19
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RNA Binding Protein Ptbp2 Is Essential for Male Germ Cell Development. Mol Cell Biol 2015; 35:4030-42. [PMID: 26391954 DOI: 10.1128/mcb.00676-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 09/14/2015] [Indexed: 11/20/2022] Open
Abstract
RNA binding proteins (RBPs) are increasingly recognized as essential factors in tissue development and homeostasis. The polypyrimidine tract binding (PTB) protein family of RBPs are important posttranscriptional regulators of gene expression. In the nervous system, the function and importance of PTB protein 2 (Ptbp2) as a key alternative splicing regulator is well established. Ptbp2 is also abundantly expressed during spermatogenesis, but its role in this developmental program has not been explored. Additionally, the importance of alternative splicing regulation in spermatogenesis is unclear. Here, we demonstrate that Ptbp2 is essential for spermatogenesis. We also describe an improved dual fluorescence flow cytometry strategy to discriminate, quantify, and collect germ cells in different stages of development. Using this approach, in combination with traditional histological methods, we show that Ptbp2 ablation results in germ cell loss due to increased apoptosis of meiotic spermatocytes and postmeiotic arrest of spermatid differentiation. Furthermore, we show that Ptbp2 is required for alternative splicing regulation in the testis, as in brain. Strikingly, not all of the alternatively spliced RNAs examined were sensitive to Ptbp2 loss in both tissues. Collectively, the data provide evidence for an important role for alternative splicing regulation in germ cell development and a central role for Ptbp2 in this process.
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20
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Lin T, Lashbrook CC, Cho SK, Butler NM, Sharma P, Muppirala U, Severin AJ, Hannapel DJ. Transcriptional analysis of phloem-associated cells of potato. BMC Genomics 2015; 16:665. [PMID: 26335434 PMCID: PMC4558636 DOI: 10.1186/s12864-015-1844-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 08/14/2015] [Indexed: 11/25/2022] Open
Abstract
Background Numerous signal molecules, including proteins and mRNAs, are transported through the architecture of plants via the vascular system. As the connection between leaves and other organs, the petiole and stem are especially important in their transport function, which is carried out by the phloem and xylem, especially by the sieve elements in the phloem system. The phloem is an important conduit for transporting photosynthate and signal molecules like metabolites, proteins, small RNAs, and full-length mRNAs. Phloem sap has been used as an unadulterated source to profile phloem proteins and RNAs, but unfortunately, pure phloem sap cannot be obtained in most plant species. Results Here we make use of laser capture microdissection (LCM) and RNA-seq for an in-depth transcriptional profile of phloem-associated cells of both petioles and stems of potato. To expedite our analysis, we have taken advantage of the potato genome that has recently been fully sequenced and annotated. Out of the 27 k transcripts assembled that we identified, approximately 15 k were present in phloem-associated cells of petiole and stem with greater than ten reads. Among these genes, roughly 10 k are affected by photoperiod. Several RNAs from this day length-regulated group are also abundant in phloem cells of petioles and encode for proteins involved in signaling or transcriptional control. Approximately 22 % of the transcripts in phloem cells contained at least one binding motif for Pumilio, Nova, or polypyrimidine tract-binding proteins in their downstream sequences. Highlighting the predominance of binding processes identified in the gene ontology analysis of active genes from phloem cells, 78 % of the 464 RNA-binding proteins present in the potato genome were detected in our phloem transcriptome. Conclusions As a reasonable alternative when phloem sap collection is not possible, LCM can be used to isolate RNA from specific cell types, and along with RNA-seq, provides practical access to expression profiles of phloem tissue. The combination of these techniques provides a useful approach to the study of phloem and a comprehensive picture of the mechanisms associated with long-distance signaling. The data presented here provide valuable insights into potentially novel phloem-mobile mRNAs and phloem-associated RNA-binding proteins. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1844-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tian Lin
- Plant Biology, Iowa State University, 253 Horticulture Hall, Ames, IA, 50011-1100, USA.
| | - Coralie C Lashbrook
- Plant Biology, Iowa State University, 253 Horticulture Hall, Ames, IA, 50011-1100, USA.
| | - Sung Ki Cho
- Plant Biology, Iowa State University, 253 Horticulture Hall, Ames, IA, 50011-1100, USA.
| | - Nathaniel M Butler
- Plant Biology, Iowa State University, 253 Horticulture Hall, Ames, IA, 50011-1100, USA. .,Department of Plant Breeding, Genetics, and Biotechnology, Michigan State University, East Lansing, MI, 48824, USA.
| | - Pooja Sharma
- Plant Biology, Iowa State University, 253 Horticulture Hall, Ames, IA, 50011-1100, USA.
| | - Usha Muppirala
- Office of Biotechnology, Iowa State University, Ames, IA, 50011-3210, USA.
| | - Andrew J Severin
- Office of Biotechnology, Iowa State University, Ames, IA, 50011-3210, USA.
| | - David J Hannapel
- Plant Biology, Iowa State University, 253 Horticulture Hall, Ames, IA, 50011-1100, USA.
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21
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Bhullar D, Jalodia R, Kalia M, Vrati S. Cytoplasmic translocation of polypyrimidine tract-binding protein and its binding to viral RNA during Japanese encephalitis virus infection inhibits virus replication. PLoS One 2014; 9:e114931. [PMID: 25545659 PMCID: PMC4278868 DOI: 10.1371/journal.pone.0114931] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 11/16/2014] [Indexed: 11/23/2022] Open
Abstract
Japanese encephalitis virus (JEV) has a single-stranded, positive-sense RNA genome containing a single open reading frame flanked by the 5′- and 3′-non-coding regions (NCRs). The virus genome replicates via a negative-sense RNA intermediate. The NCRs and their complementary sequences in the negative-sense RNA are the sites for assembly of the RNA replicase complex thereby regulating the RNA synthesis and virus replication. In this study, we show that the 55-kDa polypyrimidine tract-binding protein (PTB) interacts in vitro with both the 5′-NCR of the positive-sense genomic RNA - 5NCR(+), and its complementary sequence in the negative-sense replication intermediate RNA - 3NCR(-). The interaction of viral RNA with PTB was validated in infected cells by JEV RNA co-immunoprecipitation and JEV RNA-PTB colocalization experiments. Interestingly, we observed phosphorylation-coupled translocation of nuclear PTB to cytoplasmic foci that co-localized with JEV RNA early during JEV infection. Our studies employing the PTB silencing and over-expression in cultured cells established an inhibitory role of PTB in JEV replication. Using RNA-protein binding assay we show that PTB competitively inhibits association of JEV 3NCR(-) RNA with viral RNA-dependent RNA polymerase (NS5 protein), an event required for the synthesis of the plus-sense genomic RNA. cAMP is known to promote the Protein kinase A (PKA)-mediated PTB phosphorylation. We show that cells treated with a cAMP analogue had an enhanced level of phosphorylated PTB in the cytoplasm and a significantly suppressed JEV replication. Data presented here show a novel, cAMP-induced, PTB-mediated, innate host response that could effectively suppress JEV replication in mammalian cells.
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Affiliation(s)
| | | | - Manjula Kalia
- Vaccine and Infectious Disease Research Centre, Translational Health Science & Technology Institute, Gurgaon, India
| | - Sudhanshu Vrati
- National Institute of Immunology, New Delhi, India
- Vaccine and Infectious Disease Research Centre, Translational Health Science & Technology Institute, Gurgaon, India
- * E-mail:
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22
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Kadam US, Schulz B, lrudayaraj J. Detection and quantification of alternative splice sites in Arabidopsis genes AtDCL2 and AtPTB2 with highly sensitive surface enhanced Raman spectroscopy (SERS) and gold nanoprobes. FEBS Lett 2014; 588:1637-43. [DOI: 10.1016/j.febslet.2014.02.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/28/2014] [Indexed: 11/30/2022]
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Schmid R, Grellscheid SN, Ehrmann I, Dalgliesh C, Danilenko M, Paronetto MP, Pedrotti S, Grellscheid D, Dixon RJ, Sette C, Eperon IC, Elliott DJ. The splicing landscape is globally reprogrammed during male meiosis. Nucleic Acids Res 2013; 41:10170-84. [PMID: 24038356 PMCID: PMC3905889 DOI: 10.1093/nar/gkt811] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Meiosis requires conserved transcriptional changes, but it is not known whether there is a corresponding set of RNA splicing switches. Here, we used RNAseq of mouse testis to identify changes associated with the progression from mitotic spermatogonia to meiotic spermatocytes. We identified ∼150 splicing switches, most of which affect conserved protein-coding exons. The expression of many key splicing regulators changed in the course of meiosis, including downregulation of polypyrimidine tract binding protein (PTBP1) and heterogeneous nuclear RNP A1, and upregulation of nPTB, Tra2β, muscleblind, CELF proteins, Sam68 and T-STAR. The sequences near the regulated exons were significantly enriched in target sites for PTB, Tra2β and STAR proteins. Reporter minigene experiments investigating representative exons in transfected cells showed that PTB binding sites were critical for splicing of a cassette exon in the Ralgps2 mRNA and a shift in alternative 5′ splice site usage in the Bptf mRNA. We speculate that nPTB might functionally replace PTBP1 during meiosis for some target exons, with changes in the expression of other splicing factors helping to establish meiotic splicing patterns. Our data suggest that there are substantial changes in the determinants and patterns of alternative splicing in the mitotic-to-meiotic transition of the germ cell cycle.
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Affiliation(s)
- Ralf Schmid
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, UK, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK, School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK, Department of Health Sciences, University of 00135 Rome 'Foro Italico', Rome, Italy, Laboratories of Neuroembryology and of Cellular and Molecular Neurobiology, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy, Department of Public Health and Cell Biology, University of Rome Tor Vergata, 00133 Rome, Italy, Institute of Particle Physics Phenomenology, Durham University, Durham, DH1 3LE, UK and Life Technologies Ltd., Paisley PA4 9RF, UK
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Chapman KM, Powell HM, Chaudhary J, Shelton JM, Richardson JA, Richardson TE, Hamra FK. Linking spermatid ribonucleic acid (RNA) binding protein and retrogene diversity to reproductive success. Mol Cell Proteomics 2013; 12:3221-36. [PMID: 23938467 DOI: 10.1074/mcp.m113.030585] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Spermiogenesis is a postmeiotic process that drives development of round spermatids into fully elongated spermatozoa. Spermatid elongation is largely controlled post-transcriptionally after global silencing of mRNA synthesis from the haploid genome. Here, rats that differentially express EGFP from a lentiviral transgene during early and late steps of spermiogenesis were used to flow sort fractions of round and elongating spermatids. Mass-spectral analysis of 2D gel protein spots enriched >3-fold in each fraction revealed a heterogeneous RNA binding proteome (hnRNPA2/b1, hnRNPA3, hnRPDL, hnRNPK, hnRNPL, hnRNPM, PABPC1, PABPC4, PCBP1, PCBP3, PTBP2, PSIP1, RGSL1, RUVBL2, SARNP2, TDRD6, TDRD7) abundantly expressed in round spermatids prior to their elongation. Notably, each protein within this ontology cluster regulates alternative splicing, sub-cellular transport, degradation and/or translational repression of mRNAs. In contrast, elongating spermatid fractions were enriched with glycolytic enzymes, redox enzymes and protein synthesis factors. Retrogene-encoded proteins were over-represented among the most abundant elongating spermatid factors identified. Consistent with these biochemical activities, plus corresponding histological profiles, the identified RNA processing factors are predicted to collectively drive post-transcriptional expression of an alternative exome that fuels finishing steps of sperm maturation and fitness.
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Yang CK, Yen P. Differential translation of Dazap1 transcripts during spermatogenesis. PLoS One 2013; 8:e60873. [PMID: 23658607 PMCID: PMC3637229 DOI: 10.1371/journal.pone.0060873] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 03/04/2013] [Indexed: 01/31/2023] Open
Abstract
Deleted in AZoospermia Associated Protein 1 (DAZAP1) is a ubiquitous hnRNP protein that has been implicated in RNA transcription, splicing, and translation. It is highly expressed in testes, predominantly in late stage spermatocytes and post-meiotic spermatids. Dazap1 deficiency in mice results in growth retardation and spermatogenic arrest. The gene produces two major transcripts of 2.4 and 1.8 kb, designated Dazap1-L and Dazap1-S, respectively. Results of our previous RNA in situ hybridization and immunostaining suggested translational regulation of the Dazap1 transcripts during spermatogenesis. The main objectives of the study were to determine the origin of the two Dazap1 transcripts and to investigate whether they were similarly translated. Our Northern and 3′ RACE analyses showed that the two transcripts were generated through alternative polyadenylation. In mouse testes, the levels of both transcripts were low at postnatal day 12 (P12), increased significantly at P18, and reached maximum at P27. Sucrose gradient analyses showed that at P12 both transcripts were actively translated. Afterward, an increasing portion of Dazap1-S became associated with the translationally inactive mRNPs, and the translational repression was accompanied by an increase in the length of its poly(A) tail. A much smaller portion of Dazap1-L was also sequestered to mRNPs as testes matured, but there was no changes in its poly(A) tail length. Using RNA pull-down followed by mass spectrometry, we identified DAZL, a germ-cell specific translation regulator, as one of the proteins that bound to the 3′UTR region specific for Dazap1-L. We further showed that DAZL preferentially bound to Dazap1-L in testis lysates and stimulated the translation of a reporter gene carrying Dazap1-L 3′UTR. In summary, our study shows that the translation of the two Dazap1 transcripts is differentially regulated. It also provides a new example of translational repression associated with poly(A) tail elongation during spermatogenesis.
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Affiliation(s)
- Chi-Kai Yang
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Pauline Yen
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
- * E-mail:
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Lin S, Wang MJ, Tseng KY. Polypyrimidine tract-binding protein induces p19(Ink4d) expression and inhibits the proliferation of H1299 cells. PLoS One 2013; 8:e58227. [PMID: 23536791 PMCID: PMC3594294 DOI: 10.1371/journal.pone.0058227] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 02/01/2013] [Indexed: 11/18/2022] Open
Abstract
The expression of polypyrimidine tract-binding protein (PTB) is up-regulated in many types of cancer. Here, we studied the role of PTB in the growth of non small cell lung cancer cells. Data showed that PTB overexpression inhibited the growth of H1299 cells at least by inhibiting DNA synthesis. Quantitative real-time PCR and Western blot analyses showed that PTB overexpression in H1299 cells specifically induced the expression of p19Ink4d, an inhibitor of cyclin-dependent kinase 4. Repression of p19Ink4d expression partially rescued PTB-caused proliferation inhibition. PTB overexpression also inhibited the growth and induced the expression of p19Ink4d mRNA in A549 cells. However, Western blot analyses failed to detect the presence of p19Ink4d protein in A549 cells. To address how PTB induced p19Ink4d in H1299 cells, we showed that PTB might up-regulate the activity of p19Ink4d gene (CDKN2D) promoter. Besides, PTB lacking the RNA recognition motif 3 (RRM3) was less effective in growth inhibition and p19Ink4d induction, suggesting that RNA-binding activity of PTB plays an important role in p19Ink4d induction. However, immunoprecipitation of ribonuclearprotein complexes plus quantitative real-time PCR analyses showed that PTB might not bind p19Ink4d mRNA, suggesting that PTB overexpression might trigger the other RNA-binding protein(s) to bind p19Ink4d mRNA. Subsequently, RNA electrophoretic mobility-shift assays revealed a 300-base segment (designated as B2) within the 3′UTR of p19Ink4d mRNA, with which the cytoplasmic lysates of PTB-overexpressing cells formed more prominent complexes than did control cell lysates. Insertion of B2 into a reporter construct increased the expression of the chimeric luciferase transcripts in transfected PTB-overexpressing cells but not in control cells; conversely, overexpression of B2-containing reporter construct in PTB-overexpressing cells abolished the induction of p19Ink4d mRNA. In sum, we have shown that PTB plays as a negative regulator in H1299 cell proliferation at least by inducing p19Ink4d expression at transcriptional and post-transcriptional levels.
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Affiliation(s)
- Shankung Lin
- Institute of Cellular and System Medicine, National Health Research Institutes, Zhunan Town, Miaoli, Taiwan, Republic of China.
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Licatalosi DD, Yano M, Fak JJ, Mele A, Grabinski SE, Zhang C, Darnell RB. Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev 2012; 26:1626-42. [PMID: 22802532 DOI: 10.1101/gad.191338.112] [Citation(s) in RCA: 149] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Two polypyrimidine tract RNA-binding proteins (PTBs), one near-ubiquitously expressed (Ptbp1) and another highly tissue-restricted (Ptbp2), regulate RNA in interrelated but incompletely understood ways. Ptbp1, a splicing regulator, is replaced in the brain and differentiated neuronal cell lines by Ptbp2. To define the roles of Ptbp2 in the nervous system, we generated two independent Ptbp2-null strains, unexpectedly revealing that Ptbp2 is expressed in neuronal progenitors and is essential for postnatal survival. A HITS-CLIP (high-throughput sequencing cross-linking immunoprecipitation)-generated map of reproducible Ptbp2-RNA interactions in the developing mouse neocortex, combined with results from splicing-sensitive microarrays, demonstrated that the major action of Ptbp2 is to inhibit adult-specific alternative exons by binding pyrimidine-rich sequences upstream of and/or within them. These regulated exons are present in mRNAs encoding proteins associated with control of cell fate, proliferation, and the actin cytoskeleton, suggesting a role for Ptbp2 in neurogenesis. Indeed, neuronal progenitors in the Ptbp2-null brain exhibited an aberrant polarity and were associated with regions of premature neurogenesis and reduced progenitor pools. Thus, Ptbp2 inhibition of a discrete set of adult neuronal exons underlies early brain development prior to neuronal differentiation and is essential for postnatal survival.
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Affiliation(s)
- Donny D Licatalosi
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, New York, New York 10065, USA
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Keppetipola N, Sharma S, Li Q, Black DL. Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2. Crit Rev Biochem Mol Biol 2012; 47:360-78. [PMID: 22655688 DOI: 10.3109/10409238.2012.691456] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alternative splicing patterns are regulated by RNA binding proteins that assemble onto each pre-mRNA to form a complex RNP structure. The polypyrimidine tract binding protein, PTB, has served as an informative model for understanding how RNA binding proteins affect spliceosome assembly and how changes in the expression of these proteins can control complex programs of splicing in tissues. In this review, we describe the mechanisms of splicing regulation by PTB and its function, along with its paralog PTBP2, in neuronal development.
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Affiliation(s)
- Niroshika Keppetipola
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA, USA
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Delbes G, Yanagiya A, Sonenberg N, Robaire B. PABP interacting protein 2A (PAIP2A) regulates specific key proteins during spermiogenesis in the mouse. Biol Reprod 2012; 86:95. [PMID: 22190698 DOI: 10.1095/biolreprod.111.092619] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
During spermiogenesis, expression of the specific proteins needed for proper differentiation of male germ cells is under translational control. We have shown that PAIP2A is a major translational regulator involved in the maturation of male germ cells and male fertility. To identify the proteins controlled by PAIP2A during spermiogenesis, we characterized the proteomic profiles of elongated spermatids from wild-type (WT) mice and mice that were Paip2a/Paip2b double-null mutants (DKO). Elongated spermatid populations were obtained and proteins were extracted and separated on gradient polyacrylamide gels. The gels were digested with trypsin and peptides were identified by mass spectrometry. We identified 632 proteins with at least two unique peptides and a confidence level of 95%. Only 209 proteins were consistently detected in WT or DKO replicates with more than five spectra. Twenty-nine proteins were differentially expressed with at least a 1.5-fold change; 10 and 19 proteins were down- and up-regulated, respectively, in DKO compared to WT mice. We confirmed the significantly different expression levels of three proteins, EIF4G1, AKAP4, and HK1, by Western blot analysis. We have characterized novel proteins that have their expression controlled by PAIP2A; of these, 50% are involved in flagellar structure and sperm motility. Although several proteins affected by abrogation of Paip2a have established roles in reproduction, the roles of many others remain to be determined.
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Affiliation(s)
- Geraldine Delbes
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
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30
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Engels B, Jannot G, Remenyi J, Simard MJ, Hutvagner G. Polypyrimidine tract binding protein (hnRNP I) is possibly a conserved modulator of miRNA-mediated gene regulation. PLoS One 2012; 7:e33144. [PMID: 22427970 PMCID: PMC3302860 DOI: 10.1371/journal.pone.0033144] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2010] [Accepted: 02/10/2012] [Indexed: 11/19/2022] Open
Abstract
MiRNAs can regulate gene expression through versatile mechanisms that result in increased or decreased expression of the targeted mRNA and it could effect the expression of thousands of protein in a particular cell. An increasing body of evidence suggest that miRNAs action can be modulated by proteins that bind to the same 3′UTRs that are targeted by miRNAs, suggesting that other factors apart from miRNAs and their target sites determine miRNA-modulation of gene expression. We applied an affinity purification protocol using biotinylated let-7 miRNA inhibitor to isolate proteins that are involved in let-7 mediated gene regulation that resulted in an affinity purification of Polypyrimidine Tract Binding protein (PTB). Here we show that PTB interacts with miRNAs and human Argonaute 2 (hAgo2) through RNA as well as identified potential mammalian cellular targets that are co-regulated by PTB and hAgo2. In addition, using genetic approach, we have demonstrated that PTB genetically interacts with Caenorhabditis elegans let-7 indicating a conserved role for PTB in miRNA-mediated gene regulation.
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Affiliation(s)
- Bart Engels
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Guillaume Jannot
- Laval University Cancer Research Centre, Hôtel-Dieu de Québec (CHUQ), Québec City, Québec, Canada
| | - Judit Remenyi
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Martin J. Simard
- Laval University Cancer Research Centre, Hôtel-Dieu de Québec (CHUQ), Québec City, Québec, Canada
| | - György Hutvagner
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, United Kingdom
- Centre for Health Technologies, University of Technology, Sydney, Sydney, Australia
- * E-mail:
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Xu M, Hecht NB. Polypyrimidine tract-binding protein 2 binds to selective, intronic messenger RNA and microRNA targets in the mouse testis. Biol Reprod 2010; 84:435-9. [PMID: 20980688 DOI: 10.1095/biolreprod.110.087114] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Here we use an in vivo cross-linking and immunoprecipitation procedure to detect RNA targets of the multifunctional RNA-binding protein polypyrimidine tract-binding protein (PTBP) 2 in mouse testis. Eleven known mRNAs, including Ptbp2 mRNA, 28 RNAs matching intron sequences, and 12 small RNAs and repeat sequences are identified. The specificity of interaction between PTBP2 and its target RNAs was confirmed using RNA interference with mouse N2A cells. Reduction of PTBP2 levels led to decreases in 7 of 10 of the mRNAs, to the repression of alternative splicing of introns, and to reductions in specific miRNAs.
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Affiliation(s)
- Mingang Xu
- Center for Research on Reproduction and Women's Health, University of Pennsylvania School of Medicine, 421 Curie Boulevard, Philadelphia, PA 19104-6080, USA
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Yanagiya A, Delbes G, Svitkin YV, Robaire B, Sonenberg N. The poly(A)-binding protein partner Paip2a controls translation during late spermiogenesis in mice. J Clin Invest 2010; 120:3389-400. [PMID: 20739757 DOI: 10.1172/jci43350] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Accepted: 07/14/2010] [Indexed: 11/17/2022] Open
Abstract
Translational control plays a key role in late spermiogenesis. A number of mRNAs encoding proteins required for late spermiogenesis are expressed in early spermatids but are stored as translationally inactive messenger ribonucleoprotein particles (mRNPs). The translation of these mRNAs is associated with shortening of their poly(A) tail in late spermiogenesis. Poly(A)-binding protein (Pabp) plays an important role in mRNA stabilization and translation. Three Pabp-interacting proteins, Paip1, Paip2a, and Paip2b, have been described. Paip2a is expressed in late spermatids. To investigate the role of Paip2 in spermiogenesis, we generated mice with knockout of either Paip2a or Paip2b and double-KO (DKO) mice lacking both Paip2a and Paip2b. Paip2a-KO and Paip2a/Paip2b-DKO mice exhibited male infertility. Translation of several mRNAs encoding proteins essential to male germ cell development was inhibited in late spermiogenesis in Paip2a/Paip2b-DKO mice, resulting in defective elongated spermatids. Inhibition of translation in Paip2a/Paip2b-DKO mice was caused by aberrant increased expression of Pabp, which impaired the interaction between eukaryotic initiation factor 4E (eIF4E) and the cap structure at the 5' end of the mRNA. We therefore propose a model whereby efficient mRNA translation in late spermiogenesis occurs at an optimal concentration of Pabp, a condition not fulfilled in Paip2a/Paip2b-DKO mice.
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Affiliation(s)
- Akiko Yanagiya
- Department of Biochemistry and Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
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Hermo L, Pelletier RM, Cyr DG, Smith CE. Surfing the wave, cycle, life history, and genes/proteins expressed by testicular germ cells. Part 4: intercellular bridges, mitochondria, nuclear envelope, apoptosis, ubiquitination, membrane/voltage-gated channels, methylation/acetylation, and transcription factors. Microsc Res Tech 2010; 73:364-408. [PMID: 19941288 DOI: 10.1002/jemt.20785] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
As germ cells divide and differentiate from spermatogonia to spermatozoa, they share a number of structural and functional features that are common to all generations of germ cells and these features are discussed herein. Germ cells are linked to one another by large intercellular bridges which serve to move molecules and even large organelles from the cytoplasm of one cell to another. Mitochondria take on different shapes and features and topographical arrangements to accommodate their specific needs during spermatogenesis. The nuclear envelope and pore complex also undergo extensive modifications concomitant with the development of germ cell generations. Apoptosis is an event that is normally triggered by germ cells and involves many proteins. It occurs to limit the germ cell pool and acts as a quality control mechanism. The ubiquitin pathway comprises enzymes that ubiquitinate as well as deubiquitinate target proteins and this pathway is present and functional in germ cells. Germ cells express many proteins involved in water balance and pH control as well as voltage-gated ion channel movement. In the nucleus, proteins undergo epigenetic modifications which include methylation, acetylation, and phosphorylation, with each of these modifications signaling changes in chromatin structure. Germ cells contain specialized transcription complexes that coordinate the differentiation program of spermatogenesis, and there are many male germ cell-specific differences in the components of this machinery. All of the above features of germ cells will be discussed along with the specific proteins/genes and abnormalities to fertility related to each topic.
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Affiliation(s)
- Louis Hermo
- Department of Anatomy and Cell Biology, Faculty of Medicine, McGill University, 3640 University Street, Montreal, QC Canada H3A 2B2.
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Reid DC, Chang BL, Gunderson SI, Alpert L, Thompson WA, Fairbrother WG. Next-generation SELEX identifies sequence and structural determinants of splicing factor binding in human pre-mRNA sequence. RNA (NEW YORK, N.Y.) 2009; 15:2385-2397. [PMID: 19861426 PMCID: PMC2779669 DOI: 10.1261/rna.1821809] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Accepted: 09/18/2009] [Indexed: 05/28/2023]
Abstract
Many splicing factors interact with both mRNA and pre-mRNA. The identification of these interactions has been greatly improved by the development of in vivo cross-linking immunoprecipitation. However, the output carries a strong sampling bias in favor of RNPs that form on more abundant RNA species like mRNA. We have developed a novel in vitro approach for surveying binding on pre-mRNA, without cross-linking or sampling bias. Briefly, this approach entails specifically designed oligonucleotide pools that tile through a pre-mRNA sequence. The pool is then partitioned into bound and unbound fractions, which are quantified by a two-color microarray. We applied this approach to locating splicing factor binding sites in and around approximately 4000 exons. We also quantified the effect of secondary structure on binding. The method is validated by the finding that U1snRNP binds at the 5' splice site (5'ss) with a specificity that is nearly identical to the splice donor motif. In agreement with prior reports, we also show that U1snRNP appears to have some affinity for intronic G triplets that are proximal to the 5'ss. Both U1snRNP and the polypyrimidine tract binding protein (PTB) avoid exonic binding, and the PTB binding map shows increased enrichment at the polypyrimidine tract. For PTB, we confirm polypyrimidine specificity and are also able to identify structural determinants of PTB binding. We detect multiple binding motifs enriched in the PTB bound fraction of oligonucleotides. These motif combinations augment binding in vitro and are also enriched in the vicinity of exons that have been determined to be in vivo targets of PTB.
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Affiliation(s)
- Daniel C Reid
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island 02912, USA
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Wang MJ, Lin S. A region within the 5'-untranslated region of hypoxia-inducible factor-1alpha mRNA mediates its turnover in lung adenocarcinoma cells. J Biol Chem 2009; 284:36500-36510. [PMID: 19887373 DOI: 10.1074/jbc.m109.008904] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Previously, we showed that CL1-5 cells express more hypoxia-inducible factor-1alpha (HIF-1alpha) than the parental CL1 cells, which bestows CL1-5 cells a stronger invasive activity. Here, we investigated the mechanisms underlying the differential expression of HIF-1alpha mRNA in CL1 and CL1-5 cells. Data showed that the transcription rate of HIF-1alpha gene in CL1 cells was slightly higher than that of CL1-5 cells, suggesting that the expression of HIF-1alpha mRNA in CL1 cells was repressed by post-transcriptional mechanisms. RNA electrophoretic mobility shift assays revealed a 61-base segment (designated as D5) within the 5'-untranslated repeat of HIF-1alpha mRNA, with which the CL1 cell lysates formed more prominent complexes (including complex I) than did CL1-5 cell lysates. Insertion of D5 into a reporter construct reduced the half-life of the chimeric transcripts in transfected CL1 but not CL1-5 cells; conversely, overexpression of D5-containing reporter construct in CL1 cells increased HIF-1alpha mRNA. We also identified the polypyrimidine tract-binding protein (PTB) as a required component of complex I. Deletion of the RNA recognition motif 1 (RRM1) or RRM3 of PTB abolished the formation of complex I. Our data showed that CL1 cells expressed more PTB than CL1-5 cells. Inhibition of PTB expression in CL1 cells decreased the formation of complex I, whereas overexpression of PTB in CL1-5 cells increased the levels of complex I, decreased the stability of HIF-1alpha and D5-containing chimeric mRNAs, and decreased cell invasiveness. In sum, we have identified in lung adenocarcinoma cells a mechanism that regulates HIF-1alpha expression by modulating HIF-1alpha mRNA stability.
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Affiliation(s)
- Ming Jen Wang
- Institute of Cellular and System Medicine, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan
| | - Shankung Lin
- Institute of Cellular and System Medicine, National Health Research Institutes, Number 35, Keyan Road, Zhunan Town, Miaoli County 35053, Taiwan.
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Lin YM, Chung CL, Cheng YS. Posttranscriptional regulation of CDC25A by BOLL is a conserved fertility mechanism essential for human spermatogenesis. J Clin Endocrinol Metab 2009; 94:2650-7. [PMID: 19417033 DOI: 10.1210/jc.2009-0108] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
CONTEXT Human BOLL is known as a meiotic regulator, and CDC25A is considered as a potential RNA target of BOLL. OBJECTIVE The aim of the study was to clarify the relationship between BOLL and CDC25A expressions in human testes and to explore the mechanism by which BOLL regulates CDC25A. DESIGN AND SETTING A prospective experimental study was conducted at a university-based medical center. PARTICIPANTS AND INTERVENTIONS BOLL protein, CDC25A mRNA, and CDC25A protein expressions, as well as spermatocyte numbers in the testes of 32 infertile men were measured. The interaction between BOLL protein and CDC25A mRNA was assessed in in vitro studies. MAIN OUTCOME MEASURES Protein and RNA expressions, relationships between expression profiles, CDC25A mRNA binding site for BOLL, and the effects of BOLL on CDC25A mRNA stability and translatability were measured. RESULTS The protein expressions of BOLL and CDC25A are significantly decreased in patients with spermatogenic failure, with the lowest levels detected in patients with meiotic arrest. Both protein expressions are significantly correlated with spermatocyte numbers. Expressional profiling analysis among BOLL protein, CDC25A mRNA, and CDC25A protein suggests a causal relationship between BOLL and CDC25A. BOLL specifically binds to a 21-nucleotide region of the CDC25A 3'UTR, and this region is evolutionarily conserved. A U-rich region within this 21-nucleotide sequence is crucial for binding. BOLL stimulates CDC25A translation, and this effect does not involve alteration of mRNA stability. CONCLUSION CDC25A is subject to translational control by BOLL, which is an evolutionarily conserved mechanism. A decreased CDC25A expression caused by lack or decrease of BOLL may be associated with male infertility.
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Affiliation(s)
- Yung Ming Lin
- Department of Urology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Wang S, Okamoto T. Involvement of polypyrimidine tract-binding protein (PTB)-related proteins in pollen germination in Arabidopsis. PLANT & CELL PHYSIOLOGY 2009; 50:179-190. [PMID: 19122186 DOI: 10.1093/pcp/pcn207] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The pollen grains of most angiosperms contain stores of RNAs and their translation products required for pollen germination and subsequent early elongation of pollen tubes. Polypyrimidine tract-binding protein (PTB), which is involved in the regulation of pre-mRNA alternative splicing, internal ribosomal entry site (IRES)-mediated translation and mRNA localization/sorting, is known to act as a bridging molecule between RNAs and a variety of cellular factors to fulfill cellular functions in both the nucleus and cytoplasm. Moreover, it has been reported that PTB plays roles in the differentiation and development of animal cells and tissues. In the Arabidopsis genome, there are two PTB-related genes, tentatively termed AtPTB1 and AtPTB2. In the present study, the physiological functions of AtPTBs were investigated using genetic and cytological approaches. The AtPTB promoter was highly active in vegetative cells of mature pollen grains, and AtPTB was localized in the nucleus and cytoplasm of these vegetative cells. Mutations in the AtPTB genes resulted in decreased germination efficiency, and this effect was rescued by introduction of the AtPTB2 promoter::AtPTB2-GFP. Taken together, these findings suggest that AtPTB is involved in pollen germination through possible RNA metabolism processes in late-maturing and mature pollen grains.
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Affiliation(s)
- Shuyi Wang
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
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38
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Xu M, McCarrey JR, Hecht NB. A cytoplasmic variant of the KH-type splicing regulatory protein serves as a decay-promoting factor for phosphoglycerate kinase 2 mRNA in murine male germ cells. Nucleic Acids Res 2008; 36:7157-67. [PMID: 19015122 PMCID: PMC2602782 DOI: 10.1093/nar/gkn800] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Phosphoglycerate kinase 2 (PGK2) is a germ cell-specific protein whose mRNA is translationally regulated in the mammalian testis. Using RNA affinity chromatography with the 3'-untranslated region (UTR) of Pgk2 mRNA and adult testis extracts, several associated proteins including a novel isoform of the AU-rich element RNA-binding protein and KH-type splicing regulatory protein (KSRP) were identified. KSRP, a protein of approximately 75 kDa, is widely expressed in somatic and germ cells where it is primarily nuclear. In addition to the approximately 75-kDa KSRP, a approximately 52-kD KSRP, t-KSRP, is present in the cytoplasm of a subpopulation of germ cells. t-KSRP binds directly to a 93-nt sequence (designated the F1 region) of the 3'-UTR of the Pgk2 mRNA and destabilizes Pgk2 mRNA constructs in testis extracts and in transfected cells. We conclude that this testicular variant of the multifunctional nucleic acid-binding protein, KSRP, serves as a decay-promoting factor for Pgk2 mRNA in male germ cells.
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Affiliation(s)
- Mingang Xu
- Center for Research on Reproduction and Women's Health, University of Pennsylvania School of Medicine, Philadelphia, PA 6080, USA
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Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein. Biochem Soc Trans 2008; 36:641-7. [PMID: 18631133 DOI: 10.1042/bst0360641] [Citation(s) in RCA: 241] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
PTB (polypyrimidine-tract-binding protein) is a ubiquitous RNA-binding protein. It was originally identified as a protein with a role in splicing but it is now known to function in a large number of diverse cellular processes including polyadenylation, mRNA stability and translation initiation. Specificity of PTB function is achieved by a combination of changes in the cellular localization of this protein (its ability to shuttle from the nucleus to the cytoplasm is tightly controlled) and its interaction with additional proteins. These differences in location and trans-acting factor requirements account for the fact that PTB acts both as a suppressor of splicing and an activator of translation. In the latter case, the role of PTB in translation has been studied extensively and it appears that this protein is required for an alternative form of translation initiation that is mediated by a large RNA structural element termed an IRES (internal ribosome entry site) that allows the synthesis of picornaviral proteins and cellular proteins that function to control cell growth and cell death. In the present review, we discuss how PTB regulates these disparate processes.
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Xu M, Hecht NB. MSY2 and polypyrimidine tract binding protein 2 stabilize mRNAs in the mammalian testis. ACTA ACUST UNITED AC 2008; 31:457-61. [PMID: 18380784 DOI: 10.1111/j.1365-2605.2008.00885.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MSY2 is a highly conserved and abundant DNA/RNA-binding protein that functions as a global stabilizer/translational suppressor of mRNAs in male germ cells. The polypyrimidine tract binding protein, PTBP2, is an RNA-binding protein that splices nuclear transcripts and stabilizes specific mRNAs in the cytoplasm. The mechanisms whereby MSY2 selects and stabilizes a large group of male germ cell mRNAs and PTBP2 stabilizes specific mRNAs such as the phosphoglycerate kinase 2 mRNA in the testis and in transfected cells will be discussed.
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Affiliation(s)
- Mingang Xu
- Center for Research on Reproduction and Women's Health, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-6080, USA
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Sartini BL, Wang H, Wang W, Millette CF, Kilpatrick DL. Pre-Messenger RNA Cleavage Factor I (CFIm): Potential Role in Alternative Polyadenylation During Spermatogenesis1. Biol Reprod 2008; 78:472-82. [DOI: 10.1095/biolreprod.107.064774] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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