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Fan YJ, Ding Z, Zhang Y, Su R, Yue JL, Liang AM, Huang QW, Meng YR, Li M, Xue Y, Xu YZ. Sex-lethal regulates back-splicing and generation of the sex-differentially expressed circular RNAs. Nucleic Acids Res 2023; 51:5228-5241. [PMID: 37070178 PMCID: PMC10250224 DOI: 10.1093/nar/gkad280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 03/21/2023] [Accepted: 04/06/2023] [Indexed: 04/19/2023] Open
Abstract
Conversely to canonical splicing, back-splicing connects the upstream 3' splice site (SS) with a downstream 5'SS and generates exonic circular RNAs (circRNAs) that are widely identified and have regulatory functions in eukaryotic gene expression. However, sex-specific back-splicing in Drosophila has not been investigated and its regulation remains unclear. Here, we performed multiple RNA analyses of a variety sex-specific Drosophila samples and identified over ten thousand circular RNAs, in which hundreds are sex-differentially and -specifically back-spliced. Intriguingly, we found that expression of SXL, an RNA-binding protein encoded by Sex-lethal (Sxl), the master Drosophila sex-determination gene that is only spliced into functional proteins in females, promoted back-splicing of many female-differential circRNAs in the male S2 cells, whereas expression of a SXL mutant (SXLRRM) did not promote those events. Using a monoclonal antibody, we further obtained the transcriptome-wide RNA-binding sites of SXL through PAR-CLIP. After splicing assay of mini-genes with mutations in the SXL-binding sites, we revealed that SXL-binding on flanking exons and introns of pre-mRNAs facilitates back-splicing, whereas SXL-binding on the circRNA exons inhibits back-splicing. This study provides strong evidence that SXL has a regulatory role in back-splicing to generate sex-specific and -differential circRNAs, as well as in the initiation of sex-determination cascade through canonical forward-splicing.
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Affiliation(s)
- Yu-Jie Fan
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Zhan Ding
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Yu Zhang
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Ruibao Su
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jia-Le Yue
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - An-Min Liang
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Qi-Wei Huang
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Yan-Ran Meng
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
| | - Muwang Li
- College of Biotechnology, Jiangsu University of Science and Technology, Jiangsu 212018, China
| | - Yuanchao Xue
- Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong-Zhen Xu
- The RNA Institute, State Key Laboratory of Virology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Hubei430072, China
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Wen L, Gong Q, Du Q, Yu X, Feng Q, Liu L. Lacking of sex-lethal gene lowers the fertility of male reproduction in Spodoptera litura (Lepidoptera). PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2022; 184:105087. [PMID: 35715034 DOI: 10.1016/j.pestbp.2022.105087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/01/2022] [Accepted: 03/22/2022] [Indexed: 06/15/2023]
Abstract
Sex-lethal (Sxl) encodes an RNA-binding protein that acts as the switch of sex determination in Drosophila and influences the genitalia formation and gonadal development. However, its sex-determination roles are not conserved in all insects and its role in the gonadal development of Lepidoptera is not well documented. In this study, three splicing variants of Sxl mRNA were identified in Spodoptera litura and they highly expressed in gonads, particularly in the testis. The mRNA levels of SlSxl exhibited higher expression in the spermatid than the testis sheaths, and gradually increased with the spermiogenesis. Sex-lethal protein (SlSXL) is mainly distributed in the cytoplasm of spermatocytes and the head of spermatid. Knockout of SlSxl resulted in fewer eupyrene sperm bundles and apyrene sperm bundles in the testes of moth and a large number of undeveloped spermatocysts retained in the moth of mutant testis, and leading to the reduction of oviposition and hatch rate in the offsprings after mating with female. These results suggest that SlSxl is a critical player in the spermiogenesis of S. litura.
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Affiliation(s)
- Liang Wen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qian Gong
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qian Du
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Xiaoqiang Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou 510631, China.
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Moschall R, Rass M, Rossbach O, Lehmann G, Kullmann L, Eichner N, Strauss D, Meister G, Schneuwly S, Krahn MP, Medenbach J. Drosophila Sister-of-Sex-lethal reinforces a male-specific gene expression pattern by controlling Sex-lethal alternative splicing. Nucleic Acids Res 2019; 47:2276-2288. [PMID: 30590805 PMCID: PMC6411925 DOI: 10.1093/nar/gky1284] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/04/2018] [Accepted: 12/14/2018] [Indexed: 01/14/2023] Open
Abstract
In Drosophila, female development is governed by a single RNA-binding protein, Sex-lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Sxl expression in female flies is maintained by an auto-regulatory, positive feedback loop with Sxl controlling splicing of its own mRNA. Until now, it remained unclear how males prevent accidental triggering of the Sxl expression cascade and protect themselves against runaway protein production. Here, we identify the protein Sister-of-Sex-lethal (Ssx) as an inhibitor of Sxl auto-regulatory splicing. Sxl and Ssx have a comparable RNA-binding specificity and compete for binding to RNA regulatory elements present in the Sxl transcript. In cultured Drosophila cells, Sxl-induced changes to alternative splicing can be reverted by the expression of Ssx. Moreover, in adult male flies ablation of the ssx gene results in a low level of productive Sxl mRNA splicing and Sxl protein production in isolated, clonal cell populations. In sum, this demonstrates that Ssx safeguards male animals against Sxl protein production to reinforce a stable, male-specific gene expression pattern.
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Affiliation(s)
- Rebecca Moschall
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Mathias Rass
- Institute of Zoology, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Oliver Rossbach
- Institute of Biochemistry, Justus-Liebig-University of Giessen, Heinrich-Buff-Ring 17, D-35392 Giessen, Germany
| | - Gerhard Lehmann
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Lars Kullmann
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Norbert Eichner
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Daniela Strauss
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Gunter Meister
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Stephan Schneuwly
- Institute of Zoology, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
| | - Michael P Krahn
- Institute for Molecular and Cellular Anatomy, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany.,Medical Clinic D, University of Muenster, Domagkstrasse 3, D-48149 Muenster, Germany
| | - Jan Medenbach
- Institute of Biochemistry I, University of Regensburg, Universitaetsstrasse 31, D-93053 Regensburg, Germany
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Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM. Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. Nat Commun 2019; 10:990. [PMID: 30824702 PMCID: PMC6397201 DOI: 10.1038/s41467-019-08942-3] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/11/2019] [Indexed: 12/30/2022] Open
Abstract
Recent methodological advances allowed the identification of an increasing number of RNA-binding proteins (RBPs) and their RNA-binding sites. Most of those methods rely, however, on capturing proteins associated to polyadenylated RNAs which neglects RBPs bound to non-adenylate RNA classes (tRNA, rRNA, pre-mRNA) as well as the vast majority of species that lack poly-A tails in their mRNAs (including all archea and bacteria). We have developed the Phenol Toluol extraction (PTex) protocol that does not rely on a specific RNA sequence or motif for isolation of cross-linked ribonucleoproteins (RNPs), but rather purifies them based entirely on their physicochemical properties. PTex captures RBPs that bind to RNA as short as 30 nt, RNPs directly from animal tissue and can be used to simplify complex workflows such as PAR-CLIP. Finally, we provide a global RNA-bound proteome of human HEK293 cells and the bacterium Salmonella Typhimurium.
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Affiliation(s)
- Erika C Urdaneta
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Carlos H Vieira-Vieira
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Timon Hick
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Hans-Herrmann Wessels
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Department of Biology, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Davide Figini
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Rebecca Moschall
- Biochemistry I, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I, University of Regensburg, Universitätsstrasse 31, 93053, Regensburg, Germany
| | - Uwe Ohler
- Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
- Department of Biology, Humboldt University, Philippstr. 13, 10115, Berlin, Germany
| | - Sander Granneman
- Centre for Systems and Synthetic Biology (SynthSys), University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Matthias Selbach
- Max-Delbrück-Center for Molecular Medicine, Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Benedikt M Beckmann
- IRI Life Sciences, Humboldt University, Philippstr. 13, 10115, Berlin, Germany.
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López-Cuadros I, García-Gasca A, Gomez-Anduro G, Escobedo-Fregoso C, Llera-Herrera RA, Ibarra AM. Isolation of the sex-determining gene Sex-lethal (Sxl) in Penaeus (Litopenaeus) vannamei (Boone, 1931) and characterization of its embryogenic, gametogenic, and tissue-specific expression. Gene 2018; 668:33-47. [PMID: 29758296 DOI: 10.1016/j.gene.2018.05.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 12/11/2022]
Abstract
The Pacific white shrimp Penaeus vannamei is the most cultured shrimp species around the world. Because females grow larger than males, the culture of 'only females' is of great interest, but knowledge on sex determination and differentiation is required for producing only females. In an effort to obtain information associated with reproduction in P. vannamei, transcriptomic data from female gonads was generated, and partial sequences of a transcript were identified as Sex-lethal (Sxl). Its characterization indicated that, differently from other penaeids in which this gene has been isolated, there are six isoforms of the Sxl transcript in P. vannamei (PvanSxl 1-6). These isoforms result from alternative splicing at three splice sites (SS1, SS2, SS3). The first splice-site is unique to P. vannamei, as it has not been reported for other Arthropod species; the second splice-site (SS2) is common among crustaceans, and the third splice-site (SS3) is also unique to P. vannamei and when spliced-out, it is always together with SS2. All isoforms are expressed during embryogenesis as well as gametogenesis of both genders. The two shorter isoforms, PvanSxl-5 and PvanSxl-6, which result from the splicing of SS2 and SS3, were found mostly expressed in adult testis, but PvanSxl-6 was also expressed in oocytes during gametogenesis. During oogenesis, the second largest isoform, PvanSxl-2, which splices-out only SS1, and PvanSxl-4 that splices-out SS1 and SS2 were highly expressed. These two isoforms were also highly expressed during embryonic development. In situ hybridization allowed pinpointing more specifically the cells where the PvanSxl transcripts were expressed. During embryogenesis, hybridization was observed from the one-cell stage embryo to late gastrula. In the female gonad in previtellogenesis, hybridization occurred in the nucleus of oocytes, whereas in secondary vitellogenesis the transcript also hybridized cytoplasmic granules and cortical crypts. Finally, in situ hybridization corroborated the expression of PvanSxl also in the male gonad during spermatogenesis, mostly occurring in the cytoplasm from spermatogonia and spermatocytes.
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Affiliation(s)
- Itzia López-Cuadros
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico
| | - Alejandra García-Gasca
- Centro de Investigación en Alimentación y Desarrollo A.C., (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos S/N. Col. Estero del Yugo, C.P. 82000 Mazatlán, Sinaloa, Mexico
| | - Gracia Gomez-Anduro
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico
| | - Cristina Escobedo-Fregoso
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico; CONACYT, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de México 03940, Mexico
| | - Raúl A Llera-Herrera
- Centro de Investigación en Alimentación y Desarrollo A.C., (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos S/N. Col. Estero del Yugo, C.P. 82000 Mazatlán, Sinaloa, Mexico; CONACYT, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de México 03940, Mexico
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico.
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