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      SRSF2 is required for mRNA splicing during spermatogenesis

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          Abstract

          Background

          RNA splicing plays significant roles in fundamental biological activities. However, our knowledge about the roles of alternative splicing and underlying mechanisms during spermatogenesis is limited.

          Results

          Here, we report that Serine/arginine-rich splicing factor 2 (SRSF2), also known as SC35, plays critical roles in alternative splicing and male reproduction. Male germ cell-specific deletion of Srsf2 by Stra8-Cre caused complete infertility and defective spermatogenesis. Further analyses revealed that deletion of Srsf2 disrupted differentiation and meiosis initiation of spermatogonia. Mechanistically, by combining RNA-seq data with LACE-seq data, we showed that SRSF2 regulatory networks play critical roles in several major events including reproductive development, spermatogenesis, meiotic cell cycle, synapse organization, DNA recombination, chromosome segregation, and male sex differentiation. Furthermore, SRSF2 affected expression and alternative splicing of Stra8, Stag3 and Atr encoding critical factors for spermatogenesis in a direct manner.

          Conclusions

          Taken together, our results demonstrate that SRSF2 has important functions in spermatogenesis and male fertility by regulating alternative splicing.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12915-023-01736-6.

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          Most cited references51

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          Alternative Isoform Regulation in Human Tissue Transcriptomes

          Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of cDNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analysis of mappings of sequence reads to exon-exon junctions indicated that 92-94% of human genes undergo alternative splicing (AS), ∼86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that a majority of AS and of alternative cleavage and polyadenylation (APA) events vary between tissues, while variation between individuals was ∼2- to 3-fold less common. Extreme or ‘switch-like’ regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of AS and APA were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3′ UTRs suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation.
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            HITS-CLIP yields genome-wide insights into brain alternative RNA processing

            Summary Protein-RNA interactions play critical roles in all aspects of gene expression. Here we develop a genome-wide means of mapping protein-RNA binding sites in vivo, by high throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). HITS-CLIP analysis of the neuron-specific splicing factor Nova2 revealed extremely reproducible RNA binding maps in multiple mouse brains. These maps provide genome-wide in vivo biochemical footprints confirming the previous prediction that the position of Nova binding determines the outcome of alternative splicing; moreover, they are sufficiently powerful to predict Nova action de novo. HITS-CLIP revealed a large number of Nova-RNA interactions in 3′ UTRs, leading to the discovery that Nova regulates alternative polyadenylation in the brain. HITS-CLIP, therefore, provides a robust, unbiased means to identify functional protein-RNA interactions in vivo.
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              Expansion of the eukaryotic proteome by alternative splicing.

              The collection of components required to carry out the intricate processes involved in generating and maintaining a living, breathing and, sometimes, thinking organism is staggeringly complex. Where do all of the parts come from? Early estimates stated that about 100,000 genes would be required to make up a mammal; however, the actual number is less than one-quarter of that, barely four times the number of genes in budding yeast. It is now clear that the 'missing' information is in large part provided by alternative splicing, the process by which multiple different functional messenger RNAs, and therefore proteins, can be synthesized from a single gene.
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                Author and article information

                Contributors
                sunfeisrrsh@zju.edu.cn
                wangzb@ioz.ac.cn
                qianweipingsz@126.com
                sunqy@gd2h.org.cn
                Journal
                BMC Biol
                BMC Biol
                BMC Biology
                BioMed Central (London )
                1741-7007
                23 October 2023
                23 October 2023
                2023
                : 21
                : 231
                Affiliations
                [1 ]Guangdong and Shenzhen Key Laboratory of Reproductive Medicine and Genetics, The Center of Reproductive Medicine, Peking University Shenzhen Hospital, ( https://ror.org/03kkjyb15) 1120 Lianhua Rd, Futian District, Shenzhen, 518000 China
                [2 ]GRID grid.458489.c, ISNI 0000 0001 0483 7922, CAS Key Laboratory of Quantitative Engineering Biology, , Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, ; Shenzhen, 518055 China
                [3 ]Department of Urology & Andrology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, ( https://ror.org/00ka6rp58) #3 Qingchun East Road, Shangcheng District, Hangzhou, 310016 China
                [4 ]School of Artificial Intelligence, University of Chinese Academy of Sciences, ( https://ror.org/05qbk4x57) Beijing, 100049 China
                [5 ]GRID grid.413405.7, ISNI 0000 0004 1808 0686, Fertility Preservation Lab, Guangdong-Hongkong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, , Guangdong Second Provincial General Hospital, ; #466 Xin-Gang-Zhong-Lu, Haizhu District, Guangzhou, 510317 China
                [6 ]GRID grid.9227.e, ISNI 0000000119573309, State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, , Chinese Academy of Sciences, ; #1 Beichen West Road, Chaoyang District, Beijing, 100101 China
                [7 ]Department of Obstetrics and Gynecology, Center for Reproductive Medicine/Department of Fetal Medicine and Prenatal Diagnosis/BioResource Research Center, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, ( https://ror.org/00fb35g87) Guangzhou, 510150 China
                [8 ]Institute of Urology, Peking University Shenzhen Hospital, Shenzhen PKU-HKUST Medical Center, ( https://ror.org/03kkjyb15) Shenzhen, 518036 China
                [9 ]Department of Veterinary Pathobiology, University of Missouri, ( https://ror.org/02ymw8z06) Columbia, MO 65211 USA
                Author information
                http://orcid.org/0000-0002-0148-2414
                Article
                1736
                10.1186/s12915-023-01736-6
                10591377
                37867192
                0d585334-6bf5-4cd6-97eb-38f1d06fc8e7
                © BioMed Central Ltd., part of Springer Nature 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 17 October 2022
                : 13 October 2023
                Funding
                Funded by: National Key R&D Program of China
                Award ID: 2018YFA0107701
                Award ID: 2019YFA0109900
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001809, National Natural Science Foundation of China;
                Award ID: 82301806
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100021171, Basic and Applied Basic Research Foundation of Guangdong Province;
                Award ID: 2021A1515111118
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © BioMed Central Ltd., part of Springer Nature 2023

                Life sciences
                srsf2,male infertility,spermatogenesis,alternative splicing,lace-seq
                Life sciences
                srsf2, male infertility, spermatogenesis, alternative splicing, lace-seq

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