Identification of global alternative splicing and sex-specific splicing via comparative transcriptome analysis of gonads of Chinese tongue sole (<i>Cynoglossus semilaevis</i>)

Yi-Fang Lu; Qian Liu; Kai-Qiang Liu; Hong-Yan Wang; Cheng-Hua Li; Qian Wang; Chang-Wei Shao

doi:10.24272/j.issn.2095-8137.2021.406

Volume 43 Issue 3

May 2022

Turn off MathJax

Article Contents

Article Navigation > Zoological Research > 2022 > 43(3): 319-330

Yi-Fang Lu, Qian Liu, Kai-Qiang Liu, Hong-Yan Wang, Cheng-Hua Li, Qian Wang, Chang-Wei Shao. Identification of global alternative splicing and sex-specific splicing via comparative transcriptome analysis of gonads of Chinese tongue sole (Cynoglossus semilaevis). Zoological Research, 2022, 43(3): 319-330. doi: 10.24272/j.issn.2095-8137.2021.406

Citation:

Yi-Fang Lu, Qian Liu, Kai-Qiang Liu, Hong-Yan Wang, Cheng-Hua Li, Qian Wang, Chang-Wei Shao. Identification of global alternative splicing and sex-specific splicing via comparative transcriptome analysis of gonads of Chinese tongue sole (Cynoglossus semilaevis). Zoological Research, 2022, 43(3): 319-330. doi: 10.24272/j.issn.2095-8137.2021.406

Citation:

Yi-Fang Lu, Qian Liu, Kai-Qiang Liu, Hong-Yan Wang, Cheng-Hua Li, Qian Wang, Chang-Wei Shao. Identification of global alternative splicing and sex-specific splicing via comparative transcriptome analysis of gonads of Chinese tongue sole (Cynoglossus semilaevis). Zoological Research, 2022, 43(3): 319-330. doi: 10.24272/j.issn.2095-8137.2021.406

PDF( 11308 KB)

Identification of global alternative splicing and sex-specific splicing via comparative transcriptome analysis of gonads of Chinese tongue sole (Cynoglossus semilaevis)

doi: 10.24272/j.issn.2095-8137.2021.406

Yi-Fang Lu^{1, 2},
Qian Liu^{2, 4},
Kai-Qiang Liu^{2, 3},
Hong-Yan Wang^{2, 3},
Cheng-Hua Li¹,
Qian Wang^{2, 3
,
,},
Chang-Wei Shao^{2, 3
,
,}

1.
School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
2.
Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, Shandong 266071, China
3.
Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong 266000, China
4.
College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China

Funds: This work was supported by the National Natural Science Foundation of China (31722058, 31802275, and 31472269); National Key R&D Program of China (2018YFD0900301); AoShan Talents Cultivation Program Supported by Qingdao National Laboratory for Marine Science and Technology (2017ASTCP-ES06); Taishan Scholar Project Fund of Shandong of China to C.W.S.; National Ten-Thousands Talents Special Support Program to C.W.S.; Central Public-Interest Scientific Institution Basal Research Fund, CAFS (2020TD19); Central Public-interest Scientific Institution Basal Research Fund, YSFRI, CAFS (20603022021018); China Agriculture Research System (CARS-47-G03); and Guangdong South China Sea Key Laboratory of Aquaculture for Aquatic Economic Animals, Guangdong Ocean University (KFKT2019ZD03).

More Information

Corresponding author: E-mail: wangqian2014@ysfri.ac.cn; shaocw@ysfri.ac.cn
Received Date: 2022-01-27
Accepted Date: 2022-03-17

Published Online: 2022-03-17

Publish Date: 2022-05-18

Abstract

Abstract

Chinese tongue sole (Cynoglossus semilaevis) is an economically important marine fish species with a ZZ/ZW sex determination mechanism, which can be influenced by temperature. Alternative splicing (AS) is an important mechanism regulating the expression of genes related to sex determination and gonadal differentiation, but has rarely been reported in fish. In this study, to explore the molecular regulatory mechanisms of sex determination and gonadal differentiation, we combined isoform and RNA sequencing (Iso-Seq and RNA-Seq) to perform transcriptome profiling of male and female gonads in C. semilaevis. In total, 81 883 and 32 341 full-length transcripts were obtained in males and females, respectively. A total of 8 279 AS genes were identified, including 2 639 genes showing differential AS (DAS) between males and females. Many intersecting DAS genes and differentially expressed genes (DEGs) were enriched in the meiotic cell cycle pathway, and genes related to gonadal differentiation, such as esrrb and wt1a, were found to have sex-specific isoforms. Thus, this study revealed AS events in the gonadal transcriptomes of male and female C. semilaevis, described the characteristics of active transcription in the testes, and identified candidate genes for studying the regulatory mechanisms of AS during gonadal differentiation.
- Gonadal differentiation,
- Alternative splicing,
- Sex-specific splicing,
- Cynoglossus semilaevis,
- Iso-Seq,
- RNA-Seq

FullText(HTML)

References(59)

References

[1]	Amrein H, Gorman M, Nöthiger R. 1988. The sex-determining gene tra-2 of Drosophila encodes a putative RNA binding protein. Cell, 55(6): 1025−1035. doi: 10.1016/0092-8674(88)90247-4
[2]	Baralle FE, Giudice J. 2017. Alternative splicing as a regulator of development and tissue identity. Nature Reviews Molecular Cell Biology, 18(7): 437−451. doi: 10.1038/nrm.2017.27
[3]	Barberan-Soler S, Zahler AM. 2008. Alternative splicing regulation during C. elegans development: splicing factors as regulated targets. PLoS Genetics, 4(2): e1000001. doi: 10.1371/journal.pgen.1000001
[4]	Bártfai R, Balduf C, Hilton T, Rathmann Y, Hadzhiev Y, Tora L, et al. 2004. TBP2, a vertebrate-specific member of the TBP family, is required in embryonic development of zebrafish. Current Biology, 14(7): 593−598. doi: 10.1016/j.cub.2004.03.034
[5]	Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics, 30(15): 2114−2120. doi: 10.1093/bioinformatics/btu170
[6]	Bollig F, Mehringer R, Perner B, Hartung C, Schäfer M, Schartl M, et al. 2006. Identification and comparative expression analysis of a second wt1 gene in zebrafish. Developmental Dynamics, 235(2): 554−561. doi: 10.1002/dvdy.20645
[7]	Bourgeois CF, Mortreux F, Auboeuf D. 2016. The multiple functions of RNA helicases as drivers and regulators of gene expression. Nature Reviews Molecular Cell Biology, 17(7): 426−438. doi: 10.1038/nrm.2016.50
[8]	Braunschweig U, Barbosa-Morais NL, Pan Q, Nachman EN, Alipanahi B, Gonatopoulos-Pournatzis T, et al. 2014. Widespread intron retention in mammals functionally tunes transcriptomes. Genome Research, 24(11): 1774−1786. doi: 10.1101/gr.177790.114
[9]	Carreira-Rosario A, Bhargava V, Hillebrand J, Kollipara RK, Ramaswami M, Buszczak M. 2016. Repression of Pumilio protein expression by Rbfox1 promotes germ cell differentiation. Developmental Cell, 36(5): 562−571. doi: 10.1016/j.devcel.2016.02.010
[10]	Cesari E, Loiarro M, Naro C, Pieraccioli M, Farini D, Pellegrini L, et al. 2020. Combinatorial control of Spo11 alternative splicing by modulation of RNA polymerase II dynamics and splicing factor recruitment during meiosis. Cell Death & Disease, 11(4): 240.
[11]	Chen YX, Chen YS, Shi CM, Huang ZB, Zhang Y, Li SK, et al. 2018. SOAPnuke: a MapReduce acceleration-supported software for integrated quality control and preprocessing of high-throughput sequencing data. Gigascience, 7(1): gix120.
[12]	Clark EL, Coulson A, Dalgliesh C, Rajan P, Nicol SM, Fleming S, et al. 2008. The RNA helicase p68 is a novel androgen receptor coactivator involved in splicing and is overexpressed in prostate cancer. Cancer Research, 68(19): 7938−7946. doi: 10.1158/0008-5472.CAN-08-0932
[13]	Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. 2013. STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29(1): 15−21. doi: 10.1093/bioinformatics/bts635
[14]	Festuccia N, Owens N, Navarro P. 2018. Esrrb, an estrogen-related receptor involved in early development, pluripotency, and reprogramming. FEBS Letters, 592(6): 852−877. doi: 10.1002/1873-3468.12826
[15]	Gan Q, Chepelev I, Wei G, Tarayrah L, Cui KR, Zhao KJ, et al. 2010. Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq. Cell Research, 20(7): 763−783. doi: 10.1038/cr.2010.64
[16]	Garcia-Cruz R, Brieño MA, Roig I, Grossmann M, Velilla E, Pujol A, et al. 2010. Dynamics of cohesin proteins REC8, STAG3, SMC1β and SMC3 are consistent with a role in sister chromatid cohesion during meiosis in human oocytes. Human Reproduction, 25(9): 2316−2327. doi: 10.1093/humrep/deq180
[17]	Gazdag E, Santenard A, Ziegler-Birling C, Altobelli G, Poch O, Tora L, et al. 2009. TBP2 is essential for germ cell development by regulating transcription and chromatin condensation in the oocyte. Genes & Development, 23(18): 2210−2223.
[18]	Gómez-Redondo I, Planells B, Navarrete P, Gutiérrez-Adán A. 2021. Role of alternative splicing in sex determination in vertebrates. Sexual Development, 15(5-6): 381−391. doi: 10.1159/000519218
[19]	Han F, Wang ZJ, Wu FR, Liu ZH, Huang BF, Wang DS. 2010. Characterization, phylogeny, alternative splicing and expression of Sox30 gene. BMC Molecular Biology, 11(1): 98. doi: 10.1186/1471-2199-11-98
[20]	Isken O, Maquat LE. 2008. The multiple lives of NMD factors: balancing roles in gene and genome regulation. Nature Reviews Genetics, 9(9): 699−712. doi: 10.1038/nrg2402
[21]	Jiang DN, Chen JL, Fan Z, Tan DJ, Zhao JE, Shi HJ, et al. 2017. CRISPR/Cas9-induced disruption of wt1a and wt1b reveals their different roles in kidney and gonad development in Nile tilapia. Developmental Biology, 428(1): 63−73. doi: 10.1016/j.ydbio.2017.05.017
[22]	Kaessmann H. 2010. Origins, evolution, and phenotypic impact of new genes. Genome Research, 20(10): 1313−1326. doi: 10.1101/gr.101386.109
[23]	Kalsotra A, Cooper TA. 2011. Functional consequences of developmentally regulated alternative splicing. Nature Reviews Genetics, 12(10): 715−729. doi: 10.1038/nrg3052
[24]	Kim D, Paggi JM, Park C, Bennett C, Salzberg SL. 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature Biotechnology, 37(8): 907−915. doi: 10.1038/s41587-019-0201-4
[25]	Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, et al. 2014. A draft map of the human proteome. Nature, 509(7502): 575−581. doi: 10.1038/nature13302
[26]	Kohtz JD, Jamison SF, Will CL, Zuo P, Lührmann R, Garcia-Blanco MA, et al. 1994. Protein-protein interactions and 5'-splice-site recognition in mammalian mRNA precursors. Nature, 368(6467): 119−124. doi: 10.1038/368119a0
[27]	Kong XD, Ball Jr AR, Pham HX, Zeng WH, Chen HY, Schmiesing JA, et al. 2014. Distinct functions of human cohesin-SA1 and cohesin-SA2 in double-strand break repair. Molecular and Cellular Biology, 34(4): 685−698. doi: 10.1128/MCB.01503-13
[28]	Kuravsky ML, Aleshin VV, Frishman D, Muronetz VI. 2011. Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution. BMC Evolutionary Biology, 11(1): 160. doi: 10.1186/1471-2148-11-160
[29]	Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9(4): 357−359. doi: 10.1038/nmeth.1923
[30]	Latos PA, Goncalves A, Oxley D, Mohammed H, Turro E, Hemberger M. 2015. Fgf and Esrrb integrate epigenetic and transcriptional networks that regulate self-renewal of trophoblast stem cells. Nature Communications, 6(1): 7776. doi: 10.1038/ncomms8776
[31]	Legrand JMD, Chan AL, La HM, Rossello FJ, Änkö ML, Fuller-Pace FV, et al. 2019. DDX5 plays essential transcriptional and post-transcriptional roles in the maintenance and function of spermatogonia. Nature Communications, 10(1): 2278. doi: 10.1038/s41467-019-09972-7
[32]	Li HL, Xu WT, Zhang N, Shao CW, Zhu Y, Dong ZD, et al. 2016. Two Figla homologues have disparate functions during sex differentiation in half-smooth tongue sole (Cynoglossus semilaevis). Scientific Reports, 6(1): 28219. doi: 10.1038/srep28219
[33]	Liao JY, Suen HC, Luk ACS, Yang LL, Lee AWT, Qi HY, et al. 2021. Transcriptomic and epigenomic profiling of young and aged spermatogonial stem cells reveals molecular targets regulating differentiation. PLoS Genetics, 17(7): e1009369. doi: 10.1371/journal.pgen.1009369
[34]	Licatalosi DD, Darnell RB. 2010. RNA processing and its regulation: global insights into biological networks. Nature Reviews Genetics, 11(1): 75−87. doi: 10.1038/nrg2673
[35]	Liu Y, Chen SL, Gao FT, Meng L, Hu QM, Song WT, et al. 2014. SCAR-transformation of sex-specific SSR marker and its application in half-smooth tongue sole (Cynoglossus semiliaevis). Journal of Agricultural Biotechnology, 22(6): 787−792. (in Chinese)
[36]	Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12): 550. doi: 10.1186/s13059-014-0550-8
[37]	Luo JM, Sladek R, Bader JA, Matthyssen A, Rossant J, Giguère V. 1997. Placental abnormalities in mouse embryos lacking the orphan nuclear receptor ERR-β. Nature, 388(6644): 778−782. doi: 10.1038/42022
[38]	Mitsunaga K, Araki K, Mizusaki H, Morohashi KI, Haruna K, Nakagata N, et al. 2004. Loss of PGC-specific expression of the orphan nuclear receptor ERR-β results in reduction of germ cell number in mouse embryos. Mechanisms of Development, 121(3): 237−246. doi: 10.1016/j.mod.2004.01.006
[39]	Morrison AA, Venables JP, Dellaire G, Ladomery MR. 2006. The Wilms tumour suppressor protein WT1 (+KTS isoform) binds alpha-actinin 1 mRNA via its zinc-finger domain. Biochemistry and Cell Biology, 84(5): 789−798. doi: 10.1139/o06-065
[40]	Naro C, Jolly A, Di Persio S, Bielli P, Setterblad N, Alberdi AJ, et al. 2017. An orchestrated intron retention program in meiosis controls timely usage of transcripts during germ cell differentiation. Developmental Cell, 41(1): 82−93.e4. doi: 10.1016/j.devcel.2017.03.003
[41]	Nasmyth K, Peters J-M, Uhlmann F. 2000. Splitting the chromosome: cutting the ties that bind sister chromatids. Science, 288(5470): 1379−1384. doi: 10.1126/science.288.5470.1379
[42]	Natraj U, Richards JS. 1993. Hormonal regulation, localization, and functional activity of the progesterone receptor in granulosa cells of rat preovulatory follicles. Endocrinology, 133(2): 761−769. doi: 10.1210/endo.133.2.8344215
[43]	Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. 2008. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nature Genetics, 40(12): 1413−1415. doi: 10.1038/ng.259
[44]	Perner B, Englert C, Bollig F. 2007. The Wilms tumor genes wt1a and wt1b control different steps during formation of the zebrafish pronephros. Developmental Biology, 309(1): 87−96. doi: 10.1016/j.ydbio.2007.06.022
[45]	Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, et al. 2011. Integrative genomics viewer. Nature Biotechnology, 29(1): 24−26. doi: 10.1038/nbt.1754
[46]	Samaan S, Tranchevent LC, Dardenne E, Polay Espinoza M, Zonta E, Germann S, et al. 2014. The Ddx5 and Ddx17 RNA helicases are cornerstones in the complex regulatory array of steroid hormone-signaling pathways. Nucleic Acids Research, 42(4): 2197−2207. doi: 10.1093/nar/gkt1216
[47]	Shen SH, Park JW, Lu ZX, Lin L, Henry MD, Wu YN, et al. 2014. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America, 111(51): E5593−E5601.
[48]	Shiekhattar R, Mermelstein F, Fisher RP, Drapkin R, Dynlacht B, Wessling HC, et al. 1995. Cdk-activating kinase complex is a component of human transcription factor TFIIH. Nature, 374(6519): 283−287. doi: 10.1038/374283a0
[49]	Shiraishi E, Imazato H, Yamamoto T, Yokoi H, Abe SI, Kitano T. 2004. Identification of two teleost homologs of the Drosophila sex determination factor, transformer-2 in medaka (Oryzias latipes). Mechanisms of Development, 121(7-8): 991−996. doi: 10.1016/j.mod.2004.04.013
[50]	Smolen GA, Vassileva MT, Wells J, Matunis MJ, Haber DA. 2004. SUMO-1 modification of the Wilms' tumor suppressor WT1. Cancer Research, 64(21): 7846−7851. doi: 10.1158/0008-5472.CAN-04-1502
[51]	Sone R, Taimatsu K, Ohga R, Nishimura T, Tanaka M, Kawahara A. 2020. Critical roles of the ddx5 gene in zebrafish sex differentiation and oocyte maturation. Scientific Reports, 10(1): 14157. doi: 10.1038/s41598-020-71143-2
[52]	Soumillon M, Necsulea A, Weier M, Brawand D, Zhang XL, Gu HC, et al. 2013. Cellular source and mechanisms of high transcriptome complexity in the mammalian testis. Cell Reports, 3(6): 2179−2190. doi: 10.1016/j.celrep.2013.05.031
[53]	Tremblay AM, Giguère V. 2007. The NR3B subgroup: an overrview. Nuclear Receptor Signaling, 5(1): nrs.05009. doi: 10.1621/nrs.05009
[54]	Wang YB, Jin SB, Fu HT, Qiao H, Sun SM, Zhang WY, et al. 2019. Molecular cloning, expression pattern analysis, and in situ hybridization of a Transformer-2 gene in the oriental freshwater prawn, Macrobrachium nipponense (de Haan, 1849). 3 Biotech, 9(6): 205. doi: 10.1007/s13205-019-1737-1
[55]	Wang ZK, Gao JN, Song HY, Wu XM, Sun Y, Qi J, et al. 2014. Sexually dimorphic expression of vasa isoforms in the tongue sole (Cynoglossus semilaevis). PLoS One, 9(3): e93380. doi: 10.1371/journal.pone.0093380
[56]	Witten JT, Ule J. 2011. Understanding splicing regulation through RNA splicing maps. Trends in Genetics, 27(3): 89−97. doi: 10.1016/j.tig.2010.12.001
[57]	Yu CW, Cvetesic N, Hisler V, Gupta K, Ye T, Gazdag E, et al. 2020. TBPL2/TFIIA complex establishes the maternal transcriptome through oocyte-specific promoter usage. Nature Communications, 11(1): 6439. doi: 10.1038/s41467-020-20239-4
[58]	Yu LP, Zhang HR, Guan XB, Qin DD, Zhou J, Wu X. 2021. Loss of ESRP1 blocks mouse oocyte development and leads to female infertility. Development, 148(2): dev196931.
[59]	Zapater C, Chauvigné F, Fernández-Gómez B, Finn RN, Cerdà J. 2013. Alternative splicing of the nuclear progestin receptor in a perciform teleost generates novel mechanisms of dominant-negative transcriptional regulation. General and Comparative Endocrinology, 182: 24−40. doi: 10.1016/j.ygcen.2012.11.015