Characterization and molecular cloning of novel isoforms of human spermatogenesis associated gene SPATA3

  • 134 Accesses

  • 1 Citations


This study aimed to clone and characterize novel isoforms of the human SPATA3 gene. The isoforms of SPATA3 gene was cloned into pGMT vector using human testis cDNA as template, and Sanger sequencing was performed. Their characterizations and tissue-specific expression profiles were analyzed. The two novel isoforms were successfully cloned and deposited into GenBank as MG029442 (AYP71042) and MG029443 (AYP71043) respectively. Isoforms SPATA3-I1 and SPATA3-I2 were found with higher identity, where only 7 amino acids missed at N-terminus in SPATA3-I2, whereas SPATA3-I3 and SPATA3-I4 had more C-terminus deletion but in SPATA3-I3 no amino acid missed at N-terminus. Importantly, we found the characterization of QQPSPESTP domain with two repeats for isoforms SPATA3-I1 and SPATA3-I4, whereas three repeats for isoforms SPATA3-I1 and SPATA3-I2. The SPATA3 family of genes is orthologous conserved; the similar core PEST domain was also revealed with variable repeats, indicating that this domain may pay roles in the spermatogenesis and male development differently. Furthermore, RNA-seq data indicated that the SPATA3 gene is only expressed in testis. This further suggests that SPATA3 plays potential roles only in male development, spermatogenesis or spermatogenesis cell apoptosis. Thus, in this study we cloned the two novel isoforms of SPATA3, SPATA3-I3 and SPATA3-I4, and found interesting characteristic PEST domain (QQPSPESTP) conserved in different isoforms as well as in different species. SPATA3 is an essential gene and may functions in male reproductive system, specifically in spermatogenesis.

This is a preview of subscription content, log in to check access.

Access options

Buy single article

Instant unlimited access to the full article PDF.

US$ 39.95

Price includes VAT for USA

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Change history

  • 07 January 2020

    Unfortunately, as for the second institute name of first author Baixu Zhou, “Department of Gynecology and Obstetrics, Guangzhou Women and Children’s Hospital, Guangzhou, Guangdong, China”, should be “Department of Gynecology and Obstetrics, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China”.

  • 07 January 2020

    Unfortunately, as for the second institute name of first author Baixu Zhou, ���Department of Gynecology and Obstetrics, Guangzhou Women and Children���s Hospital, Guangzhou, Guangdong, China���, should be ���Department of Gynecology and Obstetrics, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China���.


  1. 1.

    Kimmins S, Sassone-Corsi P (2005) Chromatin remodelling and epigenetic features of germ cells. Nature 434:583–589.

  2. 2.

    da Cruz I, Rodriguez-Casuriaga R, Santinaque FF, Farias J, Curti G, Capoano CA, Folle GA, Benavente R, Sotelo-Silveira JR, Geisinger A (2016) Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage. BMC Genomics 17:294.

  3. 3.

    Sharma U, Sun F, Conine CC, Reichholf B, Kukreja S, Herzog VA, Ameres SL, Rando OJ (2018) Small RNAs are trafficked from the epididymis to developing mammalian sperm. DOI, Dev cell.

  4. 4.

    Conine CC, Sun F, Song L, Rivera-Perez JA, Rando OJ (2018) Small RNAs gained during epididymal transit of sperm are essential for embryonic development in mice. Dev Cell.

  5. 5.

    Hong SH, Kwon JT, Kim J, Jeong J, Kim J, Lee S, Cho C (2018) Profiling of testis-specific long noncoding RNAs in mice. BMC Genomics 19:539.

  6. 6.

    Ibtisham F, Wu J, Xiao M, An L, Banker Z, Nawab A, Zhao Y, Li G (2017) Progress and future prospect of in vitro spermatogenesis. Oncotarget 8:66709–66727.

  7. 7.

    O’Flynn O’Brien KL, Varghese AC, Agarwal A (2010) The genetic causes of male factor infertility: a review. Fertil Steril 93:1–12.

  8. 8.

    Kasak L, Punab M, Nagirnaja L, Grigorova M, Minajeva A, Lopes AM, Punab AM, Aston KI, Carvalho F, Laasik E et al (2018) Bi-allelic recessive loss-of-function variants in FANCM cause non-obstructive azoospermia. Am J Hum Genet 103:200–212.

  9. 9.

    Winters BR, Walsh TJ (2014) The epidemiology of male infertility. Urol Clin N Am 41:195–204.

  10. 10.

    Mita P, Piatti E, Romano A, Magro B (1998) Epidemiology of male infertility. Archivio italiano di urologia, andrologia: organo ufficiale [di] Societa italiana di ecografia urologica e nefrologica 70:85–91

  11. 11.

    Fu J, Li L, Lu G (2002) Relationship between microdeletion on Y chromosome and patients with idiopathic azoospermia and severe oligozoospermia in the Chinese. Chin Med J 115:72–75

  12. 12.

    Jaiswal MK, Agrawal V, Katara GK, Pamarthy S, Kulshrestha A, Chaouat G, Gilman-Sachs A, Beaman KD (2015) Male fertility and apoptosis in normal spermatogenesis are regulated by vacuolar-ATPase isoform a2. J Reprod Immunol 112:38–45.

  13. 13.

    Jaiswal MK, Katara GK, Mallers T, Chaouat G, Gilman-Sachs A, Beaman KD (2014) Vacuolar-ATPase isoform a2 regulates macrophages and cytokine profile necessary for normal spermatogenesis in testis. J Leukoc Biol 96:337–347.

  14. 14.

    Kanemori Y, Koga Y, Sudo M, Kang W, Kashiwabara S, Ikawa M, Hasuwa H, Nagashima K, Ishikawa Y, Ogonuki N et al (2016) Biogenesis of sperm acrosome is regulated by pre-mRNA alternative splicing of Acrbp in the mouse. Proc Natl Acad Sci USA 113:E3696–E3705.

  15. 15.

    Chen Y, Zheng Y, Gao Y, Lin Z, Yang S, Wang T, Wang Q, Xie N, Hua R, Liu M et al (2018) Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis. Cell Res.

  16. 16.

    Fu JJ, Lu GX, Li LY, Liu G, Xing XW, Liu SF (2003) Molecular cloning for testis spermatogenesis cell apoptosis related gene TSARG1 and Mtsarg1 and expression analysis for Mtsarg1 gene. Yi chuan xue bao = Acta genetica Sinica 30:25–29

  17. 17.

    Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K et al (2004) Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet 36:40–45.

  18. 18.

    Rolland T, Tasan M, Charloteaux B, Pevzner SJ, Zhong Q, Sahni N, Yi S, Lemmens I, Fontanillo C, Mosca R et al (2014) A proteome-scale map of the human interactome network. Cell 159:1212–1226.

  19. 19.

    Fu S, Cheng J, Wei C, Yang L, Xiao X, Zhang D, Stewart MD, Fu J (2017) Development of diagnostic SCAR markers for genomic DNA amplifications in breast carcinoma by DNA cloning of high-GC RAMP-PCR fragments. Oncotarget 8:43866–43877.

  20. 20.

    Fu J, Yang L, Khan MA, Mei Z (2013) Genetic characterization and authentication of Lonicera japonica Thunb. by using improved RAPD analysis. Mol Biol Rep 40:5993–5999.

  21. 21.

    Fu J, Ma L, Cheng J, Yang L, Wei C, Fu S, Lv H, Chen R, Fu J (2018) A novel, homozygous nonsense variant of the CDHR1 gene in a Chinese family causes autosomal recessive retinal dystrophy by NGS-based genetic diagnosis. J Cell Mol Med 22:5662–5669.

  22. 22.

    Imani S, Ijaz I, Shasaltaneh MD, Fu S, Cheng J, Fu J (2018) Molecular genetics characterization and homology modeling of the CHM gene mutation: a study on its association with choroideremia. Mutat Res 775:39–50.

  23. 23.

    Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR et al (2017) CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res 45:D200–D203.

  24. 24.

    Cheng J, Fu J, Zhou Q, Xiang X, Wei C, Yang L, Fu S, Khan MA, Lv H, Fu J (2019) A novel splicing mutation in the PRPH2 gene causes autosomal dominant retinitis pigmentosa in a Chinese pedigree. J Cell Mol Med 25:236.

  25. 25.

    Waclawska A, Kurpisz M (2012) Key functional genes of spermatogenesis identified by microarray analysis. Syst Biol Reprod Med 58:229–235.

  26. 26.

    Ramm SA, Scharer L, Ehmcke J, Wistuba J (2014) Sperm competition and the evolution of spermatogenesis. Mol Hum Reprod 20:1169–1179.

  27. 27.

    Fairchild MJ, Islam F, Tanentzapf G (2017) Identification of genetic networks that act in the somatic cells of the testis to mediate the developmental program of spermatogenesis. PLoS Genet 13:e1007026.

  28. 28.

    Chocu S, Calvel P, Rolland AD, Pineau C (2012) Spermatogenesis in mammals: proteomic insights. Syst Biol Reprod Med 58:179–190.

  29. 29.

    Li C, Zhou X (2012) Gene transcripts in spermatozoa: markers of male infertility. Clin Chim Acta 413:1035–1038.

  30. 30.

    Zhang JF, Zhu HB, Zhang LG, Hao HS, Zhao XM, Qin T, Lu YQ, Wang D (2013) Advance on research of gene expression during spermiogenesis at transcription level. Yi chuan = Hereditas 35:587–594

  31. 31.

    Legare C, Akintayo A, Blondin P, Calvo E, Sullivan R (2017) Impact of male fertility status on the transcriptome of the bovine epididymis. Mol Hum Reprod 23:355–369.

  32. 32.

    Wang Y, Fang R, Yuan Y, Pan M, Hu M, Zhou Y, Shen B, Zhao J (2016) Identification of host proteins, Spata3 and Dkk2, interacting with Toxoplasma gondii micronemal protein MIC3. Parasitol Res 115:2825–2835.

  33. 33.

    Malcher A, Rozwadowska N, Stokowy T, Kolanowski T, Jedrzejczak P, Zietkowiak W, Kurpisz M (2013) Potential biomarkers of nonobstructive azoospermia identified in microarray gene expression analysis. Fertil Steril 100(1686–1694):e1681–e1687.

  34. 34.

    Li L, Liu G, Fu JJ, Li LY, Tan XJ, Yang S, Lu GX (2009) Molecular cloning and characterization of a novel transcript variant of Mtsarg1 gene. Mol Biol Rep 36:1023–1032.

Download references


We gratefully acknowledge the technical assistance of our lab for this project.


This work was supported by the National Natural Science Foundation of China (30371493), supported in part by the National Natural Science Foundation of China (81172049, and 81672887), the Research Foundation of the Education Department of Sichuan Province (17ZA0427, 17ZB0467), the Research Foundation of the Science and Technology Department of Luzhou City (2015-S-42(3/4), 2016-S-65(9/9)), and the Joint Research Foundation of Luzhou City and Southwest Medical University (2018LZXNYD-YL01).

Author information

Correspondence to Junjiang Fu.

Ethics declarations

Conflict of interest

All authors declared no conflict of interest.

Ethical approval

This article does not contain any studies with animals or human participants performed by any of the authors.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Zhou, B., Wei, C., Khan, M.A. et al. Characterization and molecular cloning of novel isoforms of human spermatogenesis associated gene SPATA3. Mol Biol Rep 46, 3827–3834 (2019).

Download citation


  • SPATA3
  • Spermatogenesis
  • Splicing variant
  • Expression
  • Domain
  • Male infertility