Abstract
The late overwintering period and breeding period are two important developmental stages of testis in Onychostoma macrolepis. Small non-coding RNAs (sncRNAs) are well-known regulators of biological processes associated with numerous biological processes. This study aimed to elucidate the roles of four sncRNA classes (microRNAs [miRNAs], Piwi-interacting RNAs [piRNAs], tRNA-derived small RNAs [tsRNAs], and rRNA-derived small RNAs [rsRNAs]) across testes in the late overwintering period (in March) and breeding period (in June) by high-throughput sequencing. The testis of O. macrolepis displayed the highest levels of piRNAs and lowest levels of rsRNAs. Compared with miRNAs and tsRNAs in June, tsRNAs in March had a higher abundance, while miRNAs in March had a much lower abundance. Bioinformatics analysis identified 1,362 and 1,340 differentially expressed miRNAs and tsRNAs, respectively. Further analysis showed that miR-200–1, miR-143–1, tRFi-Lys-CTT-1, and tRFi-Glu-CTC-1 could play critical roles during the overwintering and breeding periods. Our findings provided an unprecedented insight to reveal the epigenetic mechanism underlying the overwintering and reproduction process of male O. macrolepis.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
All data generated or analyzed during this study are included in this published article [and its supplementary information files].
Abbreviations
- sncRNA:
-
Small non-coding RNA
- miRNA:
-
MicroRNA
- piRNA:
-
Piwi-interacting RNA
- tsRNA:
-
TRNA-derived small RNA
- rsRNA:
-
RRNA-derived small RNA
- O. macrolepis :
-
Onychostoma macrolepis
- tRF:
-
TRNA-derived fragment
- rRF:
-
RRNA-derived fragment
- GO:
-
Gene Ontology
- KEGG:
-
Kyoto Encyclopedia of Genes and Genomes
- RT-qPCR:
-
Reverse transcription‑quantitative polymerase chain reaction
- HE:
-
Hematoxylin–eosin
- RNA-seq:
-
RNA sequencing
- RPM:
-
Reads per million
- FDR:
-
False discovery rate
- FC:
-
Fold change
- padj:
-
Adjusted P value
- UTR:
-
Untranslated region
- Unanno:
-
Unannotated
- MG:
-
Match genome
- UMG:
-
Unmatch genome
References
Adnan M, Morton G, Hadi S (2011) Analysis of rpoS and bolA gene expression under various stress-induced environments in planktonic and biofilm phase using 2−ΔΔCT method. Mol Cell Biochem 357:275–282. https://doi.org/10.1007/s11010-011-0898-y
Ahmed N, Turchini GM (2021) Recirculating aquaculture systems (RAS): Environmental solution and climate change adaptation. J Clean Prod 297:126604
Allebrandt KV, Amin N, Müller-Myhsok B et al (2013) A KATP channel gene effect on sleep duration: from genome-wide association studies to function in Drosophila. Mol Psychiatry 18:122–132. https://doi.org/10.1038/mp.2011.142
Altschul S (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402. https://doi.org/10.1093/nar/25.17.3389
An L, Jiang H, Tang R-N (2015) The ACACB gene rs2268388 polymorphism is associated with nephropathy in Caucasian patients with diabetes: a meta-analysis. Ren Fail 37:925–928. https://doi.org/10.3109/0886022X.2015.1052978
Aravin A, Gaidatzis D, Pfeffer S et al (2006) A novel class of small RNAs bind to MILI protein in mouse testes. Nature 442:203–207. https://doi.org/10.1038/nature04916
Bhat RA, Priyam M, Foysal MJ et al (2021) Role of sex-biased miRNAs in teleosts – a review. Rev Aquac 13:269–281. https://doi.org/10.1111/raq.12474
Blighe K, Rana S, Lewis M (2019) EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling. R Packag version 1:
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Carey HV, Andrews MT, Martin SL (2003) Mammalian Hibernation: Cellular and Molecular Responses to Depressed Metabolism and Low Temperature. Physiol Rev 83:1153–1181. https://doi.org/10.1152/physrev.00008.2003
Chai A, Zhang J, Cui Q, Yuan C (2016) Mitochondrial genome of Onychostoma macrolepis (Osteichthyes: Cyprinidae). Mitochondrial DNA 27:240–241. https://doi.org/10.3109/19401736.2014.883605
Chen R, Du J, Ma L et al (2017) Comparative microRNAome analysis of the testis and ovary of the Chinese giant salamander. Reproduction 154:269–279. https://doi.org/10.1530/REP-17-0109
Chen Z, Sun Y, Yang X et al (2017) Two featured series of rRNA-derived RNA fragments (rRFs) constitute a novel class of small RNAs. PLoS One 12:e0176458. https://doi.org/10.1371/journal.pone.0176458
Czech B, Hannon GJ (2016) One loop to rule them all: the ping-pong cycle and piRNA-guided silencing. Trends Biochem Sci 41:324–337. https://doi.org/10.1016/j.tibs.2015.12.008
De Lima AO, Afonso J, Edson J et al (2021) Network analyses predict small RNAs that might modulate gene expression in the testis and epididymis of Bos indicus bulls. Front Genet 12:530. https://doi.org/10.3389/fgene.2021.610116
Deng W, Sun J, Chang Z et al (2020) Energy response and fatty acid metabolism in Onychostoma macrolepis exposed to low-temperature stress. J Therm Biol 94:102725. https://doi.org/10.1016/j.jtherbio.2020.102725
DiBella LM, Park A, Sun Z (2009) Zebrafish Tsc1 reveals functional interactions between the cilium and the TOR pathway. Hum Mol Genet 18:595–606. https://doi.org/10.1093/hmg/ddn384
Friedländer MR, Chen W, Adamidi C et al (2008) Discovering microRNAs from deep sequencing data using miRDeep. Nat Biotechnol 26:407–415. https://doi.org/10.1038/nbt1394
Friedländer MR, Mackowiak SD, Li N et al (2012) miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res 40:37–52. https://doi.org/10.1093/nar/gkr688
Goodarzi H, Liu X, Nguyen HCB et al (2015) Endogenous tRNA-Derived fragments suppress breast cancer progression via YBX1 displacement. Cell 161:790–802. https://doi.org/10.1016/j.cell.2015.02.053
Graham AM, Barreto FS (2019) Novel microRNAs are associated with population divergence in transcriptional response to thermal stress in an intertidal copepod. Mol Ecol 28:584–599. https://doi.org/10.1111/mec.14973
Ha M, Kim VN (2014) Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15:509–524
Hadj-Moussa H, Logan SM, Seibel BA, Storey KB (2018) Potential role for microRNA in regulating hypoxia-induced metabolic suppression in jumbo squids. Biochim Biophys Acta - Gene Regul Mech 1861:586–593. https://doi.org/10.1016/j.bbagrm.2018.04.007
Hammell CM, Karp X, Ambros V (2009) A feedback circuit involving let-7-family miRNAs and DAF-12 integrates environmental signals and developmental timing in Caenorhabditis elegans. Proc Natl Acad Sci 106:18668–18673. https://doi.org/10.1073/pnas.0908131106
Hou C-X, Wang L, Cai M et al (2021) Sphk1 promotes salivary adenoid cystic carcinoma progression via PI3K/Akt signaling. Pathol Pract 227:153620. https://doi.org/10.1016/j.prp.2021.153620
Huang J, Manning BD (2008) The TSC1–TSC2 complex: a molecular switchboard controlling cell growth. Biochem J 412:179–190. https://doi.org/10.1042/BJ20080281
Ishizu H, Siomi H, Siomi MC (2012) Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines. Genes Dev 26:2361–2373. https://doi.org/10.1101/gad.203786.112
Ivanov P, Emara MM, Villen J et al (2011) Angiogenin-induced tRNA fragments inhibit translation initiation. Mol Cell 43:613–623. https://doi.org/10.1016/j.molcel.2011.06.022
Jones BC, Wood JG, Chang C et al (2016) A somatic piRNA pathway in the Drosophila fat body ensures metabolic homeostasis and normal lifespan. Nat Commun 7:1–9. https://doi.org/10.1038/ncomms13856
Kalvari I, Argasinska J, Quinones-Olvera N et al (2018) Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families. Nucleic Acids Res 46:D335–D342. https://doi.org/10.1093/nar/gkx1038
Kamalidehghan B, Habibi M, Afjeh SS et al (2020) The importance of small non-coding RNAs in human reproduction: a review article. Appl Clin Genet 13:1–11. https://doi.org/10.2147/TACG.S207491
Kang HJ, Moon MJ, Lee HY, Han SW (2014) Testosterone alters testis function through regulation of piRNA expression in rats. Mol Biol Rep 41:6729–6735. https://doi.org/10.1007/s11033-014-3558-y
Karaiskos S, Naqvi AS, Swanson KE, Grigoriev A (2015) Age-driven modulation of tRNA-derived fragments in Drosophila and their potential targets. Biol Direct 10:51. https://doi.org/10.1186/s13062-015-0081-6
Kim HK, Fuchs G, Wang S et al (2017) A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature 552:57–62. https://doi.org/10.1038/nature25005
Kimura KD, Tissenbaum HA, Liu Y, Ruvkun G (1997) Daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans. Sci 277:942–946. https://doi.org/10.1126/science.277.5328.942
Kozomara A, Griffiths-Jones S (2014) miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res 42:D68–D73. https://doi.org/10.1093/nar/gkt1181
Kumar P, Anaya J, Mudunuri SB, Dutta A (2014) Meta-analysis of tRNA derived RNA fragments reveals that they are evolutionarily conserved and associate with AGO proteins to recognize specific RNA targets. BMC Med 12:78. https://doi.org/10.1186/s12915-014-0078-0
Kumar P, Kuscu C, Dutta A (2016) Biogenesis and function of transfer RNA-telated fragments (tRFs). Trends Biochem Sci 41:679–689. https://doi.org/10.1016/j.tibs.2016.05.004
Kuscu C, Kumar P, Kiran M et al (2018) tRNA fragments (tRFs) guide Ago to regulate gene expression post-transcriptionally in a Dicer-independent manner. RNA 24:1093–1105. https://doi.org/10.1261/rna.066126.118
Lambert M, Benmoussa A, Provost P (2019) Small non-coding RNAs derived from Eukaryotic ribosomal RNA. Non-Coding RNA 5:16. https://doi.org/10.3390/ncrna5010016
Li Z, Ender C, Meister G et al (2012) Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs. Nucleic Acids Res 40:6787–6799. https://doi.org/10.1093/nar/gks307
Li XZ, Roy CK, Dong X et al (2013) An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes. Mol Cell 50:67–81. https://doi.org/10.1016/j.molcel.2013.02.016
Li Y, Li J, Fang C et al (2016) Genome-wide differential expression of genes and small RNAs in testis of two different porcine breeds and at two different ages. Sci Rep 6:26852. https://doi.org/10.1038/srep26852
Li S, Lin G, Fang W et al (2020) Identification and comparison of microRNAs in the gonad of the yellowfin seabream (Acanthopagrus Latus). Int J Mol Sci 21:5690. https://doi.org/10.3390/ijms21165690
Locati MD, Pagano JFB, Abdullah F et al (2018) Identifying small RNAs derived from maternal-and somatic-type rRNAs in zebrafish development. Genome 61:371–378. https://doi.org/10.1139/gen-2017-0202
Love MI, Huber W, Anders S (2014) Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550. https://doi.org/10.1186/s13059-014-0550-8
Luo S, He F, Luo J et al (2018) Drosophila tsRNAs preferentially suppress general translation machinery via antisense pairing and participate in cellular starvation response. Nucleic Acids Res 46:5250–5268. https://doi.org/10.1093/nar/gky189
Ma L, Mondal AK, Murea M et al (2011) The effect of ACACB cis-variants on gene expression and metabolic traits. PLoS One 6:e23860. https://doi.org/10.1371/journal.pone.0023860
Nätt D, Öst A (2020) Male reproductive health and intergenerational metabolic responses from a small RNA perspective. J Intern Med 288:305–320. https://doi.org/10.1111/joim.13096
Nechooshtan G, Yunusov D, Chang K, Gingeras TR (2020) Processing by RNase 1 forms tRNA halves and distinct Y RNA fragments in the extracellular environment. Nucleic Acids Res 48:8035–8049. https://doi.org/10.1093/nar/gkaa526
Poelchau MF, Reynolds JA, Denlinger DL et al (2011) A de novo transcriptome of the Asian tiger mosquito, Aedes albopictus, to identify candidate transcripts for diapause preparation. BMC Genomics 12:619. https://doi.org/10.1186/1471-2164-12-619
Poelchau MF, Reynolds JA, Denlinger DL et al (2013) Transcriptome sequencing as a platform to elucidate molecular components of the diapause response in the Asian tiger mosquito Aedes albopictus. Physiol Entomol 38:173–181. https://doi.org/10.1111/phen.12016
Presslauer C, Tilahun Bizuayehu T, Kopp M et al (2017) Dynamics of miRNA transcriptome during gonadal development of zebrafish. Sci Rep 7:43850. https://doi.org/10.1038/srep43850
Resnick TD, McCulloch KA, Rougvie AE (2010) miRNAs give worms the time of their lives: Small RNAs and temporal control in Caenorhabditis elegans. Dev Dyn 239:1477–1489. https://doi.org/10.1002/dvdy.22260
Reynolds JA (2019) Noncoding RNA regulation of dormant states in evolutionarily diverse animals. Biol Bull 237:192–209. https://doi.org/10.1086/705484
Reynolds JA Poelchau MF Rahman Z et al (2012) Transcript profiling reveals mechanisms for lipid conservation during diapause in the mosquito, AedesAlbopictus. J Insect Physiol 58. https://doi.org/10.1016/j.jinsphys.2012.04.013
Riggs CL, Podrabsky JE (2017) Small noncoding RNA expression during extreme anoxia tolerance of annual killifish (Austrofundulus limnaeus) embryos. Physiol Genomics 49:505–518. https://doi.org/10.1152/physiolgenomics.00016.2017
Riggs CL, Summers A, Warren DE et al (2018) Small non-coding RNA expression and vertebrate anoxia tolerance. Front Genet 9:230. https://doi.org/10.3389/fgene.2018.00230
Rosace D, López J, Blanco S (2020) Emerging roles of novel small non-coding regulatory RNAs in immunity and cancer. RNA Biol 17:1196–1213. https://doi.org/10.1080/15476286.2020.1737442
Rosenkranz D, Zischler H (2012) proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinformatics 13:5. https://doi.org/10.1186/1471-2105-13-5
Rouget C, Papin C, Boureux A et al (2010) Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo. Nature 467:1128–1132. https://doi.org/10.1038/nature09465
Saito K (2006) Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome. Genes Dev 20:2214–2222. https://doi.org/10.1101/gad.1454806
Schimmel P (2018) RNA Processing and Modifications: The emerging complexity of the tRNA world: Mammalian tRNAs beyond protein synthesis. Nat Rev Mol Cell Biol 19:45–58. https://doi.org/10.1038/nrm.2017.77
Sergiev PV, Aleksashin NA, Chugunova AA et al (2018) Structural and evolutionary insights into ribosomal RNA methylation. Nat Chem Biol 14:226–235. https://doi.org/10.1038/nchembio.2569
Shi J, Ko EA, Sanders KM et al (2018) SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA-and tRNA-derived small RNAs. Genomics Proteomics Bioinformatics 16:144–151. https://doi.org/10.1016/j.gpb.2018.04.004
Shi J, Zhang Y, Tan D et al (2021) PANDORA-seq expands the repertoire of regulatory small RNAs by overcoming RNA modifications. Nat Cell Biol 23:424–436. https://doi.org/10.1038/s41556-021-00652-7
Soares AR, Fernandes N, Reverendo M et al (2015) Conserved and highly expressed tRNA derived fragments in zebrafish. BMC Mol Biol 16:1–16. https://doi.org/10.1186/s12867-015-0050-8
Su Z, Wilson B, Kumar P, Dutta A (2020) Noncanonical roles of tRNAs: tRNA fragments and beyond. Annu Rev Genet 54:47–69. https://doi.org/10.1146/annurev-genet-022620-101840
Sukocheva OA, Furuya H, Ng ML et al (2020) Sphingosine kinase and sphingosine-1-phosphate receptor signaling pathway in inflammatory gastrointestinal disease and cancers: A novel therapeutic target. Pharmacol Ther 207:107464. https://doi.org/10.1016/j.pharmthera.2019.107464
Sun F, Fu H, Liu Q et al (2008) Downregulation of CCND1 and CDK6 by miR-34a induces cell cycle arrest. FEBS Lett 582:1564–1568. https://doi.org/10.1016/j.febslet.2008.03.057
Sun L, Gao T, Wang F et al (2020) Chromosome-level genome assembly of a cyprinid fish Onychostoma macrolepis by integration of nanopore sequencing, Bionano and Hi-C technology. Mol Ecol Resour 20:1361–1371. https://doi.org/10.1111/1755-0998.13190
Suzuki T, Nagao A, Suzuki T (2011) Human mitochondrial tRNAs: biogenesis, function, structural aspects, and diseases. Annu Rev Genet 45:299–329. https://doi.org/10.1146/annurev-genet-110410-132531
Tao M, Zhou Y, Li S et al (2018) MicroRNA alternations in the testes related to the sterility of triploid fish. Mar Biotechnol 20:739–749. https://doi.org/10.1007/s10126-018-9845-1
Telonis AG, Loher P, Honda S et al (2015) Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget 6:24797–24822. https://doi.org/10.18632/oncotarget.4695
Wang F, Jia Y, Wang P et al (2017) Identification and profiling of Cyprinus carpio microRNAs during ovary differentiation by deep sequencing. BMC Genomics 18:333. https://doi.org/10.1186/s12864-017-3701-y
Wang K, Hoeksema J, Liang C (2018) piRNN: deep learning algorithm for piRNA prediction. PeerJ 6:e5429. https://doi.org/10.7717/peerj.5429
Wu P, Sato J, Zhao Y et al (1998) Starvation and diabetes increase the amount of pyruvate dehydrogenase kinase isoenzyme 4 in rat heart. Biochem J 329:197–201. https://doi.org/10.1042/bj3290197
Wu P, Inskeep K, Bowker-Kinley MM et al (1999) Mechanism responsible for inactivation of skeletal muscle pyruvate dehydrogenase complex in starvation and diabetes. Diabetes 48:1593–1599. https://doi.org/10.2337/diabetes.48.8.1593
Xu P, Vernooy SY, Guo M, Hay BA (2003) The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol 13:790–795. https://doi.org/10.1016/S0960-9822(03)00250-1
Yamasaki S, Ivanov P, Hu GF, Anderson P (2009) Angiogenin cleaves tRNA and promotes stress-induced translational repression. J Cell Biol 185:35–42. https://doi.org/10.1083/jcb.200811106
Yu H, Deng W, Zhang D et al (2017) Antioxidant defenses of Onychostoma macrolepis in response to thermal stress: Insight from mRNA expression and activity of superoxide dismutase and catalase. Fish Shellfish Immunol 66:50–61. https://doi.org/10.1016/j.fsi.2017.04.027
Zhang C (1986) On the ecological adaptation and geographical distribution of the barbing fish Varicorhinus (scaphesthes) macrolepis (bleeker). Acta Zool Sin 32:266–272
Zhang J, Feng D, Yang J et al (2015) Reproductive biology of Varicorhinus macrolepis in Shennongjia. Fish Sci 34:523–526
Zhang Y, Zhang X, Shi J et al (2018) Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nat Cell Biol 20:535–540. https://doi.org/10.1038/s41556-018-0087-2
Zhang J, Cai R, Liang J et al (2021) Molecular mechanism of Chinese alligator (Alligator sinensis) adapting to hibernation. J Exp Zool Part B Mol Dev Evol 336:32–49. https://doi.org/10.1002/jez.b.23013
Zhao Y, Gozlan R, Zhang C (2011) Out of sight out of mind: current knowledge of Chinese cave fishes. J Fish Biol 79:1545–1562. https://doi.org/10.1111/j.1095-8649.2011.03066.x
Zhou Y, Zhong H, Xiao J et al (2016) Identification and comparative analysis of piRNAs in ovary and testis of Nile tilapia (Oreochromis niloticus). Genes Genomics 38:519–527. https://doi.org/10.1007/s13258-016-0400-z
Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415. https://doi.org/10.1093/nar/gkg595
Acknowledgements
Not applicable.
Funding
This work is supported by the research and development program of China Se-enriched industry research institute, Program No. 2021FXZX04-01.
Author information
Authors and Affiliations
Contributions
GFP and WZD designed the research; CZ, QFS, and JCL conducted the research; GFP, YNC, and YJG analyzed the data; GFP and FXY wrote the manuscript; CZ, HJ, and WZD revised the manuscript. All authors read and approved the final manuscript.
Corresponding authors
Ethics declarations
Ethics approval and consent to participate
All procedures used in this study were performed in accordance with the Guide for Care and Use of Laboratory Animals and approved by the Northwest A & F University Institutional Animal Care and Use Committee.
Consent for publication
Not applicable.
Competing interests
The authors declare no conflicts of interest.
Additional information
Publisher's note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Peng, G., Zhu, C., Sun, Q. et al. Testicular miRNAs and tsRNAs provide insight into gene regulation during overwintering and reproduction of Onychostoma macrolepis. Fish Physiol Biochem 48, 481–499 (2022). https://doi.org/10.1007/s10695-022-01078-0
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10695-022-01078-0