Abstract
Regulation of microRNAs (miRNAs) on various biological processes has been a surprising and exciting field. Identification of miRNAs is the first step to comprehensively understand their functions. However, attempts on global identification and functional verification of miRNAs are very limited in penaeid shrimp Marsupenaeus japonicus, an economically important aquatic species. By performing an integrated analysis of transcriptomic profile from gastrula embryos of M. japonicus, 21 conserved miRNAs in M. japonicas (mja-miRNAs), belonging to 19 miRNA families, were identified and characterized. Of the 21 mja-miRNAs, 15 miRNAs were successfully verified to be predominantly expressed in gastrula stage, where they displayed dynamic expression patterns compared with those in naupliuin stage. Based on perfect or near-perfect match to target region, 120 target genes were predicted at transcriptome-wide level. Noteworthy, gene ontology (GO) classification and metabolic pathway annotation revealed eight targets that were actively involved in developmental processes. Of the predicted miRNA-mRNA pairs, six targets were then randomly selected and experimentally validated by dual luciferase reporter assay, where three pairs were proved with potential targeting activity. Overall, to search for conserved miRNAs potentially involved in early development of M. japonicus, we combined in silico and experimental methods, which can be applied in other organisms as well. Our data implied important roles of miRNAs in the early embryonic development and also suggested the presence of complex miRNA-mRNA functional networks in M. japonicus.
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Data Availability Statement
The datasets generated and/or analyzed during the current study are available from the corresponding author on reasonable request.
References
Abramov R, Fu G D, Zhang Y et al. 2013. Expression and regulation of miR-17a and miR-430b in zebrafish ovarian follicles. General and Comparative Endocrinology, 188: 309–315, https://doi.org/10.1016/j.ygcen.2013.02.012.
Adai A, Johnson C, Mlotshwa S et al. 2005. Computational prediction of miRNAs in Arabidopsis thaliana. Genome Research, 15(1): 78–91, https://doi.org/10.1101/gr.2908205.
Ambros V. 2004. The functions of animal microRNAs. Nature, 431(7006): 350–355, https://doi.org/10.1038/nature02871.
Ashburner M, Ball C A, Blake J A et al. 2000. Gene Ontology: tool for the unification of biology. Nature Genetics, 25(1): 25–29, https://doi.org/10.1038/75556.
Barozai M Y K. 2012. Identification and characterization of the microRNAs and their targets in Salmo salar. Gene, 499(1): 163–168, https://doi.org/10.1016/j.gene.2012.03.006.
Bartel D P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell, 116(2): 281–297, https://doi.org/10.1016/s0092-8674(04)00045-5.
Bernstein E, Caudy A A, Hammond S M et al. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature, 409(6818): 363–366, https://doi.org/10.1038/35053110.
Bizuayehu T T, Babiak J, Norberg B et al. 2012. Sex-biased miRNA expression in Atlantic halibut (Hippoglossus hippoglossus) brain and gonads. Sexual Development, 6(5): 257–266, https://doi.org/10.1159/000341378.
Brzuzan P, Woźny M, Wolińska L et al. 2010. MicroRNA expression in liver of whitefish (Coregonus lavaretus) exposed to microcystin-LR. Environmental Biotechnology, 6(2): 53–60.
Carthew R W, Sontheimer E J. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell, 136(4): 642–655, https://doi.org/10.1016/j.cell.2009.01.035.
Chen G F, Zhang C Y, Jiang F J et al. 2014. Bioinformatics analysis of hemocyte miRNAs of scallop Chlamys farreri against acute viral necrobiotic virus (AVNV). Fish & Shellfish Immunology, 37(1): 75–86, https://doi.org/10.1016/j.fsi.2014.01.002.
Chi W, Tong C B, Gan X N et al. 2011. Characterization and comparative profiling of miRNA transcriptomes in bighead carp and silver carp. PLoS One, 6(8): e23549, https://doi.org/10.1371/journal.pone.0023549.
Conesa A, Götz S, García-Gómez J M et al. 2005. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18): 3674–3676, https://doi.org/10.1093/bioinformaticx/bti610.
Crooks G E, Hon G, Chandonia J M et al. 2004. WebLogo: a sequence logo generator. Genome Research, 14(6): 1188–1190, https://doi.org/10.1101/gr.849004.
Denli A M, Tops B B J, Plasterk R H A et al. 2004. Processing of primary microRNAs by the microprocessor complex. Nature, 432(7014): 231–235, https://doi.org/10.1038/nature03049.
Flynt A S, Thatcher E J, Burkewitz K et al. 2009. miR-8 microRNAs regulate the response to osmotic stress in zebrafish embryos. Journal of Cell Biology, 185(1): 115–127, https://doi.org/10.1083/jcb.200807026.
Giraldez A J, Cinalli R M, Glasner M E et al. 2005. MicroRNAs regulate brain morphogenesis in zebrafish. Science, 308(5723): 833–838, https://doi.org/10.1126/science.1109020.
Götz S, García-Gómez J M, Terol J et al. 2008. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Research, 36(10): 3420–3435, https://doi.org/10.1093/nar/gkn176.
Grabherr M G, Haas B J, Yassour M et al. 2011. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nature Biotechnology, 29(7): 644–652, https://doi.org/10.1038/nbt.1883.
Guo H, Lu Z C, Zhu X W et al. 2018. Differential expression of microRNAs in hemocytes from white shrimp Litopenaeus vannamei under copper stress. Fish & Shellfish Immunology, 74: 152–161, https://doi.org/10.1016/j.fsi.2017.12.053.
Haas B J, Papanicolaou A, Yassour M et al. 2013. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nature Protocols, 8(8): 1494–1512, https://doi.org/10.1038/nprot.2013.084.
Han Q, Li P T, Lu X B et al. 2013. Improved primary cell culture and subculture of lymphoid organs of the greasyback shrimp Metapenaeus ensis. Aquaculture, 410–411: 101–113, https://doi.org/10.1016/j.aquaculture.2013.06.024.
He L, Wang Y L, Li Q et al. 2015. Profiling microRNAs in the testis during sexual maturation stages in Eriocheir sinensis. Animal Reproduction Science, 162: 52–61, https://doi.org/10.1016/j.anireprosci.2015.09.008.
He Y Y, Li Z X, Zhang H E et al. 2019. Genome-wide identification of Chinese shrimp (Fenneropenaeus chinensis) microRNA responsive to low pH stress by deep sequencing. Cell Stress and Chaperones, 24(4): 689–695, https://doi.org/10.1007/s12192-019-00989-x.
He Z H, Zhong Y Q, Hou D Q et al. 2022. Integrated analysis of mRNA-seq and miRNA-seq reveals the molecular mechanism of the intestinal immune response in Marsupenaeus japonicus under decapod iridescent virus 1 infection. Frontiers in Immunology, 12: 807093, https://doi.org/10.3389/fimmu.2021.807093.
Hofacker I L. 2003. Vienna RNA secondary structure server. Nucleic Acids Research, 31(13): 3429–3431, https://doi.org/10.1093/nar/gkg599.
Huang T Z, Xu D D, Zhang X B. 2012. Characterization of host microRNAs that respond to DNA virus infection in a crustacean. BMC Genomics, 13: 159, https://doi.org/10.1186/1471-2164-13-159.
John B, Enright A J, Aravin A et al. 2004. Human microRNA targets. PLoS Biology, 2(11): e363, https://doi.org/10.1371/journal.pbio.0020363.
Kanehisa M, Goto S. 2000. KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research, 28(1): 27–30, https://doi.org/10.1093/nar/28.1.27.
Kanoksinwuttipong N, Jaree P, Somboonwiwat K. 2022. Shrimp pmo-miR-750 regulates the expression of sarcoplasmic calcium-binding protein facilitating virus infection in Penaeus monodon. Fish & Shellfish Immunology, 129: 74–84, https://doi.org/10.1016/j.fsi.2022.08.046.
Kapsimali M, Kloosterman W P, de Bruijn E et al. 2007. MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system. Genome Biology, 8(8): R173, https://doi.org/10.1186/gb-2007-8-8-r173.
Kenny N J, Namigai E K O, Marlétaz F et al. 2015. Draft genome assemblies and predicted microRNA complements of the intertidal lophotrochozoans Patella vulgata (Mollusca, Patellogastropoda) and Spirobranchus (Pomatoceros) lamarcki (Annelida, Serpulida). Marine Genomics, 24: 139–146, https://doi.org/10.1016/j.margen.2015.07.004.
Kloosterman W P, Steiner F A, Berezikov E et al. 2006. Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Research, 34(9): 2558–2569, https://doi.org/10.1093/nar/gkl278.
Lai E C, Tomancak P, Williams R W et al. 2003. Computational identification of Drosophila microRNA genes. Genome Biology, 4(7): R42, https://doi.org/10.1186/gb-2003-4-7-r42.
Laity J H, Lee B M, Wright P E. 2001. Zinc finger proteins: new insights into structural and functional diversity. Current Opinion in Structural Biology, 11(1): 39–46, https://doi.org/10.1016/s0959-440x(00)00167-6.
Li P T, Wang Y H, Wang Y J et al. 2017a. Whole transcriptome sequencing and analysis of gastrula embryos of Marsupenaeus japonicus (Bate, 1888). Madridge Journal of Aquaculture Research & Development, 1(1): 1–7, https://doi.org/10.18689/mjard-1000101.
Li S K, Zhu S, Li C B et al. 2013. Characterization of microRNAs in mud crab Scylla paramamosain under Vibrio parahaemolyticus infection. PLoS One, 8(8): e73392, https://doi.org/10.1371/journal.pone.0073392.
Li X P, Meng X H, Luo K et al. 2017b. The identification of microRNAs involved in the response of Chinese shrimp Fenneropenaeus chinensis to white spot syndrome virus infection. Fish & Shellfish Immunology, 68: 220–231, https://doi.org/10.1016/j.fsi.2017.05.060.
Li Y D, Zhou F L, Huang J H et al. 2020. Transcriptome and miRNA profiles of black tiger shrimp, Penaeus monodon, under different salinity conditions. Frontiers in Marine Science, 7: 579381, https://doi.org/10.3389/fmars.2020.579381.
Li Z X, Wang J Y, He Y Y et al. 2019. Comprehensive identification and profiling of Chinese shrimp (Fenneropenaeus chinensis) microRNAs in response to high pH stress using Hiseq 2000 sequencing. Aquaculture Research, 50(11): 3154–3162, https://doi.org/10.1111/are.14269.
Lizé M, Klimke A, Dobbelstein M. 2011. MicroRNA-449 in cell fate determination. Cell Cycle, 10(17): 2874–2882, https://doi.org/10.4161/cc.10.17.17181.
Lund E, Güttinger S, Calado A et al. 2004. Nuclear export of microRNA precursors. Science, 303(5654): 95–98, https://doi.org/10.1126/science.1090599.
Lv J J, Liu P, Gao B Q et al. 2016. The identification and characteristics of salinity-related microRNAs in gills of Portunus trituberculatus. Cell Stress and Chaperones, 21(1): 63–74, https://doi.org/10.1007/s12192-015-0641-9.
Martín-Gómez L, Villalba A, Kerkhoven R H et al. 2014. Role of microRNAs in the immunity process of the flat oyster Ostrea edulis against bonamiosis. Infection, Genetics and Evolution, 27: 40–50, https://doi.org/10.1016/j.meegid.2014.06.026.
Millard R S, Bickley L K, Bateman K S et al. 2021. Global mRNA and miRNA analysis reveal key processes in the initial response to infection with WSSV in the pacific whiteleg shrimp. Viruses, 13(6): 1140, https://doi.org/10.3390/v13061140.
Miller J, McLachlan A D, Klug A. 1985. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. The EMBO Journal, 4(6): 1609–1614, https://doi.org/10.1002/j.1460-2075.1985.tb03825.x.
Mortazavi A, Williams B A, McCue K et al. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5(7): 621–628, https://doi.org/10.1038/nmeth.1226.
Ordas A, Kanwal Z, Lindenberg V et al. 2013. MicroRNA-146 function in the innate immune transcriptome response of zebrafish embryos to Salmonella typhimurium infection. BMC Genomics, 14(1): 696, https://doi.org/10.1186/1471-2164-14-696.
Ou J T, Liu Q, Bian Y X et al. 2022a. Integrated analysis of mRNA and microRNA transcriptome related to immunity and autophagy in shrimp hemocytes infected with Spiroplasma eriocheiris. Fish & Shellfish Immunology, 130: 436–452, https://doi.org/10.1016/j.fsi.2022.09.035.
Ou J T, Chen H, Luan X Q et al. 2022b. Leveraging lncRNA-miRNA-mRNA network to reveal anti-Spiroplasma eriocheiris infection mechanisms in Macrobrachium nipponense. Aquaculture, 557: 738286, https://doi.org/10.1016/j.aquaculture.2022.738286.
Pu L J, Wang J, Wang Y et al. 2018. Computational identification and characterization of microRNAs and their targets in Penaeus monodon. Journal of Oceanology and Limnology, 36(3): 853–869, https://doi.org/10.1007/s00343-018-6348-x.
Ramachandra R K, Salem M, Gahr S et al. 2008. Cloning and characterization of microRNAs from rainbow trout (Oncorhynchus mykiss): their expression during early embryonic development. BMC Developmental Biology, 8(1): 41, https://doi.org/10.1186/1471-213X-8-41.
Ramachandran R, Fausett B V, Goldman D. 2010. Ascl1a regulates Müller glia dedifferentiation and retinal regeneration through a Lin-28-dependent, let-7 microRNA signalling pathway. Nature Cell Biology, 12(11): 1101–1107, https://doi.org/10.1038/ncb2115.
Ruan L W, Bian X F, Ji Y C et al. 2011. Isolation and identification of novel microRNAs from Marsupenaeus japonicus. Fish & Shellfish Immunology, 31(2): 334–340, https://doi.org/10.1016/j.fsi.2011.05.023.
Sha Z X, Gong G Y, Wang S L et al. 2014. Identification and characterization of Cynoglossus semilaevis microRNA response to Vibrio anguillarum infection through high-throughput sequencing. Developmental & Comparative Immunology, 44(1): 59–69, https://doi.org/10.1016/j.dci.2013.11.014.
Ünlü E S, Gordon D M, Telli M. 2015. Small RNA sequencing based identification of miRNAs in Daphnia magna. PLoS One, 10(9): e0137617, https://doi.org/10.1371/journal.pone.0137617.
Wan L C, Zhang H Y, Lu S F et al. 2012. Transcriptome-wide identification and characterization of miRNAs from Pinus densata. BMC Genomics, 13(1): 132, https://doi.org/10.1186/1471-2164-13-132.
Wang J Y, Yang X D, Xu H B et al. 2012a. Identification and characterization of microRNAs and their target genes in Brassica oleracea. Gene, 505(2): 300–308, https://doi.org/10.1016/j.gene.2012.06.002.
Wang M, Wang Q L, Wang B M. 2012b. Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboretum L.). PLoS One, 7(4): e33696, https://doi.org/10.1371/journal.pone.0033696.
Wang W, Zhong P, Yi J Q et al. 2019. Potential role for microRNA in facilitating physiological adaptation to hypoxia in the Pacific whiteleg shrimp Litopenaeus vannamei. Fish & Shellfish Immunology, 84: 361–369, https://doi.org/10.1016/j.fsi.2018.09.079.
Wang Z L, Feng Y Y, Li J Y et al. 2020. Integrative microRNA and mRNA analysis reveals regulation of ER stress in the Pacific white shrimp Litopenaeus vannamei under acute cold stress. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics, 33: 100645, https://doi.org/10.1016/j.cbd.2019.100645.
Wienholds E, Kloosterman W P, Miska E et al. 2005a. MicroRNA expression in zebrafish embryonic development. Science, 309(5732): 310–311, https://doi.org/10.1126/science.1114519.
Wienholds E, Plasterk R H A. 2005b. MicroRNA function in animal development. FEBS Letters, 579(26): 5911–5922, https://doi.org/10.1016/j.febslet.2005.07.070.
Xiao J, Zhong H, Zhou Y et al. 2014. Identification and characterization of microRNAs in ovary and testis of Nile tilapia (Oreochromis niloticus) by using solexa sequencing technology. PLoS One, 9(1): e86821, https://doi.org/10.1371/journal.pone.0086821.
Xie C X, Xu S L, Yang L L et al. 2011. mRNA/microRNA profile at the metamorphic stage of olive flounder (Paralichthys olivaceus). Comparative and Functional Genomics, 2011: 256038, https://doi.org/10.1155/2011/256038.
Xu Z Q, Qin Q, Ge J C et al. 2012. Bioinformatic identification and validation of conservative microRNAs in Ictalurus punctatus. Molecular Biology Reports, 39(12): 10395–10405, https://doi.org/10.1007/s11033-012-1918-z.
Yan B, Zhao L H, Guo J T et al. 2012. miR-429 regulation of osmotic stress transcription factor 1 (OSTF1) in tilapia during osmotic stress. Biochemical and Biophysical Research Communications, 426(3): 294–298, https://doi.org/10.1016/j.bbrc.2012.08.029.
Yin Z J, Li C H, Han X L et al. 2008. Identification of conserved microRNAs and their target genes in tomato (Lycopersicon esculentum). Gene, 414(1–2): 60–66, https://doi.org/10.1016/j.gene.2008.02.007.
Yu X, Wang H, Lu Y Z et al. 2012. Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. Journal of Experimental Botany, 63(2): 1025–1038, https://doi.org/10.1093/jxb/err337.
Zeng Y, Cullen B R. 2005. Efficient processing of primary microRNA hairpins by DROSHA requires flanking nonstructured RNA sequences. Journal of Biological Chemistry, 280(30): 27595–27603, https://doi.org/10.1074/jbc.M504714200.
Zhang B H, Pan X P, Anderson T A. 2006a. Identification of 188 conserved maize microRNAs and their targets. FEBS Letters, 580(15): 3753–3762, https://doi.org/10.1016/j.febslet.2006.05.063.
Zhang B H, Pan X P, Cox S B et al. 2006b. Evidence that miRNAs are different from other RNAs. Cellular and Molecular Life Sciences, 63(2): 246–254, https://doi.org/10.1007/s00018-005-5467-7.
Zhang P J, Li C H, Shao Y N et al. 2014. Identification and characterization of miR-92a and its targets modulating Vibrio splendidus challenged Apostichopus japonicus. Fish & Shellfish Immunology, 38(2): 383–388, https://doi.org/10.1016/j.fsi.2014.04.007.
Zhang Z, Schwartz S, Wagner L et al. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology, 7(1–2): 203–214, https://doi.org/10.1089/10665270050081478.
Zheng J B, Cao J W, Mao Y et al. 2018. Identification of microRNAs with heat stress responsive and immune properties in Marsupenaeus japonicus based on next-generation sequencing and bioinformatics analysis: essential regulators in the heat stress-host interactions. Fish & Shellfish Immunology, 81: 390–398, https://doi.org/10.1016/j.fsi.2018.05.030.
Zhou Z, Wang L L, Song L S et al. 2014. The identification and characteristics of immune-related microRNAs in haemocytes of oyster Crassostrea gigas. PLoS One, 9(2): e88397, https://doi.org/10.1371/journal.pone.0088397.
Zhu F, Wang Z, Sun B Z. 2016. Differential expression of microRNAs in shrimp Marsupenaeus japonicus in response to Vibrio alginolyticus infection. Developmental & Comparative Immunology, 55: 76–79, https://doi.org/10.1016/j.dci.2015.10.012.
Acknowledgemnt
We thank Dr. Haolin XU (College of Biological Sciences, the Chinese University of Hong Kong) for kind gift of psiCHECK-2 plasmid and Sojeong JUN (Children’s Medical Center Research Institute and Department of Pediatrics, UT Southwestern Medical Center, USA) for language polishing.
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Supported by the National Natural Science Foundation of China (No. 32273116), the Natural Science Foundation of Shandong Province (China) (No. ZR2020MC189), and the National Key R&D Program of China (No. 2018YFD0901301)
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Wang, J., Pu, L., Zhang, X. et al. Integrative analysis of transcriptomic profile reveals potential roles of miRNAs in regulating development of Marsupenaeus japonicas. J. Ocean. Limnol. 42, 201–215 (2024). https://doi.org/10.1007/s00343-023-2403-3
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DOI: https://doi.org/10.1007/s00343-023-2403-3