Computational identification and characterization of microRNAs and their targets in <italic style="font-style: italic">Penaeus monodon</italic>

濮龙军; 王晶; 王玉; 左建伟; 郭华荣

doi:10.1007/s00343-018-6348-x

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Computational identification and characterization of microRNAs and their targets in Penaeus monodon

Biology | Updated：2023-05-19

- Computational identification and characterization of microRNAs and their targets in Penaeus monodon
- Computational identification and characterization of microRNAs and their targets in Penaeus monodon
- 海洋湖沼学报（英文） 2018年36卷第3期页码：853-869
- Affiliations：
  
  1.Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
  2.Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China
- Author bio：
  
  GUO Huarong, huarongguo@ouc.edu.cn
- Funds：
  
  the National Natural Science Foundation of China(31172391);the National Natural Science Foundation of China(31472274);the Fundamental Research Funds for Central Universities(201762003);the Scholarship Foundation for Excellent Scientists of Shandong Province(BS2011SW054);the National HighTech R&D Program of China (863 Program)(2012AA10A402);the Open Funds of Institute of Biodiversity and Evolution, Ocean University of China(201362017)
- DOI：10.1007/s00343-018-6348-x
  中图分类号：
- 收稿：2016-12-26，
  
  录用：2017-2-3，
  
  网络首发：2017-02-28，
  
  纸质出版：2018-05
- Accepted：
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濮龙军, 王晶, 王玉, 等. Computational identification and characterization of microRNAs and their targets in Penaeus monodon[J]. 海洋湖沼学报（英文）, 2018,36(3):853-869.

Longjun PU, Jing WANG, Yu WANG, et al. Computational identification and characterization of microRNAs and their targets in Penaeus monodon[J]. Chinese Journal of Oceanology and Limnology, 2018, 36(3): 853-869.
濮龙军, 王晶, 王玉, 等. Computational identification and characterization of microRNAs and their targets in Penaeus monodon[J]. 海洋湖沼学报（英文）, 2018,36(3):853-869. DOI： 10.1007/s00343-018-6348-x.

Longjun PU, Jing WANG, Yu WANG, et al. Computational identification and characterization of microRNAs and their targets in Penaeus monodon[J]. Chinese Journal of Oceanology and Limnology, 2018, 36(3): 853-869. DOI： 10.1007/s00343-018-6348-x.

摘要

Abstract

Study on shrimp miRNAs was limited and just 7 mature miRNA sequences of

Marsupenaeus japonicus

are deposited in mirBase database. In this study

miRNAs and their target gene candidates were computationally identified from shrimp

Penaeus monodon

and then experimentally validated. Using 39 908 expressed sequence tags (ESTs) and 21 124 genome survey sequences (GSSs) of

P. monodon

(pmo) as reference dataset

a comprehensive approach based on inter-species homolog search was employed to investigate the candidate miRNAs (i.e. pmo-miRNA). A total of eight miRNAs belonging to 7 families were computationally identified and five out of them were subsequently validated by PCR and sequencing. Of these

pmo-miR-4961a

pmo-miR-4961b

pmo-miR-4979 and pmo-miR-3819 were first identified from shrimps. Both the mature pmo-miRNAs and the corresponding precursors were conserved among different species. Based on perfect or near-perfect match to the target region

the target gene candidates of pmomiRNAs were predicted from 10 331 mRNA sequences of

P. monodon

. A total of 20 genes were predicted as the targets of pmo-miR-4961a

pmo-miR-4961b

pmo-miR-4979 and pmo-miR-6492. Experimental validation by dual luciferase reporter assay confirmed the targeting between 3 pmo-miRNAs and one or two of their target genes

especially the pmo-miR-4979 which could significantly down-regulate the expression of target gene (JR226772). This study updates the miRNAs and their targets in

P. monodon

and lays a solid foundation for future RNAi study.

关键词

Keywords

references

Adai A, Johnson C, Mlotshwa S, Archer-Evans S, Manocha V, Vance V, Sundaresan V. 2005. Computational prediction of miRNAs in Arabidopsis thaliana . Genome Research, 15(1):78-91.

Altschul S F, Madden T L, Schäffer A A, Zhang J H, Zhang Z, Miller W, Lipman D J. 1997. Gapped BLAST and PSIBLAST:a new generation of protein database search programs. Nucleic Acids Res., 25(17):3 389-3 402.

Alvarez-Garcia I, Miska E A. 2005. MicroRNA functions in animal development and human disease. Development, 132(21):4 653-4 662.

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.

Ason B, Darnell D K, Wittbrodt B, Berezikov E, Kloosterman W P, Wittbrodt J, Antin P B, Plasterk R H. 2006.Differences in vertebrate microRNA expression.Proceedings of the National Academy of Sciences of the United States of America, 103(39):14 385-14 389.

Axtell M J, Westholm J O, Lai E C. 2011. Vive la différence:biogenesis and evolution of microRNAs in plants and animals. Genome Biol., 12(4):221.

Bar M, Wyman S K, Fritz B R et al. 2008. MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells, 26(10):2 496-2 505.

Bartel D P. 2004. MicroRNAs:genomics, biogenesis, mechanism, and function. Cell, 116(2):281-297.

Baskerville S, Bartel D P. 2005. Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11(3):241-247.

Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk R H A, Cuppen E. 2005. Phylogenetic shadowing and computational identification of human microRNA genes.Cell, 120(1):21-24.

Brown J R, Sanseau P. 2005. A computational view of microRNAs and their targets. Drug Discovery Today , 10(8):595-601.

Carrington J C, Ambros V. 2003. Role of microRNAs in plant and animal development. Science, 301(5631):336-338.

Carthew R W, Sontheimer E J. 2009. Origins and mechanisms of miRNAs and siRNAs. Cell, 136(4):642-655.

Chan S M, Gu P L, Chu K H, Tobe S S. 2003. Crustacean neuropeptide genes of the CHH/MIH/GIH family:implications from molecular studies. General and Comparative Endocrinology, 134(3):214-219.

Chen X M. 2005. MicroRNA biogenesis and function in plants.FEBS Letters, 579(26):5 923-5 931.

Cheng A M, Byrom M W, Shelton J, Ford L P. 2005. Antisense inhibition of human miRNAs and indications for an involvement of miRNA in cell growth and apoptosis.Nucleic Acids Res., 33(4):1 290-1 297.

Chi W, Tong C B, Gan X N, He S P. 2011. Characterization and comparative profiling of miRNA transcriptomes in bighead carp and silver carp. PLoS One, 6(8):e23549.

Conesa A, Götz S, García-Gómez J M, Terol J, Talón M, Robles M. 2005. Blast2GO:a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 21(18):3 674-3 676.

Cui Y L, Huang T Z, Zhang X B. 2015. RNA editing of microRNA prevents RNA-induced silencing complex recognition of target mRNA. Open Biology, 5(12):150 126.

Davis B N, Hata A. 2009. Regulation of MicroRNA biogenesis:a miRiad of mechanisms. Cell Communication and Signaling, 7(1):18.

Fabbri M, Garzon R, Cimmino A et al. 2007. MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B. Proceedings of the National Academy of Sciences of the United States of America, 104(40):15 805-15 810.

Fanjul-Moles M L. 2006. Biochemical and functional aspects of crustacean hyperglycemic hormone in decapod crustaceans:review and update. Comparative Biochemistry and Physiology Part C:Toxicology & Pharmacology, 142(3-4):390-400.

Gomes C P C, Cho J H, Hood L, Franco O L, Pereira R W, Wang K. 2013. A review of computational tools in microRNA discovery. Front. Genet., 4:81.

Götz S, García-Gómez J M, Terol J, Williams T D, Nagaraj S H, Nueda M J, Robles M, Talón M, Dopazo J, Conesa A. 2008. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res., 36(10):3 420-3 435.

Gregory R I, Chendrimada T P, Cooch N, Shiekhattar R. 2005.Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell, 123(4):631-640.

Griffiths-Jones S, Grocock R J, Van Dongen S, Bateman A, Enright A J. 2006. miRBase:microRNA sequences, targets and gene nomenclature. Nucleic Acids Res., 34(S1):D140-D144.

Guo H S, Xie Q, Fei J F, Chua N H. 2005. MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development. The Plant Cell, 17(5):1 376-1 386.

Hofacker I L. 2003. Vienna RNA secondary structure server.Nucleic Acids Res., 31(13):3 429-3 431.

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(1):159.

Huang T Z, Zhang X B. 2012. Functional analysis of a crustacean microRNA in host-virus interactions. Journal of Virology, 86(23):12 997-13 004.

John B, Enright A J, Aravin A, Tuschl T, Sander C, Marks D S. 2004. Human microRNA targets. PLoS Biology, 2(11):e363.

Kanehisa M, Goto S. 2000. KEGG:kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28(1):27-30.

Kato M, Putta S, Wang M, Yuan H, Lanting L, Nair I, Gunn A, Nakagawa Y, Shimano H, Todorov I, Rossi J J, Natarajan R. 2009. TGF-β activates Akt kinase through a microRNAdependent amplifying circuit targeting PTEN. Nature Cell Biology, 11(7):881-889.

Kim V N. 2005. MicroRNA biogenesis:coordinated cropping and dicing. Nature Reviews Molecular Cell Biology, 6(5):376-385.

Kloosterman W P, Plasterk R H A. 2006. The diverse functions of microRNAs in animal development and disease.Developmental Cell, 11(4):441-450.

Kloosterman W P, Steiner F A, Berezikov E, de Bruijn E, van de Belt J, Verheul M, Cuppen E, Plasterk R H A. 2006.Cloning and expression of new microRNAs from zebrafish. Nucleic Acids Res., 34(9):2 558-2 569.

Lagos-Quintana M, Rauhut R, Yalcin A, Meyer J, Lendeckel W, Tuschl T. 2002. Identification of tissue-specific microRNAs from mouse. Current Biology, 12(9):735-739.

Lai E C, Tomancak P, Williams R W, Rubin G M. 2003.Computational identification of Drosophila microRNA genes. Genome Biol., 4(7):R42.

Li L, Xu J Z, Yang D Y, Tan X R, Wang H F. 2010.Computational approaches for microRNA studies:a review. Mammalian Genome, 21(1-2):1-12.

Li Y, Wang F, Lee J A, Gao F B. 2006. MicroRNA-9a ensures the precise specification of sensory organ precursors in Drosophila . Genes & Development, 20(20):2 793-2 805.

Lim L P, Lau N C, Weinstein E G, Abdelhakim A, Yekta S, Rhoades M W, Burge C B, Bartel D P. 2003. The microRNAs of Caenorhabditis elegans . Genes & Development, 17(8):991-1 008.

Liu C G, Calin G A, Meloon B, Gamliel N, Sevignani C, Ferracin M, Dumitru C D, Shimizu M, Zupo S, Dono M, Alder H, Bullrich F, Negrini M, Croce C M. 2004. An oligonucleotide microchip for genome-wide microRNA profiling in human and mouse tissues. Proceedings of the National Academy of Sciences of the United States of America, 101(26):9 740-9 744.

Lu C, Jeong D H, Kulkarni K et al. 2008. Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proceedings of the National Academy of Sciences of the United States of America, 105(12):4 951-4 956.

Meemak P, Phongdara A, Chotigeat W, Tammi M T. 2013.Computational identification of Penaeus monodon microRNA genesan d their targets. Songklanakarin Journal of Science & Technology, 35(2):143-148.

O'Connell R M, Chaudhuri A A, Rao D S, Baltimore D. 2009.Inositol phosphatase SHIP1 is a primary target of miR-155. Proceedings of the National Academy of Sciences of the United States of America, 106(17):7 113-7 118.

Pierce M L, Weston M D, Fritzsch B, Gabel H W, Ruvkun G, Soukup G A. 2008. MicroRNA-183 family conservation and ciliated neurosensory organ expression. Evolution & Development, 10(1):106-113.

Ramachandra R K, Salem M, Gahr S, Rexroad C E, Yao J B. 2008. Cloning and characterization of microRNAs from rainbow trout ( Oncorhynchus mykiss ):their expression during early embryonic development. BMC Developmental Biology, 8(1):41.

Re A, Corá D, Taverna D, Caselle M. 2009. Genome-wide survey of microRNA-transcription factor feed-forward regulatory circuits in human. Molecular BioSystems, 5(8):854-867.

Rengpipat S, Phianphak W, Piyatiratitivorakul S, Menasveta P. 1998. Effects of a probiotic bacterium on black tiger shrimp Penaeus monodon survival and growth.Aquaculture, 167(3-4):301-313.

Rodriguez A, Griffiths-Jones S, Ashurst J L, Bradley A. 2004.Identification of mammalian microRNA host genes and transcription units. Genome Research, 14(10a):1 902-1 910.

Saini H K, Griffiths-Jones S, Enright A J. 2007. Genomic analysis of human microRNA transcripts. Proceedings of the National Academy of Sciences of the United States of America, 104(45):17 719-17 724.

Sethupathy P, Megraw M, Hatzigeorgiou A G. 2006. A guide through present computational approaches for the identification of mammalian microRNA targets. Nature Methods, 3(11):881-886.

Soares A R, Pereira P M, Santos B, Egas C, Gomes A C, Arrais J, Oliveira J L, Moura G R, Santos M A. 2009. Parallel DNA pyrosequencing unveils new zebrafish microRNAs.BMC Genomics, 10(1):195.

Stark A, Bushati N, Jan C H, Kheradpour P, Hodges E, Brennecke J, Bartel D P, Cohen S M, Kellis M. 2008. A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes & Development, 22(1):8-13.

Strimmer K, von Haeseler A. 1996. Quartet puzzling:a quartet maximum-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution, 13(7):964-969.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5:molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution, 28(10):2 731-2 739.

Wang J Y, Yang X D, Xu H B, Chi X Y, Zhang M, Hou X L. 2012. Identification and characterization of microRNAs and their target genes in Brassica oleracea . Gene, 505(2):300-308.

Weston M D, Pierce M L, Rocha-Sanchez S R, Beisel K W, Soukup G A. 2006. MicroRNA gene expression in the mouse inner ear. Brain Research, 1111(1):95-104.

Wienholds E, Kloosterman W P, Miska E, Alvarez-Saavedra E, Berezikov E, de Bruijn E, Horvitz H R, Kauppinen S, Plasterk R H A. 2005. MicroRNA expression in zebrafish embryonic development. Science, 309(5732):310-311.

Xi Q Y, Xiong Y Y, Wang Y M, Cheng X, Qi Q E, Shu G, Wang S B, Wang L N, Gao P, Zhu X T, Jiang Q Y, Zhang Y L, Liu L. 2015. Genome-wide discovery of novel and conserved microRNAs in white shrimp ( Litopenaeus vannamei ). Molecular Biology Reports, 42(1):61-69.

Xie C X, Xu S L, Yang L L, Ke Z H, Xing J B, Gai J W, Gong X L, Xu L X, Bao B L. 2011. mRNA/microRNA profile at the metamorphic stage of olive flounder ( Paralichthys olivaceus ). Comparative And functional Genomics, 2011:256 038.

Xu Z Q, Qin Q, Ge J C, Pan J L, Xu X F. 2012. Bioinformatic identification and validation of conservative microRNAs in Ictalurus punctatus . Molecular Biology Reports, 39(12):10 395-10 405.

Yang G, Yang L, Zhao Z, Wang J J, Zhang X B. 2012. Signature miRNAs involved in the innate immunity of invertebrates.PLoS One, 7(6):e39015.

Yang L D, He S P. 2014. A bioinformatics-based update on microRNAs and their targets in rainbow trout( Oncorhynchus mykiss ). Gene, 533(1):261-269.

Yin Z J, Li C H, Han X L, Shen F F. 2008. Identification of conserved microRNAs and their target genes in tomato( Lycopersicon esculentum ). Gene, 414(1-2):60-66.

Zhang B H, Pan X P, Cannon C H, Cobb G P, Anderson T A. 2006b. Conservation and divergence of plant microRNA genes. The Plant Journal, 46(2):243-259.

Zhang B H, Pan X P, Cox S B, Cobb G P, Anderson T A. 2006a.Evidence that miRNAs are different from other RNAs.Cellular and Molecular Life Sciences, 63(2):246-254.

Zhang B H, Pan X P, Wang Q L, Cobb G P, Anderson T A. 2005. Identification and characterization of new plant microRNAs using EST analysis. Cell Research, 15(5):336-360.

Zhang B H, Wang Q L, Wang K B, Pan X P, Liu F, Guo T L, Cobb G P, Anderson T A. 2007. Identification of cotton microRNAs and their targets. Gene, 397(1-2):26-37.

Zhang Z, Schwartz S, Wagner L, Miller W. 2000. A greedy algorithm for aligning DNA sequences. Journal of Computational Biology, 7(1-2):203-214.

Zhou L G, Liu Y H, Liu Z C, Kong D Y, Duan M, Luo L J. 2010. Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa . Journal of Experimental Botany, 61(15):4 157-4 168.

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Computational identification and characterization of microRNAs and their targets in Penaeus monodon

DOI：10.1007/s00343-018-6348-x

摘要

Abstract

关键词

Keywords

references