[an error occurred while processing this directive]
Research Articles

The identification and verification of species-specific microRNAs and their precursors in Lampetra japonica

Expand
  • 1. School of Life Science, Liaoning Normal Uuniversity, Dalian 116081, China;
    2. Lamprey Research Center, Liaoning Normal University, Dalian 116081, China

Received date: 2014-11-25

  Revised date: 2015-01-19

  Online published: 2015-02-10

Abstract

MicroRNAs (miRNAs) negatively regulate genes which are involved in various biological processes of metabolism at both transcriptional and post-transcriptional levels. In recent years, the existence and function of miRNAs have been extensively studied in plants and animals with the application of deep sequencing and microarray technology. In this study, small RNAs from leucocytes of Lampetra japonica (L. japonica) were sequenced using the second generation high-throughput sequencing technology. A total of 5 207 787 small RNA sequences were identified, and 4 739 346 of them assembled into 10 989 variants. Based on sequence similarity analysis, the sequences of these variants matched known miRNAs of 306 conserved families, among which 6 conserved miRNA family members expressed at an extremely high level which reflected the conservatism of miRNAs among species. In addition, 70 unannotated sequences were predicted to be new miRNAs, and 34 of them were further verified expressing in antigen-treated L. japonica leucocytes by miRNA microarray assay. Moreover, the minimal folding free energy indexes for 16 of the 34 miRNA precursors exceed 0.85, indicating the existence of species-specific miRNAs in L. japonica which may play important roles in regulating, growth, development and disease response of L. japonica leukocytes.

Cite this article

Xin Liu, Jie Zhang, Chunhui Zhao, Tiesong Li, Jihong Wang, Qingwei Li . The identification and verification of species-specific microRNAs and their precursors in Lampetra japonica[J]. Hereditas(Beijing), 2015 , 37(3) : 283 -291 . DOI: 10.16288/j.yczz.14-411

References

[1] Lee RC, Feinbaum RL, Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 . Cell , 1993, 75(5): 843-854.
[2] Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans . Nature , 2000, 403(6772): 901-906.
[3] Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. Identification of novel genes coding for small expressed RNAs. Science , 2001, 294(5543): 853-858.
[4] Lee RC, Ambros V. An extensive class of small RNAs in Caenorhabditis elegans . Science , 2001, 294(5543): 862-864.
[5] Lau NC, Lim LP, Weinstein EG, Bartel DP. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans . Science , 2001, 294(5543): 858-862.
[6] Berezikov E, Plasterk RH. Camels and zebrafish, viruses and cancer: a microRNA update. Hum Mol Genet , 2005, 14(S2): R183-R190.
[7] Lai EC, Tomancak P, Williams RW, Rubin GM. Computational identification of Drosophila microRNA genes. Genome Biol , 2003, 4: R42.
[8] Berezikov E, Guryev V, van de Belt J, Wienholds E, Plasterk RH, Cuppen E. Phylogenetic shadowing and computational identification of human microRNA genes. Cell , 2005, 120(1): 21-24.
[9] Lim LP, Glasner ME, Yekta S, Burge CB, Bartel DP. Vertebrate microRNA genes. Science , 2003, 299(5612): 1540.
[10] Lim LP, Lau NC, Weinstein EG, Abdelhakim A, Yekta S, Rhoades MW, Burge CB, Bartel DP. The microRNAs of Caenorhabditis elegans. Genes Dev , 2003, 17(8): 991-1008.
[11] Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z. Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet , 2005, 37(7): 766-770.
[12] Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP. MicroRNAs in plants. Genes Dev , 2002, 16(13): 1616-1626.
[13] Sunkar R, Zhu JK. Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis . Plant Cell , 2004, 16(8): 2001-2019.
[14] Park W, Li JJ, Song RT, Messing J, Chen XM. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana . Curr Biol , 2002, 12(17): 1484-1495.
[15] Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grässer FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju JY, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T. Identification of microRNAs of the herpesvirus family. Nat Methods , 2005, 2(4): 269-276.
[16] Pfeffer S, Zavolan M, Grässer FA, Chien M, Russo JJ, Ju JY, John B, Enright AJ, Marks D, Sander C, Tuschl T. Identification of virus-encoded microRNAs. Science , 2004, 304(5671): 734-736.
[17] Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ. miR-Base: tools for microRNA genomics. Nucleic Acids Res , 2008, 36(S1): D154-D158.
[18] Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM. Bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila . Cell , 2003, 113(1): 25-36.
[19] Xu PZ, Vernooy SY, Guo M, Hay BA. The Drosophila microRNA mir-14 suppresses cell death and is required for normal fat metabolism. Curr Biol , 2003, 13(9): 790-795.
[20] Chen CZ, Li L, Lodish HF, Bartel DP. MicroRNAs modulate hematopoietic lineage differentiation. Science , 2004, 303(5654): 83-86.
[21] Park JK, Liu X, Strauss TJ, McKearin DM, Liu QH. The miRNA pathway intrinsically controls self-renewal of Drosophila germline stem cells. Curr Biol , 2007, 17(6): 533-538.
[22] Alvarez-Garcia I, Miska EA. MicroRNA functions in animal development and human disease. Development , 2005, 132(21): 4653-4662.
[23] Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs
Outlines

/