日本七鳃鳗物种特异性microRNAs及其前体识别与验证

doi:10.16288/j.yczz.14-411

[an error occurred while processing this directive]

HEREDITAS(Beijing) ›› 2015, Vol. 37 ›› Issue (3): 283-291.doi: 10.16288/j.yczz.14-411

• Research Articles • Previous Articles Next Articles

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

Xin Liu^{1, 2}, Jie Zhang^{1, 2}, Chunhui Zhao^{1, 2}, Tiesong Li^{1, 2}, Jihong Wang^{1, 2}, Qingwei Li^{1, 2}

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

Received:2014-11-25 Revised:2015-01-19 Online:2015-03-20 Published:2015-02-10

Abstract

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.

Key words: Lampetra japonica, species-specific miRNA, high-throughput sequencing, microarray assay

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.

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

Metrics

Comments

www.chinagene.cn
备案号：京ICP备09063187号

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

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 11

Recommended Articles

Metrics

Comments

[1]	Jie Wu, Jianping Quan, Yong Ye, ZhenFang Wu, Jie Yang, Ming Yang, Enqin Zheng. Advances in assay for transposase-accessible chromatin with high-throughput sequencing [J]. Hereditas(Beijing), 2020, 42(4): 333-346.
[2]	Xin Li, Chengming Qu, Yinglun Han, Xin Liu, Qingwei Li. Identification, recombinant expression and immunological study of Lja-SHP2 in Lampetra japonica [J]. Hereditas(Beijing), 2020, 42(2): 183-193.
[3]	Gang Liu,Feizhou Sun,Fangxian Zhu,Haiyong Feng,Xu Han. Runs of homozygosity and its application on livestock genome study [J]. Hereditas(Beijing), 2019, 41(4): 304-317.
[4]	Xiangyuan Zhang,Chao He,Bingyu Ye,Dejian Xie,Minglei Shi,Yan Zhang,Wenlong Shen,Ping Li,Zhihu Zhao. Optimization and quality control of genome-wide Hi-C library preparation [J]. Hereditas(Beijing), 2017, 39(9): 847-855.
[5]	Dongyi Bai, Yiping Zhao, Bei Li, Bou Gerelchimeg, Xinzhuang Zhang, Manglai Dugarjaviin. Progress in the whole genome of Equus by using high-throughput sequencing technologies [J]. Hereditas(Beijing), 2017, 39(11): 974-983.
[6]	Ke Fang, Kaixiang Zhang, Jian Wang, Zhimeng Fu, Xianghui Zhao. Advances on the profiling of 5-hydroxymethylcytosine [J]. HEREDITAS(Beijing), 2016, 38(3): 206-216.
[7]	Cairui Lu, Changsong Zou, Guoli Song. Recent progress in gene mapping through high-throughput sequencing technology and forward genetic approaches [J]. HEREDITAS(Beijing), 2015, 37(8): 765-776.
[8]	Xin Liu,Xueying Song,Xiaoping Zhang,Yinglun Han,Ting Zhu,Rong Xiao,Qingwei Li. Genetic basis of immune response of lymphocyte-like cells in the mucosal immune system of Lampetra japonica [J]. HEREDITAS(Beijing), 2015, 37(11): 1149-1159.
[9]	Lu Wen, Fuchou Tang. Recent progress in single-cell RNA-Seq analysis [J]. HEREDITAS(Beijing), 2014, 36(11): 1069-1076.
[10]	LAI Xiao-Juan, CHEN Hai-Min, YANG Rui, YAN Xiao-Jun. Advances on the genome of algae [J]. HEREDITAS, 2013, 35(6): 735-744.
[11]	JIN Ping, ZHANG Wei-Wei, HUANG Hui-Fang, MA Fei. Cloning and analysis of Lyb gene from Lampetra japonica [J]. HEREDITAS, 2008, 30(12): 1597-1602.