Skip to main content

Advertisement

SpringerLink
Log in

Identification and Characteristics of Cattle MicroRNAs by Homology Searching and Small RNA Cloning

  • Published:
Biochemical Genetics Aims and scope Submit manuscript

Abstract

MicroRNAs (miRNA) are a class of noncoding RNA molecules that regulate gene expression by an RNA-interfering pathway through cleavage or inhibition of the translation of target mRNA. The 254 cattle miRNA candidates found by homology searching frequently clustered at certain chromosomes, and some are possibly expressed from more than one genomic locus. They were partially verified by cloning from a small cattle RNA library, where 31 distinct miRNAs were identified: 18 previously registered in the database of miRBase, 11 novel and homologous to known mammalian miRNAs, and 2 potentially novel without homology to any known miRNAs. Partial miRNA expression was detected by RT-PCR in cattle tissues, such as brain, liver, lung, and heart; some were expressed in all tissues and others in a specific tissue. Sequence alignments revealed that many had end variants, most of which differed in the 3′ end; a small number differed in the 5′ end. This indicates that the same miRNA gene can be individually modified in the process of miRNA biogenesis and could have a different role in regulating target gene expression.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3

Similar content being viewed by others

References

  • Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355

    Article  CAS  PubMed  Google Scholar 

  • Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  PubMed  Google Scholar 

  • 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 (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37:766–770

    Article  CAS  PubMed  Google Scholar 

  • Blow MJ, Grocock RJ, van Dongen S, Enright AJ, Dicks E, Futreal PA, Wooster R, Stratton MR (2006) RNA editing of human microRNAs. Genome Biol 7:R27

    Article  PubMed  Google Scholar 

  • Chen PY, Manninga H, Slanchev K, Chien M, Russo JJ, Ju J, Sheridan R, John B, Marks DS, Gaidatzis D, Sander C, Zavolan M, Tuschl T (2005) The developmental miRNA profiles of zebrafish as determined by small RNA cloning. Genes Dev 19:1288–1293

    Article  CAS  PubMed  Google Scholar 

  • Coutinho LL, Matukumalli LK, Sonstegard TS, Van Tassell CP, Gasbarre LC, Capuco AV, Smith TP (2007) Discovery and profiling of bovine microRNAs from immune-related and embryonic tissues. Physiol Genomics 29:35–43

    CAS  PubMed  Google Scholar 

  • Fu H, Tie Y, Xu C, Zhang Z, Zhu J, Shi Y, Jiang H, Sun Z, Zheng X (2005) Identification of human fetal liver miRNAs by a novel method. FEBS Lett 579:3849–3854

    Article  CAS  PubMed  Google Scholar 

  • Fu HJ, Zhu J, Yang M, Zhang ZY, Tie Y, Jiang H, Sun ZX, Zheng XF (2006) A novel method to monitor the expression of microRNAs. Mol Biotechnol 32:197–204

    Article  CAS  PubMed  Google Scholar 

  • Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J (2003) Computational and experimental identification of C. elegans microRNAs. Mol Cell 11:1253–1263

    Article  CAS  PubMed  Google Scholar 

  • Gu Z, Eleswarapu S, Jiang H (2007) Identification and characterization of microRNAs from the bovine adipose tissue and mammary gland. FEBS Lett 581:981–988

    Article  CAS  PubMed  Google Scholar 

  • He L, Thomson JM, Hemann MT, Hernando-Monge E, Mu D, Goodson S, Powers S, Cordon-Cardo C, Lowe SW, Hannon GJ, Hammond SM (2005) A microRNA polycistron as a potential human oncogene. Nature 435:828–833

    Article  CAS  PubMed  Google Scholar 

  • Hwang HW, Wentzel EA, Mendell JT (2007) A hexanucleotide element directs microRNA nuclear import. Science 315:97–100

    Article  CAS  PubMed  Google Scholar 

  • Jones-Rhoades MW, Bartel DP (2004) Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell 14:787–799

    Article  CAS  PubMed  Google Scholar 

  • Kawahara Y, Zinshteyn B, Sethupathy P, Iizasa H, Hatzigeorgiou AG, Nishikura K (2007) Redirection of silencing targets by adenosine-to-inosine editing of miRNAs. Science 315:1137–1140

    Article  CAS  PubMed  Google Scholar 

  • Kim VN (2005) MicroRNA biogenesis: coordinated cropping and dicing. Nat Rev Mol Cell Biol 6:376–385

    Article  CAS  PubMed  Google Scholar 

  • Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T (2001) Identification of novel genes coding for small expressed RNAs. Science 294:853–858

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Lagos-Quintana M, Rauhut R, Meyer J, Borkhardt A, Tuschl T (2003) New microRNAs from mouse and human. RNA 9:175–179

    Article  CAS  PubMed  Google Scholar 

  • Lai EC, Tomancak P, Williams RW, Rubin GM (2003) Computational identification of Drosophila microRNA genes. Genome Biol 4:R42

    Article  PubMed  Google Scholar 

  • Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A, Pfeffer S, Rice A, Kamphorst AO, Landthaler M, Lin C, Socci ND, Hermida L, Fulci V, Chiaretti S, Foa R, Schliwka J, Fuchs U, Novosel A, Muller RU, Schermer B, Bissels U, Inman J, Phan Q, Chien M, Weir DB, Choksi R, De Vita G, Frezzetti D, Trompeter HI, Hornung V, Teng G, Hartmann G, Palkovits M, Di Lauro R, Wernet P, Macino G, Rogler CE, Nagle JW, Ju J, Papavasiliou FN, Benzing T, Lichter P, Tam W, Brownstein MJ, Bosio A, Borkhardt A, Russo JJ, Sander C, Zavolan M, Tuschl T (2007) A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 129:1401–1414

    Article  CAS  PubMed  Google Scholar 

  • Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854

    Article  CAS  PubMed  Google Scholar 

  • Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115:787–798

    Article  CAS  PubMed  Google Scholar 

  • Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20

    Article  CAS  PubMed  Google Scholar 

  • Liang H, Landweber LF (2007) Hypothesis: RNA editing of microRNA target sites in humans? RNA 13:463–467

    Article  CAS  PubMed  Google Scholar 

  • Mourelatos Z, Dostie J, Paushkin S, Sharma A, Charroux B, Abel L, Rappsilber J, Mann M, Dreyfuss G (2002) MiRNPs: a novel class of ribonucleoproteins containing numerous microRNAs. Genes Dev 16:720–728

    Article  CAS  PubMed  Google Scholar 

  • Plasterk RH (2006) Micro RNAs in animal development. Cell 124:877–881

    Article  CAS  PubMed  Google Scholar 

  • Rajewsky N (2006) MicroRNA target predictions in animals. Nat Genet 38 Suppl:S8–S13

    Article  PubMed  Google Scholar 

  • Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207

    Article  CAS  PubMed  Google Scholar 

  • Weber MJ (2005) New human and mouse microRNA genes found by homology search. FEBS J 272:59–73

    Article  CAS  PubMed  Google Scholar 

  • Wightman B, Ha I, Ruvkun G (1993) Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75:855–862

    Article  CAS  PubMed  Google Scholar 

  • Zhang B, Pan X, Anderson TA (2006) Identification of 188 conserved maize microRNAs and their targets. FEBS Lett 580:3753–3762

    Article  CAS  PubMed  Google Scholar 

  • Zhang R, Peng Y, Wang W, Su B (2007) Rapid evolution of an X-linked microRNA cluster in primates. Genome Res 17:612–617

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was partially supported by grants from the National Natural Science Foundation of China (No. 30500301), the National "973" Project (2002CB512803), and the Foundation of Shanghai Medical Sciences (No. 044038).

Author information

Authors and Affiliations

  1. Laboratory of Medical Microbiology, Department of Medical Microbiology and Parasitology, Shang Medical College of Fudan University, 138 Yixueyuan Rd, Shanghai, 200032, People’s Republic of China

    Jian-Er Long

  2. Institute of Medical Genetics, Shanghai Jiaotong University, 24/1400 West Beijing Rd, Shanghai, 200040, People’s Republic of China

    Jian-Er Long & Hai-Xuan Chen

Authors
  1. Jian-Er Long
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hai-Xuan Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jian-Er Long.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

(DOC 33 kb)

(RTF 1223 kb)

(RTF 189 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Long, JE., Chen, HX. Identification and Characteristics of Cattle MicroRNAs by Homology Searching and Small RNA Cloning. Biochem Genet 47, 329–343 (2009). https://doi.org/10.1007/s10528-009-9234-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10528-009-9234-6

Keywords

Search

Navigation