Genes & Genomics

, Volume 37, Issue 5, pp 419–427 | Cite as

Deep sequencing identifies conserved and novel microRNAs from antlers cartilage of Chinese red deer (Cervus elaphus)

  • Yanxia Chen
  • Xuedong Liu
  • Xiaoguang Yang
  • Yuhui Liu
  • Xiaomeng Pi
  • Qingzhen Liu
  • Dong Zheng
Research Article
First Online:
Received:
Accepted:

Abstract

Deer antlers are the only mammalian appendages subject to an annual cycle of epimorphic regeneration. Within the rapid-growth stage, they display the fastest cartilage development in the animal kingdom. To identify microRNA (miRNA) profiling in red deer (Cervus elaphus) antler cartilage, we applied deep sequencing technology to a small RNA library constructed from pooled cartilage (three antlers from three individuals). We generated 9,520,645 mappable reads with a size distribution of between 15 and 30 nucleotides (miRNAs of 18 nucleotides were the most abundant group: 31 %). Bioinformatics data mining revealed 399 miRNAs in antler cartilage, of which 345 were highly conserved and expressed in 25 other mammals, including the cattle (Bos taurus) and in humans (Homo sapiens). The remaining 54 miRNAs we identified were novel and likely to be antler-cartilage specific, but were expressed at low levels. The identification of these known and newly identified miRNAs in antler cartilage significantly enhances our understanding of the miRNA profiling of regenerating antler cartilage. Further studies are necessary to better understand miRNAs-regulated antlerogenesis.

Keywords

Red deer Cartilage microRNA Regeneration 
This is a preview of subscription content, log in to check access.

Notes

Acknowledgments

We thank Mr. Shouzhuang YANG at the Qinghuangdao Safari Park for his help and technical support.

Conflict of interest

The authors declare that there is no conflict of interest.

Ethical Statement

This study was subject to approval by the Animal Ethics Committee of the Northeast Forestry University (AEC-NEFU; Permit Number: 2012-0016).

Funding

This work was funded by the Fundamental Research Funds for the Central Universities (No. 2572014EA05-01 to DZ) and the Program for New Century Excellent Talents in University (No. NCET-11-0609 to DZ).

Supplementary material

13258_2015_270_MOESM1_ESM.docx (229 kb)
Supplementary material 1 (DOCX 228 kb)
13258_2015_270_MOESM2_ESM.xlsx (55 kb)
Supplementary material 2 (XLSX 55 kb)
13258_2015_270_MOESM3_ESM.xlsx (596 kb)
Supplementary material 3 (XLSX 596 kb)

References

  1. Allen SP, Maden M, Price JS (2002) A role for retinoic acid in regulating the regeneration of deer antlers. Dev Biol 251:409–423CrossRefPubMedGoogle Scholar
  2. Ambady S, Wu Z, Dominko T (2012) Identification of novel MicroRNAs in Xenopus laevis metaphase II arrested eggs. Genesis 50:286–299PubMedCentralCrossRefPubMedGoogle Scholar
  3. Ambros V (2001) microRNAs: tiny regulators with great potential. Cell 107:823–826CrossRefPubMedGoogle Scholar
  4. Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X, Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M et al (2003) A uniform system for microRNA annotation. RNA 9:277–279PubMedCentralCrossRefPubMedGoogle Scholar
  5. Banks JW, Newbrey WJ (1983a) Light microscopic studies of the ossification process in developing antlers. In: Brown RD (ed) Antler Development in cervidea: a proceedings of the first international symposium of the Caesar Kleberg Wildlife Research Institute, College of Agriculture, Texas A&I University, Kingsville, Texas. Kingsville: Caesar Kleberg Wildlife Research Institute, pp 231–260Google Scholar
  6. Banks JW, Newbry WJ (1983) Antler development as a unique modification of mammalian endochondral ossification. In: Banks RD (ed) Antler developments in cervidae. Caesar Kleburg Wildlife Research Institute, Kingsville, pp 279–306Google Scholar
  7. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297CrossRefPubMedGoogle Scholar
  8. Cai Y, Yu X, Zhou Q, Yu C, Hu H, Liu J, Lin H, Yang J, Zhang B, Cui P et al (2010) Novel microRNAs in silkworm (Bombyx mori). Funct Integr Genomics 10:405–415CrossRefPubMedGoogle Scholar
  9. Cai EH, Gao YX, Wei ZZ, Chen WY, Yu P, Li K (2012) Serum miR-21 expression in human esophageal squamous cell carcinomas. Asian Pac J Cancer Prev 13:1563–1567CrossRefPubMedGoogle Scholar
  10. Camarillo C, Swerdel M, Hart RP (2011) Comparison of microarray and quantitative real-time PCR methods for measuring MicroRNA levels in MSC cultures. Methods Mol Biol 698:419–429PubMedCentralCrossRefPubMedGoogle Scholar
  11. Caponi S, Funel N, Frampton AE, Mosca F, Santarpia L, Van der Velde AG, Jiao LR, De Lio N, Falcone A, Kazemier G et al (2012) The good, the bad and the ugly: a tale of miR-101, miR-21 and miR-155 in pancreatic intraductal papillary mucinous neoplasms. Ann Oncol 24:734–741CrossRefPubMedGoogle Scholar
  12. Chapman DI (1975) Antlers-bones of contention. Mamm Rev 5:121–172CrossRefGoogle Scholar
  13. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR et al (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33:e179–e187PubMedCentralCrossRefPubMedGoogle Scholar
  14. Chen X, Li Q, Wang J, Guo X, Jiang X, Ren Z, Weng C, Sun G, Wang X, Liu Y et al (2009) Identification and characterization of novel amphioxus microRNAs by Solexa sequencing. Genome Biol 10:R78–R90PubMedCentralCrossRefPubMedGoogle Scholar
  15. Chen YH, Wang SQ, Wu XL, Shen M, Chen ZG, Chen XG, Liu YX, Zhu XL, Guo F, Duan XZ et al (2011) Characterization of microRNAs expression profiling in one group of Chinese urothelial cell carcinoma identified by Solexa sequencing. Urol Oncol 31:219–227CrossRefPubMedGoogle Scholar
  16. Chen C, Deng B, Qiao M, Zheng R, Chai J, Ding Y, Peng J, Jiang S (2012) Solexa sequencing identification of conserved and novel microRNAs in backfat of Large White and Chinese Meishan pigs. PLoS One 7:e31426–e31435PubMedCentralCrossRefPubMedGoogle Scholar
  17. Danks J, Dacke C, Flik G, Gay C (1999) Calcium metabolism: comparative endocrinology. Bio Scientifica Ltd, Bristol, pp 131–138Google Scholar
  18. de Crombrugghe B, Lefebvre V, Behringer RR, Bi W, Murakami S, Huang W (2000) Transcriptional mechanisms of chondrocyte differentiation. Matrix Biol 19:389–394CrossRefPubMedGoogle Scholar
  19. Dippold RP, Vadigepalli R, Gonye GE, Hoek JB (2012) Chronic ethanol feeding enhances miR-21 induction during liver regeneration while inhibiting proliferation in rats. Am J Physiol Gastrointest Liver Physiol 303:G733–G743PubMedCentralCrossRefPubMedGoogle Scholar
  20. Drayton RM (2012) The role of microRNA in the response to cisplatin treatment. Biochem Soc Trans 40:821–825CrossRefPubMedGoogle Scholar
  21. Faragalla H, Youssef YM, Scorilas A, Khalil B, White NM, Mejia-Guerrero S, Khella H, Jewett MA, Evans A, Lichner Z et al (2012) The clinical utility of miR-21 as a diagnostic and prognostic marker for renal cell carcinoma. J Mol Diagn 14:385–392CrossRefPubMedGoogle Scholar
  22. Faucheux C, Nesbitt SA, Horton MA, Price JS (2001) Cells in regenerating deer antler cartilage provide a microenvironment supports osteoclast differentiation. J Exp Biol 204:443–455PubMedGoogle Scholar
  23. Faucheux C, Horton MA, Price JS (2002) Nuclear localization of type I parathyroid hormone/parathyroid hormone-related protein receptors in deer antler osteoclasts: evidence for parathyroid hormone-related protein and receptor activator of NF-κB-dependent effects on osteoclast formation in regenerating mammalian bone. J Bone Miner Res 17:455–464CrossRefPubMedGoogle Scholar
  24. Faucheux C, Nicholls BM, Allen S, Danks JA, Horton MA, Price JS (2004) Parathyroid hormone-related peptide may play a role in deer antler regeneration. Dev Dyn 231:88–97CrossRefPubMedGoogle Scholar
  25. Friedman RC, Farh KK, Burge CB, Bartel DP (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 19:92–105PubMedCentralCrossRefPubMedGoogle Scholar
  26. Goss RJ (1970) Problems of antlerogenesis. Clin Orthopaed 69:227–238CrossRefGoogle Scholar
  27. Goss RJ (1983) Deer antlers: regeneration, function and evolution. Academic Press, New YorkGoogle Scholar
  28. Gu Z, Eleswarapu S, Jiang H (2007) Identification and characterization of microRNAs from the bovine adipose tissue and mammary gland. FEBS Lett 581:981–988CrossRefPubMedGoogle Scholar
  29. Hannon GJ (2002) RNA interference. Nature 418:244–251CrossRefPubMedGoogle Scholar
  30. Hermansen SK, Dahlrot RH, Nielsen BS, Hansen S, Kristensen BW (2012) MiR-21 expression in the tumor cell compartment holds unfavorable prognostic value in gliomas. J Neurooncol 111:71–81CrossRefPubMedGoogle Scholar
  31. Hu W, Meng X, Lu T, Wu L, Li T, Li M, Tian Y (2013) MicroRNA-1 inhibits the proliferation of Chinese sika deer-derived cartilage cells by binding to the 3′-untranslated region of IGF-1. Mol Med Rep 8:523–528PubMedGoogle Scholar
  32. Hu W, Li T, Wu L, Li M, Meng X (2014) Identification of microRNA-18a as a novel regulator of the insulin-like growth factor-1 in the proliferation and regeneration of deer antler. Biotechnol Lett 36:703–710CrossRefPubMedGoogle Scholar
  33. Huang J, Ju Z, Li Q, Hou Q, Wang C, Li J, Li R, Wang L, Sun T, Hang S et al (2011) Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle. Int J Biol Sci 7:1016–1026PubMedCentralCrossRefPubMedGoogle Scholar
  34. Ji Z, Wang G, Xie Z, Zhang C, Wang J (2012) Identification and characterization of microRNA in the dairy goat (Capra hircus) mammary gland by Solexa deep-sequencing technology. Mol Biol Rep 39:9361–9371CrossRefPubMedGoogle Scholar
  35. Jiang J, Lee EJ, Gusev Y, Schmittgen TD (2005) Real-time expression profiling of microRNA precursors in human cancer cell lines. Nucl Acids Res 33:5394–5403PubMedCentralCrossRefPubMedGoogle Scholar
  36. Kierdorf U, Li C, Price JS (2009) Improbable appendages: deer antler renewal as a unique case of mammalian regeneration. Semin Cell Dev Biol 20:535–542CrossRefPubMedGoogle Scholar
  37. Kobayashi T, Lu J, Cobb BS, Rodda SJ, McMahon AP, Schipani E, Merkenschlager M, Kronenberg HM (2008) Dicer-dependent pathways regulate chondrocyte proliferation and differentiation. Proc Natl Acad Sci USA 105:1949–1954PubMedCentralCrossRefPubMedGoogle Scholar
  38. Lee RC, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75:843–854CrossRefPubMedGoogle Scholar
  39. Legeai F, Rizk G, Walsh T, Edwards O, Gordon K, Lavenier D, Leterme N, Méreau A, Nicolas J, Tagu D et al (2010) Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum. BMC Genom 11:281–289CrossRefGoogle Scholar
  40. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB (2003) Prediction of mammalian microRNA targets. Cell 115:787–798CrossRefPubMedGoogle Scholar
  41. Lewis BP, Burge CB, Bartel DP (2005) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell 120:15–20CrossRefPubMedGoogle Scholar
  42. Li C (2012) Deer antler regeneration: a stem cell-based epimorphic process. Birth Defects Res C Embryo Today 96:51–62CrossRefPubMedGoogle Scholar
  43. Li C, Clark DE, Lord EA, Stanton JA, Suttie JM (2002) Sampling technique to discriminate the different tissue layers of growing antler tips for gene discovery. Anat Rec 268:125–130CrossRefPubMedGoogle Scholar
  44. Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769–773CrossRefPubMedGoogle Scholar
  45. Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA et al (2005) MicroRNA expression profiles classify human cancers. Nature 435:834–838CrossRefPubMedGoogle Scholar
  46. Nakamura Y, Inloes JB, Katagiri T, Kobayashi T (2011) Chondrocyte-specific microRNA-140 regulates endochondral bone development and targets Dnpep to modulate bone morphogenetic protein signaling. Mol Cell Biol 31:3019–3028PubMedCentralCrossRefPubMedGoogle Scholar
  47. Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P et al (2000) Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA. Nature 408:86–89CrossRefPubMedGoogle Scholar
  48. Pillai RS, Bhattacharyya SN, Artus CG, Zoller T, Cougot N, Basyuk E, Bertrand E, Filipowicz W (2005) Inhibition of translational initiation by let-7 microRNA in human cells. Science 309:1573–1576CrossRefPubMedGoogle Scholar
  49. Price JS, Oyajobi BO, Oreffo RO, Russell RG (1994) Cells cultured from the growing tip of red deer antler express alkaline phosphatase and proliferate in response to insulin-like growth factor-I. J Endocrinol 143:R9–R16CrossRefPubMedGoogle Scholar
  50. Price JS, Oyajobi BO, Nalin AM, Frazer A, Russell RG, Sandell LJ (1996) Chondrogenesis in the regenerating antler tip in red deer: expression of collagen types I, IIA, IIB, and X demonstrated by in situ nucleic acid hybridization and immunocytochemistry. Dev Dyn 205:332–347CrossRefPubMedGoogle Scholar
  51. Reinhart BJ, Weinstein EG, Rhoades MW, Bartel B, Bartel DP (2002) MicroRNAs in plants. Genes Dev 16:1616–1626PubMedCentralCrossRefPubMedGoogle Scholar
  52. Sayed D, Abdellatif M (2011) MicroRNAs in development and disease. Physiol Rev 91:827–887CrossRefPubMedGoogle Scholar
  53. Schmittgen TD, Jiang J, Liu Q, Yang L (2004) A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res 32:e43–e52PubMedCentralCrossRefPubMedGoogle Scholar
  54. Sdassi N, Silveri L, Laubier J, Tilly G, Costa J, Layani S, Vilotte JL, Le Provost F (2009) Identification and characterization of new miRNAs cloned from normal mouse mammary gland. BMC Genom 10:149–158CrossRefGoogle Scholar
  55. Sun J, Zhong N, Li Q, Min Z, Zhao W, Sun Q, Tian L, Yu H, Shi Q, Zhang F et al (2011) MicroRNAs of rat articular cartilage at different developmental stages identified by Solexa sequencing. Osteoarthr Cartil 19:1237–1245CrossRefPubMedGoogle Scholar
  56. Szuwart T, Kierdorf H, Kierdorf U, Clemen G (2002) Histochemical and ultrastructural studies of cartilage resorption and acid phosphatase activity during antler growth in fallow deer (Dama dama). Anat Rec 268:66–72CrossRefPubMedGoogle Scholar
  57. Vaz C, Ahmad HM, Sharma P, Gupta R, Kumar L, Kulshreshtha R, Bhattacharya A (2010) Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genom 11:288–305CrossRefGoogle Scholar
  58. Wei Z, Liu X, Feng T, Chang Y (2011) Novel and conserved microRNAs in Dalian purple urchin (Strongylocentrotus nudus) identified by next generation sequencing. Int J Biol Sci 7:180–192PubMedCentralCrossRefPubMedGoogle Scholar
  59. Wheeler BM, Heimberg AM, Moy VN, Sperling EA, Holstein TW, Heber S, Peterson KJ (2009) The deep evolution of metazoan microRNAs. Evol Dev 11:50–68CrossRefPubMedGoogle Scholar
  60. Yekta S, Shih IH, Bartel DP (2004) MicroRNA-directed cleavage of HOXB8 mRNA. Science 304:594–596CrossRefPubMedGoogle Scholar
  61. Zhang BH, Wang QL, Pan XP (2007) MicroRNAs and their regulatory roles in animals and plants. J Cell Physiol 210:279–289CrossRefPubMedGoogle Scholar
  62. Zhao Y, Yao B, Zhang M, Wang S, Zhang H, Xiao W (2013) Comparative analysis of differentially expressed genes in Sika deer antler at different stages. Mol Biol Rep 40:1665–1676CrossRefPubMedGoogle Scholar
  63. Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31:3406–3415PubMedCentralCrossRefPubMedGoogle Scholar

Copyright information

© The Genetics Society of Korea and Springer-Science and Media 2015

Authors and Affiliations

  • Yanxia Chen
    • 1
  • Xuedong Liu
    • 1
  • Xiaoguang Yang
    • 1
  • Yuhui Liu
    • 1
  • Xiaomeng Pi
    • 1
  • Qingzhen Liu
    • 1
  • Dong Zheng
    • 1
  1. 1.Laboratory of Genetics and Molecular BiologyNortheast Forestry UniversityHarbinChina

Personalised recommendations