microRNA Discovery by RNA-Seq

MicroRNAs (miRNAs) are key regulators of gene expression and contribute to a variety of biological processes including cell growth, differentiation, and development. Abnormal microRNA expression has been reported in various diseases including various cancers, cardiovascular disease, and neurological disorders. Therefore microRNAs are considered to be promising diagnostic and therapeutic candidates for the treatment of human disease.

The miRBase sequence database, is the public repository for all known microRNAs. Newly discovered microRNAs are routinely added and it has grown rapidly with approximately >10,000 entries to date. Despite this rapid growth, many miRNAs have not yet been validated, and many believe there are numerous microRNAs yet to be identified. A lack of a full complement of miRNAs has imposed limitations on recognizing their important roles in development and disease.

Now researchers are using the latest in deep sequencing technology along with advanced bioinformatics packages to identify novel microRNAs in various tissue types and species.

  • Ryu S, Joshi N, McDonnell K, Woo J, Choi H, et al. (2011) Discovery of Novel Human Breast Cancer MicroRNAs from Deep Sequencing Data by Analysis of Pri-MicroRNA Secondary Structures. PLoS ONE 6(2), e16403. [article]
  • Xie SS, Li XY, Liu T, Cao JH, Zhong Q, Zhao SH. (2011) Discovery of Porcine microRNAs in Multiple Tissues by a Solexa Deep Sequencing Approach. PLoS One 6(1), e16235. [article]
  • Creighton CJ, Benham AL, Zhu H, Khan MF, Reid JG, Nagaraja AK, Fountain MD, Dziadek O, Han D, Ma L, Kim J, Hawkins SM, Anderson ML, Matzuk MM, Gunaratne PH. (2010) Discovery of novel microRNAs in female reproductive tract using next generation sequencing. PLoS One 5(3), e9637. [article]
  • Huang QX, Cheng XY, Mao ZC, Wang YS, Zhao LL, Yan X, Ferris VR, Xu RM, Xie BY. (2010) MicroRNA discovery and analysis of pinewood nematode (Bursaphelenchus xylophilus) by deep sequencing. PLoS One 5(10), e13271. [article]
  • Song C, Wang C, Zhang C, Korir NK, Yu H, Ma Z, Fang J. (2010) Deep sequencing discovery of novel and conserved microRNAs in trifoliate orange (Citrus trifoliata). BMC Genomics 11, 431. [article]
  • Zhao CZ, Xia H, Frazier TP, Yao YY, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ. (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10, 3. [article]