Computational approaches for microRNA studies: a review
- 2.6k Downloads
MicroRNAs (miRNAs) are one class of tiny, endogenous RNAs that can regulate messenger RNA (mRNA) expression by targeting homologous sequences in mRNAs. Their aberrant expressions have been observed in many cancers and several miRNAs have been convincingly shown to play important roles in carcinogenesis. Since the discovery of this small regulator, computational methods have been indispensable tools in miRNA gene finding and functional studies. In this review we first briefly outline the biological findings of miRNA genes, such as genomic feature, biogenesis, gene structure, and functional mechanism. We then discuss in detail the three main aspects of miRNA computational studies: miRNA gene finding, miRNA target prediction, and regulation of miRNA genes. Finally, we provide perspectives on some emerging issues, including combinatorial regulation by miRNAs and functional binding sites beyond the 3′-untranslated region (3′UTR) of target mRNAs. Available online resources for miRNA computational studies are also provided.
KeywordsmiRNA Target miRNA Gene Target Prediction miRNA Binding Site Viral miRNAs
miRNA-induced silencing complexes
Support vector machine
Hidden Markov model
High-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation
- Pol II or Pol III
RNA polymerase II or III
Transcription start site
We apologize for the failure to cite many of the important and relevant papers in this field due to space limitations. We thank Dr. Baowei Peng and Ms. Jian Fan for critical reading of the manuscript. This work was partially supported by the National Natural Science Foundation of China (Grant No. 60601010), the Science Foundation of the education department of Henan province (Grant No. 2006210002), and the Award for Outstanding Young Teacher of Tongji University (No.TJYQ08014).
- Olson AJ, Brennecke J, Aravin AA, Hannon GJ, Sachidanandam R (2008) Analysis of large-scale sequencing of small RNAs. Pac Symp Biocomput 126-136Google Scholar