Computational approaches for microRNA studies: a review

• Published in: Mammalian genome Vol. 21; no. 1-2; pp. 1 - 12
• Main Authors: Li, Li, Xu, Jianzhen, Yang, Deyin, Tan, Xiaorong, Wang, Hongfei
• Format: Journal Article
• Language: English
• Published: New York New York : Springer-Verlag 01.02.2010; Springer-Verlag; Springer Nature B.V
• Subjects: 3' Untranslated Regions - physiology; Animal Genetics and Genomics; Animals; Artificial Intelligence; Binding Sites; Biomedical and Life Sciences; Cell Biology; Computational Biology - methods; Gene Regulatory Networks - physiology; Genome - physiology; Human Genetics; Humans; Life Sciences; MicroRNAs - chemistry; MicroRNAs - genetics; MicroRNAs - physiology; Transcription Factors - genetics; Transcription Factors - physiology; miRNA Gene; Viral miRNAs; Target Prediction; miRNA Binding Site; miRNA Target
• ISSN: 0938-8990; 1432-1777
• DOI: 10.1007/s00335-009-9241-2

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.