MicroRNA target prediction: theory and practice

• Published in: Molecular genetics and genomics : MGG 2014-12, Vol.289 (6), p.1085-1101
• Main Authors: Wagner, Mathias, Vicinus, Benjamin, Frick, Vilma Oliveira, Auchtor, Michael, Rubie, Claudia, Jeanmonod, Pascal, Richards, Tereza A, Linder, Roland, Weichert, Frank
• Format: Article
• Language: English
• Subjects: 3' Untranslated Regions; adenocarcinoma; Adult; Aged; Aged, 80 and over; Algorithms; Animal Genetics and Genomics; Binding Sites; Biochemistry; Bioinformatics; Biomedical and Life Sciences; Cancer; Chemokine CCL20 - genetics; Colorectal Neoplasms - genetics; Colorectal Neoplasms - mortality; Computers; enzyme-linked immunosorbent assay; Female; Gene expression; genes; Genomics; Human Genetics; Humans; Life Sciences; luciferase; Male; Medical libraries; messenger RNA; Microbial Genetics and Genomics; microRNA; MicroRNAs; MicroRNAs - chemistry; MicroRNAs - metabolism; Middle Aged; Original Paper; Plant Genetics and Genomics; prediction; Regulatory Sequences, Ribonucleic Acid; reverse transcriptase polymerase chain reaction; RNA Folding; RNA, Messenger - chemistry; RNA, Messenger - metabolism; Software; tissue analysis
• ISSN: 1617-4615; 1617-4623
• DOI: 10.1007/s00438-014-0871-z

The present study is one of the few that includes tissue samples in the evaluation of target prediction algorithms designed to detect microRNA (miRNA) sequences that might interact with particular messenger RNA (mRNA) sequences. Twelve different target prediction tools were used to find miRNA sequences that might interact with CCL20 gene expression. Different algorithms predicted controversial miRNA sequences for CCL20 regulation due to a different weighting of parameters. Hsa-miR-21 and hsa-miR-145 suggested by four or more programs were chosen for further investigation. Possible real interaction of these miRNA sequences with CCL20 gene expression was monitored using luciferase assays and expression analyses of tissue samples of colorectal adenocarcinoma by either qRT-PCR or ELISA. Folding status of seed-binding sites in complete mRNA and 3′UTR of CCL20 was predicted. Prediction of miRNA expression was attempted based on CCL20 expression data. Eight of the target prediction tools forecasted a role for hsa-miR-21 and four mentioned hsa-miR-145 in CCL20 gene regulation. Laboratory experimentation showed that CCL20 may serve as a target of hsa-miR-21 but not hsa-miR-145. Expression of the molecules resulted in no clear assertion. Folding of seed-binding sites was predicted to be relatively constant for the complete mRNA and 3′UTR. Predicting miRNA expression based on target gene expression was impossible. This might be attributable to the fact that effects of miRNA activity may oscillate between gene product repression and activation. Additional systematic studies are needed to address this issue.