A database that identify CDS-located and 5'UTR-located miRNA binding sites and systematically evaluate miRNA regulatory effects on mRNA stability and translation by integrating multiple high-throughput experimental datasets such as Ago CLIP-seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH), mRNA profiles, ribosome-protected fragment sequencing (RPF) and pulsed stable isotope labeling with amino acids in culture (pSILAC). MtiBase used 61 Ago CLIP-seq datasets to reduce the rates of false positive target prediction. To assess miRNA regulatory effects on mRNA stability, 222 mRNA profiles in response to miRNA overexpression, knockdown, or knockout were integrated. Moreover, 28 RPF and six pSILAC were applied to assess the effects of miRNAs on translational efficiency and protein synthesis, respectively. The SNP influence to the regulatory effects of CDS-located and 5'UTR-located miRNA binding sites was also systematically investigated.
Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, Sun Yat-Sen University, Guangzhou, China; Key Laboratory of Liver Disease of Guangdong Province, The Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA; Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangzhou, China
MtiBase funding source(s)
This work was supported by project grants from the National Basic Research Program of China (2011CB811305); the National Natural Science Foundation of China (81230073, 31370791, 91440110, 91442205); project of Science and Technology New Star in ZhuJiang Guangzhou city (2012J2200025).