Screening for possible miRNA–mRNA associations in a colon cancer cell line |
| |
Authors: | Sotaro Kanematsu Kousuke Tanimoto Yutaka Suzuki Sumio Sugano |
| |
Institution: | 1. Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan;2. Genome Laboratory, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan |
| |
Abstract: | MicroRNAs (miRNAs) are small non-coding RNAs mediating the regulation of gene expression in various biological contexts, including carcinogenesis. Here, we screened putative associations between 34, 45, and 103 miRNAs and 164, 391, and 81 mRNAs via Argonaute1 (Ago1) or Ago2 immunoprecipitation (IP) experiments in a colon cancer cell line. We used a combination of RIP Seq analysis. RNAs that were co-immunoprecipitated with Ago1 or Ago2 were used for massively parallel small RNA and mRNA sequencing. The detected miRNAs and mRNAs were further associated with one another based on in silico target predictions. Analysis of the putative associations indicated that, although Ago1 and Ago2 shared a similar repertory of miRNAs, the mRNAs possibly regulated by those miRNAs seemed different. The mRNAs detected with Ago1 IP were indicated to be frequently associated with genes having constitutive cellular functions, regulated by a smaller number of miRNAs, and appeared to receive more stringent translational regulation. In contrast, putative miRNA-mRNA associations detected with Ago2 IP appeared to be related to signal transduction genes, which had a larger number of possible miRNA binding sites. We then conducted a similar analysis using the colon cancer cells cultured under hypoxia and identified potential hypoxia-induced miRNA-mRNA associations, which included several well-characterized cancer-related genes as novel putative miRNA targets. |
| |
Keywords: | Ago Argonaute BCL2 B-cell CLL/lymphoma 2 BIM BCL2-interacting mediator of cell death miRNPs miRNA-silencing effector protein complexes VEGF vascular endothelial growth factor HIF1A hypoxia inducible factor 1 alpha subunit HMGA2 high mobility group AT-hook 2 RPLP2 ribosomal protein large P2 HIC2 hypermethylated in cancer 2 TSC tuberous sclerosis mTOR mechanistic target of rapamycin CAMKK2 calcium/calmodulin-dependent protein kinase kinase 2 DACT1 dapper antagonist of beta-catenin homolog 1 ATRX alpha thalassemia/mental retardation syndrome X-linked |
本文献已被 ScienceDirect 等数据库收录! |
|