Screening for possible miRNA-mRNA associations in a colon cancer cell line

详细信息    查看全文

• 作者：Sotaro Kanematsu ; Kousuke Tanimoto ; Yutaka Suzuki ; Sumio Sugano
• 关键词：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 bet
• 刊名：Gene
• 出版年：10 January, 2014
• 年：2014
• 卷：533
• 期：2
• 页码：520-531
• 全文大小：770 K

文摘

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.