TY - JOUR T1 - miR-106b-responsive gene landscape identifies regulation of Kruppel-like factor family JF - bioRxiv DO - 10.1101/088229 SP - 088229 AU - Cody J. Wehrkamp AU - Sathish Kumar Natarajan AU - Ashley M. Mohr AU - Mary Anne Phillippi AU - Justin L. Mott Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/11/17/088229.abstract N2 - MicroRNA dysregulation is a common feature of cancer and due to the promiscuity of microRNA binding this can result in a wide array of genes whose expression is altered. miR-106b is an oncomiR overexpressed in cholangiocarcinoma and its upregulation in this and other cancers often leads to repression of anti-tumorigenic targets. The goal of this study was to identify the miR-106b-regulated gene landscape in cholangiocarcinoma cells using a genome-wide, unbiased mRNA analysis. Through RNA-Seq we found 112 mRNAs significantly repressed by miR-106b. The majority of these genes contain the specific miR-106b seed-binding site. We have validated 11 genes from this set at the mRNA level and demonstrated regulation by miR-106b of five proteins. Combined analysis of our miR-106b-regulated mRNA data set plus published reports indicate that miR-106b binding is anchored by G:C pairing in and near the seed. Novel targets Kruppel-like factor 2 (KLF2) and KLF6 were verified both at the mRNA and at the protein level. Further investigation showed regulation of four other KLF family members by miR-106b. We have discovered coordinated repression of several members of the KLF family by miR-106b that may play a role in cholangiocarcinoma tumor biology.List of abbreviationsMTT3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromideDAPI4’,6-diamidine-2’-phenylindole dihydrochlorideCLASHCrosslinking, ligation, and sequencing of hybridsDR5Death receptor-5DMEMDulbecco’s Modified Eagle’s MediumFDRFalse discovery rateFBSFetal bovine serumKLFKruppel-like factorLNALocked-nucleic acidqRT-PCRQuantitative reverse-transcription PCRSDS-PAGESodium dodecylsulfate-polyacrylamide gel electrophoresisUTRUntranslated region ER -