title: Two-tiered approach identifies a network of cancer and liver disease-related genes regulated by miR-122.
abstract: MicroRNAs function as important regulators of gene expression and are commonly linked to development, differentiation, and diseases such as cancer. To better understand their roles in various biological processes, identification of genes targeted by microRNAs is necessary. Although prediction tools have significantly helped with this task, experimental approaches are ultimately required for extensive target search and validation. We employed two independent yet complementary high throughput approaches to map a large set of mRNAs regulated by miR-122, a liver-specific microRNA implicated in regulation of fatty acid and cholesterol metabolism, hepatitis C infection, and hepatocellular carcinoma. The combination of luciferase reporter-based screening and shotgun proteomics resulted in the identification of 260 proteins significantly down-regulated in response to miR-122 in at least one method, 113 of which contain predicted miR-122 target sites. These proteins are enriched for functions associated with the cell cycle, differentiation, proliferation, and apoptosis. Among these miR-122-sensitive proteins, we identified a large group with strong connections to liver metabolism, diseases, and hepatocellular carcinoma. Additional analyses, including examination of consensus binding motifs for both miR-122 and target sequences, provide further insight into miR-122 function.
authors.affiliation: Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA. dboutz@mail.utexas.edu
authors.forename: Daniel R
authors.initials: DR
authors.lastname: Boutz
authors.forename: Patrick J
authors.initials: PJ
authors.lastname: Collins
authors.forename: Uthra
authors.initials: U
authors.lastname: Suresh
authors.forename: Mingzhu
authors.initials: M
authors.lastname: Lu
authors.forename: Cristina M
authors.initials: CM
authors.lastname: Ramírez
authors.forename: Carlos
authors.initials: C
authors.lastname: Fernández-Hernando
authors.forename: Yufei
authors.initials: Y
authors.lastname: Huang
authors.forename: Raquel de Sousa
authors.initials: Rde S
authors.lastname: Abreu
authors.forename: Shu-Yun
authors.initials: SY
authors.lastname: Le
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Shapiro
authors.forename: Angela M
authors.initials: AM
authors.lastname: Liu
authors.forename: John M
authors.initials: JM
authors.lastname: Luk
authors.forename: Shelley Force
authors.initials: SF
authors.lastname: Aldred
authors.forename: Nathan D
authors.initials: ND
authors.lastname: Trinklein
authors.forename: Edward M
authors.initials: EM
authors.lastname: Marcotte
authors.forename: Luiz O F
authors.initials: LO
authors.lastname: Penalva
mesh_terms: D006528:Carcinoma, Hepatocellular / Q000235:genetics / Q000378:metabolism*; D002460:Cell Line; D052138:Genes, Neoplasm; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics / Q000378:metabolism*; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D009363:Neoplasm Proteins / Q000096:biosynthesis* / Q000235:genetics; D012334:RNA, Neoplasm / Q000235:genetics / Q000378:metabolism*
chemical_list: C531907:MIRN122 microRNA, human; D035683:MicroRNAs; D009363:Neoplasm Proteins; D012334:RNA, Neoplasm