title: Characterization of hnRNP K protein-RNA interactions.
abstract: The heterogeneous nuclear ribonucleoprotein K protein is an RNA-binding protein found in several subcellular compartments where it is thought to be involved in signaling multiple processes that compose gene expression. K protein contains three K homology (KH) domains that mediate RNA-binding. We used a serial analysis of gene expression (SAGE)-based strategy, yeast three-hybrid screen, RNA pull-down assays and computational analysis to characterize K protein-associated RNAs. We demonstrate that K protein interacts with many sense and antisense nuclear and mitochondrial transcripts through both direct and indirect binding. The highly specific direct binding of transcripts to K protein is mediated by a consensus sequence comprising three C-rich patches. Structural analysis suggests a three-prong interaction model whereby each of the three KH domains binds one of the C-rich patches. Genome-wide and yeast three-hybrid clone analysis revealed that these sequences are located preferentially in the 3' untranslated regions, which are known to regulate mRNA translation and processing.
authors.affiliation: Department of Gastroenterology, Medical Center for Postgraduate Education at Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, 02-781 Warsaw, Poland.
authors.forename: Karolina
authors.initials: K
authors.lastname: Klimek-Tomczak
authors.forename: Lucjan S
authors.initials: LS
authors.lastname: Wyrwicz
authors.forename: Sanjeev
authors.initials: S
authors.lastname: Jain
authors.forename: Karol
authors.initials: K
authors.lastname: Bomsztyk
authors.forename: Jerzy
authors.initials: J
authors.lastname: Ostrowski
mesh_terms: D000818:Animals; D001483:Base Sequence; D045744:Cell Line, Tumor; D034641:Heterogeneous-Nuclear Ribonucleoprotein K / Q000378:metabolism*; D008956:Models, Chemical; D011233:Precipitin Tests; D011485:Protein Binding; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D051381:Rats; D012689:Sequence Homology, Nucleic Acid; D020798:Two-Hybrid System Techniques
chemical_list: D034641:Heterogeneous-Nuclear Ribonucleoprotein K; D012313:RNA