title: HEXIM1-binding elements on mRNAs identified through transcriptomic SELEX and computational screening.
abstract: The positive transcription elongation factor b (P-TEFb) is one of the main regulatory factors of the transcription mediated by RNA polymerase II (RNAPII). P-TEFb promotes transcriptional elongation by phosphorylating its targets, which include the C-terminal domain of RNAPII. The activity of P-TEFb is negatively regulated by an RNA-binding protein HEXIM1 in association with 7SK snRNA. To search for other cellular RNAs that bind to HEXIM1, we used systematic evolution of ligands by exponential enrichment (SELEX) with the HeLa cDNA library as the initial pool source. We identified cad mRNA as a HEXIM1-binding RNA and confirmed their association in HeLa cells. In vitro mutational analysis showed that cad mRNA binds to HEXIM1 through its bulged stem structure located in exon 11. In addition, a computational search revealed other RNAs with similar stem structures, including brd4 and tcf3 mRNAs, both of which were shown to be coimmunoprecipitable with anti-HEXIM1 antibody in HeLa cells. Our findings suggest a possible role for HEXIM1 in the regulation of specific gene expressions.
authors.affiliation: Department of Basic Medical Sciences, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Fujimoto
authors.forename: Yoshikazu
authors.initials: Y
authors.lastname: Nakamura
authors.forename: Shoji
authors.initials: S
authors.lastname: Ohuchi
mesh_terms: D020816:Amino Acid Motifs; D001221:Aspartate Carbamoyltransferase / Q000235:genetics; D001483:Base Sequence; D051792:Basic Helix-Loop-Helix Proteins / Q000235:genetics; D002223:Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing) / Q000235:genetics; D018797:Cell Cycle Proteins; D019295:Computational Biology / Q000379:methods*; D004080:Dihydroorotase / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D006367:HeLa Cells; D006801:Humans; D009687:Nuclear Proteins / Q000235:genetics; D042925:Positive Transcriptional Elongation Factor B / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012342:RNA, Small Nuclear / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D052156:SELEX Aptamer Technique / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics; D000092468:Bromodomain Containing Proteins
chemical_list: D001221:Aspartate Carbamoyltransferase; D051792:Basic Helix-Loop-Helix Proteins; D002223:Carbamoyl-Phosphate Synthase (Glutamine-Hydrolyzing); D018797:Cell Cycle Proteins; D004080:Dihydroorotase; D009687:Nuclear Proteins; D042925:Positive Transcriptional Elongation Factor B; D012333:RNA, Messenger; D012342:RNA, Small Nuclear; D016601:RNA-Binding Proteins; D014157:Transcription Factors; C441289:BRD4 protein, human; D000092468:Bromodomain Containing Proteins; C033626:CAD trifunctional enzyme; C476123:HEXIM1 protein, human; C407909:TCF3 protein, human