title: A coregulatory network of NR2F1 and microRNA-140.
abstract: BACKGROUND
  Both nuclear receptor subfamily 2 group F member 1 (NR2F1) and microRNAs (miRNAs) have been shown to play critical roles in the developing and functional inner ear. Based on previous studies suggesting interplay between NR2F1 and miRNAs, we investigated the coregulation between NR2F1 and miRNAs to better understand the regulatory mechanisms of inner ear development and functional maturation.
  
  
  RESULTS
  Using a bioinformatic approach, we identified 11 potential miRNAs that might coregulate target genes with NR2F1 and analyzed their targets and potential roles in physiology and disease. We selected 6 miRNAs to analyze using quantitative real-time (qRT) -PCR and found that miR-140 is significantly down-regulated by 4.5-fold (P=0.004) in the inner ear of NR2F1 knockout (Nr2f1(-/-)) mice compared to wild-type littermates but is unchanged in the brain. Based on this, we performed chromatin-immunoprecipitation followed by qRT-PCR and confirmed that NR2F1 directly binds and regulates both miR-140 and Klf9 in vivo. Furthermore, we performed luciferase reporter assay and showed that miR-140 mimic directly regulates KLF9-3'UTR, thereby establishing and validating an example coregulatory network involving NR2F1, miR-140, and Klf9.
  
  
  CONCLUSIONS
  We have described and experimentally validated a novel tissue-dependent coregulatory network for NR2F1, miR-140, and Klf9 in the inner ear and we propose the existence of many such coregulatory networks important for both inner ear development and function.
authors.affiliation: Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America ; Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: David Y
authors.initials: DY
authors.lastname: Chiang
authors.affiliation: Bobby R. Alford Department of Otolaryngology- Head and Neck Surgery, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: David W
authors.initials: DW
authors.lastname: Cuthbertson
authors.affiliation: Huffington Center on Aging and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Fernanda R
authors.initials: FR
authors.lastname: Ruiz
authors.affiliation: Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Na
authors.initials: N
authors.lastname: Li
authors.affiliation: Bobby R. Alford Department of Otolaryngology- Head and Neck Surgery, Baylor College of Medicine, Houston, Texas, United States of America ; Huffington Center on Aging and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America.
authors.forename: Fred A
authors.initials: FA
authors.lastname: Pereira
mesh_terms: D020413:3' Untranslated Regions / Q000502:physiology; D000818:Animals; D051838:COUP Transcription Factor I / Q000235:genetics / Q000378:metabolism*; D015536:Down-Regulation / Q000502:physiology; D007758:Ear, Inner / Q000166:cytology / Q000378:metabolism*; D053263:Gene Regulatory Networks / Q000502:physiology*; D006801:Humans; D051741:Kruppel-Like Transcription Factors / Q000096:biosynthesis / Q000235:genetics; D051379:Mice; D018345:Mice, Knockout; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*
chemical_list: D020413:3' Untranslated Regions; D051838:COUP Transcription Factor I; C489675:Klf9 protein, mouse; D051741:Kruppel-Like Transcription Factors; C547828:MIRN140 microRNA, mouse; D035683:MicroRNAs; C497590:Nr2f1 protein, mouse