title: Transcriptional interference by antisense RNA is required for circadian clock function.
abstract: Eukaryotic circadian oscillators consist of negative feedback loops that generate endogenous rhythmicities. Natural antisense RNAs are found in a wide range of eukaryotic organisms. Nevertheless, the physiological importance and mode of action of most antisense RNAs are not clear. frequency (frq) encodes a component of the Neurospora core circadian negative feedback loop, which was thought to generate sustained rhythmicity. Transcription of qrf, the long non-coding frq antisense RNA, is induced by light, and its level oscillates in antiphase to frq sense RNA. Here we show that qrf transcription is regulated by both light-dependent and light-independent mechanisms. Light-dependent qrf transcription represses frq expression and regulates clock resetting. Light-independent qrf expression, on the other hand, is required for circadian rhythmicity. frq transcription also inhibits qrf expression and drives the antiphasic rhythm of qrf transcripts. The mutual inhibition of frq and qrf transcription thus forms a double negative feedback loop that is interlocked with the core feedback loop. Genetic and mathematical modelling analyses indicate that such an arrangement is required for robust and sustained circadian rhythmicity. Moreover, our results suggest that antisense transcription inhibits sense expression by mediating chromatin modifications and premature termination of transcription. Taken together, our results establish antisense transcription as an essential feature in a circadian system and shed light on the importance and mechanism of antisense action.
authors.affiliation: Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Xue
authors.affiliation: Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.
authors.forename: Qiaohong
authors.initials: Q
authors.lastname: Ye
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.
authors.forename: Simon R
authors.initials: SR
authors.lastname: Anson
authors.affiliation: Department of Clinical Sciences, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.
authors.forename: Jichen
authors.initials: J
authors.lastname: Yang
authors.affiliation: Department of Clinical Sciences, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.
authors.forename: Guanghua
authors.initials: G
authors.lastname: Xiao
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
authors.forename: David
authors.initials: D
authors.lastname: Kowbel
authors.affiliation: Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA.
authors.forename: N Louise
authors.initials: NL
authors.lastname: Glass
authors.affiliation: Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.
authors.forename: Susan K
authors.initials: SK
authors.lastname: Crosthwaite
authors.affiliation: Department of Physiology, The University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.
authors.forename: Yi
authors.initials: Y
authors.lastname: Liu
mesh_terms: D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D057906:Circadian Clocks / Q000235:genetics* / Q000502:physiology; D002940:Circadian Rhythm / Q000235:genetics / Q000502:physiology / Q000528:radiation effects; D025461:Feedback, Physiological; D015966:Gene Expression Regulation, Fungal / Q000235:genetics / Q000528:radiation effects; D020868:Gene Silencing; D005800:Genes, Fungal / Q000235:genetics; D008027:Light; D009492:Neurospora crassa / Q000235:genetics* / Q000502:physiology / Q000528:radiation effects; D012319:RNA Polymerase II / Q000378:metabolism; D016372:RNA, Antisense / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics; D061806:Transcription Termination, Genetic / Q000528:radiation effects; D014158:Transcription, Genetic / Q000235:genetics* / Q000528:radiation effects
chemical_list: D002843:Chromatin; D016372:RNA, Antisense; D022661:RNA, Untranslated; D012319:RNA Polymerase II