Transcriptional interference by antisense RNA is required for circadian clock function

Abstract

Eukaryotic circadian oscillators consist of negative feedback loops that generate endogenous rhythmicities1. Natural antisense RNAs are found in a wide range of eukaryotic organisms2-5. Nevertheless, the physiological importance and mode of action of most antisense RNAs is not clear6-9. frequency (frq) encodes a component of the Neurospora core circadian negative feedback loop which was thought to generate sustained rhythmicity10. Transcription of qrf, the long non-coding frq antisense RNA, is light induced, and its level oscillates in antiphase to frq sense RNA3. Here we show that qrf transcription is regulated by both light-dependent and -independent mechanisms. Light-dependent qrf transcription represses frq expression and regulates clock resetting. qrf expression in the dark, on the other hand, is required for circadian rhythmicity. frq transcription also inhibits qrf expression and surprisingly, 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 modeling 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 transcription termination. Together, our results established antisense transcription as an essential feature in a circadian system and shed light on the importance and mechanism of antisense action.

The frequency natural antisense transcript first promotes, then represses, frequency gene expression via facultative heterochromatin

“…In other words, colliding RNA polymerases (PolII) from the sense/antisense pair generate premature termination and abortive transcripts because they run into each other (46). This model, although attractive, seems to contradict normal light-induced frq and qrf expression and does not account for what we observe in heterochromatin as a mechanism, even though some of their prior work indicates DNA methylation at convergent transcripts.…”

Suppression of WHITE COLLAR-independent frequency Transcription by Histone H3 Lysine 36 Methyltransferase SET-2 Is Necessary for Clock Function in Neurospora

“…One major function of the Set-2 pathway in yeast is to suppress cryptic transcription originated from transcribed ORF. However, cryptic transcripts from frq locus were not found in the set-2 KO mutants (21). Instead, SET-2 is required to regulate the transcription of the full-length frq gene, which is supposed to be transcribed from its normal promoter (based on the length of frq mRNA in wild-type and set-2 KO mutant strains).…”

Le nouveau paradigme de l’origine développementale de la santé et des maladies (DOHaD)

“…Ils sont dynamiques au cours de la vie [42] et des rythmes circadiens [23]. De fait, l'élément central de l'horloge circadienne, le facteur de transcription CLOCK (clock circadian regulator), possède également une activité acétyltransférase d'histone et plusieurs modificateurs de la chromatine sont recrutés de manière circadienne au niveau des promoteurs des gènes contrôlés par l'horloge ; des ARN antisens jouent également un rôle important dans cette régulation [43,62]. Il est maintenant également admis que des processus épigénétiques sous-tendent les états fonctionnels des neurones qui peuvent rester stables pendant plusieurs années.…”