ZFIN ID: ZDB-PUB-140318-7
The light-induced transcriptome of the zebrafish pineal gland reveals complex regulation of the circadian clockwork by light
Ben-Moshe, Z., Alon, S., Mracek, P., Faigenbloom, L., Tovin, A., Vatine, G.D., Eisenberg, E., Foulkes, N.S., and Gothilf, Y.
Date: 2014
Source: Nucleic acids research   42(6): 3750-67 (Journal)
Registered Authors: Foulkes, Nicholas-Simon, Gothilf, Yoav, Tovin, Adi, Vatine, Gad
Keywords: none
Microarrays: GEO:GSE53288
MeSH Terms:
  • 3' Untranslated Regions
  • Animals
  • Circadian Clocks/genetics*
  • HEK293 Cells
  • Humans
  • Light*
  • Locomotion
  • Metabolic Networks and Pathways/genetics
  • MicroRNAs/biosynthesis
  • MicroRNAs/metabolism
  • Pineal Gland/metabolism
  • RNA, Messenger/metabolism
  • Transcription Factors/metabolism
  • Transcriptional Activation/radiation effects*
  • Transcriptome/radiation effects*
  • Zebrafish/genetics*
  • Zebrafish/growth & development
  • Zebrafish/metabolism
PubMed: 24423866 Full text @ Nucleic Acids Res.

Light constitutes a primary signal whereby endogenous circadian clocks are synchronized (‘entrained’) with the day/night cycle. The molecular mechanisms underlying this vital process are known to require gene activation, yet are incompletely understood. Here, the light-induced transcriptome in the zebrafish central clock organ, the pineal gland, was characterized by messenger RNA (mRNA) sequencing (mRNA-seq) and microarray analyses, resulting in the identification of multiple light-induced mRNAs. Interestingly, a considerable portion of the molecular clock (14 genes) is light-induced in the pineal gland. Four of these genes, encoding the transcription factors dec1, reverbb1, e4bp4-5 and e4bp4-6, differentially affected clock- and light-regulated promoter activation, suggesting that light-input is conveyed to the core clock machinery via diverse mechanisms. Moreover, we show that dec1, as well as the core clock gene per2, is essential for light-entrainment of rhythmic locomotor activity in zebrafish larvae. Additionally, we used microRNA (miRNA) sequencing (miR-seq) and identified pineal-enhanced and light-induced miRNAs. One such miRNA, miR-183, is shown to downregulate e4bp4-6 mRNA through a 32UTR target site, and importantly, to regulate the rhythmic mRNA levels of aanat2, the key enzyme in melatonin synthesis. Together, this genome-wide approach and functional characterization of light-induced factors indicate a multi-level regulation of the circadian clockwork by light.