The Light Responsive Transcriptome of the Zebrafish: Function and Regulation

Abstract

Most organisms possess circadian clocks that are able to anticipate the day/night cycle and are reset or “entrained” by the ambient light. In the zebrafish, many organs and even cultured cell lines are directly light responsive, allowing for direct entrainment of the clock by light. Here, we have characterized light induced gene transcription in the zebrafish at several organizational levels. Larvae, heart organ cultures and cell cultures were exposed to 1- or 3-hour light pulses, and changes in gene expression were compared with controls kept in the dark. We identified 117 light regulated genes, with the majority being induced and some repressed by light. Cluster analysis groups the genes into five major classes that show regulation at all levels of organization or in different subset combinations. The regulated genes cover a variety of functions, and the analysis of gene ontology categories reveals an enrichment of genes involved in circadian rhythms, stress response and DNA repair, consistent with the exposure to visible wavelengths of light priming cells for UV-induced damage repair. Promoter analysis of the induced genes shows an enrichment of various short sequence motifs, including E- and D-box enhancers that have previously been implicated in light regulation of the zebrafish period2 gene. Heterologous reporter constructs with sequences matching these motifs reveal light regulation of D-box elements in both cells and larvae. Morpholino-mediated knock-down studies of two homologues of the D-box binding factor Tef indicate that these are differentially involved in the cell autonomous light induction in a gene-specific manner. These findings suggest that the mechanisms involved in period2 regulation might represent a more general pathway leading to light induced gene expression.

Circadian rhythms in Mexican blind cavefish Astyanax mexicanus in the lab and in the field

“…We isolated two DNA repair genes from populations of Astyanax mexicanus: CPD photolyase (CPD phr), involved in photoreactivation, and damage-specific DNA binding protein 2 (ddb2), part of the nucleotide excision repair pathway. Consistent with previous studies in zebrafish 25,26 , CPD phr is strongly induced after a 3-hour light pulse in surface fish (Fig. 5a).…”

“…We next examined the expression of thyrotroph embryonic factor 1 (tef1), which lies upstream of per2 and is itself a lightinducible gene in zebrafish 25,26 . TEF1 is a transcriptional activator and belongs to the family of bZIP PAR domain containing DNA binding proteins, which recognize D-box regulatory sequences (TTAYGTAA or TTATACAA).…”

“…Per1 amplitude was estimated by averaging peak to trough ratios in LD, and was 20. 23,25,26 . Without this light-dependent induction, animals appear to have reduced tolerance to environmental stress and increased mortality 23,40 .…”

“…Light has a profound impact on gene expression and physiology in fish 25,26 . Consequently, one would predict that isolation in a cave would influence a wide range of biological processes.…”

“…Independent circadian clocks are found in virtually all zebrafish tissues, and these tissues are themselves directly light responsive 18,19 . Light signals have a strong impact, not only on resetting of the zebrafish circadian clock [20][21][22] , but also on numerous aspects of zebrafish cell biology, such as the activation of DNA repair processes [23][24][25][26] and the regulation of cell cycle events [27][28][29][30] . Evolving in a completely dark environment is therefore likely to impact fish physiology in a dramatic manner.…”