Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora

White collar‐1 (WC‐1) and white collar‐2 (WC‐2) are essential for light‐mediated responses in Neurospora crassa, but the molecular mechanisms underlying gene induction and the roles of other real and putative photoreceptors remain poorly characterized. Unsupervised hierarchical clustering of genome‐...

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Bibliographic Details
Published in:The EMBO journal 2009-04, Vol.28 (8), p.1029-1042
Main Authors: Chen, Chen-Hui, Ringelberg, Carol S, Gross, Robert H, Dunlap, Jay C, Loros, Jennifer J
Format: Article
Language:English
Subjects:
Base Sequence
Biological Clocks - physiology
Circadian rhythm
Circadian Rhythm - physiology
Cluster Analysis
DNA-Binding Proteins - genetics
DNA-Binding Proteins - metabolism
Fungal Proteins - genetics
Fungal Proteins - metabolism
Fungi
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Fungal
Genome, Fungal
Genomics
Light
microarray
Molecular biology
Molecular Sequence Data
Neurospora
Neurospora crassa - genetics
Neurospora crassa - metabolism
Oligonucleotide Array Sequence Analysis
photoreceptors
Promoter Regions, Genetic
Signal Transduction - physiology
Transcription Factors - genetics
Transcription Factors - metabolism
Transcription, Genetic
wc-1
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Summary:White collar‐1 (WC‐1) and white collar‐2 (WC‐2) are essential for light‐mediated responses in Neurospora crassa, but the molecular mechanisms underlying gene induction and the roles of other real and putative photoreceptors remain poorly characterized. Unsupervised hierarchical clustering of genome‐wide microarrays reveals 5.6% of detectable transcripts, including several novel mediators, that are either early or late light responsive. Evidence is shown for photoreception in the absence of the dominant, and here confirmed, white collar complex (WCC) that regulates both types of light responses. VVD primarily modulates late responses, whereas light‐responsive submerged protoperithecia‐1 (SUB‐1), a GATA family transcription factor, is essential for most late light gene expression. After a 15‐min light stimulus, the WCC directly binds the sub‐1 promoter. Bioinformatics analysis detects many early light response elements (ELREs), as well as identifying a late light response element (LLRE) required for wild‐type activity of late light response promoters. The data provide a global picture of transcriptional response to light, as well as illuminating the cis‐ and trans‐acting elements comprising the regulatory signalling cascade that governs the photobiological response.
ISSN:0261-4189
1460-2075
DOI:10.1038/emboj.2009.54