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

ABSTRACT: 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.

SUBMITTER: Chen CH

PROVIDER: S-EPMC2683703 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature

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

Chen Chen-Hui CH Ringelberg Carol S CS Gross Robert H RH Dunlap Jay C JC Loros Jennifer J JJ

The EMBO journal 20090305 8

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 d ...[more]

PMID: 19262566

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Project description:To better understand the roles of WC-1, WC-2 and other putative photoreceptors in mediation of light signals and to identify new components in light sensing cascades, we used microarrays with genome-wide coverage to characterize light-inducible transcriptional changes in Neurospora crassa. After unsupervised hierarchical clustering of 90 microarrays, 316 genes, representing about 3.21% of the total genome, showed robust and consistent light responses. As expected, WC-1 and WC-2 knockout strains both exhibited severe impairments in response to a continuous white light stimulus, confirming their dominant roles in light sensing cascades. Knockout strains of 5 newly-identified light-inducible transcription factors were further characterized for their potential function in mediating light signals. Interestingly, one early light-inducible transcription factor, Submerged Protoperithecia-1 (SUB-1), appeared to be essential in mediating a large number of late light response, providing a direct molecular connection between early and late light responses. Furthermore, a novel motif, which is overrepresented among late light responsive genes, was demonstrated to be necessary for full induction of late light responses in vivo. Taken together, these results reveal a simple hierarchical light-sensing cascade in Neurospora, which is initially invoked by light-activated White Collar Complex (WCC) binding to Light Response Elements (LREs) of the primary target genes, including SUB-1. Subsequently, the induction of SUB-1 and other activators activate downstream targets. Thus, light responses of well-defined timing and amplitude can be orchestrated to meet the differential needs of underlying biological processes. Keywords: time course, light response Two-color microarray, totally 135 arrays were used to characterize light response in different photoreceptor knockout strains. Alexa Fluor 555 was consistently used to label cDNA synthesized from reference RNA, which is a mixture containing equal amounts of RNA samples harvested from different circadian time points and light treatment durations. The same batch of pooled RNA was used as a reference for each array experiment. Alexa Fluor 647 was used exclusively to label cDNA representing sample RNA.

Dataset Information

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

Publications

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

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