Genome-wide analysis of light-inducible responses reveals hierarchical light signalling in Neurospora
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TLDR
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.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.read more
Citations
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The circadian clock of Neurospora crassa.
TL;DR: This review will introduce the basics of circadian rhythms, the model filamentous fungus N. crassa, and provide an overview of the molecular components and regulation of the circadian clock.
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Transcription Factors in Light and Circadian Clock Signaling Networks Revealed by Genomewide Mapping of Direct Targets for Neurospora White Collar Complex
Kristina M. Smith,Gencer Sancar,Rigzin Dekhang,Christopher M. Sullivan,Shaojie Li,Andrew G. Tag,Cigdem Sancar,Erin L. Bredeweg,Henry D. Priest,Ryan F. McCormick,Terry L. Thomas,James C. Carrington,Jason E. Stajich,Deborah Bell-Pedersen,Michael Brunner,Michael Freitag +15 more
TL;DR: ChIP sequencing is used to uncover direct targets of the Neurospora crassa circadian regulator White Collar Complex, and shows that WCC directly controls the expression of 24 transcription factor genes, including the clock-controlled adv-1 gene, which controls a circadian output pathway required for daily rhythms in development.
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References
More filters
Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Journal ArticleDOI
Significance analysis of microarrays applied to the ionizing radiation response
TL;DR: A method that assigns a score to each gene on the basis of change in gene expression relative to the standard deviation of repeated measurements is described, suggesting that this repair pathway for UV-damaged DNA might play a previously unrecognized role in repairing DNA damaged by ionizing radiation.
Journal ArticleDOI
The genome sequence of the filamentous fungus Neurospora crassa
James E. Galagan,Sarah E. Calvo,Katherine A. Borkovich,Eric U. Selker,Nick O. Read,David B. Jaffe,William Fitzhugh,Li-Jun Ma,Serge Smirnov,Seth Purcell,Bushra Rehman,Timothy Elkins,Reinhard Engels,Shunguang Wang,Cydney B. Nielsen,Jonathan Butler,Matthew G. Endrizzi,Dayong Qui,Peter Ianakiev,Deborah Bell-Pedersen,Mary Anne Nelson,Margaret Werner-Washburne,Claude P. Selitrennikoff,John A. Kinsey,Edward L. Braun,Alex Zelter,Alex Zelter,Ulrich Schulte,Gregory O. Kothe,Gregory Jedd,Werner Mewes,Chuck Staben,Edward M. Marcotte,David Greenberg,Alice Roy,Karen Foley,Jerome Naylor,Nicole Stange-Thomann,Robert Barrett,Sante Gnerre,Michael Kamal,Manolis Kamvysselis,Evan Mauceli,Cord Bielke,Stephen Rudd,Dmitrij Frishman,Svetlana Krystofova,Carolyn G. Rasmussen,Robert L. Metzenberg,David D. Perkins,Scott Kroken,Carlo Cogoni,Giuseppe Macino,David E. A. Catcheside,Weixi Li,Robert J. Pratt,Stephen A. Osmani,Colin P.C. DeSouza,Louise Glass,Marc J. Orbach,J. Andrew Berglund,Rodger B. Voelker,Oded Yarden,Michael Plamann,Stephan Seiler,Jay C. Dunlap,Alan Radford,Rodolfo Aramayo,Donald O. Natvig,Lisa A. Alex,Gertrud Mannhaupt,Daniel J. Ebbole,Michael Freitag,Ian T. Paulsen,Matthew S. Sachs,Eric S. Lander,Chad Nusbaum,Bruce W. Birren +77 more
TL;DR: A high-quality draft sequence of the N. crassa genome is reported, suggesting that RIP has had a profound impact on genome evolution, greatly slowing the creation of new genes through genomic duplication and resulting in a genome with an unusually low proportion of closely related genes.
Journal ArticleDOI
Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock
Stacey L. Harmer,John B. Hogenesch,Marty Straume,Hur-Song Chang,Bin Han,Tong Zhu,Xun Wang,Joel A. Kreps,Steve A. Kay,Steve A. Kay +9 more
TL;DR: This study presents a comprehensive view of the temporal compartmentalization of physiological pathways by the circadian clock in a eukaryote.
Journal ArticleDOI
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes
Andreas Ruepp,Alfred Zollner,Dieter Maier,Kaj Albermann,Jean Hani,Martin Mokrejs,Igor V. Tetko,Ulrich Güldener,Gertrud Mannhaupt,Martin Münsterkötter,H. Werner Mewes +10 more
TL;DR: The Functional Catalogue (FunCat), a hierarchically structured, organism-independent, flexible and scalable controlled classification system enabling the functional description of proteins from any organism, is presented.