title: A Tool Set for the Genome-Wide Analysis of Neurospora crassa by RT-PCR.
abstract: Neurospora crassa is an important model organism for filamentous fungi as well as for circadian biology and photobiology. Although the community-accumulated tool set for the molecular analysis of Neurospora is extensive, two components are missing: (1) dependable reference genes whose level of expression are relatively constant across light/dark cycles and as a function of time of day and (2) a catalog of primers specifically designed for real-time PCR (RT-PCR). To address the first of these we have identified genes that are optimal for use as reference genes in RT-PCR across a wide range of expression levels; the mRNA/transcripts from these genes have potential for use as reference noncycling transcripts outside of Neurospora. In addition, we have generated a genome-wide set of RT-PCR primers, thereby streamlining the analysis of gene expression. In validation studies these primers successfully identified target mRNAs arising from 70% (34 of 49) of all tested genes and from all (28) of the moderately to highly expressed tested genes.
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, New Hampshire 03755.
authors.forename: Jennifer H
authors.initials: JH
authors.lastname: Hurley
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, New Hampshire 03755.
authors.forename: Arko
authors.initials: A
authors.lastname: Dasgupta
authors.affiliation: Institute for Biomedical Informatics, Perelman School of Medicine, Philadelphia, Pennsylvania 19104.
authors.forename: Peter
authors.initials: P
authors.lastname: Andrews
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, New Hampshire 03755.
authors.forename: Alexander M
authors.initials: AM
authors.lastname: Crowell
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, New Hampshire 03755.
authors.forename: Carol
authors.initials: C
authors.lastname: Ringelberg
authors.affiliation: Department of Biochemistry, Geisel School of Medicine, Hanover, New Hampshire 03755.
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Loros
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, New Hampshire 03755 jay.c.dunlap@dartmouth.edu.
authors.forename: Jay C
authors.initials: JC
authors.lastname: Dunlap
mesh_terms: D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal; D016681:Genome, Fungal; D055106:Genome-Wide Association Study / Q000379:methods; D023281:Genomics / Q000379:methods*; D008027:Light; D009492:Neurospora crassa / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods
keywords: Neurospora crassa; circadian; light induction; quinic acid induction; reference genes