title: Genome-wide characterization of light-regulated genes in Neurospora crassa.
abstract: The filamentous fungus Neurospora crassa responds to light in complex ways. To thoroughly study the transcriptional response of this organism to light, RNA-seq was used to analyze capped and polyadenylated mRNA prepared from mycelium grown for 24 hr in the dark and then exposed to light for 0 (control) 15, 60, 120, and 240 min. More than three-quarters of all defined protein coding genes (79%) were expressed in these cells. The increased sensitivity of RNA-seq compared with previous microarray studies revealed that the RNA levels for 31% of expressed genes were affected two-fold or more by exposure to light. Additionally, a large class of mRNAs, enriched for transcripts specifying products involved in rRNA metabolism, showed decreased expression in response to light, indicating a heretofore undocumented effect of light on this pathway. Based on measured changes in mRNA levels, light generally increases cellular metabolism and at the same time causes significant oxidative stress to the organism. To deal with this stress, protective photopigments are made, antioxidants are produced, and genes involved in ribosome biogenesis are transiently repressed.
authors: Department of Biology, Texas A&M University, College Station, Texas 77843-3258.
authors: Cheng
authors: C
authors: Wu
authors: Department of Biology, Texas A&M University, College Station, Texas 77843-3258.
authors: Fei
authors: F
authors: Yang
authors: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305.
authors: Kristina M
authors: KM
authors: Smith
authors: Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215.
authors: Matthew
authors: M
authors: Peterson
authors: Department of Biology, Texas A&M University, College Station, Texas 77843-3258.
authors: Rigzin
authors: R
authors: Dekhang
authors: Department of Biology, Texas A&M University, College Station, Texas 77843-3258.
authors: Ying
authors: Y
authors: Zhang
authors: The Eli and Edy L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142.
authors: Jeremy
authors: J
authors: Zucker
authors: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305.
authors: Erin L
authors: EL
authors: Bredeweg
authors: Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755-3844.
authors: Chandrashekara
authors: C
authors: Mallappa
authors: Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755-3844.
authors: Xiaoying
authors: X
authors: Zhou
authors: Bioinformatics Program, Boston University, Boston, Massachusetts 02215.
authors: Anna
authors: A
authors: Lyubetskaya
authors: Department of Ecology and Evolutionary Biology, Yale University, New Haven Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06520.
authors: Jeffrey P
authors: JP
authors: Townsend
authors: Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 The Eli and Edy L. Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142 Bioinformatics Program, Boston University, Boston, Massachusetts 02215 Department of Microbiology, Boston University, Boston, Massachusetts 02215.
authors: James E
authors: JE
authors: Galagan
authors: Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305.
authors: Michael
authors: M
authors: Freitag
authors: Department of Genetics, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire 03755-3844.
authors: Jay C
authors: JC
authors: Dunlap
authors: Department of Biology, Texas A&M University, College Station, Texas 77843-3258.
authors: Deborah
authors: D
authors: Bell-Pedersen
authors: Department of Biology, Texas A&M University, College Station, Texas 77843-3258 msachs@bio.tamu.edu.
authors: Matthew S
authors: MS
authors: Sachs
mesh_terms: D018076:DNA, Complementary / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D015966:Gene Expression Regulation, Fungal / Q000528:radiation effects*; D005800:Genes, Fungal; D016681:Genome, Fungal / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D008027:Light; D009492:Neurospora crassa / Q000235:genetics / Q000528:radiation effects*; D010641:Phenotype; D012331:RNA, Fungal / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D018076:DNA, Complementary; D004271:DNA, Fungal; D012331:RNA, Fungal; D012333:RNA, Messenger
keywords: Neurospora; RNA-seq; light