title: Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential.
abstract: Neurospora crassa has been for decades a principal model for filamentous fungal genetics and physiology as well as for understanding the mechanism of circadian clocks. Eukaryotic fungal and animal clocks comprise transcription-translation-based feedback loops that control rhythmic transcription of a substantial fraction of these transcriptomes, yielding the changes in protein abundance that mediate circadian regulation of physiology and metabolism: Understanding circadian control of gene expression is key to understanding eukaryotic, including fungal, physiology. Indeed, the isolation of clock-controlled genes (ccgs) was pioneered in Neurospora where circadian output begins with binding of the core circadian transcription factor WCC to a subset of ccg promoters, including those of many transcription factors. High temporal resolution (2-h) sampling over 48 h using RNA sequencing (RNA-Seq) identified circadianly expressed genes in Neurospora, revealing that from ∼10% to as much 40% of the transcriptome can be expressed under circadian control. Functional classifications of these genes revealed strong enrichment in pathways involving metabolism, protein synthesis, and stress responses; in broad terms, daytime metabolic potential favors catabolism, energy production, and precursor assembly, whereas night activities favor biosynthesis of cellular components and growth. Discriminative regular expression motif elicitation (DREME) identified key promoter motifs highly correlated with the temporal regulation of ccgs. Correlations between ccg abundance from RNA-Seq, the degree of ccg-promoter activation as reported by ccg-promoter-luciferase fusions, and binding of WCC as measured by ChIP-Seq, are not strong. Therefore, although circadian activation is critical to ccg rhythmicity, posttranscriptional regulation plays a major role in determining rhythmicity at the mRNA level.
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755;
authors.forename: Jennifer M
authors.initials: JM
authors.lastname: Hurley
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755;
authors.forename: Arko
authors.initials: A
authors.lastname: Dasgupta
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755;
authors.forename: Jillian M
authors.initials: JM
authors.lastname: Emerson
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755;
authors.forename: Xiaoying
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755;
authors.forename: Carol S
authors.initials: CS
authors.lastname: Ringelberg
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755;
authors.forename: Nicole
authors.initials: N
authors.lastname: Knabe
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Anna M
authors.initials: AM
authors.lastname: Lipzen
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Erika A
authors.initials: EA
authors.lastname: Lindquist
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Christopher G
authors.initials: CG
authors.lastname: Daum
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Kerrie W
authors.initials: KW
authors.lastname: Barry
authors.affiliation: US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598;
authors.forename: Igor V
authors.initials: IV
authors.lastname: Grigoriev
authors.affiliation: Department of Biochemistry and Biophysics, Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331;
authors.forename: Kristina M
authors.initials: KM
authors.lastname: Smith
authors.affiliation: Departments of Biomedical Engineering and Microbiology, Boston University, Boston, MA 02215;
authors.forename: James E
authors.initials: JE
authors.lastname: Galagan
authors.affiliation: Department of Biology, Texas A&M University, College Station, TX 77843; and.
authors.forename: Deborah
authors.initials: D
authors.lastname: Bell-Pedersen
authors.affiliation: Department of Biochemistry and Biophysics, Center of Genome Research and Biocomputing, Oregon State University, Corvallis, OR 97331;
authors.forename: Michael
authors.initials: M
authors.lastname: Freitag
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755;
authors.forename: Chao
authors.initials: C
authors.lastname: Cheng
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755; Department of Biochemistry, Geisel School of Medicine, Hanover, NH 03755.
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Loros
authors.affiliation: Department of Genetics, Geisel School of Medicine, Hanover, NH 03755; jay.c.dunlap@dartmouth.edu.
authors.forename: Jay C
authors.initials: JC
authors.lastname: Dunlap
mesh_terms: D057906:Circadian Clocks; D004734:Energy Metabolism / Q000235:genetics; D025461:Feedback, Physiological; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D005800:Genes, Fungal / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D009492:Neurospora crassa / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D015398:Signal Transduction / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*
chemical_list: D005656:Fungal Proteins; D012333:RNA, Messenger
keywords: Neurospora; RNA-Seq; circadian; clock-controlled genes; transcription