title: CHD1 remodels chromatin and influences transient DNA methylation at the clock gene frequency.
abstract: Circadian-regulated gene expression is predominantly controlled by a transcriptional negative feedback loop, and it is evident that chromatin modifications and chromatin remodeling are integral to this process in eukaryotes. We previously determined that multiple ATP-dependent chromatin-remodeling enzymes function at frequency (frq). In this report, we demonstrate that the Neurospora homologue of chd1 is required for normal remodeling of chromatin at frq and is required for normal frq expression and sustained rhythmicity. Surprisingly, our studies of CHD1 also revealed that DNA sequences within the frq promoter are methylated, and deletion of chd1 results in expansion of this methylated domain. DNA methylation of the frq locus is altered in strains bearing mutations in a variety of circadian clock genes, including frq, frh, wc-1, and the gene encoding the frq antisense transcript (qrf). Furthermore, frq methylation depends on the DNA methyltransferase, DIM-2. Phenotypic characterization of Δdim-2 strains revealed an approximate WT period length and a phase advance of approximately 2 hours, indicating that methylation plays only an ancillary role in clock-regulated gene expression. This suggests that DNA methylation, like the antisense transcript, is necessary to establish proper clock phasing but does not control overt rhythmicity. These data demonstrate that the epigenetic state of clock genes is dependent on normal regulation of clock components.
authors.affiliation: Department of Genetics, Dartmouth Medical School, Hanover, New Hampshire, United States of America.
authors.forename: William J
authors.initials: WJ
authors.lastname: Belden
authors.forename: Zachary A
authors.initials: ZA
authors.lastname: Lewis
authors.forename: Eric U
authors.initials: EU
authors.lastname: Selker
authors.forename: Jennifer J
authors.initials: JJ
authors.lastname: Loros
authors.forename: Jay C
authors.initials: JC
authors.lastname: Dunlap
mesh_terms: D001683:Biological Clocks / Q000235:genetics; D015152:Blotting, Northern; D015139:Blotting, Southern; D015153:Blotting, Western; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D042002:Chromatin Assembly and Disassembly; D047369:Chromatin Immunoprecipitation; D002940:Circadian Rhythm; D004265:DNA Helicases / Q000235:genetics* / Q000378:metabolism; D019175:DNA Methylation; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D015257:DNA-Cytosine Methylases / Q000235:genetics / Q000378:metabolism; D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D009154:Mutation; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; C087405:FRQ protein, Neurospora crassa; D005656:Fungal Proteins; D016372:RNA, Antisense; D014157:Transcription Factors; C105589:wc-1 protein, Neurospora crassa; C103772:white collar 2 protein, Neurospora; D015257:DNA-Cytosine Methylases; D004265:DNA Helicases