Project description:Composed of negative feedback loops, circadian oscillations are thought to be noise-resistant. Yet, individual cells in culture are remarkably heterogenous, oscillating independently and with different period lengths. To assess whether differential methylation contributes to heritable heterogeneity of circadian periods, we used reduced representation bisulfite sequencing (RRBS) to explore DNA methylation profiles and their correlation with the transcriptome in the 10 clonal cell lines. To investigate the mechanisms underlying this heterogeneity, we generated and characterized hundreds of clonal cell lines from the same parent culture. By comparing clonal lines with different circadian periods, we identified a group of differentially methylated regions (DMRs).
Project description:Composed of negative feedback loops, circadian oscillations are thought to be noise-resistant. Yet, individual cells in culture are remarkably heterogenous, oscillating independently and with different period lengths. To investigate the mechanisms underlying this heterogeneity, we generated and characterized hundreds of clonal cell lines from the same parent culture as well as subclones from clonal lines. By comparing clonal lines with different circadian periods, we identified a pool of candidate genes that determine periodicity.
Project description:As a time-keeping system, circadian clock times numerous key processes to the appropriate time of day. The proper phasing of the plant circadian clock, which is mainly determined by circadian period, can provide the growth fitness for plants by facilitating the endogenous rhythms to match the external day–night cycle. Here we provide the comprehensive evidences that genomic 5-methylcytosine is critical for regulating circadian period. We found that chemical inhibition of DNA methyltransferases could significantly lengthen circadian period in the seedlings of Arabidopsis. Dysfunction of methyltransferases met1-3 and drm1 drm2 cmt3 cmt2 for both hypo-CG and hypo-non-CG texts can dramatically lengthen circadian period. To find the target genes of 5mC for modulating the circadian period, we conducted RNAseq experiments of Aza vs Mock at ZT1 h or ZT13 h time window and ddcc vs Col-0 at LL 24 h or LL36 time window. Each sample has two biological replicates.
Project description:Our objective was to identify candidate genes that contribute to the long 31-hour circadian period previously observed in DGRP_892. We performed transcriptional profiling of whole fly heads from two genotypes: DGRP_892, and Canton-S B, a line with a normal 24-hour circadian period. We collected fly heads every two hours over a 24-hour period. We quantified differential expression among genotype, time, and sex.
Project description:The period-2 (prd-2) mutant of Neurospora crassa is characterized by recessive inheritance of a 26-hour long period phenotype of the circadian clock. PRD-2 encodes a putative RNA-binding protein. To identify PRD-2 target genes and its role in the clock, we performed transcript profiling in delta prd-2 compared to control samples using RNA-Sequencing. Hundreds of genes are affected by loss of prd-2, including decreased levels of Casein Kinase I (ck-1a, NCU00685). The circadian period length in Neurospora is exquisitely sensitive to ck-1a levels, and we attribute the long period length defect in the prd-2 mutant to low levels of ck-1a transcript, decreased ck-1a transcript stability, and lower levels of CKI protein. Thus, Casein Kinase I gene expression is subject to complex regulation in the circadian clock.
Project description:Circadian clocks coordinate time-of-day specific metabolic and physiological processes to maximize performance and fitness. In addition to light, which is considered the strongest time cue to entrain animal circadian clocks, metabolic input has emerged as an important signal for clock modulation and entrainment, especially in peripheral clocks. Circadian clock proteins have been to be substrates of O-GlcNAcylation, a nutrient sensitive post-translational modification (PTM), and the interplay between clock protein O-GlcNAcylation and other PTMs, like phosphorylation, is expected to facilitate the regulation of circadian physiology by metabolic signals. Here, we used mass spectrometry proteomics to identify PTMs on PERIOD, the key biochemical timer of the Drosophila clock, over the circadian cycle.