Sunrise, Sunset. The tempo of a day can quickly pass us by while filling our brain with all epigenetics has to offer. But whether our brains are aware of it or not, with each sunrise and sunset comes a rhythmic genome-wide DNA methylation profile.
To gain insight into exactly what makes our brain’s rhythmically tick, the lab of Janine LaSalle at the University of California, Davis, utilized a Snord116 deletion mouse model of Prader-Willi syndrome (PWS). PWS and Angelman syndrome (AS) are reciprocal imprinting disorders that arise from aberrations of the SNRPN-UBE3A locus, with AS caused by a loss of maternal UBE3A and PWS by a loss of the paternal SNORD116 cluster. Notably, these two disorders produce distinct neurodevelopmental profiles characterized by sleep and metabolic problems.
Here’s what the group found in the brain’s cortex when they compared adult male Snord116+/− mice to matched wild-type controls across six different time points on the clock:
- Whole-genome bisulfite sequencing (WGBS) of wild type cortex revealed cycling of >4,000 differentially methylated regions (DMRs), which are comprised of >23,000 CpGs!
- However, PWS mice display a loss or a shift in rhythmicity at the majority of these DMRs
- Rhythmic DMRs belong to genes with functions related to body-weight and metabolism, where disruption of these traits represent hallmarks of PWS and AS
- The genes identified display a strong overlap with differentially methylated genes in the brains of PWS patients as well as another study of circadian rhythm in humans
- Integration with previous RNA-seq data revealed a time-lagged relationship between the cycling of DNA methylation and transcription
- Both WGBS and RNA-seq revealed cross-talk with the only other locus containing imprinted clusters snoRNAs (Dlk1-Dio3), which results in reciprocal disorders known as Temple and Kagami-Ogata syndromes (TS and KOS)
- DNA fluorescence in situ hybridization (FISH) demonstrated that Snord116 modifies the unique allele-specific chromatin decondensation occurring at these imprinted loci
Clocking In With the Time Keepers
First author Rochelle Coulson shares, “DNA methylation is dynamic. Far more so than has historically been appreciated. We found a unique set of CpGs that are rhythmically methylated across diurnal time in wildtype mouse cortex, and this pattern is disrupted by the loss of Snord116, a long noncoding RNA from the PWS locus. These rhythmic CpGs are not randomly scattered throughout the genome, but are clustered into specific regions important for gene regulation, and we were surprised at how well conserved these sites were between mouse and human. They also linked the PWS locus to another imprinted locus, strengthening the imprinted gene network we’ve started to see come up again and again. Sleep difficulties are a common feature of neurological disorders, and Prader-Willi syndrome is no exception. The co-regulatory networks between sleep, metabolism and imprinted loci suggest that understanding the disrupted epigenetic rhythms in PWS may hold promise for the future application of chronotherapy in the treatment of a wide variety of neurodevelopmental, neuropsychiatric, metabolic, sleep, and imprinted disorders.”
Senior author Janine LaSalle concludes, “We were pleasantly surprised by several findings in this study. First, that there were significant rhythmic methylation dynamics in the cortex. Less than 1% of possible CpGs were rhythmic, so it’s not as though the whole methylome is getting erased and re-established while we sleep, but still enough to be important and relevant. Second, that loss of a single imprinted noncoding RNA locus was required for the proper rhythmicity of 97% of these methylation sites. Third, that there was a strong overlap in both of these effects between mouse and human. Fourth, that the identified genes highlighted functions in circadian entrainment and body weight, relevant to PWS. The whole study was a remarkable demonstration of a time by genotype interaction in brain. I now like to think that “time is the new sex” as important biological variables to consider in neuroscience and genetics.”
Clock in to the brains epigenome over at Nature Communications, April 2018