PUBLICATION
Long non-coding RNAs have age-dependent diurnal expression that coincides with age-related changes in genome-wide facultative heterochromatin
- Authors
- Park, J., Belden, W.J.
- ID
- ZDB-PUB-190212-10
- Date
- 2018
- Source
- BMC Genomics 19: 777 (Journal)
- Registered Authors
- Keywords
- Aging, Circadian rhythm, Diurnal, Heterochromatin, Histone H3 lysine 9 methylation, Long non-coding RNA
- Datasets
- GEO:GSE109854, GEO:GSE109855, GEO:GSE109856
- MeSH Terms
-
- Aging/genetics*
- Animals
- Chromatin Immunoprecipitation
- Gene Expression Profiling
- Genome*
- Genome-Wide Association Study*
- Heterochromatin/genetics*
- Heterochromatin/metabolism
- High-Throughput Nucleotide Sequencing
- RNA, Long Noncoding/genetics*
- Zebrafish
- PubMed
- 30373515 Full text @ BMC Genomics
Citation
Park, J., Belden, W.J. (2018) Long non-coding RNAs have age-dependent diurnal expression that coincides with age-related changes in genome-wide facultative heterochromatin. BMC Genomics. 19:777.
Abstract
Background Disrupted diurnal rhythms cause accelerated aging and an increased incidence in age-related disease and morbidity. The circadian clock governs cell physiology and metabolism by controlling transcription and chromatin. The goal of this study is to further understand the mechanism of age-related changes to circadian chromatin with a focus on facultative heterochromatin and diurnal non-coding RNAs.
Results We performed a combined RNA-seq and ChIP-seq at two diurnal time-points for three different age groups to examine the connection between age-related changes to circadian transcription and heterochromatin in neuronal tissue. Our analysis focused on uncovering the relationships between long non-coding RNA (lncRNA) and age-related changes to histone H3 lysine 9 tri-methylation (H3K9me3), in part because the Period (Per) complex can direct facultative heterochromatin and models of aging suggest age-related changes to heterochromatin and DNA methylation. Our results reveal that lncRNAs and circadian output change dramatically with age, but the core clock genes remain rhythmic. Age-related changes in clock-controlled gene (ccg) expression indicate there are age-dependent circadian output that change from anabolic to catabolic processes during aging. In addition, there are diurnal and age-related changes in H3K9me3 that coincide with changes in transcription.
Conclusions The data suggest a model where some age-related changes in diurnal expression are partially attributed to age-related alterations to rhythmic facultative heterochromatin. The changes in heterochromatin are potentially mediated by changes in diurnal lncRNA creating an interlocked circadian-chromatin regulatory network that undergoes age-dependent metamorphosis.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping