Epigenetic inheritance of circadian period in clonal cells

Yan Li, Yongli Shan, Gokhul Kilaru, Stefano Berto, Guang Zhong Wang, Kimberly H. Cox, Seung Hee Yoo, Shuzhang Yang, Genevieve Konopka, Joseph S. Takahashi

Research output: Contribution to journalArticlepeer-review

11 Scopus citations


Circadian oscillations are generated via transcriptional-translational negative feedback loops. However, individual cells from fibroblast cell lines have heterogeneous rhythms, oscillating independently and with different period lengths. Here we showed that heterogeneity in circadian period is heritable and used a multi-omics approach to investigate underlying mechanisms. By examining large-scale phenotype-associated gene expression profiles in hundreds of mouse clonal cell lines, we identified and validated multiple novel candidate genes involved in circadian period determination in the absence of significant genomic variants. We also discovered differentially co-expressed gene networks that were functionally associated with period length. We further demonstrated that global differential DNA methylation bidirectionally regulated these same gene networks. Interestingly, we found that depletion of DNMT1 and DNMT3A had opposite effects on circadian period, suggesting non-redundant roles in circadian gene regulation. Together, our findings identify novel gene candidates involved in periodicity, and reveal DNA methylation as an important regulator of circadian periodicity.

Original languageEnglish (US)
Article numbere54186
Pages (from-to)1-36
Number of pages36
StatePublished - May 2020

ASJC Scopus subject areas

  • General Neuroscience
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology


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