Genomic interactome of circadian genes in mouse tissues

Mammals exhibit daily recurring biological changes imposed by circadian rhythms ranging from
physiological level to a molecular level. This molecular output from environmental cues is
controlled in each cell by a set of core clock genes involved in a transcriptional-translational
feedback loop mechanism. One such temporal rhythm is the robust oscillation in expression of
tissue specific genes.

Recently, chromatin conformation capture (3C) techniques allow the study of three-dimensional
(3D) genome architecture which along with functional assays have determined a crucial role of the
3D genomic topology in transcriptional regulation from a global level of compartments to a more
local level of chromatin loops. Despite the vast information now available, it remains unclear how
dynamic changes in topology can alter specific gene expression.

Therefore, our model provides a unique system in which there are recursive changes in mRNA
levels approximately every 24 hours whithout changes in cell identity. In our study we examine the
interactome of mouse liver during a circadian cycle to determine the dynamics of chromatin
contacts in relation to changing levels of .We wish to understand whether differences in rhythmic
mRNA abundance between time points correlate with changes in the genomic interactome of
circadian genes and to a greater extent if these chromatin contacts differ between tissues.

Moreover, this study will allow us to identify gene-specific chromatin contacts, specifically with
potential regulatory elements that can be further explored in functional studies.