Diurnal control of H3K27me1 deposition shapes expression of a subset of cell cycle and DNA damage response genes [ChIP-seq]

Rhythmic oscillation of biological processes helps organisms to adapt their physiological responses to the most appropriate time of the day. Chromatin remodeling has been described as one of the molecular mechanisms controlling these oscillations. The importance of these changes in transcriptional activation, as well as in the maintenance of heterochromatic regions has been widely demonstrated. However, little is still known on how diurnal changes can impact the global status of chromatin modifications and, hence, control gene expression. In plants, the repressive mark H3K27me1, deposited by ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5 and 6 (ATXR5 and 6) methyltransferases, is largely associated with transposable elements but it also covers lowly expressed genes. Here we show that this histone modification is preferentially deposited during the night. In euchromatic regions it is found along the bodies of DNA damage response genes (DDR), where it is needed for their proper expression. The absence of H3K27me1 translates in an enhanced expression of DDR genes that follows a rhythmic oscillation pattern. This evidences a link between chromatin modifications and their synchronization with the diurnal cycle in order to accurately modulate the activation of biological processes to the most appropriate time of the day. Overall design: We profiled H3K27me1 and H3 marks by chromatin-immunoprecipitation DNA-sequencing (ChIP-seq) and analyzed the H3K27me1 data normalized to total H3 in wild type (WT) and atxr5/6 double mutant plants at two time points, ZT4 (midday) and ZT16 (midnight). Seedlings were gown under short days (8h light - 16h dark) conditions and harvested 14 days after sowing. Two biological replicates were performed and 1 gr of seedlings was used as starting material.