Nucleosome positioning dynamics during the cold-induced silencing of the Arabidopsis FLC gene using targeted MNase-seq

Micrococcal nuclease (MNase) has been extensively used to map nucleosomes genome wide. Here, we used a targeted MNase-seq approach to map nucleosomes at high resolution at the FLC locus during the cold-induced silencing. This strategy uncovered that the +1 nucleosome at FLC is repositioned closer to the promoter in response to cold. The nucleosome repositioning alters the chromatin structure locally at the 5' end of FLC and is linked to the silencing of the gene. Moreover, this is in part modulated by VRN1, a non-sequence-specific DNA binding protein that associates with FLC promoter and is required for its silencing. Overall design: Arabidopsis Col-0 with an active FRIGIDA allele (WT FRI), and vrn1-4 FRI seedlings were grown at ambient temperature and subject to 1 week of cold. Seedlings before and after cold were used for MNase-seq.