Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana

In this work, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in Arabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development-related transcription factors, resulting in either inhibition of transcription or a bivalent status of the genes. Lastly, FLC-like and VIN3-like genes were identified that appear to be novel components of the vernalization pathway. ChIP-seq of H3K27me3, H3K4me3, H3K36me3, each from 3 vernalization time points and 2 replicates; RNA-seq from 7 vernalization time points and 2 replicates