Decipher Plant Gene Regulatory Networks Using Single Plant Cell Types

Gene expression is under the control of transcription factors and various epigenomic modifications of the chromatin such as the methylation patterns of the genomic DNA (gDNA) and various chemical changes of histone proteins. Small RNAs are another important regulator of plant chromatin structure and gene expression [1,2]. The integration of different epigenomic marks (i.e. gDNA methylome, histone modifications) with nucleosome occupancy, pool of small RNA, cis-elements recognized by transcription factors and transcriptome profiling is essential to fully understand how the epigenome and transcription factors controls chromatin structure and gene expression. In plants, histone post-translational modifications and gDNA methylation are reliable marks of euchromatin (transcriptionally active genes) or heterochromatin (transcriptionally inactive genes; for review, [3]). For instance, in Arabidopsis thaliana, 5-methyl cytosine (5mC) is present predominantly over repetitive DNA sequences (e.g. silent transposable elements) but is also detected in the body of expressed genes [1,3-11]. H3K4me3 and H3K27me3 are mainly associated with actively expressed and repressed/ lowly expressed genes, respectively, and not with intergenic or heterochromatic sequences [7,12,13].