DNase I hypersensitivity mapping, genomic footprinting, and transcription factor networks in plants

Understanding gene regulatory networks in plants requires knowledge of cis-regulatory DNA, trans-acting factors, and their dynamics across development and in response to stimuli. Active cis-regulatory elements are hypersensitive to cleavage by the endonuclease DNase I. Motifs within DNase I hypersensitive sites indicate potential trans-acting factor occupancy and, when combined with DNase I cleavage data, can be used to construct provisional regulatory networks. Several recent studies have applied genome-wide DNase I hypersensitivity mapping to Arabidopsis thaliana and rice, generating chromatin accessibility landscapes for an array of tissues, cell types, and treatments. Here, we discuss these studies, with an emphasis on building regulatory networks and possible directions for improvements.