Genome-Wide Transcription Factor Binding in Leaves from C(3) and C(4) Grasses

The majority of plants use C(3) photosynthesis, but over 60 independent lineages of angiosperms have evolved the C(4) pathway. In most C(4) species, photosynthesis gene expression is compartmented between mesophyll and bundle-sheath cells. We performed DNaseI sequencing to identify genome-wide profiles of transcription factor binding in leaves of the C(4) grasses Zea mays, Sorghum bicolor, and Setaria italica as well as C(3) Brachypodium distachyon. In C(4) species, while bundle-sheath strands and whole leaves shared similarity in the broad regions of DNA accessible to transcription factors, the short sequences bound varied. Transcription factor binding was prevalent in gene bodies as well as promoters, and many of these sites could represent duons that influence gene regulation in addition to amino acid sequence. Although globally there was little correlation between any individual DNaseI footprint and cell-specific gene expression, within individual species transcription factor binding to the same motifs in multiple genes provided evidence for shared mechanisms governing C(4) photosynthesis gene expression. Furthermore, interspecific comparisons identified a small number of highly conserved transcription factor binding sites associated with leaves from species that diverged around 60 million years ago. These data therefore provide insight into the architecture associated with C(4) photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.