PT - JOURNAL ARTICLE AU - Steven J. Burgess AU - Ivan Reyna-Llorens AU - Katja Jaeger AU - Julian M. Hibberd TI - A transcription factor binding atlas for photosynthesis in cereals identifies a key role for coding sequence in the regulation of gene expression AID - 10.1101/165787 DP - 2017 Jan 01 TA - bioRxiv PG - 165787 4099 - http://biorxiv.org/content/early/2017/07/24/165787.short 4100 - http://biorxiv.org/content/early/2017/07/24/165787.full AB - The gene regulatory architecture associated with photosynthesis is poorly understood. Most plants use the ancestral C3 pathway, but our most productive cereal crops use C4 photosynthesis. In these C4 cereals, large-scale alterations to gene expression allow photosynthesis to be partitioned between cell types of the leaf. Here we provide a genome-wide transcription factor binding atlas for grasses that operate either C3 or C4 photosynthesis. Most of the >950,000 sites bound by transcription factors are preferentially located in genic sequence rather than promoter regions, and specific families of transcription factors preferentially bind coding sequence. Cell specific patterning of gene expression in C4 leaves is associated with combinatorial modifications to transcription factor binding despite broadly similar patterns of DNA accessibility between cell types. A small number of DNA motifs bound by transcription factors are conserved across 60 million years of grass evolution, and C4 evolution has repeatedly co-opted at least one of these hyper-conserved cis-elements. The grass cistrome is highly divergent from that of the model plant Arabidopsis thaliana.