RT Journal Article
SR Electronic
T1 Genome-wide transcription factor binding in leaves from C<sub>3</sub> and C<sub>4</sub> grasses
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 165787
DO 10.1101/165787
A1 Steven J. Burgess
A1 Ivan Reyna-Llorens
A1 Sean R. Stevenson
A1 Pallavi Singh
A1 Katja Jaeger
A1 Julian M. Hibberd
YR 2019
UL http://biorxiv.org/content/early/2019/06/05/165787.abstract
AB The majority of plants use C3 photosynthesis, but over sixty independent lineages of angiosperms have evolved the C4 pathway. In most C4 species, photosynthesis gene expression is compartmented between mesophyll and bundle sheath cells. We performed DNaseI-SEQ to identify genome-wide profiles of transcription factor binding in leaves of the C4 grasses Zea mays, Sorghum bicolor and Setaria italica as well as C3 Brachypodium distachyon. In C4 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 impact 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 C4 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 C4 photosynthesis gene expression in particular and characteristics of transcription factor binding in cereal crops in general.One sentence summary Genome-wide patterns of transcription factor binding in vivo defined by DNaseI for leaves of C3 and C4 grasses