Subgenome-specific usage of transposable element-derived promoters and enhancers in bread wheat development

Transcription start site (TSS) is the hub integrating regulatory input from promoters and enhancers. Common wheat converged three subgenomes adapted to different environment and established as a major crop worldwide. Detection of more precise and new TSS of both genes and enhancers in common wheat is the basis in interpreting transcriptional regulatory networks as well as the subgenome divergent regulation in their entirety. Overall design: In the present study, we profiled the genome wide TSS by CAGE-seq together with DNA methylation and histone modifications from four typical tissues in common wheat, the resulting catalogue of enhancers enabled more precise detection of ubiquitous and tissue specific TSS usage of coding genes and enhancers.