Summary of the conserved and novel characteristics of PEs. This diagram summarizes the identification and characterization of the identified intragenic putative plant enhancers (PEs) carrying epigenomic signatures of canonical mammalian enhancers. Distinct from putative plant enhancers reported previously, almost all PEs are intragenic and associated with the 3′ ends of protein-coding genes. The TESs located upstream of the midpoint on both DNA strands in a pattern that resembles strand-specific RNA expression profile. The data collectively suggest that a high number of genes end their transcription in the vicinity of PE midpoints. In accord, PAS-like motifs are clustered in this region. PEs can physically form intrachromosomal chromatin loops with other regions (eILs), majority of which are protein-coding genes. Additionally, more than half of PEs can interact with protein-coding genes via their 5′ or 3′ UTRs. The sizes of the intrachromosomal chromatin loops ranged from a few kb to 27 Mb.
