Regulation of target gene expression by chromatin-associated protein-coding transcripts in plants

Protein-coding transcripts are regarded as intermediates that mediate DNA-to-protein information flow, leaving their noncoding regulatory potential largely underappreciated. Genome-wide profiling of RNA–chromatin interactions in Arabidopsis has uncovered widespread associations between protein-coding transcripts and distinct genomic loci, implying that they possess regulatory functions. Here, we found that BT2 and GSL8 transcripts modulate target gene transcription independently of their protein products through distinct mechanisms. The BT2 transcript represses transcription of its targets CEP2 and MRF4 by forming RNA–DNA triplexes, thereby restricting root growth and promoting flowering, whereas GSL8 acts through a triplex-independent pathway. Our findings unveil intrinsic regulatory activities of protein-coding transcripts, challenging the canonical definition of mRNA function and blurring the functional distinction between coding and noncoding RNAs in the context of genome evolution.