Widespread transcriptional regulation from within transcribed regions in plants

Animals and plants have evolved separately for over 1.5 billion years and independently invented multicellularity, suggesting a possible divergence in their mode of transcription regulation. Here, we set out to elucidate fundamental features of transcription regulatory sequences in plants. Using a massively parallel reporter assay in four species, we show that sequences downstream of the transcription start site (TSS) play a major role in controlling transcription. Swapping regulatory sequences from one side of the TSS to the other yields different outcomes, unlike animal enhancers which act independently of their position. A GATC-containing DNA motif, positioned downstream of the TSS, was sufficient to enhance gene expression in a dose-dependent manner. Its effect on gene expression was tissue-dependent and conserved across vascular plants. These results identify a unique characteristic of transcriptional regulation in plants, and suggest fundamental differences in gene regulation might exist between plants and animals. ### Competing Interest Statement The authors have declared no competing interest.