Epigenetic regulation of spurious transcription initiation in Arabidopsis

In plants, epigenetic regulation is critical for silencing repetitive sequences and maintaining proper expression of transcription units. However, its functional impacts on genome-wide transcription initiation landscape remains largely elusive. To dissect the role of epigenetic regulation in shaping plant transcription initiation landscape we generated genome-wide maps of transcription start sites (TSSs) at a single-nucleotide resolution in representative mutants of epigenetic modifiers in the model plant Arabidopsis thaliana (A.thaliana) by Cap Analysis of Gene Expression followed by sequencing (CAGE-seq). Our analysis revealed that about one-third of the TSSs identified across all conditions are exclusively activated in the mutant backgrounds, where epigenetic control is compromised. Thousands of these sites have yet been annotated, suggesting that they are likely cryptic TSSs silenced under normal condition by epigenetic mechanisms. Consistently, these TSSs mainly locate at genomic regions highly decorated with heterochromatic modifications and possessing sequence architecture similar to that of regular plant promoters. Maintenance DNA methylation pathway facilitated by METHYLTRANSFERASE 1 (MET1) regulates the largest number of cryptic TSSs, which also largely overlap with targets regulated by other epigenetic pathways. Transposable elements (TEs) from both retro- and DNA transposon families, which function as a reservoir of putative regulatory elements in A.thaliana genome, contribute up to 65% of the cryptic TSSs. Importantly, the activation of cryptic TSSs significantly attenuates regular transcription initiated from nearby TSSs, likely through a poorly characterized mechanism of transcriptional interference. Such attenuation may affect the plant's development and ability to respond to environmental stresses. Our study, therefore, sheds lights on a novel role of epigenetic regulation in maintaining proper gene functions in plants by suppressing spurious transcription from cryptic TSSs.