In plants, epigenetic regulation is critical for silencing transposons and maintaining proper gene expression. However, its impact on the genome-wide transcription initiation landscape remains elusive. By conducting a genome-wide analysis of transcription start sites (TSSs) using cap analysis of gene expression (CAGE) sequencing, we show that thousands of TSSs are exclusively activated in various epigenetic mutants of Arabidopsis thaliana and referred to as cryptic TSSs. Many have not been identified in previous studies, of which up to 65% are contributed by transposons. They possess similar genetic features to regular TSSs and their activation is strongly associated with the ectopic recruitment of RNAPII machinery. The activation of cryptic TSSs significantly alters transcription of nearby TSSs, including those of genes important for development and stress responses. Our study, therefore, sheds light on the role of epigenetic regulation in maintaining proper gene functions in plants by suppressing transcription from cryptic TSSs.

在植物中，表观遗传调控对于沉默转座子和维持适当的基因表达至关重要。但是，它对全基因组转录起始环境的影响仍然难以捉摸。通过使用基因表达（CAGE）测序的上限分析进行转录起始位点（TSS）的全基因组分析，我们显示成千上万的TSS在拟南芥的各种表观遗传突变体中被独家激活并称为隐式TSS。在以前的研究中尚未发现很多，其中转座子的贡献高达65％。它们具有与常规TSS相似的遗传特征，其激活与RNAPII机制的异位募集密切相关。隐性TSS的激活会显着改变附近TSS的转录，包括对发育和应激反应重要的基因的转录。因此，我们的研究揭示了表观遗传调控通过抑制隐性TSS的转录来维持植物适当基因功能的作用。