Plant Epigenetics Unit, Okinawa Institute of Science and Technology (OIST), 1919-1 Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
Wageningen University & Research, Droevendaalsesteeg 4, 6708 PB Wageningen, Netherlands.
Nat Commun. 2020 Jun 26;11(1):3224. doi: 10.1038/s41467-020-16951-w.
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。然而，它对全基因组转录起始景观的影响仍然难以捉摸。通过使用基因表达的帽分析（CAGE）测序对转录起始位点（TSS）进行全基因组分析，我们表明，在拟南芥的各种表观遗传突变体中，有数千个 TSS 仅被激活，并被称为隐匿 TSS。许多在以前的研究中没有被识别出来，其中多达 65%是由转座子贡献的。它们具有与常规 TSS 相似的遗传特征，其激活与 RNAPII 机制的异位募集强烈相关。隐匿 TSS 的激活显著改变了附近 TSS 的转录，包括那些对发育和应激反应很重要的基因。因此，我们的研究阐明了表观遗传调控通过抑制隐匿 TSS 的转录在植物中维持适当基因功能的作用。
