Epigenetic regulation of spurious transcription initiation in Arabidopsis

Ngoc Tu Le, Yoshiko Harukawa, Saori Miura, Damian Boer, Akira Kawabe and Hidetoshi Saze ()
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Ngoc Tu Le: Okinawa Institute of Science and Technology (OIST)
Yoshiko Harukawa: Okinawa Institute of Science and Technology (OIST)
Saori Miura: Okinawa Institute of Science and Technology (OIST)
Damian Boer: Wageningen University & Research
Akira Kawabe: Kyoto Sangyo University
Hidetoshi Saze: Okinawa Institute of Science and Technology (OIST)

Nature Communications, 2020, vol. 11, issue 1, 1-15

Abstract: Abstract 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.

Date: 2020
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DOI: 10.1038/s41467-020-16951-w

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