Epigenetic regulation of spurious transcription initiation in Arabidopsis

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.

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All studies must disclose on these points even when the disclosure is negative. Sequencing data generated in this study have been deposited to the DDBJ Sequence Read Archive under the accession codes DRA009134 and DRA009847. Their identifications are described in the Methods section. Processed CAGE-seq data are also accessible via the following web link: https://plantepigenetics.oist.jp/.
No sample size calculation was performed. Sample size was chosen according to the standard in the plant biology field.
One replicate of met1 CAGE samples was excluded from the analyses in the revised manuscript due to a low correlation to the other replicates and according to the reviewers' comments. Another met1 CAGE replicate was discarded due to low mapping coverage.
All the experiments were reproducible in the repeated experiments.
Plant samples were placed randomly in the plant facility.
No blinding was applied for sampling. Since most of the data were obtained by bioinformatic analysis with identical parameter settings in our study, blind sampling was not essential.