Cryptic promoter activation occurs by at least two different mechanisms in the Arabidopsis genome.

Autor: Kudo H; Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan., Matsuo M; Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan., Satoh S; Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan., Hata T; Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan., Hachisu R; Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan., Nakamura M; Center for G Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan., Yamamoto YY; Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagito, Gihu-shi, Gifu, 501-1193, Japan., Kimura H; Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama City, Kanagawa, 226-8501, Japan., Matsui M; RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan., Obokata J; Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5 Hangi-cho, Sakyo-ku, Kyoto, 606-8522, Japan.
Jazyk: angličtina
Zdroj: The Plant journal : for cell and molecular biology [Plant J] 2021 Oct; Vol. 108 (1), pp. 29-39. Date of Electronic Publication: 2021 Aug 02.
DOI: 10.1111/tpj.15420
Abstrakt: In gene-trap screening of plant genomes, promoterless reporter constructs are often expressed without trapping of annotated gene promoters. The molecular basis of this phenomenon, which has been interpreted as the trapping of cryptic promoters, is poorly understood. Here, we found that cryptic promoter activation occurs by at least two different mechanisms using Arabidopsis gene-trap lines in which a firefly luciferase (LUC) open reading frame (ORF) without an apparent promoter sequence was expressed from intergenic regions: one mechanism is 'cryptic promoter capturing', in which the LUC ORF captured pre-existing promoter-like chromatin marked by H3K4me3 and H2A.Z, and the other is 'promoter de novo origination', in which the promoter chromatin was newly formed near the 5' end of the inserted LUC ORF. The latter finding raises a question as to how the inserted LUC ORF sequence is involved in this phenomenon. To examine this, we performed a model experiment with chimeric LUC genes in transgenic plants. Using Arabidopsis psaH1 promoter-LUC constructs, we found that the functional core promoter region, where transcription start sites (TSSs) occur, cannot simply be determined by the upstream nor core promoter sequences; rather, its positioning proximal to the inserted LUC ORF sequence was more critical. This result suggests that the insertion of the coding sequence alters the local distribution of TSSs in the plant genome. The possible impact of the two types of cryptic promoter activation mechanisms on plant genome evolution and endosymbiotic gene transfer is discussed.
(© 2021 Society for Experimental Biology and John Wiley & Sons Ltd.)
Databáze: MEDLINE
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