The core clock transcription factor TOC1 binds directly to defence gene promoters regulating immunity in Arabidopsis

Shannon-Leigh Sparks; Laura Roden; Robert Ingle

doi:10.1038/s42003-026-09667-y

The core clock transcription factor TOC1 binds directly to defence gene promoters regulating immunity in Arabidopsis

Shannon-Leigh Sparks
, Laura Roden
, Robert Ingle

Research output: Contribution to journal › Article › peer-review

Abstract

The plant circadian clock drives temporal differences in susceptibility to pathogens. We investigated the role of TIMING OF CAB EXPRESSION 1 (TOC1) in the regulation of defence against Botrytis cinerea in Arabidopsis. The temporal variation in susceptibility to B. cinerea observed in wild-type Arabidopsis was abolished in TOC1-ox and toc1-2 plants under both diurnal and constant conditions. In addition, TOC1-ox plants were more susceptible than Col0 following inoculation at dawn, while inoculation at night lead to enhanced resistance in toc1-2 plants versus C24 plants, suggesting TOC1 is a negative regulator of immunity. RNA-seq analysis showed that the genes mis-regulated in toc1-2 plants had significant enrichment for terms related to biotic stress, an overrepresentation of G-box elements in their promoters and included genes encoding key transcription factors (TFs) involved in defence against necrotrophic pathogens. Chromatin immunoprecipitation-qPCR showed that TOC1 occupies G-box containing regions of the defence TFs ERF4, ORA47, ORA59 and WRKY33 in a pathogenresponsive and MYC2-dependent manner. We suggest that the phased TOC1 occupancy of defence gene promoters contributes to the gating of plant immunity against necrotrophic pathogens, while the MYC2-dependent release of TOC1 in response to pathogen detection allows plants to mount an acute immune response.

Original language	English
Pages (from-to)	(In-Press)
Number of pages	42
Journal	Communications Biology
Volume	(In-Press)
Early online date	11 Feb 2026
DOIs	https://doi.org/10.1038/s42003-026-09667-y
Publication status	E-pub ahead of print - 11 Feb 2026

Bibliographical note

This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit
to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not
have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this
article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the
article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain
permission directly from the copyright holder.

Funding

This work was funded by the National Research Foundation of South Africa (Competitive support for rated researcher grant numbers 105819 and 118504).

Funders	Funder number
National Research Foundation	105819 , 118504

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Sparks et al REVISION V2Accepted author manuscript, 1.07 MB
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Cite this

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title = "The core clock transcription factor TOC1 binds directly to defence gene promoters regulating immunity in Arabidopsis",

abstract = "The plant circadian clock drives temporal differences in susceptibility to pathogens. We investigated the role of TIMING OF CAB EXPRESSION 1 (TOC1) in the regulation of defence against Botrytis cinerea in Arabidopsis. The temporal variation in susceptibility to B. cinerea observed in wild-type Arabidopsis was abolished in TOC1-ox and toc1-2 plants under both diurnal and constant conditions. In addition, TOC1-ox plants were more susceptible than Col0 following inoculation at dawn, while inoculation at night lead to enhanced resistance in toc1-2 plants versus C24 plants, suggesting TOC1 is a negative regulator of immunity. RNA-seq analysis showed that the genes mis-regulated in toc1-2 plants had significant enrichment for terms related to biotic stress, an overrepresentation of G-box elements in their promoters and included genes encoding key transcription factors (TFs) involved in defence against necrotrophic pathogens. Chromatin immunoprecipitation-qPCR showed that TOC1 occupies G-box containing regions of the defence TFs ERF4, ORA47, ORA59 and WRKY33 in a pathogenresponsive and MYC2-dependent manner. We suggest that the phased TOC1 occupancy of defence gene promoters contributes to the gating of plant immunity against necrotrophic pathogens, while the MYC2-dependent release of TOC1 in response to pathogen detection allows plants to mount an acute immune response. ",

author = "Shannon-Leigh Sparks and Laura Roden and Robert Ingle",

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The core clock transcription factor TOC1 binds directly to defence gene promoters regulating immunity in Arabidopsis

Abstract

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