Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean

Mar 9, 2026The Plant cell

Daily cycles in DNA accessibility control rhythmic gene activity in soybean

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Abstract

Eleven core co-oscillation groups (CCOGs) were identified in soybean, showing synchronized chromatin accessibility and mRNA oscillations.

Chromatin accessibility within CCOGs is associated with the binding motifs of core circadian oscillators that regulate gene expression.
Two distinct accessible chromatin regions (ACRs) were characterized, influencing both circadian rhythmicity and stable expression of GmLHY1a.
Natural variants of ACRs correlate with the latitudinal adaptation of soybean.
Mutations in core oscillator components, such as GmLHYs and GmLUXs, disrupt chromatin oscillation in CCOGs.
Altered chromatin accessibility was observed at key binding sites, specifically where GmLHY1a interacts with the ACR linked to GmPIF4.

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In soybean (Glycine max (L) Merr.), the circadian clock orchestrates rhythmic molecular, metabolic, and physiological processes that determine yield potential and restrict cultivars to a narrow latitudinal range. However, the role of dynamic chromatin states in rhythmic transcription remains elusive. Here, we integrated time-series ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing), ChIP-seq (Chromatin Immunoprecipitation sequencing), and RNA-seq to map the genome-wide circadian chromatin accessibility landscape under free-running conditions in soybean. We identified 11 core co-oscillation groups (CCOGs), whose chromatin accessibility was synchronized with mRNA oscillations. Accessible chromatin regions (ACRs) within these CCOGs are enriched for binding motifs of the core circadian oscillators, which regulate the expression of their target genes. Two functionally distinct ACRs, which respectively regulate the circadian rhythmicity and stable expression of LATE ELONGATED HYPOCOTYL 1a (GmLHY1a), were characterized. Natural variants of these ACRs were correlated with the latitudinal adaptation of soybean. In addition, mutations in core oscillator components, including GmLHYs and LUX ARRHYTHMO (GmLUXs), disrupt chromatin oscillation in CCOGs. For instance, altered chromatin accessibility was detected at key binding sites, such as the region where GmLHY1a interacts with the ACR associated with GmPIF4 (PHYTOCHROME INTERACTING FACTOR 4). Collectively, these findings reveal a mechanism wherein chromatin accessibility rhythms orchestrate genome-scale transcriptional programs, and provide a large-scale, time-resolved multi-omics resource to facilitate crop breeding for improved environmental adaptation.

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Circadian oscillations in chromatin accessibility systematically orchestrate rhythmic gene transcription in soybean

Abstract

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