Chromatin accessibility–transcription coupling is dynamically reconfigured during Arabidopsis embryo maturation

Chromatin accessibility (CA) is widely profiled alongside transcription because it is generally associated with transcriptional activity. How directly the two layers are linked remains unclear. We addressed this in Arabidopsis thaliana embryos. We profiled CA and transcription across the torpedo, bent-cotyledon, and mature-green stages using stage-resolved nicking enzyme-assisted sequencing (NicE-seq) and nanopore RNA sequencing. To test whether their relationship is genetically regulated, we also analyzed ld-1, a mutant of LUMINIDEPENDENS (LD) linked to global transcriptional repression. Transcriptomes formed discrete stage-specific programmes, but CA did not. Accessibility at both promoters and transcription-factor motifs largely followed a common developmental trajectory that peaked at the bent-cotyledon stage and declined thereafter, rather than mirroring module-specific expression patterns. Loss of LD preserved promoter architecture but extensively remodelled motif accessibility, increasing its concordance with module-specific expression timing and strengthening CA-transcription coupling. Chromatin accessibility and transcription are subject to partly independent regulation during embryo maturation. The ability of LD loss to strengthen accessibility-transcription concordance demonstrates that their coupling is a regulated rather than fixed property of developmental chromatin.