Sunflower seed-specific HSFA9 induces persistent chromatin accessibility during seed-to-seedling developmental transition

Abstract

HSFA9 (A9) is a seed-specific transcription factor that contributes to seed longevity in sunflower. A9 also links the regulation of seed maturation with that of early seedling greening through its effects on various light receptors. Transcriptomic analyses of transgenic tobacco seeds suggested that A9 might affect chromatin remodeling. Here, using formaldehyde-assisted isolation of regulatory elements (FAIRE) and micrococcal nuclease digestion, we analyzed the A9 effects on chromatin accessibility shortly after seed imbibition in the proximal promoter region of developmentally relevant genes, including HY5 and PHYA. A9, expressed from a seed-specific promoter, enhanced chromatin accessibility in the analyzed regions. Converse, promoter-specific, effects were observed upon loss-of-function of tobacco A9 (NtA9) in transgenic seeds. Furthermore, a memory effect was observed, as the induced chromatin accessibility persisted for up to 4 days after seed imbibition, when A9 was no longer detected. The A9-induced chromatin effects involved labile/unstable nucleosomes placed at proximal promoter locations where A9 induced substantial nucleosomal depletion. Specific inhibitors of BRAHMA-like ATPase subunits of SWI/SNF (SWItch/Sucrose Non-Fermentable) chromatin-remodeling complexes and histone deacetylase (HDAC) impaired A9-induced memory. Thus, SWI/SNF remodeling and HDAC activity mechanistically contribute to the A9-induced memory. Furthermore, SWI/SNF inhibition specifically reduced the HY5 and PHYA promoter accessibility in both transgenic and non-transgenic seeds. Our results identify HSFA9 as a potential master, short-term, ‘epigenetic’ regulator that operates in seeds in anticipation of seedling establishment. The new, A9-induced, somatic memory effect reported here may facilitate early seedling greening and stress tolerance during the seed-to-seedling developmental transition.