The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility

Abstract

BackgroundPlant adaptive responses to changing environments involve complex molecular interplays between intrinsic and external signals. Whilst much is known on the signaling components mediating diurnal, light, and temperature controls on plant development, their influence on chromatin-based transcriptional controls remains poorly explored.ResultsIn this study we show that a SWI/SNF chromatin remodeler subunit, BAF60, represses seedling growth by modulating DNA accessibility of hypocotyl cell size regulatory genes. BAF60 binds nucleosome-free regions of multiple G box-containing genes, opposing in cis the promoting effect of the photomorphogenic and thermomorphogenic regulator Phytochrome Interacting Factor 4 (PIF4) on hypocotyl elongation. Furthermore, BAF60 expression level is regulated in response to light and daily rhythms.ConclusionsThese results unveil a short path between a chromatin remodeler and a signaling component to fine-tune plant morphogenesis in response to environmental conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1246-7) contains supplementary material, which is available to authorized users.

The histone variant H2A.Z and chromatin remodeler BRAHMA act coordinately and antagonistically to regulate transcription and nucleosome dynamics in Arabidopsis

“…These results expand on previous locus‐specific studies by both finding that well positioned nucleosomes surrounding BRM binding sites is a general genomic trend and that the stability of many of these flanking nucleosomes depends on BRM (Sacharowski et al ., ; Wu et al ., ). Since the BAF60 subunit of the SWI2/SNF2 complex has been observed localizing to open chromatin, we provide further evidence that the SWI2/SNF2 complex binds to NDRs by finding that the BRM SWI2/SNF2 ATPase also binds to NDRs (Jegu et al ., ). The fact that we see an increase in +1 nucleosome occupancy in the absence of BRM and H2A.Z at genes where both are needed for proper transcriptional regulation (especially classes 1 and 2) is consistent with studies showing that both factors disrupt interactions between DNA and nucleosomes (Schnitzler et al ., ; Rudnizky et al ., ).…”

“…However, H2A.Z and/or BRM may have more consistent roles in chromatin regulation through interactions with specific transcription factors (TFs). Some previously reported interactions between either H2A.Z or BRM and TFs prompted us to evaluate how H2A.Z and BRM might contribute to nucleosome organization surrounding TF binding sites where they co-localize (John et al, 2008;Wu, 2012;Efroni et al, 2013;Vercruyssen et al, 2014;Sacharowski et al, 2015;Zhao and Garcia, 2015;Buszewicz et al, 2016;Cortijo et al, 2017;Jegu et al, 2017;Zhang et al, 2017a).…”

Unwinding BRAHMA Functions in Plants

“…Similar to KNAT2 and KNAT6 regulations, the H3K4me3 level is increased in brm plants and the H3K27me3 level is unchanged at PORC locus. Interestingly, the BAF60/SWP73B/CHC1 subunit of the SWI/SNF complex is also regulated by light and represses seedling growth by opposing in cis the photomorphogenic effect of PIF4 [31]. Later during leaf development, BRM, AtSWI3C, and BSH5 all act as repressors of seed maturation genes (2S family) in leaves and bind to their promoters [32].…”

Linking crop traits to transcriptome differences in a progeny population of tetraploid potato

“…Three of the most highly correlated transcripts with P. infestans leaf resistance were an Arabinogalactan protein (DMG402032565), a Sodium/potassium/calcium exchanger (DMG400006339) and an Associate of C-myc transcript (DMG400025428) with unknown function, all of which were detected by the differentially expression analysis as well. A transcript encoding a chromodomain remodeling complex (DMG400006925) was clearly positively regulated with resistance and highly similar to AtBAF60 (AT5G14170), which was recently shown to mediate repression of seedling growth [20].…”