The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis  

Abstract

SWI/SNF complexes mediate ATP-dependent chromatin remodeling to regulate gene expression. Many components of these complexes are evolutionarily conserved, and several subunits of Arabidopsis thaliana SWI/SNF complexes are involved in the control of flowering, a process that depends on the floral repressor FLOWERING LOCUS C (FLC). BAF60 is a SWI/SNF subunit, and in this work, we show that BAF60, via a direct targeting of the floral repressor FLC, induces a change at the highorder chromatin level and represses the photoperiod flowering pathway in Arabidopsis. BAF60 accumulates in the nucleus and controls the formation of the FLC gene loop by modulation of histone density, composition, and posttranslational modification. Physiological analysis of BAF60 RNA interference mutant lines allowed us to propose that this chromatinremodeling protein creates a repressive chromatin configuration at the FLC locus.

SWP73 Subunits of Arabidopsis SWI/SNF Chromatin Remodeling Complexes Play Distinct Roles in Leaf and Flower Development

“…In addition to promoter regions showing altered nucleosome occupancy in our MNaseSeq study, the ChIP-Seq data also identified characteristic peaks of SWP73B representation in the coding sequences and 39-UTRs of the AS1, AS2, and YAB5, as well as AGL24, LFY, AP1, AP3, and SEP3 genes involved in leaf and flower development, suggesting an overall role of SWP73B-containing SWI/SNF complexes in their transcription (Figures 3C and 3D;Supplemental Figures 7C and 7D). In the shared upregulated ChIP-Seq and MNase-Seq data set, we identified the FLC gene, in which peaks of SWP73B occupancy were also detected in both 59-and 39-UTRs, confirming previous data on the location of SWP73B target sites in this locus (Jégu et al, 2014;Supplemental Figures 7C and 7D). In summary, our comparative transcript profiling and MNase-Seq and ChIP-Seq studies consistently identified a small set of genes that are known regulators of leaf and flower development and show association with SWP73B, in addition to altered nucleosome occupancy in the 59-UTRs and altered transcript levels in the swp73b mutant.…”

“…In these lines, a reduction of SWP73B transcript level was reported to correlate with dwarfism and enhanced resistance to Agrobacterium tumefaciens-mediated root transformation (Crane and Gelvin, 2007). Recently, these lines were found to show a late flowering phenotype under inductive long-day conditions (Jégu et al, 2014). In addition, a homozygous SALK_113834 line carrying a T-DNA insertion in the SWP73B promoter region has been used in a study to demonstrate the involvement of SWP73B in DNA repair after UV-B treatment (Campi et al, 2012).…”

“…Association of SWI/SNF subunits SWI3C, SWI3D, and SWP73B with AN-GUSTIFOLIA3 (AN3), recruitment of SWP73B to promoters of AN3-regulated target genes GROWTH-REGULATING FACTOR3 (GRF3), GRF5, HECATE1 (HEC1), CONSTANS-LIKE5 (COL5), CYTOKININ RESPONSE FACTOR2 (CRF2), and RESPONSE REGULATOR4, and altered expression of these genes in the brahma (brm) SNF2-ATPase mutant suggest an important role of SWI/SNF complexes in the regulation of leaf development (Vercruyssen et al, 2014). Another major role of SWI/SNF complexes in flowering time control is indicated by the recent finding that SWP73B (BAF60) is involved in chromatin loop formation of the flowering time repressor FLOWERING LOCUS C (FLC) gene (Jégu et al, 2014).…”

“…In addition, a homozygous SALK_113834 line carrying a T-DNA insertion in the SWP73B promoter region has been used in a study to demonstrate the involvement of SWP73B in DNA repair after UV-B treatment (Campi et al, 2012). Although this mutation was reported to reduce the SWP73B transcript level by 50% compared with the wild type (Campi et al, 2012), Jégu et al (2014) found that the line has wild-type SWP73B mRNA levels and is therefore not suitable for genetic analysis. Intriguingly, although this SALK_113834 mutant is distributed as a homozygous line, we found that it is in fact heterozygous and segregates the swp73b-1 T-DNA insertion allele.…”

“…qRT-PCR analysis of a 39 segment of SWP73B located downstream of insertion indicated that the transcript level was ;3% compared with the wild type in the homozygous swp73b-1 mutant ( Figure 2B). Analogously, we examined a second mutant line swp73b-2 (SALK_071739), which was supposed to be homozygous but was found to show normal SWP73B transcript levels by Jégu et al (2014). As in the case of swp73b-1, the swp73b-2 line also proved to be heterozygous and carried a T-DNA insertion in the first intron, which caused a target site deletion of 19 bp ( Figure 2A).…”