BCL7A and BCL7B potentiate SWI/SNF-complex-mediated chromatin accessibility to regulate gene expression and vegetative phase transition in plants

Switch defective/sucrose non-fermentable (SWI/SNF) chromatin remodeling complexes are multi-subunit machineries that establish and maintain chromatin accessibility and gene expression by regulating chromatin structure. However, how the remodeling activities of SWI/SNF complexes are regulated in eukaryotes remains elusive. B-cell lymphoma/leukemia protein 7A/B/C (BCL7A/B/C) have been reported as subunits of SWI/SNF complexes for decades in animals and recently in plants; however, the role of BCL7 subunits in SWI/SNF function remains undefined. Here, we identify a unique role for plant BCL7A and BCL7B homologous subunits in potentiating the genome-wide chromatin remodeling activities of BRAHMA-SWI/SNF complexes in plants. BCL7A/B require the catalytic ATPase BRAHMA (BRM) to assemble with the signature subunits of the BRM-SWI/SNF complexes and for genomic binding at a subset of target genes. Loss of BCL7A and BCL7B diminishes BRM-mediated genome-wide chromatin accessibility without changing the stability and genomic targeting of the BRM-SWI/SNF complex, highlighting the specialized role of BCL7A/B in regulating remodeling activity. We further show that BCL7A/B fine-tunes the remodeling activity of BRM-SWI/SNF complexes to generate accessible chromatin at the juvenility resetting region (JRR) of the microRNAs MIR156A/C for plant juvenile identity maintenance. In summary, our work uncovers the function of previously elusive SWI/SNF subunits in multicellular eukaryotes and provides insights into the mechanisms whereby plants memorize the juvenile identity through SWI/SNF-mediated control of chromatin accessibility. Overall design: For ChIP-seq and MNase-seq assays, Arabidopsis seeds were sterilized with 10% sodium hypochlorite solution, washed with sterile water four times, and then stratified at 4 °C in darkness for three days. Seeds were then sown on ½-strength Murashige and Skoog (MS) medium containing 1% sucrose and 0.6% agar. Seedlings were grown under cold white light (approximately 120 µmol·m-2·s-1) with short-day conditions (10 h light/14 h dark) at 22 °C. For ChIP-seq, 14-day-old seedlings (~0.5 g for each biological replicate) grown on ½-strength?MS medium under short-day conditions were fixed using 1% formaldehyde under a vacuum for 15?min and then ground into a fine powder in liquid nitrogen. The chromatin was sonicated into ~300-bp fragments using a Bioruptor sonicator with a 30/30-s on/off cycle (27 total on cycles) at the high setting. Immunoprecipitation was performed using 1 µl of anti-GFP (Abcam, Cat. No. ab290) at 4°C overnight. For MNase-seq, Approximately 0.4g of seedlings were used per sample. For MNase treatment, the prepared nuclei were resuspended in prewarmed MNase digestion buffer (20 mM Tris-HCl, pH 8.0, 5 mM NaCl, and 2.5 mM CaCl2), followed by the addition of 0.5 units of MNase (Takara, Cat. No. 2910A,) and incubation (10 min at 37?C with periodic agitation). Finally, the mono-nucleosome DNA was isolated from 2% agarose gels and quantified by the Qubit dsDNA HS assay kit (ThermoFisher, Cat. No. Q32851).