Sacharowski Sebastian P, Kubala Szymon, Cwiek Pawel, Steciuk Jaroslaw, Gratkowska-Zmuda Dominika, Oksinska Paulina, Bucior Ernest, Rolicka Anna T, Ciesla Monika, Nowicka Klaudia, Alseekh Saleh, Tohge Takayuki, Giavalisco Patrick, Zugaj Dorota L, Stolze Sara C, Harzen Anne, Franzen Rainer, Huettel Bruno, Grzesiuk Elzbieta, Hajirezaei Mohammad-Reza, Nakagami Hirofumi, Koncz Csaba, Fernie Alisdair R, Sarnowski Tomasz J
Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106, Warsaw, Poland.
Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
New Phytol. 2025 Jul;247(2):791-812. doi: 10.1111/nph.70182. Epub 2025 May 22.
Evolutionarily conserved switch-defective/sucrose nonfermentable (SWI/SNF) ATP-dependent chromatin remodelling complexes (CRCs) alter nucleosome positioning and chromatin states, affecting gene expression to regulate important processes such as proper development and hormonal signalling pathways. We employed transcript profiling, chromatin immunoprecipitation (ChIP), mass spectrometry, yeast two-hybrid and bimolecular fluorescence complementation protein-protein interaction studies, along with hormone and metabolite profiling and phenotype assessments, to distinguish the SWP73A and SWP73B subunit functions in Arabidopsis. We identified a novel subclass of SWI/SNF CRCs defined by the presence of the SWP73A subunit. Therefore, we propose a refined classification of SWI/SNF CRCs in Arabidopsis, introducing BRM-associated SWI/SNF (BAS)-A (containing SWP73A) and BAS-B (containing SWP73B) subclasses. The SWP73A- and SWP73B-carrying SWI/SNF CRCs exhibit differential properties, demonstrated by distinct chromatin binding patterns and divergent effects on hormone biosynthesis and metabolism. We additionally found that SWP73A plays a specific role in the regulation of auxin signalling, root development, metabolism and germination that cannot be fully compensated by SWP73B. We recognised that some atypical subclasses of SWI/SNF CRCs may be likely formed in mutant lines with inactivated SWP73 subunits. Our study reveals that the duplication of the SWP73 subunit genes contributes to unique and shared functions of SWI/SNF CRC subclasses in the regulation of various processes in Arabidopsis.
进化上保守的开关缺陷型/蔗糖非发酵型（SWI/SNF）ATP依赖的染色质重塑复合体（CRCs）可改变核小体定位和染色质状态，影响基因表达，从而调节诸如正常发育和激素信号通路等重要过程。我们运用转录谱分析、染色质免疫沉淀（ChIP）、质谱分析、酵母双杂交和双分子荧光互补蛋白-蛋白相互作用研究，以及激素和代谢物谱分析与表型评估，来区分拟南芥中SWP73A和SWP73B亚基的功能。我们鉴定出了一个由SWP73A亚基的存在所定义的SWI/SNF CRCs新亚类。因此，我们提出了拟南芥中SWI/SNF CRCs的细化分类，引入了与BRM相关的SWI/SNF（BAS）-A（包含SWP73A）和BAS-B（包含SWP73B）亚类。携带SWP73A和SWP73B的SWI/SNF CRCs表现出不同的特性，这通过不同的染色质结合模式以及对激素生物合成和代谢的不同影响得以证明。我们还发现SWP73A在生长素信号传导、根发育、代谢和萌发的调节中发挥特定作用，而SWP73B无法完全补偿这一作用。我们认识到，在SWP73亚基失活的突变系中可能会形成一些非典型的SWI/SNF CRCs亚类。我们的研究表明，SWP73亚基基因的复制有助于SWI/SNF CRC亚类在拟南芥各种过程调节中发挥独特和共享的功能。
