COMPASS functions as a module of the INO80 complex

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Shang et al. explore the function of a chromatin-remodeling complex in the regulation of gene expression. Plant Cell. https://doi.org/10.1093/plcell/koab187

By Ji-Yun Shang and Xin-Jian He

 Background: In eukaryotic cells, the INO80 chromatin remodeling complex uses energy derived from ATP hydrolysis to change chromatin structure and the accessibility of chromatin-related proteins to DNA. The histone methyltransferase COMPASS complexes can add three methyl groups (me3) on histone 3 lysine 4 (H3K4me3) in actively transcribed genes and promote transcription. INO80 and COMPASS are two independent complexes in yeast and metazoans, with well-characterized compositions and functions. Although the biological functions of INO80 and COMPASS complexes were extensively studied in plants, the compositions of these complexes were less studied.

Question: We wanted to investigate the composition of the Arabidopsis INO80 chromatin remodeling complex and figure out how the INO80 complex regulates gene expression.

Findings: We found that the Arabidopsis INO80 complex contained ~26 conserved and non-conversed components bind to three domains of INO80: the N-terminal domain (NTD), HSA domain, and ATPase domain. In particular, a subclass of the COMPASS complex, containing the histone H3K4 methyltransferase ATX4 or ATX5, binds to the NTD of INO80 through JMJ24, a protein belonging to the H3K9me2 demethylase family. The ATX4/5-containing COMPASS complex and the other NTD-binding subunits form the NTD module, which promotes plant growth and represses flowering under short-day conditions. Furthermore, we found that the NTD module can activate gene expression by promoting H3K4me3 deposition at a subset of genes targeted by the INO80 complex in an ATPase activity-independent way.

Next steps: We will carry out chromatin immunoprecipitation and sequencing analysis to identify the target genomic loci of INO80 complex at the whole-genome level. Based on the resulting data, we will investigate how the ATPase-dependent and -independent functions of INO80 are coordinated in the regulation of gene expression, growth, and flowering time.

Reference:

Ji-Yun Shang, Yu-Jia Lu, Xue-Wei Cai, Yin-Na Su, Chao Feng, Lin Li, She Chen, Xin-Jian He (2021). COMPASS functions as a module of the INO80 chromatin remodeling complex to mediate histone H3K4 methylation in Arabidopsis. https://doi.org/10.1093/plcell/koab187