Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis

Abstract

Active DNA demethylation is critical for controlling the DNA methylomes in plants and mammals. However, little is known about how DNA demethylases are recruited to target loci, and the involvement of chromatin marks in this process. Here, we identify 2 components of the SWR1 chromatin-remodeling complex, PIE1 and ARP6, as required for ROS1-mediated DNA demethylation, and discover 2 SWR1-associated bromodomain-containing proteins, AtMBD9 and nuclear protein X1 (NPX1). AtMBD9 and NPX1 recognize histone acetylation marks established by increased DNA methylation 1 (IDM1), a known regulator of DNA demethylation, redundantly facilitating H2A.Z deposition at IDM1 target loci. We show that at some genomic regions, H2A.Z and DNA methylation marks coexist, and H2A.Z physically interacts with ROS1 to regulate DNA demethylation and antisilencing. Our results unveil a mechanism through which DNA demethylases can be recruited to specific target loci exhibiting particular histone marks, providing a conceptual framework to understand how chromatin marks regulate DNA demethylation.

A novel protein complex that regulates active DNA demethylation inArabidopsis

“…To date, two proteins, H2A.Z and MET18, have been reported to physically interact with ROS1 and to regulate active DNA demethylation in Arabidopsis plants (Nie et al, 2019; Duan et al, 2015). H2A.Z is required for ROS1 to target specific genomic regions defined by the IDM and SWR1 protein complexes (Qian et al, 2012; Lang et al, 2015; Nie et al, 2019). MET18 is a critical enzyme in the biosynthesis of the MoCo cofactor required for the methyl-DNA glycosylase/lyase activity of ROS1 (Duan et al, 2015).…”

“…Several transcription factors have been shown to interact with and to target Tet enzymes to genes critical for cell differentiation and reprogramming (Costa et al, 2013; de la Rica et al, 2013; Sardina et al, 2018; Wang et al, 2015; Xiong et al, 2016). In Arabidopsis , the IDM histone acetyltransferase complex is required for directing ROS1 to a subset of active DNA demethylation target regions (Duan et al, 2017; Lang et al, 2015; Nie et al, 2019; Qian et al, 2014; Qian et al, 2012). MBD7 in the IDM complex recognizes dense mCpG sites and thus ensures that ROS1 is eventually targeted to genomic regions with densely methylated CpG sequences (Lang et al, 2015).…”

SIZ1-mediated SUMOylation of ROS1 Enhances Its Stability and Positively Regulates Active DNA Demethylation inArabidopsis

“…In recent years, several studies have elucidated the mechanisms of ROS1 targeting and activity regulation. The newly discovered IDM complex functions together with the SWR1 complex in recruiting ROS1 to specific genomic loci for active DNA demethylation (Duan et al ., 2017; Lang et al ., 2015; Li et al ., 2015; Nie et al ., 2019; Qian et al ., 2014; Qian et al ., 2012; Wang et al ., 2015). MET18 is critical for the regulation of enzymatic activity of ROS1 (Duan et al , 2015; Wang et al ., 2016).…”

“…Bisulfite treatment, library construction, and deep sequencing were performed by the Genomics Core Facility at the Shanghai Center for Plant Stress Biology, China. Data analysis was conducted as previously reported (Nie et al ., 2019).…”

“…The Arabidopsis 5-methylcytosine DNA glycosylase/lyase ROS1 is critical for pruning DNA methylation to keep a proper DNA methylation pattern genome-wide (Gong et al , 2002; Qian et al ., 2012). The recruitment of ROS1 to specific genomic loci requires the Increased DNA Methylation (IDM) complex to catalyze histone acetylations, which in turn attact the SWR1 complex for the deposition of H2A.Z required for the direct recruitment of ROS1 (Lang et al ., 2015; Li et al ., 2015; Li et al ., 2012; Nie et al ., 2019; Qian et al ., 2012; Wang et al ., 2015). ROS1 belongs to a small family of enzymes that also includes DME, DML2 and DML3 (Zhu, 2009), which are iron-sulfur proteins requiring Fe-S clusters as cofactors for enzymatic activities (Balk and Pilon, 2011; Netz et al ., 2014).…”