In Arabidopsis, the histone H3K9 methyltransferases SUVH4, SUVH5, and SUVH6 can directly bind to methylated DNA by their SRA domains ( Rajakumara et al., 2011 Du et al., 2014 Li et al., 2018). Because histone modifications function at the nucleosome level and co-exist with DNA, many regulators of histone modifications have direct or indirect DNA binding modules. An ISWI complex was shown to associate with the histone modifications H3K4me3 and H4K16ac through its the DDT-domain–containing subunit BPTF in humans ( Li et al., 2006 Wysocka et al., 2006 Ruthenburg et al., 2011). Histone modifications are important epigenetic regulators that can mediate the association of chromatin-remodeling proteins with chromatin in a locus-specific manner. It remains to be determined whether the Arabidopsis ISWI complexes contain any other accessory subunits and how the accessory subunits function in the complexes. To date, only the DDT-domain proteins RINGLET1 (RTL1) and RTL2 have been reported to be accessory subunits of ISWI complexes in Arabidopsis ( Li et al., 2012 Dong et al., 2013).

Loss-of-function of CHR11/17 results in pleiotropic developmental defects and early flowering ( Li et al., 2012 Smaczniak et al., 2012). Like ISWI chromatin remodelers in yeast ( Saccharomyces cerevisiae) and metazoans, CHR11/17 are required for the even spacing of nucleosomes in the gene body ( Li et al., 2014). In Arabidopsis ( Arabidopsis thaliana), there are two closely related ISWI chromatin-remodeling proteins, CHROMATIN-REMODELING PROTEIN11 (CHR11) and CHR17 (CHR11/17 Huanca-Mamani et al., 2005 Li et al., 2012 Smaczniak et al., 2012). Accessory subunits of the ISWI complexes either regulate nucleosome mobilization or facilitate the association of the ISWI complexes with specific chromatin sites ( Toto et al., 2014). ISWI proteins typically associate with one to three accessory subunits and form multiple ISWI complexes in eukaryotes ( Yadon and Tsukiyama, 2011 Bartholomew, 2014). By mediating nucleosome mobility, ISWI proteins regulate the appropriate spacing of nucleosomes within the genome ( Gkikopoulos et al., 2011 Li et al., 2012). Imitation Switch (ISWI) is one of four families of ATP-dependent chromatin-remodeling proteins (ISWI, SWI/SNF, CHD, and INO80) in eukaryotes ( Clapier and Cairns, 2009). The results suggest that the dual recognition of AT-rich DNA and H3K4me3 by the ARID5 ARID-PHD cassette may facilitate the association of the ISWI complex with specific chromatin regions to regulate development and floral transition.ĪTP-dependent chromatin-remodeling proteins regulate the packaging, unwrapping, and mobilization of nucleosomes and thereby affect DNA replication, DNA repair, and transcription ( Narlikar, 2010 Toto et al., 2014). Both PHD and ARID domains are necessary for the association of ARID5 with chromatin. The H3K4me3 peptide is combinatorially recognized by the PHD and ARID domains, while the DNA is specifically recognized by the ARID domain. We determined the ternary complex structure of the ARID5 ARID-PHD cassette with an H3K4me3 peptide and an AT-containing DNA. The ARID-PHD dual domain cassette of ARID5 recognizes both the H3K4me3 histone mark and AT-rich DNA. We found that AT-RICH INTERACTING DOMAIN5 (ARID5), a subunit of a plant-specific ISWI complex, can regulate development and floral transition. Here, we identified three types of Imitation Switch (ISWI) chromatin-remodeling complexes in Arabidopsis ( Arabidopsis thaliana).

However, it is largely unknown whether and how these two epigenetic regulators coordinately regulate the important biological processes. Chromatin remodeling and histone modifications are important for development and floral transition in plants.

Gmod file name for dead ringer