Uncovering the mechanistic basis for specific recognition of monomethylated H3K4 by the CW domain of Arabidopsis histone methyltransferase SDG8

Abstract

Chromatin consists of DNA and histones, and specific histone modifications that determine chromatin structure and activity are regulated by three types of proteins, called writer, reader, and eraser. Histone reader proteins from vertebrates, vertebrate-infecting parasites, and higher plants possess a CW domain, which has been reported to read histone H3 lysine 4 (H3K4). The CW domain of SDG8 (also called ASHH2), a histone H3 lysine 36 methyltransferase, preferentially binds monomethylated H3K4 (H3K4me1), unlike the mammalian CW domain protein, which binds trimethylated H3K4 (H3K4me3). However, the molecular basis of the selective binding by the CW domain of SDG8 (SDG8-CW) remains unclear. Here, we solved the 1.6-Å-resolution structure of SDG8-CW in complex with H3K4me1, which revealed that residues in the C-terminal α-helix of SDG8-CW determine binding specificity for low methylation levels at H3K4. Moreover, substitutions of key residues, specifically Ile-915 and Asn-916, converted SDG8-CW binding preference from H3K4me1 to H3K4me3. Sequence alignment and mutagenesis studies revealed that the CW domain of SDG725, the homolog of SDG8 in rice, shares the same binding preference with SDG8-CW, indicating that preference for low methylated H3K4 by the CW domain of ASHH2 homologs is conserved among higher-order plants. Our findings provide first structural insights into the molecular basis for specific recognition of monomethylated H3K4 by the H3K4me1 reader protein SDG8 from.

Arabidopsis SDG8 Potentiates the Sustainable Transcriptional Induction of the Pathogenesis-Related Genes PR1 and PR2 During Plant Defense Response

“…The CW domain is found in a small number of chromatin-related proteins in animals and plants, and is thought to be a "reader" of methylated H3K4 (Hoppmann et al, 2011). The one found in SDG8 has preference for H3K4me1/me2 (Liu and Huang, 2018). SDG8 thus combines both an H3K4 methylation-reading module and an H3K36me3 writing module, making it the only reader and writer of histone methylation.…”

Interactive and noninteractive roles of histone H2B monoubiquitination and H3K36 methylation in the regulation of active gene transcription and control of plant growth and development

“…Because SDG8 does not possess the G-box, TGGGCC/T and TAATTA binding domain, it is tempting to speculate that it may act in a combination with other transcription factors that are able to bind G-box and/or FORC A motifs directly to regulate downstream genes. Finally, other processes may enable SDG8 recruitment, especially when considering its interaction with the RNA PolII, the zinc finger domain-containing H3K27 demethylase ELF6 or even H3K4me1 through its CW domain (Hoppmann et al, 2011;Yang et al, 2016;Liu & Huang, 2018).…”

The Arabidopsis (ASHH2) CW domain binds monomethylated K4 of the histone H3 tail through conformational selection

“…The role of the CW domain in most proteins is to recognize and bind to methylated histone H3 (H3) N-terminal tails at the K4 position (H3K4meX, where X is the number of methyl groups). Depending on the protein, the CW domain displays a different specificity for the degree of methylation [7,8,14]. The other mammalian CW domain-containing proteins ZCWPW1, ZCWPW2, MORC3 and MORC4 display specificity for H3K4me2/me3 [7,11].…”