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 Arabidopsis 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.
Highlights
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
The CW domains in mammalian MORC1, MORC2, and LSD2 have been reported to have no ability to bind any histone H3K4 peptides, whereas the CW domains of mammalian ZCWPW1, ZCWPW2, MORC3, and MORC4 bind to H3K4me3 [20, 23, 29]
The results showed that ART of histone H3 is important for the recognition of H3K4me1 by OsSDG725-CW, the same as SDG8
Summary
SDG8 harbors a CW domain in the middle of its amino acid sequence and a SET domain that is C-terminal to the CW domain (Fig. 1A). We determined the structure of SDG8-CW in complex with H3K4me (residues 1–9) by the single-wavelength anomalous dispersion method using the anomalous zinc ion signal. The monomethylated side chain of Lys-4 inserts into a pocket formed by five residues, Trp-865 on 1, Trp-874 on 2, Ile-915, Asn-916, and Leu-919 on ␣1 (Fig. 1G). The methyl group of Ala-1 inserts into a hydrophobic pocket formed by Val-866, Ile-885, and Trp-891 (Fig. 2D). Arg-2 and K4me form hydrogen bonds with the main chains of Arg-867 and Trp-865 on 1, respectively (Fig. 2B). Hydroxyl group of Thr-3 is involved in water-mediated hydrogen bond interactions with the main chains of Val-882 and Ile885. The K4me binds in a straight concave surface of SDG-CW, which is different from the canonical trimethyllysinebinding pocket formed by three or more aromatic residues to
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