Specificity of the Chromodomain Y Chromosome Family of Chromodomains for Lysine-methylated ARK(S/T) Motifs

Abstract

Previous studies have shown two homologous chromodomain modules in the HP1 and Polycomb proteins exhibit discriminatory binding to related methyllysine residues (embedded in ARKS motifs) of the histone H3 tail. Methylated ARK(S/T) motifs have recently been identified in other chromatin factors (e.g. linker histone H1.4 and lysine methyltransferase G9a). These are thought to function as peripheral docking sites for the HP1 chromodomain. In vertebrates, HP1-like chromodomains are also present in the chromodomain Y chromosome (CDY) family of proteins adjacent to a putative catalytic motif. The human genome encodes three CDY family proteins, CDY, CDYL, and CDYL2. These have putative functions ranging from establishment of histone H4 acetylation during spermiogenesis to regulation of transcription co-repressor complexes. To delineate the biochemical functions of the CDY family chromodomains, we analyzed their specificity of methyllysine recognition. We detected substantial differences among these factors. The CDY chromodomain exhibits discriminatory binding to lysinemethylated ARK(S/T) motifs, whereas the CDYL2 chromodomain binds with comparable strength to multiple ARK(S/T) motifs. Interestingly, subtle amino acid changes in the CDYL chromodomain prohibit such binding interactions in vitro and in vivo. However, point mutations can rescue binding. In support of the in vitro binding properties of the chromodomains, the full-length CDY family proteins exhibit substantial variability in chromatin localization. Our studies underscore the significance of subtle sequence differences in a conserved signaling module for diverse epigenetic regulatory pathways.The human Y chromosome has been thoroughly sequenced and compared with partially sequenced Y chromosomes of chimpanzee and mouse (1-3). The Y chromosomes are believed to be enriched in genes essential for spermatogenesis and testis development. Interstitial Y chromosome deletions are associated with spermatogenic failure and male infertility (1,4,5). One gene that is present in multiple copies on the human Y chromosome is CDY, 5 which exhibits testis-specific expression (1). Interestingly, the mouse Y chromosome does not encode CDY, suggesting a developmentally advanced usage of CDY in primates (3).The human CDY gene seems to be derived from the autosomal homologs CDYL or CDYL2 (Fig. 1, A and B) (6). CDYL is ubiquitously expressed, whereas CDYL2 exhibits selective expression in tissues of testis, prostate, spleen, and leukocytes (6). The mouse genome also encodes related CDYL and CDYL2 genes (Fig. 1B). The presence of CDY-like genes appears to be a hallmark of echinoderm and vertebrate genomes. In sea urchin and chicken genomes we found only one CDY-like gene that corresponds to mammalian CDYL2 (Fig. 1B).CDY family proteins have two conserved domains implicated in histone modification and recognition; that is, a chromodomain followed by an enoyl-coenzyme A hydratase/isomerase (ECH) putative catalytic domain (Fig. 1A). Previously, it was shown that the chromodomain of hum...

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The C Terminus of the Alb3 Membrane Insertase Recruits cpSRP43 to the Thylakoid Membrane

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