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 lysine-methylated 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.