Arabidopsis thaliana requires a prolonged period of cold exposure during winter
to initiate flowering in a process termed vernalization. Exposure to cold
induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb
group (PcG) proteins. A key role in this epigenetic switch is played by
transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY
DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of
PcG silencing machinery. To understand the structural mechanism of site-specific
DNA recognition by VAL1, we have solved the crystal structure of VAL1 B3 domain
(VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA
sequence 5'-CATGCA-3'/5'-TGCATG-3'. We find that VAL1-B3 makes H-bonds and van
der Waals contacts to DNA bases of all six positions of the canonical Sph/RY
element. In agreement with the structure, in vitro DNA binding studies show that
VAL1-B3 does not tolerate substitutions at any position of the 5'-TGCATG-3'
sequence. The VAL1-B3-DNA structure presented here provides a structural model
for understanding the specificity of plant B3 domains interacting with the
Sph/RY and other DNA sequences.
