The puff-specific RRM protein NonA is a single-stranded nucleic acid binding protein

The chromatin protein NonA from Drosophila present in many puffs on polyten e chromosomes, belongs to the growing class of RRM proteins. Exchange of am ino acids within the RNP1 and RNP2 consensus sequences, known from other RR M proteins to be essential for RNA binding, has been shown drastically to r educe NonA function in vivo. Here we compare NonA binding to RNA from the S gs-4 gene, an in situ target for NonA, with binding to Sgs-3 RNA, which is not a target of NonA. Using an immunoprecipitation assay in vitro we show t hat NonA binds to single-stranded (ss)DNA and RNA with moderate affinity (K -D=8x10(-8) M). However, we did not observe sequence-specific binding to th e Sgs-4 transcript nor to Sgs-4 DNA containing upstream regulatory sequence s. Point mutations within the RNP1 and RNP2 consensus sequences that interf ere with NonA function in vivo do not significantly change chromosomal bind ing nor the general affinity for RNA. The expression of Sgs-4 RNA relative to the expression of Sgs-3 RNA remains the same in the presence or absence of NonA protein.