The open reading frame transcribed from the unr gene (immediately upstream of N-ras) in mammals consists of multiple repeats similar to the cold- shock domain, a specific DNA-binding motif found in prokaryotic cold-shock proteins and eukaryotic DNA-binding proteins. Alignment of the CSD sequences of unr with those from other proteins reveals a core of similarity for which a consistent secondary structure prediction can be derived. This prediction suggests that the CSD consists primarily of beta- sheet. Further sequence analysis has shown that there is a short motif of 8 amino acids, corresponding to the RNP-1 motif found in canonical RNA-binding domains. Many RNA-binding proteins contain the RNP-1 and RNP-2 motifs in an RNA-binding domain.The CSD family of proteins, which includes several transcription factors, has been identified to contain a motif similar to RNP-1. A non-redundant protein sequence database was searched with regular expressions and with a weight/residue position matrix of the RNP-1 motif resulting in the identification of numerous known members of the RNA-binding family of proteins. In addition, the search identified that the CSD-containing family of proteins includes a motif which is almost identical to the RNP-1 motif. It is conceivable that the RNP-1 in the CSD-containing proteins enables them to function as both double- and single-stranded, DNA- and RNA-binding proteins. The analogy between a member of the CSD-containing family of proteins and TFIIIA, the X. laevis transcription factor, has previously been drawn by others.This suggests that the CSD-containing proteins could be involved in transcription as well as in gene regulation post-transcriptionally by binding RNA. The initial phases of modelling a CSD based on the crystal structure of an RNA-binding protein have been attempted. The structural co-ordinates of the human U1 small nuclear ribonucleoprotein A are being used to model four predicted ~ regions in CSD on the four-stranded beta sheet found in this protein.
