Polyadenylylated nuclear RNA contains branches.

A highly charged component can be isolated from a total RNase T2 digest of nuclear polyadenylylated RNA from HeLa cells that is separable from caps by (dihydroxyboryl)aminoethyl-cellulose chromatography. Chemical and enzymatic analyses show that the component contains a 2'-5' phosphodiester bond that creates a branch at the 2'-hydroxyl group of one nucleotide already linked to an adjoining nucleotide through the usual 3'-5' phosphodiester bond. [Formula: see text] This structure was confirmed by analysis of a similar component isolated from nuclease P1 digests of the same nuclear polyadenylylated RNA. Branches occur in roughly 10% of nuclear polyadenylylated RNAs, including those >10S in size, but are absent from cytoplasmic polyadenylylated RNA. Possible implications for branches as intermediates in mRNA processing are discussed.