Determination of the nucleotide sequences in mouse U14 small nuclear RNA and 18S ribosomal RNA responsible for in vitro intermolecular base‐pairing

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Abstract
U14 small nuclear RNA (snRNA) is an evolutionarily conserved RNA species that plays a role in rRNA processing. The conserved ability of fungal, amphibian and mammalian U14 snRNAs to hybridize with both homolous and heterologous eukaryotic 18S rRNAs indicates a potential role for this intermolecular RNA/RNA interaction in U14 snRNA function. To understand better the possible role of this intermolecular base‐pairing in rRNA processing, we have defined those nucleotide sequences in mouse U14 snRNA and 18S rRNA responsible for the observed in vitro hybridization. We have constructed, using synthetic DNA oligonucleotides, a U14 snRNA gene which has been positioned behind a T7 RNA polymerase promoter site and then inserted into a plasmid. The presence of natural or engineered restriction endonuclease sites within this construct has permitted the in vitro transcription of full‐length mouse U14 snRNA transcripts (an 87‐nucleotide mouse U14 snRNA minus 5′ or 3′ leader sequences) or 3′ terminally truncated U14 snRNA fragments. Hybridization of full‐length or truncated fragments of U14 snRNA to mouse 18S rRNA demonstrated the utilization of a previously proposed 18S rRNA complementary sequence located near the 3′ end of mouse U14 snRNA (nucleotides 65–78) for intermolecular hybridization. Conversely, RNase‐T1‐generated fragments of 18S rRNA capable of hybrid‐selection by U14 snRNA have been isolated and sequenced. A nested set of hybrid‐selected 18S rRNA fragments define a mouse 18S rRNA sequence (nucleotides 459–472) which exhibits perfect complementarity to the defined U14 snRNA sequence 65–78. Primer‐extension/chain‐termination mapping of mouse U14‐snRNA · 18S‐rRNA hybrids has confirmed the formation of the proposed hybrid structure. A second set of observed complementary sequences in mouse U14 snRNA (nucleotides 25–38) and mouse 18S rRNA (nucleotides 82–95) are not used for the in vitro hybridization of these two RNAs. Presumably the involvement of this prevents its base‐pairing with 18S rRNA. However, the strong evolutionary conservation of both U14‐snRNA · 18S‐rRNA hybrid structures and their juxtapositioning within the folded secondary structure of 18S rRNAs argues for a biological role for each in U14 snRNA function.