We previously reported common structural features within the 3′‐terminal regions of U1, U4, and U5 RNAs. To check whether these features also exist in U2 RNA, the primary and secondary structures of the 3′‐terminal regions of chicken, pheasant, and rat U2 RNAs were examined. Whereas no difference was observed between pheasant and chicken, the chicken and rat sequences were only 82.5% homologous. Such divergence allowed us to propose a unique model of secondary structure based on maximum base‐pairing and secondary structure conservation. The same model was obtained from the results of limited digestion of U2 RNA with various nucleases. Comparison of this structure with those of U1, U4, and U5 RNAs shows that the four RNAs share a common structure designated as domain A, and consisting of a free single‐stranded region with the sequence Pu‐A‐(U)n‐G‐Pup flanked by two hairpins. The hairpin on the 3′ side is very stable and has the sequence Py‐N‐Py‐Gp in the loop. The presence of this common domain is discussed in connection with relationships among U RNAs and common protein binding sites.

Chicken, rat and human U1A RNAs in solution, were examined for secondary structure, using several methods including hydrolysis by various nucleases, hybridization to DNA oligomers and analysis of fragment interactions. The experimental results showed that the three U1A RNAs have the same structure, stable over a wide range of pH and ionic conditions. They allowed the selection of one out of several possible models constructed from the data of primary structure. This model is characterized by 4 hairpins and two single-stranded regions, the two hairpins from the 3' part of the molecule bearing very stable stems. In addition, the experimental results showed that in contrast to the 5' half of the molecule, the 3' half has a compact conformation probably stabilized by tertiary interactions. The 5' end of U1A RNA is accessible and free of base-pairing so that it might base-pair with regions of other RNA molecules, for instance, with the extremities of introns as has been recently proposed in a model of splicing.

SUMMARYThe methods of enzymatic and chemical treatment of end-labeled RNA were applied to the determination of the nucleotide sequence of chicken and man UlA RNA and to the reexamination of that of rat UlA RNA. The chemical method allowed the easy demonstration of the cap structure. All three RNA were 165 nucleotide long. Two hitherto non described modified pyrimidines were detected close to the 5' end. Only 9 base substitutions were observed from chicken to man indicating a high degree of conservation of UlA RNA through evolution. INTRODUCTIONMetabolically stable low molecular weight RNA were found in the nuclei of a variety of cell types (1-4). Four of these small RNA (4.5SI, U1A, U2 and U3B RNA) isolated from rat Novikoff Hepatoma cells were sequenced by Busch and coworkers (5-8). The interest for the small nuclear RNA was renewed by the finding that they may be hydrogen-bonded to premessenger RNA (9, 10) and that they were present in the ribonucleoproteins containing the premessenger RNA (11-14) which are assumed to be the site of splicing. Therefore, it was proposed that the small RNA might insure the proper alignment of premessenger RNA sequences for splicing (15)(16)(17). This idea was reinforced by the observation of at certain complementari:ty between a single sequence a the 5' end of UlA RNA and a consensus of the intron sequences adjacent to the splice point in premessenger RNA. As premessenger RNA from various animal species were used for the establishment of the consensus sequence and as only the published sequence of rat UlA RNA was available (6), the model implied a high conservation of the primary structure of UlA RNA through evolution (16). This prompted us to determine the complete nucleotide sequence of UlA RNA from 2 other animal species, chicken