U2 RNA shares a structural domain with U1, U4, and U5 RNAs.

Abstract

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.

The linked units of 5S rDNA and U1 snDNA of razor shells (Mollusca: Bivalvia: Pharidae)

“…They were compared with the two gastropod sequences (see above), the ones from the insect D. melanogaster (Lo and Mount, 1990), and those from crustaceans Asellus aquaticus and Proasellus coxalis (Barzotti et al, 2003). Considering as a reference the E. magnus U1 sequence (see U1 predicted secondary structures), they correspond to the following positions: the 5 0 end (includes the 5 0 splice site, Zhuang and Weiner, 1986 Branlant et al, 1982). The most conserved region was the 5 0 end (11 nt) that was identical in all sequences.…”

“…The secondary structure of stem-loop IV was conserved in razor shells and gastropods and consisted of one hairpin loop, one internal loop, two stems and a central nonpaired region containing the 5 0 splice site (Zhuang and Weiner, 1986 and references therein) and the Sm proteins binding region ('domain A', Branlant et al, 1982). The predicted secondary structure of stem-loop I was similar in all U1s, except E. macha type A U1 and L. gigantea sequences (Supplementary file S6 c and i), whose internal loops were 2-3 nts bigger.…”

Schizosaccharomyces pombe U4 small nuclear RNA closely resembles vertebrate U4 and is required for growth

“…This demonstrates that Schiz. pombe V4 retains a functional "Sm-binding site": a short nucleotide sequence, which is apparently sufficient to permit the association of RNA species with the "Sm-proteins" that are common between VI, 2, 4 and 5 (Branlant et al, 1982;Mattaj & De Robertis, 1985). A sequence (AGVVVUGG) similar to a consensus Sm-binding site is found in a singlestranded region of Schizo pombe U4.…”

The 5′-terminal sequence of U1 RNA complementary to the consensus 5′ splice site of hnRNA is single-stranded in intact U1 snRNP particles

“…The T1 fingerprint analysis ( Figure 5) strongly suggests that this fragment is derived by cleavage of Ul RNA at the region between nucleotides 132 and 136 ( Figure 6). This region is part of the so-called domain A, a common structural feature of all snRNAs Ul, U2, U4 and U5 (17). Domain A has been suggested to be the primary binding site for one or more of the snRNP proteins (33), and in support of this, pentanucleotide 3 induces RNase H cleavage only in the isolated Ul RNA but not in Ul RNA as part of the snRNP.…”

“…RNase H will only hydrolyse Ul RNA if the sequence complementary to an individual DNA oligonucleotide is single-stranded and thus able to form a short DNA-RNA hybrid. One of the oligodeoxynucleotides employed is also complementary to a region of Ul RNA between nucleotides 132 and 136 which is part of the so-called domain A (17). The snRNPs used for this study were purified by immune affinity chromatography with antibodies specific for the 2,2,7-trimethylguanosine(m3G)-containing cap structure of the snRNAs (18 (18).…”