A mechanism for RNA splicing.

Abstract

ABSrRACT The most abundant of the stable small nuclear RNAs of eukaryotic cells, U-1 small nuclear RNA, is exactly complementary to the consensus sequences at RNA splice sites.We propose that this RNA is the recognition component of the nuclear RNA splicing enzyme and forms base pairs with both ends of an intron so as to align them for cutting and splicing.Intramolecular RNA splicing, first discovered for the adenovirus-specific RNA (1-3), occurs in the expression of numerous eukaryotic genes (4). At present there are three known classes of DNA sequences at splice sites, found in genes for a chloroplast tRNA (5), yeast tRNAs (6), and vertebrate mRNAs (7-9). Each class has distinctive sequence characteristics. For the splice sites of vertebrate genes, comparisons of a limited set of sequences (7,8) showed that introns were flanked in every case by 5'-/ G-T-(intron)-A-G/-3'. Subsequent sequences have borne this out (9) and have shown that the 5' ("upstream") and 3' ("downstream") ends of introns have approximately the following consensus or "optimal" sequences: 5'-(exon)-A-G/G-T-A-A-G-T-A-(intron) -T-T-T-T-Y-T-T-T-T-T-T-C-T-T-N-C-A-G/G-(exon)-3'.The upstream and downstream splice sites in nuclear RNA molecules presumably must be brought together for RNA splicing to occur. This could be achieved by intramolecular base pairing, but no appropriate complementary structures have been found reproducibly in the vicinity of splice sites (10). We propose an alternative mechanism in which upstream and downstream splicing sites form base pairs with another RNA molecule which could be a structural component of the splicing enzyme(s). There may be an example comparable to this proposed splicing system in RNase P of Escherichia coli, which is a site-specific RNase with an essential RNA component (I1).THE MODEL We considered that such an effector RNA might be found among the discrete; stable, small nuclear RNAs (snRNAs) that are ubiquitous in eukaryotic cells (12). Sequences have been reported for several of these (13-17). When we compared the sequence of U-i snRNA from rat hepatoma (13) with sequences of the optimal splice site (Fig. 1), we discovered that the first 10 nucleotides after the U-1 RNA cap are perfectly complementary to the 9 nucleotides of the optimal upstream site and to the tetranucleotide C-A-G/G from the optimal downstream site. The next 11 nucleotides of U-I are purine-rich and can be aligned with the pyrimidine-rich segment of the downstream site. This striking complementarity with splicing sites is not found in any of the other snRNAs now sequenced, which are U-2 (14), 4.5S (15), and adenovirus VA-I RNAs (16,17). We therefore propose that U-1 snRNA in the RNA splicing complex forms base pairs with both ends of an intron in a large nuclear RNA molecule as shown in Fig. 2, bringing

Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes

“…These consensus sequences, termed the donor site or 5h splice site [5h (C\A)AGGU(A\-G)AGU 3h] and acceptor site or 3h splice site [5h (U\C)11N-(U\C)AG(G\A) 3h], signal the precise location for excision by the spliceosome and subsequent removal of an intron [24,25]. The two splice sites overlap the intron\exon boundaries.…”

Structure-function relations in E. coli 16S RNA

“…For example, Ul RNA has been linked to mRNA splicing (Lerner et al, 1980;Rogers and Wall, 1980) while the RNA moiety of RNAase P has been shown to be absolutely required for its activity (Kole et al, 1980). RNA has even been shown to be capable of making and breaking phosphodiester bonds in the complete absence of protein (Kruger et al, 1982).…”

Sequences of mRNAs derived from genome RNA segment 7 of influenza virus: colinear and interrupted mRNAs code for overlapping proteins.

“…For M2 mRNA, the junction is between nucleotides 51 and 740; for mRNA3, the junction is between nucleotides 11 and 740. More complicated consensus sequences involving nucleotides complementary with the U1 small nuclear RNA have been observed (20,21 Al and A2, probable 3' junctions of the intervening sequences, which are the same for M2 mRNA and mRNA3.…”