Alternative splicing caused by RNA secondary structure

Solnick, David

doi:10.1016/0092-8674(85)90239-9

Cited by 254 publications

(162 citation statements)

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“…In an effort to understand the possible role of RNA secondary structure in alternative splicing, pre-mRNAs containing artificial inverted repeats were studied. The results of these analyses indicated that the alternative splicing patterns of such premRNAs could be influenced by certain RNA secondary structures, both in vitro (34) and in vivo (14). The relative contribution of RNA secondary structure to splice site selection in vivo may be low, however, because in one study (35) such inverted repeats affected splicing at most only slightly.…”

mentioning

confidence: 86%

Multiple cis-acting sequence elements are required for efficient splicing of simian virus 40 small-t antigen pre-mRNA.

Fu¹,

Colgan²,

Manley³

1988

Mol. Cell. Biol.

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We have determined the effects of a number of mutations in the small-t antigen mRNA intron on the alternative splicing pattern of the simian virus 40 early transcript. Expansion of the distance separating the small-t pre-mRNA lariat branch point and the shared large T-small t 3' splice site from 18 to 29 nucleotides (nt) resulted in a relative enhancement of small-t splicing in vivo. This finding, coupled with the observation that large-T pre-RNA splicing in vitro was not affected by this expansion, suggests that small-t splicing is specifically constrained by a short branch point-3' splice site distance. Similarly, the distance separating the 5' splice site and branch point (48 nt) was found to be at or near a minimum for small-t splicing, because deletions in this region as small as 2 nt dramatically reduced the ratio of small-t to large-T mRNA that accumulated in transfected cells. Finally, a specific sequence within the small-t intron, encompassing the upstream branch sites used in large-T splicing, was found to be an important element in the cell-specific pattern of early alternative splicing. Substitutions within this region reduced the ratio of small-t to large-T mRNA produced in HeLa cells but had only minor effects in human 293 cells.One of the most intriguing questions concerning premRNA splicing in higher eucaryotes is how splice sites are selected. The conserved consensus sequences found at splice sites (6, 26) are of course important factors. However, they are unlikely to be the sole determinants, since "cryptic" splice sites, which are sequences in pre-mRNA that resemble a consensus sequence, are not normally used. More interestingly, some pre-mRNAs undergo alternative splicing, which results in the production of different mature mRNAs from a common precursor by use of different splice sites (for reviews, see references 7, 17, 20, and 29). What factors dictate how splice sites are chosen in such premRNAs, especially in those in which splice site selection is regulated?The view that sequences besides the conserved splice site sequences are involved in alternative splicing has received some experimental support. For example, the alternative splicing patterns of simian virus 40 (SV40) late pre-mRNAs (36) and adenovirus early-region 3 pre-mRNAs (2, 3) were altered in viral mutants containing deletions within exon sequences. In addition, in mutants containing tandem duplications of 5' and 3' splice sites of the ,-globin first intron, splice site selection in vitro appeared to be influenced by the length of adjacent exon sequences (30). One way in which distal sequences might influence splice site selection is through higher-order RNA structure. In an effort to understand the possible role of RNA secondary structure in alternative splicing, pre-mRNAs containing artificial inverted repeats were studied. The results of these analyses indicated that the alternative splicing patterns of such premRNAs could be influenced by certain RNA secondary structures, both in vitro (34) and in vivo (14). The relative ...

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mentioning

confidence: 86%

Multiple cis-acting sequence elements are required for efficient splicing of simian virus 40 small-t antigen pre-mRNA.

Fu¹,

Colgan²,

Manley³

1988

Mol. Cell. Biol.

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“…More recently, a third site which shows some sequence requirements for splicing in vivo has been identified -the branch point, which lies about 30 nucleotides upstream of the 3' splice site (8). Results with deletion mutants and chimeric RNA's have indicated little or no sequence requirements for exon sequences and intron regions not already mentioned (7,9,10) -these other regions may only have a role in determining three-dimensional structures which facilitate the bringing together of companion splice sites as originally proposed (11)(12)(13).…”

Section: Introductionmentioning

confidence: 99%

The length but not the sequence of the polyoma virus late leader exon is important for both late RNA splicing and stability

Adami¹,

Carmichael

1987

Nucl Acids Res

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ABSTRACT'Polyoma virus late RNA processing provides a convenient model system in which to study the mechanics of splicing in vivo. In order to understand further the role of the untranslated "late leader" unit in late RNA processing we have constructed a group of polyoma viruses with deletions and substitutions in the leader exon. This has allowed us to determine that there is a minimum exon size required for both pre-mRNA splicing and stability in this system. We show here that the non-viability of a mutant (ALM) with a 9 base late leader unit is due to a general defect in late RNA splicing. In addition, ALM-infected cells show at least 40-fold depression in the accumulation of late nuclear RNA (spliced or unspliced). The ALM late promoter, however, functions nearly normally. Substituted leader variants with 51-to 96-base long exons of unrelated sequence are viable (G. Adami and G. Carmichael, J. Virol. 58, 417-425, 1986). We show here that late RNA from one of these substituted leader mutants (containing a 51-base leader exon) is spliced at wild type levels, with virtually no defect in accumulation. Thus, in the polyoma system, splice sites separated by only 9 bases can inhibit each others usage, presumably by steric interference. We suggest that this type of inhibition leads to extreme RNA instability. INTRODUCTION Much work in recent years has been directed towards further understanding the mechanism of splicing of mRNA precursors. Analyses of intron sequence requirements for in vivo mRNA splicing in higher eukaryotes originally indicated the importance of the 5' splice site, including the highly conserved GU dinucleotide at the 5' exon-intron boundary, and the 3' splice site, which consists of a similarly highly conserved dinucleotide, AG, at the 3' boundary, but which additionally includes an upstream stretch of pyrimidines (1-7). More recently, a third site which shows some sequence requirements for splicing in vivo has been identified -the branch point,

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“…Secondary structure effects on splicing have previously been introduced artificially by the insertion of inverted repeats that sequester an exon or splice site (Solnick 1985;Solnick and Lee 1987). In some cases, this has resulted in exon skipping in vitro and in vivo.…”

Section: Mechanisms For Activationmentioning

confidence: 99%

A Sequential splicing mechanism promotes selection of an optimal exon by repositioning a downstream 5' splice site in preprotachykinin pre-mRNA.

Nasim¹,

Spears²,

Hoffmann³

et al. 1990

Genes Dev.

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To explore the structural basis of alternative splicing, we have analyzed the splicing of pre-mRNAs containing an optional exon, E4, from the preprotachykinin gene. This gene encodes substance P and related tachykinin peptides by alternative splicing of a common pre-mRNA. We have shown that alternative splicing of preprotachykinin pre-mRNA occurs by preferential skipping of optional E4. The competing mechanism that incorporates E4 into the final spliced RNA is constrained by an initial block to splicing of the immediate upstream intervening sequence (IVS), IVS3. This block is relieved by sequential splicing, in which the immediate downstream IVS4 is removed first. The structural change resulting from the first splicing event is directly responsible for activation of IVS3 splicing. This structural rearrangement replaces IVS4 sequences with E5 and its adjacent IVS5 sequences. To determine how this structural change promoted IVS3 splicing, we asked what structural change(s) would restore activity of IVS3 splicing-defective mutants. The most significant effect was observed by a 2-nucleotide substitution that convened the 5' splice site of E4 to an exact consensus match, GUAAGU. Exon 5 sequences alone were found not to promote splicing when present in one or multiple copies. However, when a 15-nucleotide segment of IVS5 containing GUAAGU was inserted into a splicing-defective mutant just downstream of the hybrid exon segment E4E5, splicing activity was recovered. Curiously, the 72-nucleotide L2 exon of adenovirus, without its associated 5' splice site, activates splicing when juxtaposed to E4. Models for the activation of splicing by an RNA structural change are discussed.

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Alternative splicing caused by RNA secondary structure

Cited by 254 publications

References 46 publications

Multiple cis-acting sequence elements are required for efficient splicing of simian virus 40 small-t antigen pre-mRNA.

Multiple cis-acting sequence elements are required for efficient splicing of simian virus 40 small-t antigen pre-mRNA.

The length but not the sequence of the polyoma virus late leader exon is important for both late RNA splicing and stability

A Sequential splicing mechanism promotes selection of an optimal exon by repositioning a downstream 5' splice site in preprotachykinin pre-mRNA.

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