Genetic and Biochemical Analysis of Alternative RNA Splicing

Hodges, Dianne; Bernstein, Sanford I.

doi:10.1016/s0065-2660(08)60399-5

Cited by 61 publications

(36 citation statements)

References 349 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Exon splicing enhancers have been shown to be important elements in the efficiency of exon recognition (2,14,26). One major class of exon enhancers are the purine-rich enhancers, exemplified by the caldesmon and cTNT enhancers compared in this study (4, 5, 8, 9, 15, 20, 22, 25, 31-34, 36, 38, 41-43).…”

Section: Discussionmentioning

confidence: 75%

“…Even short purine-rich enhancers can have major effects on the efficiency of exon inclusion. Most characterized purine-rich enhancers reside in alternative exons and have been shown to be essential sequence elements for exon inclusion, usually via the activation of weak 3Ј splice sites (2,14,26). Exon enhancers are often interchangeable in their ability to activate weak 3Ј splice sites, not only between genes (8,17,20,36,(41)(42)(43), but also between species (13), suggesting that either most enhancers bind the same factors or the bound factors have interchangeable activities.…”

mentioning

confidence: 99%

See 1 more Smart Citation

A Short Sequence within Two Purine-Rich Enhancers Determines 5′ Splice Site Specificity

Elrick¹,

Humphrey²,

Cooper

et al. 1998

Molecular and Cellular Biology

View full text Add to dashboard Cite

Purine-rich enhancers are exon sequences that promote inclusion of alternative exons, usually via activation of weak upstream 3 splice sites. A recently described purine-rich enhancer from the caldesmon gene has an additional activity by which it directs selection of competing 5 splice sites within an alternative exon. In this study, we have compared the caldesmon enhancer with another purine-rich enhancer from the chicken cardiac troponin T (cTNT) gene for the ability to regulate flanking splice sites. Although similar in sequence and length, the two enhancers demonstrated strikingly different specificities towards 5 splice site choice when placed between competing 5 splice sites in an internal exon. The 32-nucleotide caldesmon enhancer caused effective usage of the exon-internal 5 splice site, whereas the 30-nucleotide cTNT enhancer caused effective usage of the exon-terminal 5 splice site. Both enhancer-mediated splicing pathways represented modulation of the default pathway in which both 5 splice sites were utilized. Each enhancer is multipartite, consisting of two purine-rich sequences of a simple (GAR) n repeat interdigitated with two enhancer-specific sequences. The entire enhancer was necessary for maximal splice site selectivity; however, a 5-to 7-nucleotide region from the 3 end of each enhancer dictated splice site selectivity. Mutations that interchanged this short region of the two enhancers switched specificity. The portion of the cTNT enhancer determinative for 5 splice site selectivity was different than that shown to be maximally important for activation of a 3 splice site, suggesting that enhancer environment can have a major impact on activity. These results are the first indication that individual purine-rich enhancers can differentiate between flanking splice sites. Furthermore, localization of the specificity of splice site choice to a short region within both enhancers indicates that subtle differences in enhancer sequence can have profound effects on the splicing pathway.Sequences within exons in addition to splice sites have emerged in the last several years as powerful determinants of splicing efficiency (2, 13, 24). Of these sequences, the purinerich exon enhancers containing the generic core sequence (GAR) n (R ϭ G or A) (42) have received the most attention (4,6,9,17,20,23,25,32,(41)(42)(43). Even short purine-rich enhancers can have major effects on the efficiency of exon inclusion. Most characterized purine-rich enhancers reside in alternative exons and have been shown to be essential sequence elements for exon inclusion, usually via the activation of weak 3Ј splice sites (2,14,26). Exon enhancers are often interchangeable in their ability to activate weak 3Ј splice sites, not only between genes (8,17,20,36,(41)(42)(43), but also between species (13), suggesting that either most enhancers bind the same factors or the bound factors have interchangeable activities.Purine-rich enhancers bind to members of the arginineserine-rich class of splicing factors (29, 44), the S/R proteins (re...

show abstract

Section: Discussionmentioning

confidence: 75%

mentioning

confidence: 99%

A Short Sequence within Two Purine-Rich Enhancers Determines 5′ Splice Site Specificity

Elrick¹,

Humphrey²,

Cooper

et al. 1998

Molecular and Cellular Biology

View full text Add to dashboard Cite

show abstract

“…The question remains as to which regulatory mechanism is involved in reversing the proportions of the shorter and longer variants when cells become malignant. Alternative splicing is often regulated in a tissue, sex, and/or developmental stage-specific fashion 24,25 and regulated by factors that are expressed in a tissue-specific manner and are necessary for the splicing events to occur. 26 It may thus well be possible that proliferating cells have different regulation of splicing.…”

Section: Discussionmentioning

confidence: 99%

A comparison of genomic structures and expression patterns of two closely related flanking genes in a critical lung cancer region at 3p21.3

et al. 1999

View full text Add to dashboard Cite

In the search for a tumour suppressor gene in the 3p21.3 region we isolated two genes, RBM5 and RBM6. Gene RBM5 maps to the region which is homozygously deleted in the small cell lung cancer cell line GLC20; RBM6 crosses the telomeric breakpoint of this deletion. Sequence comparison revealed that at the amino acid level both genes show 30% identity. They contain two zinc finger motifs, a bipartite nuclear signal and two RNA binding motifs, suggesting that the proteins for which RBM5 and RBM6 are coding have a DNA/RNA binding function and are located in the nucleus. Northern and Southern analysis did not reveal any abnormalities. By SSCP analysis of 16 lung cancer cell lines we found only in RBM5 a single presumably neutral mutation. By RT-PCR we demonstrated the existence of two alternative splice variants of RBM6, one including and one excluding exon 5, in both normal lung tissue and lung cancer cell lines. Exclusion of exon 5 results in a frameshift which would cause a truncated protein of 520 amino acids instead of 1123 amino acids. In normal lung tissue, the relative amount of the shorter transcript was much greater than that in the lung tumour cell lines, which raises the question whether some tumour suppressor function may be attributed to the derived shorter protein.

show abstract

“…The choice of splicing pattern is thought to be determined by proteins that bind to regulatory sequences in the pre-mRNA and act to enhance or suppress spliceosome assembly at specific splice sites. Although several proteins have been identified in Drosophila that act in this way, the regulatory molecules that direct alternative splicing are mostly unknown and poorly understood (McKeown 1992;Hodges and Bernstein 1994;Inoue et al 1995;Adams et al 1996).…”

mentioning

confidence: 99%

A new regulatory protein, KSRP, mediates exon inclusion through an intronic splicing enhancer.

Min

Turck²,

Nikolic³

et al. 1997

Genes Dev.

311

253

View full text Add to dashboard Cite

We have purified and cloned a new splicing factor, KSRP. KSRP is a component of a multiprotein complex that binds specifically to an intronic splicing enhancer element downstream of the neuron-specific c-src N1 exon. This 75-kD protein induces the assembly of five other proteins, including the heterogeneous nuclear ribonucleoprotein F, onto the splicing enhancer. The sequence of the KSRP cDNA indicates that the protein contains four K homology RNA-binding domains and an unusual carboxy-terminal domain. KSRP is similar to two proteins, FUSE-binding protein and P-element somatic inhibitor. KSRP is expressed in both neural and non-neural cell lines, although it is present at higher levels in neural cells. Antibodies specific for KSRP inhibit the splicing of the N1 exon in vitro. Moreover, this inhibition of N1 splicing can be rescued by the addition of purified KSRP. KSRP is likely to regulate splicing from a number of intronic splicing enhancer sequences.[Key Words: Alternative splicing; regulatory protein; KSRP; intronic splicing enhancer; RNA-binding protein]

show abstract

Genetic and Biochemical Analysis of Alternative RNA Splicing

Cited by 61 publications

References 349 publications

A Short Sequence within Two Purine-Rich Enhancers Determines 5′ Splice Site Specificity

A Short Sequence within Two Purine-Rich Enhancers Determines 5′ Splice Site Specificity

A comparison of genomic structures and expression patterns of two closely related flanking genes in a critical lung cancer region at 3p21.3

A new regulatory protein, KSRP, mediates exon inclusion through an intronic splicing enhancer.

Contact Info

Product

Resources

About