Prototype Based Recognition of Splice Sites

2006 ◽  
pp. 25-55
Author(s):  
Barbara Hammer ◽  
Marc Strickert ◽  
Thomas Villmann
Keyword(s):  
Splice Sites

Role of small nuclear RNAs in eukaryotic gene expression

2013 ◽  
Vol 54 ◽  
pp. 79-90 ◽  
Author(s):  
Saba Valadkhan ◽  
Lalith S. Gunawardane
Keyword(s):  
Gene Expression ◽  
Protein Interactions ◽  
Rna Stability ◽  
Splice Sites ◽  
Branch Site ◽  
Small Nuclear Rnas ◽  
Eukaryotic Gene Expression ◽  
Eukaryotic Gene ◽  
Rna Biogenesis

Eukaryotic cells contain small, highly abundant, nuclear-localized non-coding RNAs [snRNAs (small nuclear RNAs)] which play important roles in splicing of introns from primary genomic transcripts. Through a combination of RNA–RNA and RNA–protein interactions, two of the snRNPs, U1 and U2, recognize the splice sites and the branch site of introns. A complex remodelling of RNA–RNA and protein-based interactions follows, resulting in the assembly of catalytically competent spliceosomes, in which the snRNAs and their bound proteins play central roles. This process involves formation of extensive base-pairing interactions between U2 and U6, U6 and the 5′ splice site, and U5 and the exonic sequences immediately adjacent to the 5′ and 3′ splice sites. Thus RNA–RNA interactions involving U2, U5 and U6 help position the reacting groups of the first and second steps of splicing. In addition, U6 is also thought to participate in formation of the spliceosomal active site. Furthermore, emerging evidence suggests additional roles for snRNAs in regulation of various aspects of RNA biogenesis, from transcription to polyadenylation and RNA stability. These snRNP-mediated regulatory roles probably serve to ensure the co-ordination of the different processes involved in biogenesis of RNAs and point to the central importance of snRNAs in eukaryotic gene expression.

scholarly journals Comparative Analysis of the Human Dystrophin and Utrophin Gene Structures

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 793-798
Author(s):  
Uberto Pozzoli ◽  
Manuela Sironi ◽  
Rachele Cagliani ◽  
Giacomo P Comi ◽  
Alessandra Bardoni ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Splice Sites ◽  
Gene Structures ◽  
Human Dystrophin

Abstract We present analysis of intronic sequences in the human DMD and UTRN genes. In both genes accumulation of repeated elements could account for intron expansion. Out-of-frame rod-domain exons have stronger splice sites and are separated by significantly longer introns as compared to in-frame exons. These features are unique for the two homologs and not shared by other spectrin superfamily genes.

scholarly journals Induction of cryptic pre-mRNA splice-switching by antisense oligonucleotides

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kristin A. Ham ◽  
Niall P. Keegan ◽  
Craig S. McIntosh ◽  
May T. Aung-Htut ◽  
Khine Zaw ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Antisense Oligonucleotides ◽  
Live Cells ◽  
Splice Sites ◽  
Cryptic Splice Site ◽  
Exon Definition ◽  
Rna Targets ◽  
Cryptic Splice Sites ◽  
Six Genes ◽  
Intended Effect

AbstractAntisense oligomers (AOs) are increasingly being used to modulate RNA splicing in live cells, both for research and for the development of therapeutics. While the most common intended effect of these AOs is to induce skipping of whole exons, rare examples are emerging of AOs that induce skipping of only part of an exon, through activation of an internal cryptic splice site. In this report, we examined seven AO-induced cryptic splice sites in six genes. Five of these cryptic splice sites were discovered through our own experiments, and two originated from other published reports. We modelled the predicted effects of AO binding on the secondary structure of each of the RNA targets, and how these alterations would in turn affect the accessibility of the RNA to splice factors. We observed that a common predicted effect of AO binding was disruption of the exon definition signal within the exon’s excluded segment.

Functional splice sites in a zebrafish LINE and their influence on zebrafish gene expression

Gene ◽  
2007 ◽  
Vol 390 (1-2) ◽  
pp. 221-231 ◽  
Author(s):  
Masato Tamura ◽  
Masaki Kajikawa ◽  
Norihiro Okada
Keyword(s):  
Gene Expression ◽  
Splice Sites

scholarly journals Breast Cancer Patient Prognosis Is Determined by the Interplay between TP53 Mutation and Alternative Transcript Expression: Insights from TP53 Long Amplicon Digital PCR Assays

Cancers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1531
Author(s):  
Annette Lasham ◽  
Nicholas Knowlton ◽  
Sunali Y. Mehta ◽  
Antony W. Braithwaite ◽  
Cristin G. Print
Keyword(s):  
Breast Cancer ◽  
Gene Locus ◽  
Tp53 Mutation ◽  
P53 Protein ◽  
Tp53 Gene ◽  
Digital Pcr ◽  
Protein Isoforms ◽  
Alternative Transcript ◽  
Transcript Expression ◽  
Splice Sites

The TP53 gene locus is capable of producing multiple RNA transcripts encoding the different p53 protein isoforms. We recently described multiplex long amplicon droplet digital PCR (ddPCR) assays to quantify seven of eight TP53 reference transcripts in human tumors. Here, we describe a new long amplicon ddPCR assay to quantify expression of the eighth TP53 reference transcript encoding ∆40p53α. We then applied these assays, alongside DNA sequencing of the TP53 gene locus, to tumors from a cohort of New Zealand (NZ) breast cancer patients. We found a high prevalence of mutations at TP53 splice sites in the NZ breast cancer cohort. Mutations at TP53 intron 4 splice sites were associated with overexpression of ∆133TP53 transcripts. Cox proportional hazards survival analysis showed that interplay between TP53 mutation status and expression of TP53 transcript variants was significantly associated with patient outcome, over and above standard clinical and pathological information. In particular, patients with no TP53 mutation and a low ratio of TP53 transcripts t2 to t1, which derive from alternative intron 1 acceptor splice sites, had a remarkably good outcome. We suggest that this type of analysis, integrating mutation and transcript expression, provides a step-change in our understanding of TP53 in cancer.

Unusual splice sites in the E1A?E1B cotranscripts synthesized in adenovirus type 40-infected A549 cells

1994 ◽  
Vol 139 (3-4) ◽  
pp. 389-402 ◽  
Author(s):  
S. Ishida ◽  
Y. Fujinaga ◽  
K. Fujinaga ◽  
N. Sakamoto ◽  
S. Hashimoto
Keyword(s):  
A549 Cells ◽  
Adenovirus Type ◽  
Splice Sites
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