A novel approach to describe a U1 snRNA binding site

Freund, Marcel; Asang, Corinna; Kammler, Susanne; Konermann, Carolin; Krummheuer, Jörg; Hipp, Marianne; Meyer, Imke; Gierling, Wolfram; Theiss, Stephan; Preuss, Thorsten; Schindler, Detlev; Kjems, Jørgen; Schaal, Heiner

doi:10.1093/nar/gkg901

Cited by 89 publications

(94 citation statements)

References 59 publications

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“…2). As recently described, this approach has been successfully applied to compare and predict the strength of U1 snRNP binding to the 59-splice site (Freund et al 2003). The U1 snRNA sequence 59-ACUUACCUG-39 was tested for complementarity to each queried 59-splice site sequence spanning nucleotides À3 to +6.…”

Section: Probability Of Yag and Gu Utilizationmentioning

confidence: 99%

Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site

Dou

Fox-Walsh²,

Baldi³

et al. 2006

RNA

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Alternative pre-mRNA splicing may be the most efficient and widespread mechanism to generate multiple protein isoforms from single genes. Here, we describe the genomic analysis of one of the most frequent types of alternative pre-mRNA splicing, alternative 59-and 39-splice-site selection. Using an EST-based alternative splicing database recording >47,000 alternative splicing events, we determined the frequency and location of alternative 59-and 39-splice sites within the human genome. The most common alternative splice sites used in the human genome are located within 6 nucleotides (nt) of the dominant splice site. We show that the EST database overrepresents alternative splicing events that maintain the reading frame, thus supporting the concept that RNA quality-control steps ensure that mRNAs that encode for potentially harmful protein products are destroyed and do not serve as templates for translation. The most frequent location for alternative 59-splice sites is 4 nt upstream or downstream from the dominant splice site. Sequence analysis suggests that this preference is a consequence of the U1 snRNP binding sequence at the 59-splice site, which frequently contains a GU dinucleotide 4 nt downstream from the dominant splice site. Surprisingly, ;50% of duplicated 39-YAG splice junctions are subject to alternative splicing. This high probability of alternative 39-splice-site activation in close proximity of the dominant 39-splice site suggests that the second step of the splicing may be prone to violate splicing fidelity.

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Section: Probability Of Yag and Gu Utilizationmentioning

confidence: 99%

Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site

Dou

Fox-Walsh²,

Baldi³

et al. 2006

RNA

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show abstract

“…Second, an algorithm developed by Freund et al (2003) was used to evaluate the hydrogen bonding potential between 59 splice sites and the U1 snRNA 59 end. By this measure, 59 splice sites associated with exons 12, 12a, and 13 were in the high complementary (i.e., strong) class, while the 59 splice site associated with exon 13a was in the low complementarity (i.e., weak) class (Table 1).…”

Section: Resultsmentioning

confidence: 99%

“…In almost all cases where sequence divergence occurred, Number of uninterrupted hydrogen bonds to U1 snRNA. (HC) high complimentarity; (LC) low complimentarity (Freund et al 2003). The consensus 59 splice site mutants have H-bond scores of 23.…”

Section: Resultsmentioning

confidence: 99%

A DNA damage signal activates and derepresses exon inclusion in Drosophila TAF1 alternative splicing

Marengo

Wassarman²

2008

RNA

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Signal-dependent alternative splicing is important for regulating gene expression in eukaryotes, yet our understanding of how signals impact splicing mechanisms is limited. A model to address this issue is alternative splicing of Drosophila TAF1 pre-mRNA in response to camptothecin (CPT)-induced DNA damage signals. CPT treatment of Drosophila S2 cells causes increased inclusion of TAF1 alternative cassette exons 12a and 13a through an ATR signaling pathway. To evaluate the role of TAF1 premRNA sequences in the alternative splicing mechanism, we developed a TAF1 minigene (miniTAF1) and an S2 cell splicing assay that recapitulated key aspects of CPT-induced alternative splicing of endogenous TAF1. Analysis of miniTAF1 indicated that splice site strength underlies independent and distinct mechanisms that control exon 12a and 13a inclusion. Mutation of the exon 13a weak 59 splice site or weak 39 splice site to a consensus sequence was sufficient for constitutive exon 13a inclusion. In contrast, mutation of the exon 12a strong 59 splice site or moderate 39 splice site to a consensus sequence was only sufficient for constitutive exon 12a inclusion in the presence of CPT-induced signals. Analogous studies of the exon 13 39 splice site suggest that exon 12a inclusion involves signal-dependent pairing between constitutive and alternative splice sites. Finally, intronic elements identified by evolutionary conservation were necessary for full repression of exon 12a inclusion or full activation of exon 13a inclusion and may be targets of CPT-induced signals. In summary, this work defines the role of sequence elements in the regulation of TAF1 alternative splicing in response to a DNA damage signal.

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“…3A, with the exception of Dbl3, which was not detected by PCR, and therefore its structure is only putative. Furthermore, cryptic SD sites utilized by splice variants were evaluated by their capability to form H bonds with U1 snRNA (26). The H-bond scores of cryptic sites 1, 2, and 3 were found to be 15, 16.9, and 13.8, respectively (http://www.uni-duesseldorf.de/rna/html/hbond-score .php), which corresponds to 14 hydrogen bonds found as a proper consensus.…”

Section: Reevaluation Of Rsv-transformed Rodent Cells and Selected Chmentioning

confidence: 99%

Molecular Events Accompanying Rous Sarcoma Virus Rescue from Rodent Cells and the Role of Viral Gene Complementation

Lounková

Dráberová

Šenigl

et al. 2014

J Virol

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Transformation of rodent cells with avian Rous sarcoma virus (RSV) opened new ways to studying virus integration and expression in nonpermissive cells. We were interested in (i) the molecular changes accompanying fusion of RSV-transformed mammalian cells with avian cells leading to virus rescue and (ii) enhancement of this process by retroviral gene products. The RSV-transformed hamster RSCh cell line was characterized as producing only a marginal amount of env mRNA, no envelope glycoprotein, and a small amount of unprocessed Gag protein. Egress of viral unspliced genomic RNA from the nucleus was hampered, and its stability decreased. Cell fusion of the chicken DF-1 cell line with RSCh cells led to production of env mRNA, envelope glycoprotein, and processed Gag and virus-like particle formation. Proteosynthesis inhibition in DF-1 cells suppressed steps leading to virus rescue. Furthermore, new aberrantly spliced env mRNA species were found in the RSCh cells. Finally, we demonstrated that virus rescue efficiency can be significantly increased by complementation with the env gene and the highly expressed gag gene and can be increased the most by a helper virus infection. In summary, Env and Gag synthesis is increased after RSV-transformed hamster cell fusion with chicken fibroblasts, and both proteins provided in trans enhance RSV rescue. We conclude that the chicken fibroblast yields some factor(s) needed for RSV replication, particularly Env and Gag synthesis, in nonpermissive rodent cells. IMPORTANCE One of the important issues in retrovirus heterotransmission is related to cellular factors that prevent virus replication. Rous sarcoma virus (RSV), a member of the avian sarcoma and leukosis family of retroviruses, is able to infect and transform mammalian cells; however, such transformed cells do not produce infectious virus particles.Using the well-defined model of RSVtransformed rodent cells, we established that the lack of virus replication is due to the absence of chicken factor(s), which can be supplemented by cell fusion. Cell fusion with permissive chicken cells led to an increase in RNA splicing and nuclear export of specific viral mRNAs, as well as synthesis of respective viral proteins and production of virus-like particles. RSV rescue by cell fusion can be potentiated by in trans expression of viral genes in chicken cells. We conclude that rodent cells lack some chicken factor(s) required for proper viral RNA processing and viral protein synthesis.

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A novel approach to describe a U1 snRNA binding site

Cited by 89 publications

References 59 publications

Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site

Genomic splice-site analysis reveals frequent alternative splicing close to the dominant splice site

A DNA damage signal activates and derepresses exon inclusion in Drosophila TAF1 alternative splicing

Molecular Events Accompanying Rous Sarcoma Virus Rescue from Rodent Cells and the Role of Viral Gene Complementation

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