Generation of Stable mRNA Fragments and Translation of N-Truncated Proteins Induced by Antisense Oligodeoxynucleotides

Thoma, Christian; Hasselblatt, Peter; Köck, Josef; Chang, Shau-Feng; Hockenjos, Birgit; Will, Hans; Hentze, Matthias W.; Blum, Hubert E.; Weizsäcker, Fritz von; Offensperger, Wolf‐Bernhard

doi:10.1016/s1097-2765(01)00364-1

Cited by 37 publications

(37 citation statements)

References 40 publications

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“…6E). The ability of similarly cleaved transcripts to be translated as functionally distinct proteins has been previously reported (Thoma et al 2001;Hasselblatt et al 2005;Snider et al 2009). Although an N-terminal proteomics study, analogous to the 59-terminal transcriptomic analysis conducted here, is required to determine the full contribution of this process to protein diversity, examination of publicly available N-terminal peptide sequences reveals an enrichment of peptides with N-terminal methionine downstream from cleavage sites relative to random positions in the coding sequence (Supplemental Fig.…”

Section: Post-transcriptional Cleavage Generates a Diversity Of Long mentioning

confidence: 82%

“…Although such long RNAs may ultimately be cleaved into smaller RNAs, we propose that truncated mRNA isoforms may also potentially be translated to C-or N-terminal truncated proteins. There are numerous precedents to support this proposal (Thoma et al 2001;Hasselblatt et al 2005;Snider et al 2009). For example, a recent study found that a range of endogenous small and long RNA transcripts are generated from the DUX4 gene, including a 39-cleaved isoform that undergoes translation from an internal methionine to generate a functionally distinct truncated protein that lacks the N-terminal domain (Snider et al 2009).…”

Section: Discussionmentioning

confidence: 95%

“…Also, small antisense RNAs may direct cleavage by annealing with complementary RNA and forming a doublestranded substrate for RNase H cleavage (Cerritelli and Crouch 2009). Although the cleavage of these transcripts results in rapid degradation of the upstream capped, non-polyadenylated fragment, the 39-uncapped polyadenylated fragment can exhibit remarkable stability, being efficiently translated even when the site of cleavage occurs within a few nucleotides upstream of the initiation codon (Thoma et al 2001;Hasselblatt et al 2005). Furthermore, the resultant N-terminal-truncated proteins have distinct functional differences from the full-length form.…”

Section: Discussionmentioning

confidence: 99%

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Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Mercer¹,

Dinger²,

Bracken³

et al. 2010

Genome Res.

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The complexity of the eukaryotic transcriptome is generated by the interplay of transcription initiation, termination, alternative splicing, and other forms of post-transcriptional modification. It was recently shown that RNA transcripts may also undergo cleavage and secondary 59 capping. Here, we show that post-transcriptional cleavage of RNA contributes to the diversification of the transcriptome by generating a range of small RNAs and long coding and noncoding RNAs. Using genomewide histone modification and RNA polymerase II occupancy data, we confirm that the vast majority of intraexonic CAGE tags are derived from post-transcriptional processing. By comparing exonic CAGE tags to tissue-matched PARE data, we show that the cleavage and subsequent secondary capping is regulated in a developmental-stage-and tissue-specific manner. Furthermore, we find evidence of prevalent RNA cleavage in numerous transcriptomic data sets, including SAGE, cDNA, small RNA libraries, and deep-sequenced size-fractionated pools of RNA. These cleavage products include mRNA variants that retain the potential to be translated into shortened functional protein isoforms. We conclude that post-transcriptional RNA cleavage is a key mechanism that expands the functional repertoire and scope for regulatory control of the eukaryotic transcriptome.

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Section: Post-transcriptional Cleavage Generates a Diversity Of Long mentioning

confidence: 82%

Section: Discussionmentioning

confidence: 95%

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Mercer¹,

Dinger²,

Bracken³

et al. 2010

Genome Res.

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show abstract

“…4B, lanes 8 and 9) or together (data not shown). Inhibition was specific, as reprobing the same Western blot showed no changes in the level of either GAPDH or ␣-tubulin, and long exposures of the Western blot failed to detect truncated ASA protein, as can happen with antisense oligodeoxynucleotides (data not shown) (28). It was also possible that the anti-ASA U1 snRNAs were inhibiting expression by inducing aberrant splicing.…”

Section: Effects Of Increased Distance Multiple Binding Sites and Imentioning

confidence: 88%

Inhibiting expression of specific genes in mammalian cells with 5′ end-mutated U1 small nuclear RNAs targeted to terminal exons of pre-mRNA

Fortes

Cuevas

Guan

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

127

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Reducing or eliminating expression of a given gene is likely to require multiple methods to ensure coverage of all of the genes in a given mammalian cell. We and others [Furth, P. A., Choe, W. T., Rex, J. H., Byrne, J. C., and Baker, C. C. (1994) Mol. Cell. Biol. 14, 5278 -5289] have previously shown that U1 small nuclear (sn) RNA, both natural or with 5 end mutations, can specifically inhibit reporter gene expression in mammalian cells. This inhibition occurs when the U1 snRNA 5 end base pairs near the polyadenylation signal of the reporter gene's pre-mRNA. This base pairing inhibits poly(A) tail addition, a key, nearly universal step in mRNA biosynthesis, resulting in degradation of the mRNA. Here we demonstrate that expression of endogenous mammalian genes can be efficiently inhibited by transiently or stably expressed 5 end-mutated U1 snRNA. Also, we determine the inhibitory mechanism and establish a set of rules to use this technique and to improve the efficiency of inhibition. Two U1 snRNAs base paired to a single pre-mRNA act synergistically, resulting in up to 700-fold inhibition of the expression of specific reporter genes and 25-fold inhibition of endogenous genes. Surprisingly, distance from the U1 snRNA binding site to the poly(A) signal is not critical for inhibition, instead the U1 snRNA must be targeted to the terminal exon of the pre-mRNA. This could reflect a disruption by the 5 end-mutated U1 snRNA of the definition of the terminal exon as described by the exon definition model. mutant U1 snRNAs ͉ gene expression inhibition ͉ polyadenylation inhibition

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“…This means that the mRNA encoding Mos could itself play a role in the meiotic maturation and that its integrity is required. The degradation of Mos mRNA could, for example, lead to the release of regulatory RNA-binding proteins or generate new stable mRNA fragments encoding for N-terminal truncated proteins, 64 which proteins could dramatically interfere with meiotic maturation. 63 Although not necessary for GVBD, Mos remains a powerful inducer of meiotic maturation when microinjected.…”

Section: The Role Of Mos Synthesismentioning

confidence: 99%

Oocyte Maturation, Mos and Cyclins—A Matter of Synthesis: Two Functionally Redundant Ways to Induce Meiotic Maturation

Haccard

Jessus²

2006

Cell Cycle

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The development of an immature oocyte into a fertilizable gamete is a process known as meiotic maturation. In vertebrates, it corresponds to the transition from the prophase arrest of the first meiotic division (usually considered as a late G 2 phase) to the metaphase arrest of the second meiotic division. This transition is controlled by modulating the activity of the cyclin B-Cdc2 complex, MPF (M-phase promoting factor), the universal regulator of the G 2 /M transition. Meiotic maturation of frog oocytes is triggered by steroid hormones through a rapid, necessary and sufficient suppression of PKA and requires ongoing protein synthesis. A long-standing question has been to identify key protein(s) required to trigger the activation of MPF in response to the hormonal signal. Here we will discuss data supporting the view that steroids bring about meiotic maturation through functionally redundant pathways involving synthesis of Mos or of cyclin proteins, reinforcing the robustness of the system.

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Generation of Stable mRNA Fragments and Translation of N-Truncated Proteins Induced by Antisense Oligodeoxynucleotides

Cited by 37 publications

References 40 publications

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome

Inhibiting expression of specific genes in mammalian cells with 5′ end-mutated U1 small nuclear RNAs targeted to terminal exons of pre-mRNA

Oocyte Maturation, Mos and Cyclins—A Matter of Synthesis: Two Functionally Redundant Ways to Induce Meiotic Maturation

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