p53 activation by knockdown technologies.
Morpholino phosphorodiamidate antisense oligonucleotides (MOs) and short interfering RNAs (siRNAs) are commonly used platforms to study gene function by sequence-specific knockdown. Both technologies, however, can elicit undesirable off-target effects. We have used several model genes to study these...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2007-05-01
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| Series: | PLoS Genetics |
| Online Access: | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.0030078&type=printable |
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| author | Mara E Robu Jon D Larson Aidas Nasevicius Soraya Beiraghi Charles Brenner Steven A Farber Stephen C Ekker |
| author_facet | Mara E Robu Jon D Larson Aidas Nasevicius Soraya Beiraghi Charles Brenner Steven A Farber Stephen C Ekker |
| author_sort | Mara E Robu |
| collection | DOAJ |
| description | Morpholino phosphorodiamidate antisense oligonucleotides (MOs) and short interfering RNAs (siRNAs) are commonly used platforms to study gene function by sequence-specific knockdown. Both technologies, however, can elicit undesirable off-target effects. We have used several model genes to study these effects in detail in the zebrafish, Danio rerio. Using the zebrafish embryo as a template, correct and mistargeting effects are readily discernible through direct comparison of MO-injected animals with well-studied mutants. We show here indistinguishable off-targeting effects for both maternal and zygotic mRNAs and for both translational and splice-site targeting MOs. The major off-targeting effect is mediated through p53 activation, as detected through the transferase-mediated dUTP nick end labeling assay, acridine orange, and p21 transcriptional activation assays. Concurrent knockdown of p53 specifically ameliorates the cell death induced by MO off-targeting. Importantly, reversal of p53-dependent cell death by p53 knockdown does not affect specific loss of gene function, such as the cell death caused by loss of function of chordin. Interestingly, quantitative reverse-transcriptase PCR, microarrays and whole-mount in situ hybridization assays show that MO off-targeting effects are accompanied by diagnostic transcription of an N-terminal truncated p53 isoform that uses a recently recognized internal p53 promoter. We show here that MO off-targeting results in induction of a p53-dependent cell death pathway. p53 activation has also recently been shown to be an unspecified off-target effect of siRNAs. Both commonly used knockdown technologies can thus induce secondary but sequence-specific p53 activation. p53 inhibition could potentially be applicable to other systems to suppress off-target effects caused by other knockdown technologies. |
| format | Article |
| id | doaj-art-7a76f464ccd845ad8bc0f250bb3941db |
| institution | OA Journals |
| issn | 1553-7390 1553-7404 |
| language | English |
| publishDate | 2007-05-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS Genetics |
| spelling | doaj-art-7a76f464ccd845ad8bc0f250bb3941db2025-08-20T02:00:55ZengPublic Library of Science (PLoS)PLoS Genetics1553-73901553-74042007-05-0135e7810.1371/journal.pgen.0030078p53 activation by knockdown technologies.Mara E RobuJon D LarsonAidas NaseviciusSoraya BeiraghiCharles BrennerSteven A FarberStephen C EkkerMorpholino phosphorodiamidate antisense oligonucleotides (MOs) and short interfering RNAs (siRNAs) are commonly used platforms to study gene function by sequence-specific knockdown. Both technologies, however, can elicit undesirable off-target effects. We have used several model genes to study these effects in detail in the zebrafish, Danio rerio. Using the zebrafish embryo as a template, correct and mistargeting effects are readily discernible through direct comparison of MO-injected animals with well-studied mutants. We show here indistinguishable off-targeting effects for both maternal and zygotic mRNAs and for both translational and splice-site targeting MOs. The major off-targeting effect is mediated through p53 activation, as detected through the transferase-mediated dUTP nick end labeling assay, acridine orange, and p21 transcriptional activation assays. Concurrent knockdown of p53 specifically ameliorates the cell death induced by MO off-targeting. Importantly, reversal of p53-dependent cell death by p53 knockdown does not affect specific loss of gene function, such as the cell death caused by loss of function of chordin. Interestingly, quantitative reverse-transcriptase PCR, microarrays and whole-mount in situ hybridization assays show that MO off-targeting effects are accompanied by diagnostic transcription of an N-terminal truncated p53 isoform that uses a recently recognized internal p53 promoter. We show here that MO off-targeting results in induction of a p53-dependent cell death pathway. p53 activation has also recently been shown to be an unspecified off-target effect of siRNAs. Both commonly used knockdown technologies can thus induce secondary but sequence-specific p53 activation. p53 inhibition could potentially be applicable to other systems to suppress off-target effects caused by other knockdown technologies.https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.0030078&type=printable |
| spellingShingle | Mara E Robu Jon D Larson Aidas Nasevicius Soraya Beiraghi Charles Brenner Steven A Farber Stephen C Ekker p53 activation by knockdown technologies. PLoS Genetics |
| title | p53 activation by knockdown technologies. |
| title_full | p53 activation by knockdown technologies. |
| title_fullStr | p53 activation by knockdown technologies. |
| title_full_unstemmed | p53 activation by knockdown technologies. |
| title_short | p53 activation by knockdown technologies. |
| title_sort | p53 activation by knockdown technologies |
| url | https://journals.plos.org/plosgenetics/article/file?id=10.1371/journal.pgen.0030078&type=printable |
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