p53 activation by knockdown technologies.

Mara E. Robu, Jon D. Larson, Aidas Nasevicius, Soraya Beiraghi, Charles Brenner, Steven A. Farber, Stephen C Ekker

Research output: Contribution to journalArticle

615 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
JournalPLoS Genetics
Volume3
Issue number5
DOIs
StatePublished - May 25 2007
Externally publishedYes

Fingerprint

Morpholinos
Antisense Oligonucleotides
oligonucleotides
targeting
Technology
cell death
Zebrafish
Cell Death
Danio rerio
small interfering RNA
Small Interfering RNA
assay
assays
Stored Messenger RNA
Genes
RNA
gene
acridine orange
Acridine Orange
genes

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics
  • Cancer Research
  • Genetics(clinical)

Cite this

Robu, M. E., Larson, J. D., Nasevicius, A., Beiraghi, S., Brenner, C., Farber, S. A., & Ekker, S. C. (2007). p53 activation by knockdown technologies. PLoS Genetics, 3(5). https://doi.org/10.1371/journal.pgen.0030078

p53 activation by knockdown technologies. / Robu, Mara E.; Larson, Jon D.; Nasevicius, Aidas; Beiraghi, Soraya; Brenner, Charles; Farber, Steven A.; Ekker, Stephen C.

In: PLoS Genetics, Vol. 3, No. 5, 25.05.2007.

Research output: Contribution to journalArticle

Robu, ME, Larson, JD, Nasevicius, A, Beiraghi, S, Brenner, C, Farber, SA & Ekker, SC 2007, 'p53 activation by knockdown technologies.', PLoS Genetics, vol. 3, no. 5. https://doi.org/10.1371/journal.pgen.0030078
Robu ME, Larson JD, Nasevicius A, Beiraghi S, Brenner C, Farber SA et al. p53 activation by knockdown technologies. PLoS Genetics. 2007 May 25;3(5). https://doi.org/10.1371/journal.pgen.0030078
Robu, Mara E. ; Larson, Jon D. ; Nasevicius, Aidas ; Beiraghi, Soraya ; Brenner, Charles ; Farber, Steven A. ; Ekker, Stephen C. / p53 activation by knockdown technologies. In: PLoS Genetics. 2007 ; Vol. 3, No. 5.
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