Genetic compensation induced by deleterious mutations but not gene knockdowns

Nature

Volumn 524, Issue 7564, 2015, Pages 230-233

  Rossi, Andrea ^a   Kontarakis, Zacharias ^a   Gerri, Claudia ^a   Nolte, Hendrik ^a,b   Hölper, Soraya ^a   Krüger, Marcus ^a,b   Stainier, Didier Y R ^a  

^a MAX PLANCK INSTITUTE FOR HEART AND LUNG RESEARCH   (Germany)

^b UNIVERSITY OF COLOGNE   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; EGF LIKE DOMAIN MULTIPLE 7; GUIDE RNA; MESSENGER RNA; MORPHOLINO OLIGONUCLEOTIDE; PROTEIN P53; PROTEOME; TRANSCRIPTOME; UNCLASSIFIED DRUG; EGFL7 PROTEIN, ZEBRAFISH; ELASTIN MICROFIBRIL INTERFACE LOCATED PROTEIN; MEMBRANE PROTEIN; VASCULOTROPIN A; VEGF PROTEIN, ZEBRAFISH; ZEBRAFISH PROTEIN;

CELLS AND CELL COMPONENTS; CYPRINID; DICOTYLEDON; GENE EXPRESSION; GENETIC ANALYSIS; MUTATION; PHENOTYPE; PROTEIN; RODENT;

5' UNTRANSLATED REGION; ANGIOGENESIS; ARTICLE; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; DISEASE SEVERITY; EMBRYO; EXTRACELLULAR MATRIX; GENE DELETION; GENE EXPRESSION REGULATION; GENE SILENCING; HUMAN; KNOCKOUT GENE; NONHUMAN; PHENOTYPE; PHENOTYPIC VARIATION; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; RNA SEQUENCE; RNA TRANSLATION; STOP CODON; TRANSCRIPTION ELONGATION; TRANSCRIPTION INITIATION; UPREGULATION; VASCULAR DISEASE; WESTERN BLOTTING; ZEBRA FISH; ALLELE; ANIMAL; BRAIN; COMPARATIVE STUDY; CRISPR CAS SYSTEM; EMBRYOLOGY; GENE REPRESSION; GENETICS; LARVA; METABOLISM; MUTATION; PATHOLOGY; RNA INTERFERENCE;

ANIMALIA; ARABIDOPSIS; DANIO RERIO;

ALLELES; ANIMALS; BRAIN; CRISPR-CAS SYSTEMS; GENE KNOCKDOWN TECHNIQUES; LARVA; MEMBRANE GLYCOPROTEINS; MORPHOLINOS; MUTATION; PHENOTYPE; PROTEOME; RNA INTERFERENCE; SUPPRESSION, GENETIC; TRANSCRIPTOME; UP-REGULATION; VASCULAR ENDOTHELIAL GROWTH FACTOR A; ZEBRAFISH; ZEBRAFISH PROTEINS;

EID: 84939482880     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14580     Document Type: Article

References (29)

1. Kok, F. O. et al. Reverse genetic screening reveals poor correlation between morpholino-induced and mutant phenotypes in zebrafish. Dev. Cell 32, 97-108 (2015).
2. Stainier, D. Y., Kontarakis, Z. and Rossi, A. Making sense of anti-sense data. Dev. Cell 32, 7-8 (2015).
3. Law, S. H. and Sargent, T.D. The serine-threonine protein kinase PAK4 is dispensable in zebrafish: identification of a morpholino-generated pseudophenotype. PLoS ONE 9, e100268 (2014).
4. Daude, N. et al. Knockout of the prion protein (PrP)-like Sprn gene does not produce embryonic lethality in combination with PrP(C)-deficiency. Proc. Natl Acad. Sci. USA 109, 9035-9040 (2012).
5. De Souza, A. T. et al. Transcriptional and phenotypic comparisons of Ppara knockout and siRNA knockdown mice. Nucleic Acids Res. 34, 4486-4494 (2006).
6. Smart, N. and Riley,P.R. Thymosinb4invasculardevelopment, responseto research commentary. Circ. Res. 112, 29-30 (2013).
7. Gao, Y. et al. Auxin binding protein 1 (ABP1) is not required for either auxin signaling or Arabidopsis development. Proc. Natl Acad. Sci. USA 112, 2275-2280 (2015).
8. Anon. RNA interference on target. Nature Methods 3, 659 (2006).
9. Robu, M. E. et al. p53 activation by knockdown technologies. PLoS Genet. 3, e78 (2007).
10. Schmidt, M. et al. EGFL7 regulates the collective migration of endothelial cells by restricting their spatial distribution. Development 134, 2913-2923 (2007).
11. Kuhnert, F. et al. Attribution of vascular phenotypes of themurine Egfl7 locus to the microRNA miR-126. Development 135, 3989-3993 (2008).
12. Parker, L. S. et al. The endothelial-cell-derived secreted factor Egfl7 regulates vascular tube formation. Nature 428, 754-758 (2004).
13. Charpentier, M. S. et al. CASZ1 promotes vascular assembly and morphogenesis through the direct regulation of an EGFL7/RhoA-mediated pathway. Dev. Cell 25, 132-143 (2013).
14. Huang, C. et al. VE-statin/Egfl7 siRNA inhibits angiogenesis inmalignant glioma in vitro. Int. J. Clin. Exp. Pathol. 7, 1077-1084 (2014).
15. Cermak, T. et al. Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting. Nucleic Acids Res. 39, e82 (2011).
16. Nichol, D. and Stuhlmann, H. EGFL7: a unique angiogenic signaling factor in vascular development and disease. Blood 119, 1345-1352 (2012).
17. Chi,N.C. et al. Foxn4 directly regulates tbx2b expression and atrioventricular canal formation. Genes Dev. 22, 734-739 (2008).
18. Jin, S. W., Beis, D., Mitchell, T., Chen, J. N. and Stainier, D. Y. Cellular and molecular analyses of vascular tube and lumen formation in zebrafish. Development 132, 5199-5209 (2005).
19. Larson, M. H. et al. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nature Protocols 8, 2180-2196 (2013).
20. Zanetti, M. et al. EMILIN-1 deficiency induces elastogenesis and vascular cell defects. Mol. Cell. Biol. 24, 638-650 (2004).
21. Lelievre, E. et al. VE-statin/egfl7 regulates vascular elastogenesis by interacting with lysyl oxidases. EMBO J. 27, 1658-1670 (2008).
22. Sulem, P. et al. Identification of a large set of rare complete human knockouts. Nature Genet. 47, 448-452 (2015).
23. Doyle, E. L. et al. TAL effector specificity for base 0 of the DNA target is altered in a complex, effector- and assay-dependent manner by substitutions for the tryptophan in cryptic repeat -1. PLoS ONE 8, e82120 (2013).
24. Bedell, V. M. et al. In vivo genome editing using a high-efficiency TALEN system. Nature 491, 114-118 (2012).
25. Jao, L. E., Wente, S. R. and Chen, W. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc. Natl Acad. Sci. USA 110, 13904-13909 (2013).
26. Nolte, H. et al. Global protein expression profiling of zebrafish organs based on in vivo incorporation of stable isotopes. J. Proteome Res. 13, 2162-2174 (2014).
27. Cox, J. and Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnol. 26, 1367-1372 (2008).
28. Cox, J. et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. J. Proteome Res. 10, 1794-1805 (2011).
29. Tusher, V. G., Tibshirani, R. and Chu, G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl Acad. Sci. USA 98, 5116-5121 (2001).