PUBLICATION

mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay

Authors
Anderson, J.L., Mulligan, T.S., Shen, M.C., Wang, H., Scahill, C.M., Tan, F.J., Du, S.J., Busch-Nentwich, E.M., Farber, S.A.
ID
ZDB-PUB-171122-14
Date
2017
Source
PLoS Genetics   13: e1007105 (Journal)
Registered Authors
Anderson, Jennifer, Busch-Nentwich, Elisabeth, Farber, Steven, Mulligan, Tim
Keywords
none
MeSH Terms
  • Animals
  • Clustered Regularly Interspaced Short Palindromic Repeats/genetics
  • Codon, Nonsense
  • Exons/genetics
  • Gene Editing/methods
  • Gene Expression/genetics
  • Genome
  • Genomics
  • Mutagenesis/genetics
  • Mutation/genetics
  • Nonsense Mediated mRNA Decay/genetics*
  • Nonsense Mediated mRNA Decay/physiology
  • RNA Stability/genetics
  • RNA, Messenger/genetics
  • RNA, Messenger/metabolism
  • Zebrafish/genetics*
PubMed
29161261 Full text @ PLoS Genet.
Abstract
As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes. We analyzed mRNA processing in seven zebrafish lines with mutations expected to disrupt gene function, generated by CRISPR/Cas9 or ENU mutagenesis methods. Five of the seven lines showed evidence of altered mRNA processing: one through a skipped exon that did not lead to a frame shift, one through nonsense-associated splicing that did not lead to a frame shift, and three through the use of cryptic splice sites. These results highlight the need for a methodical analysis of the mRNA produced in mutant lines before making conclusions or embarking on studies that assume loss of function as a result of a given genomic change. Furthermore, recognition of the types of adaptations that can occur may inform the strategies of mutant generation.
Genes / Markers
Figures
Show all Figures
Expression
Phenotype
Mutation and Transgenics
Human Disease / Model Data
Sequence Targeting Reagents
Fish
Antibodies
Orthology
Engineered Foreign Genes
Mapping
Errata and Notes