Optimizing Nervous System-Specific Gene Targeting with Cre Driver Lines: Prevalence of Germline Recombination and Influencing Factors

Neuron. 2020 Apr 8;106(1):37-65.e5. doi: 10.1016/j.neuron.2020.01.008. Epub 2020 Feb 5.


The Cre-loxP system is invaluable for spatial and temporal control of gene knockout, knockin, and reporter expression in the mouse nervous system. However, we report varying probabilities of unexpected germline recombination in distinct Cre driver lines designed for nervous system-specific recombination. Selective maternal or paternal germline recombination is showcased with sample Cre lines. Collated data reveal germline recombination in over half of 64 commonly used Cre driver lines, in most cases with a parental sex bias related to Cre expression in sperm or oocytes. Slight differences among Cre driver lines utilizing common transcriptional control elements affect germline recombination rates. Specific target loci demonstrated differential recombination; thus, reporters are not reliable proxies for another locus of interest. Similar principles apply to other recombinase systems and other genetically targeted organisms. We hereby draw attention to the prevalence of germline recombination and provide guidelines to inform future research for the neuroscience and broader molecular genetics communities.

Keywords: Cre-lox; conditional gene targeting; conditional knockin; conditional knockout; conditional reporter; germline recombination; molecular genetics; mosaic recombination; parental sex bias; site-specific recombinase.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Female
  • Gene Targeting / methods*
  • Genes, Reporter
  • Germ Cells
  • Integrases / genetics*
  • Male
  • Mice
  • Mice, Transgenic
  • Mosaicism
  • Neurons / metabolism*
  • Oocytes / metabolism*
  • Recombination, Genetic / genetics*
  • Spermatozoa / metabolism*


  • Cre recombinase
  • Integrases