How Cre Recombinase Works
Cre recombinase is a 38 kDa enzyme derived from bacteriophage P1 that catalyzes site specific recombination between LoxP sequences without requiring cofactors or additional proteins.
Recognition
Cre recognizes the 34 base pair LoxP sequence, consisting of two 13 bp inverted repeats flanking an 8 bp asymmetric spacer region.
Recombination
When two LoxP sites flank a DNA segment in the same orientation, Cre excises the intervening sequence as a circular DNA molecule, leaving a single LoxP site behind.
Irreversibility
Excision is essentially irreversible in vivo because the excised circle is rapidly degraded and reintegration probability is extremely low.
Types of Cre Driver Lines
Neuronal Cre Lines
Immune Cell Cre Lines
Metabolic Tissue Cre Lines
Cardiovascular Cre Lines
Selecting the Right Cre Line
Expression Pattern Verification
- Review published characterization and Cre Portal data
- Cross to Rosa26 reporter to visualize actual recombination
- Some Cre lines have broader expression than names suggest
Timing Considerations
- When does Cre expression begin?
- Early activity may cause embryonic phenotypes
- Cre marks cell lineage permanently
Efficiency Factors
- Not all Cre lines achieve 100% recombination
- Efficiency varies by target locus and Cre level
- Mosaicism may be acceptable or problematic
Cre Line Quality Considerations
Germline Recombination
Problem: Cre expression in germ cells causes global recombination transmitted to offspring, eliminating conditional control.
- •Maintain floxed allele through female if Cre is male germline active
- •Use Cre lines validated for germline silence
- •Always genotype for recombined allele in non Cre tissues
Cre Toxicity
Problem: High Cre expression can cause cellular toxicity independent of target gene through DNA damage at pseudo LoxP sites.
- •Include Cre positive, flox negative controls
- •Distinguish Cre toxicity from gene deletion phenotypes
- •Monitor for growth abnormalities with chronic Cre
Selected Publications Featuring Cre Technology
Research utilizing Cre recombinase mice generated by ingenious targeting laboratory:
Wang L, Noyer L, Jishage M, et al. (2025).
CLNS1A regulates genome stability and cell cycle progression to control CD4 T cell function and autoimmunity. ↗Sci Immunol 10(108): eadq8860
Clausen BE et al. (1999).
Conditional gene targeting in macrophages and granulocytes using LysMcre mice. ↗Transgenic Research 8(4): 265-277
What Researchers Say
“The Hephaestin flox model ingenious has made for us has been great. It has helped generate eight research publications.”
— Joshua Dunaief, PhD, MD
University of Pennsylvania
Start Your Cre Recombinase Project
Our scientific consultants can help you select the optimal Cre driver line or design custom Cre knockin models for your research goals. We also design optimal floxed alleles for Cre dependent conditional knockout.