Mouse Genetics Glossary

An allele is a specific version of a gene, a genotype is the combination of alleles an organism carries, and a phenotype is the observable outcome of that genetic makeup interacting with environmental factors.

The process of introducing genetically modified cells into a developing mouse blastocyst to create a chimera—an organism composed of cells from both the host embryo and the engineered cells.

Planned mating strategies used to generate offspring of specific genotypes—such as heterozygous, homozygous, or compound mutant combinations—from established genetically modified lines.

Comprehensive evaluation of an engineered mouse line's physiological, molecular, and behavioral traits before any experimental intervention. This establishes a reference dataset that differentiates inherent strain variability from phenotypic changes.

A genetically engineered mouse in which a specific gene can be selectively inactivated in chosen tissues, cell types, or developmental stages—enabling precise studies of gene function while avoiding embryonic lethality or systemic effects.

A genetically engineered mouse in which a target gene is permanently deleted or disrupted in every cell of the body from the earliest stages of development. This classical approach provides foundational insight into gene function.

A bacteriophage P1-derived site-specific recombination technology that utilizes Cre recombinase to mediate genomic modifications at engineered LoxP sequences. This technology underpins conditional gene engineering approaches in mammalian genetics.

A mouse line that expresses Cre recombinase from a promoter specific to certain tissues, cell types, or developmental stages, enabling targeted genomic recombination only in those cells.

Procedures necessary to maintain healthy and genetically defined mouse lines. Backcrossing involves introducing a targeted mutation onto a standardized inbred background to minimize genetic variability.

The genetic replacement of mouse cytokines, receptors, or ligand–receptor pairs with their human equivalents. These models recreate critical components of the human immune network for accurate evaluation of human biologics.

The most widely used inbred mouse strain in biomedical research and the reference strain for the mouse genome sequence. C57BL/6 mice are preferred for gene targeting due to extensive phenotypic characterization, ES cell compatibility, robust breeding performance, and compatibility with the majority of tissue-specific Cre driver lines.

Two major substrains of C57BL/6 mice that diverged decades ago through separate breeding programs at Jackson Laboratory (J) and NIH (N). Key differences include: C57BL/6J carries an Nnt deletion affecting glucose metabolism and insulin secretion; C57BL/6N has intact Nnt but some colonies carry the rd8 Crb1 retinal degeneration allele. C57BL/6N is the standard background for IKMC knockout resources.

A mutant allele that encodes a protein that not only loses its normal function but also interferes with the activity of the wild-type protein. The resulting phenotype mimics or exceeds the severity of a full loss-of-function mutation.

An independent site-specific recombination platform derived from bacteriophage D6, using Dre recombinase to recognize rox sites for DNA rearrangements orthogonal to both Cre-lox and Flp-FRT.

A genetic alteration caused by the insertion or deletion of nucleotides that shifts the reading frame of a gene's coding sequence. This shift changes the downstream amino acid sequence and often introduces premature stop codons, resulting in truncated or nonfunctional proteins.

A floxed gene contains two LoxP sites flanking an essential DNA segment, allowing Cre recombinase to mediate excision or inversion for conditional gene regulation. LoxP sites are 34 base pair sequences recognized by Cre recombinase.

A yeast-derived site-specific recombination mechanism enabling targeted DNA excision, inversion, or integration through the interaction of Flp recombinase with FRT sites. It serves as an orthogonal complement to Cre-lox in mammalian genetics.

A gain-of-function mutation increases or creates a new activity for a gene or protein, while a loss-of-function mutation reduces or abolishes normal function. Both mutation types play central roles in disease biology and are critical tools in genetic research.

The process by which a genetic modification introduced into an organism is passed on to its offspring through reproductive (germ) cells. It confirms that the engineered change is stably integrated into the genome and can be inherited by future generations.

Molecular methods used to detect, confirm, and quantify genetic modifications in engineered mouse models. These assays verify whether the targeted allele, wild-type allele, or transgene is present in an individual animal's DNA.

Ensures that a targeted genetic modification has been successfully passed through reproductive cells to offspring. Coat-color markers serve as a visible indicator of ES cell contribution in chimeric founder animals.

Immunological compatibility factors that influence successful transplantation and maintenance of human cells or tissues in humanized mouse models. These parameters determine whether engrafted human immune systems function properly.

A precise DNA repair and genetic engineering mechanism that uses a homologous sequence as a template to exchange or replace genetic material. It allows for accurate correction or insertion of DNA sequences at defined genomic loci.

A high-fidelity DNA repair mechanism that uses a homologous DNA sequence as a template to accurately fix double-strand breaks. Unlike NHEJ, HDR ensures precise integration or correction of genetic material.

A genetically engineered mouse in which one or more human genes, immune system components, or biological pathways have been introduced to replicate aspects of human physiology, bridging the gap between basic research and clinical translation.

Hypomorphic alleles partially reduce gene function, and null alleles abolish it entirely. Both are critical tools in mouse model research for studying gene dosage and loss-of-function effects.

Genetically engineered mice with key inhibitory immune receptors—such as PD-1, PD-L1, and CTLA-4—replaced with their human equivalents. Essential for evaluating antibody and biologic therapies targeting immune checkpoint pathways.

Genetically engineered mice in which murine major histocompatibility complex (MHC) genes are replaced with human leukocyte antigen (HLA) alleles. These models recapitulate key aspects of human antigen presentation and adaptive immunity.

A genetically engineered version of a gene that can be activated or deleted at a specific time by an external stimulus. The most widely used approach is the Cre-ER system, allowing researchers to precisely control the timing of gene modification in vivo.

A system that fuses Cre recombinase to a modified estrogen-receptor ligand-binding domain (ERT2), confining it to the cytoplasm until activation by tamoxifen, thus providing temporal control of recombination.

The orientation of recombination sites determines genetic outcomes: direct repeats drive excision (deletion) of the intervening DNA, whereas inverted repeats cause inversion of the DNA segment.

A genetically engineered mouse in which a specific gene has been permanently inactivated ('knocked out') to study its biological function, role in disease, and potential as a therapeutic target.

A genetically engineered mouse in which a specific DNA sequence—such as a gene, cDNA, mutation, reporter, or human ortholog—is inserted into a defined genomic locus to add or modify gene function.

A cassette containing a transcriptional STOP sequence flanked by LoxP sites that blocks gene expression until excised by Cre recombinase. This molecular 'gatekeeper' design is essential for gain-of-function models requiring precise gene induction.

Introducing extended genomic DNA segments—often spanning 100–300 kilobases—into the mouse genome using bacterial artificial chromosomes (BACs) to preserve native gene context and regulatory elements.

Missense mutations change a single nucleotide in a coding region, resulting in a different amino acid in the protein sequence. Nonsense mutations convert a codon into a premature stop signal, producing truncated and often nonfunctional proteins.

The presence of two or more genetically distinct cell populations within the same organism that originated from a single fertilized egg. In genetic engineering, mosaicism arises when not all cells carry the intended genetic modification.

A DNA double-strand break repair pathway that directly ligates broken DNA ends without requiring a homologous template. It is an efficient but error-prone mechanism that can introduce small insertions or deletions (indels).

A continuous stretch of DNA or RNA sequence that can be translated into a protein. It begins with a start codon (typically AUG in mRNA) and ends with a stop codon (UAA, UAG, or UGA). ORFs represent the protein-coding potential of a gene.

Procedures to determine whether unintended genomic changes have occurred during editing, while also verifying that the targeted locus remains structurally sound and functionally unaffected.

A single-nucleotide change in a DNA sequence that can modify how a gene is expressed or how its protein product functions. Even a one-base change can dramatically alter phenotype, making point mutations crucial to understanding genetic disease, evolution, and therapeutic intervention.

Non-coding DNA sequences that control when, where, and how genes are expressed. They function as molecular switches that coordinate transcriptional activity by interacting with transcription factors, chromatin modifiers, and the basal transcription machinery.

A technique used to generate transgenic mice by directly introducing foreign DNA into the pronucleus of a fertilized one-cell embryo. The injected DNA integrates randomly into the mouse genome.

A reporter gene is an easily detectable genetic marker—such as GFP, LacZ, or luciferase—inserted into a mouse genome to visualize gene expression, monitor cellular activity, or trace lineage in vivo.

A genetic construct introduced to restore the normal function of a gene that has been disrupted, deleted, or mutated. Complementation confirms that an observed phenotype results directly from loss of that gene's function.

A well-characterized safe harbor site in the mouse genome, located on chromosome 6. It supports stable and ubiquitous expression of inserted genes without interfering with nearby genomic functions and is the standard integration site for transgenic constructs.

A ubiquitously expressed safe harbor locus on mouse chromosome 6 used for targeted transgene insertion. The Rosa26 locus supports stable, position-independent expression without disrupting neighboring genes, making it the most commonly used integration site for constitutive or conditional transgene expression, Cre driver lines, and reporter alleles.

A genetically engineered mouse in which a reporter gene (GFP, tdTomato, LacZ, or luciferase) is inserted at an endogenous locus to visualize gene expression under native regulatory control. Unlike transgenic reporters, knockin reporters are subject to all endogenous transcriptional and post-transcriptional regulation, providing accurate spatiotemporal expression patterns.

Unintended recombinase activity occurring without inducer presence or outside targeted tissues, leading to unwanted genomic alterations or mosaicism. Understanding its sources is essential for accurate genetic modeling.

Measurable signals—typically fluorescent, enzymatic, or luminescent—produced by genetically encoded reporter genes such as GFP, LacZ, and luciferase. These are integrated into mouse models to visualize gene expression and track cell lineages.

A defined region of the genome where a transgene or targeted DNA sequence can be inserted without disrupting endogenous genes or regulatory networks. Integration at a safe harbor site allows stable, predictable expression.

Genes incorporated into targeting vectors to identify and isolate cells that have successfully integrated a genetic modification. Common markers include neomycin resistance (NeoR) and puromycin resistance (PuroR).

The precise insertion of a single copy of a DNA construct into a defined location within the genome. This approach prevents the variability, gene silencing, and expression artifacts associated with random multi-copy insertions.

A precise genome engineering strategy in which a transgene is inserted into a well-characterized, transcriptionally active, and non-disruptive genomic locus to ensure predictable and stable expression.

A classical DNA analysis method that remains the gold standard for verifying correct targeting, integration patterns, and copy number of inserted constructs in engineered mouse models.

Sequencing tools for verifying the accuracy of DNA junctions at targeted integration sites. These assays confirm that homologous recombination or HDR occurred precisely without insertions, deletions, or rearrangements.

Single humanized models express one human gene of an interacting pair, while double humanized models replace both receptor and ligand to achieve full human-to-human signaling compatibility within the mouse system.

Tetracycline-responsive transcription systems that regulate gene expression reversibly through doxycycline administration, allowing dose- and time-dependent control of transgene activity.

A temporal gene deletion system using CreERT2 fusion protein—Cre recombinase fused to a mutant estrogen receptor ligand-binding domain (ERT2). Without tamoxifen, CreERT2 is sequestered in the cytoplasm by HSP90 chaperones. Tamoxifen administration triggers nuclear translocation and LoxP recombination, enabling gene deletion at defined timepoints in adult animals.

A synthetic DNA construct designed to introduce specific genetic modifications into a genome through homologous recombination or HDR. It contains sequences known as homology arms that align precisely with the genomic target locus.

A genetically engineered mouse model in which a target gene is selectively deleted or inactivated in a specific tissue or cell type, rather than throughout the entire organism. Typically relies on the Cre-LoxP recombination system.

The activation or deactivation of a genetic modification at a specific time or during a defined developmental window. This strategy allows researchers to study gene function dynamically and distinguish developmental effects from later ones.

How effectively a mouse model replicates key aspects of human biology, ensuring findings are predictive of clinical outcomes. Disease modeling involves engineering mice to mimic specific human pathological conditions for studying mechanisms and testing therapies.

Describes whether the two copies of a gene in an organism are identical (homozygous) or different (heterozygous). Determining zygosity is crucial for interpreting phenotypes and designing experiments.