Genome-editing terminology
What is ‘Base Editing’ and what does ‘dCas9’ mean? New to the world of genome-editing? Learn and review common abbreviations and definitions in the field of genome-engineering here.
Need a reminder about key terminology for stem cells? Explore common stem cell terminology with our stem cell glossary.
A
- Allele: One of two or more versions of a gene. An individual inherits two alleles for each gene, one from each parent.
B
- Base Editing: A form of gene editing that enables the direct, irreversible conversion of one DNA base pair into another at a target genomic locus without making double-stranded DNA breaks.
- Bioinformatics: The science of collecting and analyzing complex biological data such as genetic codes.
C
- Cas12 (formerly Cpf1): A class 2 type V CRISPR system characterized by its ability to create staggered DNA double-strand breaks and has been utilized for genome editing and as a diagnostic tool due to its collateral cleavage activity.
- Cas13 (formerly C2c2): A class 2 type VI CRISPR system known for targeting RNA instead of DNA, offering potential for RNA editing and viral interference applications.
- Cas14: A smaller class 2 type V CRISPR system known for targeting single-stranded DNA (ssDNA) and being applicable in precise DNA editing and diagnostics.
- Cas9: An enzyme that uses a guide RNA to cut DNA at a specific sequence, allowing for gene editing. It is the most widely used Cas enzyme in CRISPR technologies.
- CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats): A family of DNA sequences in bacteria and archaea that forms the basis of the CRISPR-Cas9 genome editing technology. It allows for precise editing of DNA at specific locations.
- CRISPR Library: A collection of gRNA sequences that target multiple genes, used for large-scale screening experiments to study gene function.
- CRISPRa (CRISPR activation): Similar to CRISPRi, but designed to enhance gene expression by targeting activation domains to specific DNA sequences.
- CRISPRi (CRISPR interference): A CRISPR-based technology that uses dead Cas9 (dCas9) to block transcription without cutting the DNA, effectively silencing gene expression.
D
- dCas9 (Dead Cas9): A modified form of the Cas9 protein that can bind to DNA but cannot cut it. Used in CRISPRi and CRISPRa for gene regulation without altering the DNA sequence.
- DNA Ligase: An enzyme that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond.
- Double Strand Break (DSB): A type of DNA damage that involves the breakage of both strands of the DNA double helix. DSBs are key intermediates in various forms of gene editing, including CRISPR-Cas9 mediated genome editing, where they are introduced at specific genomic locations to induce repair mechanisms that can result in targeted mutations or insertions.
E
- Electroporation: A technique used to introduce nucleic acids into cells by applying an electrical field to increase cell membrane permeability.
- Ethical Considerations in Gene Editing: The set of moral principles and debates surrounding the modification of genetic material, especially in humans, including concerns about safety, consent, and the potential for unintended consequences.
G
- Gene Drive: A genetic engineering technology that promotes the inheritance of a particular gene to increase its prevalence in a population.
- Gene Editing: A method by which the genetic material of living organisms is altered. It can involve inserting, deleting, or replacing DNA within the organism’s genome.
- Gene Silencing: The process of suppressing gene expression, which can be achieved through various methods including RNA interference (RNAi) and CRISPRi.
- Gene Therapy: A technique that uses genes to treat or prevent disease by inserting a gene into a patient’s cells instead of using drugs or surgery.
- Genetic Drift: A mechanism of evolution that refers to random fluctuations in the frequencies of alleles from one generation to the next.
- Genome: The complete set of DNA in an organism, including all of its genes and noncoding sequences.
- Genome Engineering: The field of science that involves modifying an organism’s genetic material to achieve desired traits or outcomes.
- Germline Gene Therapy: The transfer of genes into the germline cells (sperm or eggs) of an organism, leading to changes that are heritable by offspring.
H
- HDR (Homology Directed Repair): A mechanism for repairing double-strand DNA breaks using a homologous sequence as a template, allowing for precise gene editing when a donor template is provided.
- Homology Arms: Short sequences of DNA that flank a DNA insert in genetic engineering. They are identical to sequences at the target site and facilitate homologous recombination.
I
- Indel: A mutation resulting from the insertion or deletion of bases in the genome.
K
- Knock-in: Inserting a specific gene or sequence into a particular locus within an organism’s genome.
- Knockout: Completely disabling a gene’s function, often by deleting a portion of the gene’s sequence.
M
- Molecular Clone: The process of making multiple copies of a specific DNA sequence using recombinant DNA technology.
- Multiplexing: The process of editing multiple genes at once, which can be achieved with CRISPR technology by using several sgRNAs targeting different genes simultaneously.
N
- NHEJ (Non-Homologous End Joining): A pathway that repairs double-strand breaks in DNA by directly ligating the break ends together without the need for a homologous template, often leading to insertions or deletions.
O
- Off-Target Effects: Unintended modifications made by gene-editing tools at locations in the genome other than the intended target site.
P
- PAM (Protospacer Adjacent Motif): A short DNA sequence following the DNA region targeted by CRISPR-Cas9. It is essential for Cas9 binding and cleavage.
- Plasmid: A small DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. Widely used as a vector in genetic engineering.
- Precision Medicine: An approach to patient care that allows doctors to select treatments that are most likely to help patients based on a genetic understanding of their disease.
- Prime Editing: A versatile and precise method of gene editing that combines a Cas9 nickase with a reverse transcriptase, allowing for the introduction of insertions, deletions, and all 12 possible base-to-base conversions without requiring double-strand breaks or donor DNA templates.
- Protospacer: The target DNA sequence in the genome that CRISPR-Cas systems are programmed to target and cleave.
R
- Recombinant DNA: DNA that has been formed artificially by combining constituents from different organisms.
- Regulatory Frameworks for Gene Editing: The legal and policy structures established by governments and international bodies to oversee and control the use of gene-editing technologies.
- RNA Interference (RNAi): A biological process in which RNA molecules inhibit gene expression or translation, by neutralizing targeted mRNA molecules.
S
- sgRNA (Single-guide RNA): A synthetic RNA molecule designed to guide Cas9 to a specific location in the genome by base pairing with the target DNA sequence.
- Somatic Cell Gene Therapy: The transfer of genes into the somatic cells of a patient to treat a genetic disease.
- Synthetic Biology: An interdisciplinary branch of biology and engineering that involves designing and constructing new biological parts, devices, and systems.
T
- TALENs (Transcription Activator-Like Effector Nucleases): Customizable proteins that can be engineered to cut specific DNA sequences, similar to ZFNs but with a different DNA-binding mechanism.
- Transfection: The process of deliberately introducing nucleic acids into cells. Various methods exist, including chemical, lipid-based, and physical methods like electroporation.
- Transgenic Organism: An organism that has been genetically modified to contain DNA from another organism, often from a different species.
V
- Vector: In molecular biology, a vehicle used to artificially carry foreign genetic material into another cell, where it can be replicated and/or expressed. Examples include plasmids, viruses, and artificial chromosomes.
- Viral Transduction: A method of gene delivery where viruses are used as vectors to insert genetic material into cells.
Z
- Zinc Finger Nucleases (ZFNs): Engineered DNA-binding proteins that facilitate targeted editing of the genome by creating double-strand breaks in DNA at specific locations.