Genome Editing Techniques in Plant and Animal Systems

Advances in genome editing have transformed our capacity to interrogate and engineer biological systems across both plant and animal kingdoms. Early platforms based on zinc-finger nucleases and transcription activator-like effector nucleases (TALENs) established precise double-strand cleavage but were labour-intensive to design. The emergence of RNA-guided nucleases, most notably CRISPR/Cas systems, has democratised genome engineering by combining ease of programmability with high efficiency. Variants of Cas9, Cas12 and newly characterised effectors such as Fanzor extend the scope of targeted DNA cleavage, base conversion and epigenetic modulation. Base editors and prime editors enable single-base substitutions or small insertions without double-strand breaks, reducing cytotoxicity and off-target activity. Delivering these reagents in vivo relies on viral and nonviral vectors, nanoparticle vehicles or ribonucleoprotein complexes, each balancing efficiency, tissue specificity and immune compatibility. In plants, multiplex editing of gene families and metabolic pathways accelerates trait stacking and functional genomics. In animals, precise edits underpin disease modelling, gene therapy and xenotransplantation. Ongoing innovations address off-target prediction, allele-specific correction and long-range genomic rearrangements. Together, these methods offer unprecedented opportunities for sustainable agriculture, biodiversity conservation and human health, while raising considerations for biosafety and regulatory frameworks.

Research from Nature Portfolio

Recent studies have identified a eukaryotic RNA-guided endonuclease, termed Fanzor, which shares ancestral relationships with prokaryotic OMEGA effectors and Cas12. Biochemical characterisation and cryogenic electron microscopy reveal structural conservation of the catalytic core and guide-RNA recognition, enabling reprogramming of Fanzor for precise human genome engineering. This discovery broadens the toolkit of programmable nucleases beyond the bacterial immune system and suggests novel avenues for editing in complex eukaryotic contexts. Another report demonstrates a dual-CRISPR/Cas12a assay configured for one-pot amplification and visual detection of viral RNA at point-of-care. Although primarily applied to pathogen diagnostics, this system exemplifies multiplexed CRISPR collateral cleavage and minimal-instrument workflows, underscoring the adaptability of CRISPR platforms for both editing and rapid molecular readouts in animal health.

Genome Editing Techniques in Plant and Animal Systems publication trend

The graph below shows the total number of articles in genome editing techniques in plant and animal systems across all publications each year (not limited to Nature Index journals).

Technical terms

CRISPR/Cas9: RNA-guided nuclease system that induces site-specific double-strand breaks in DNA.

Cas12 (Cpf1): Alternative RNA-guided endonuclease with distinct PAM requirements and staggered cleavage.

Base editor: Fusion of a deaminase enzyme to Cas protein allowing direct conversion of single nucleotides without double-strand breaks.

Prime editor: Cas9 nickase fused to reverse transcriptase for programmable insertions, deletions or substitutions using a prime editing guide RNA.

Guide RNA (gRNA): Short RNA molecule that directs Cas effectors to complementary genomic loci.

Homology‐directed repair (HDR): DNA repair pathway using a homologous template to introduce precise edits at a break site.

Non-homologous end joining (NHEJ): Error-prone repair mechanism that rejoins double‐strand breaks, often generating insertions or deletions.

References

1. CRISPR/Cas9 therapeutics: progress and prospects. Signal Transduction and Targeted Therapy (2023).
2. Fanzor is a eukaryotic programmable RNA-guided endonuclease. Nature (2023).
3. A CRISPR/Cas9 toolkit for multiplex genome editing in plants. BMC Plant Biology (2014).
4. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biology (2016).
5. Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay. Nature Communications (2020).