Uncovering the Dynamics of Precise Repair at CRISPR/Cas9-induced Double-Strand Breaks

Ben‐Tov, Daniela; Mafessoni, Fabrizio; Cucuy, Amit; Honig, Arik; Melamed-Bessudo, Cathy; Levy, Avraham A.

doi:10.1101/2023.01.10.523377

Cited by 2 publications

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“…This difference could also explain why we often find that dsODN integrations at target sites for Cas12a are often accompanied by deletions, which is not the case for Cas9 (Chapter 4). We should remember that most of the induced DSBs are likely repaired perfectly without the formation of mutations (Bétermier et al 2014;Ben-Tov et al 2023). These sequences will be cut repeatedly until an error is made, a mutation is introduced, and the target site is lost, which is the visible end-point.…”

Section: Mutation Patterns and Their Implications For Nuclease Select...mentioning

confidence: 99%

“…In HDR, the sister chromatid or another stretch of homologous DNA is used as a template to repair the damage (Chatterjee & Walker, 2017;Manova & Gruszka, 2015) (Figure 1). Especially NHEJ is not always perfect -although far more perfect than often portrayed -and during repair, mutations may arise (Ben-Tov et al, 2023;Bétermier et al, 2014). These mutations frequently take the form of small insertions or deletions (indels) that can disrupt open reading frames or other genetic elements.…”

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CRISPR specificity in tomato

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are re-ligated without the use of a repair template. In HDR, the sister chromatid or another stretch of homologous DNA is used as a template to repair the damage (Chatterjee & Walker, 2017;Manova & Gruszka, 2015) (Figure 1). Especially NHEJ is not always perfect -although far more perfect than often portrayed -and during repair, mutations may arise (Ben-Tov et al., 2023;Bétermier et al., 2014). These mutations frequently take the form of small insertions or deletions (indels) that can disrupt open reading frames or other genetic elements. DNA repair through the HDR pathways is generally perfect, leaves no scars in the form of indels, and can be used to modify the targeted locus precisely or to introduce a piece of genetic material by providing a DNA template. Thus, DSB creation is the first step in producing mutations or specific modifications at a pre-defined genomic region of interest. Figure 1 -Repair of double-strand breaks. The two most frequently employed repair pathways are non-homologous end joining (NHEJ, left) and homology-directed repair (HDR, right). NHEJ may lead to gene disruption by resulting in small insertions and deletions. HDR is generally perfect. Methods for the targeted induction of DSBs Meganucleases Prokaryotes employ sequence-specific DNA cleavage to protect themselves against invading DNA, such as that of bacteriophages. Many prokaryotic genomes encode restriction endonucleases: enzymes that recognize and bind to a specific DNA sequence, which they subsequently cleave. These recognition sites are frequently between 4 and 8 bases and often palindromic (Loenen et al., C H A P T E R 1 -G e n e r a l I n t r o d u c t i o n | 11problems can be partially overcome by utilizing zinc fingers that bind "GNN" motifs, but this, in turn, severely limits the number of genomic loci that can be targeted. Transcription-activator-like effector nucleasesTranscription activator-like effectors (TALEs) are proteins encoded by the plant pathogen Xanthomonas. This bacterium injects TALEs into plant cells, where they bind promoters of specific genes and induce transcription, hijacking the cellular machinery of the plant to the benefit of the bacterium (Boch & Bonas, 2010). Similar to zinc fingers recognizing three bases, each TALE repeat recognizes one specific base. These repeats can be combined in a modular way to produce proteins that bind the desired genomic locus. Like ZFN, TALEs can be fused to a FokI endonuclease domain, forming TALE nucleases (TALENs). A pair of TALENs can form the FokI dimer that causes the DSB (Figure 2). A significant advantage of TALENs over ZFNs is that the binding specificity of a TALE repeat is not affected by a neighbouring repeat, making TALEN design more straightforward than ZFN design. Like ZFNs, TALENs have been applied for targeted genome editing in the animal and plant kingdoms ). Yet, for every target, a new TALEN must be designed and constructed, which can be challenging due to their repetitive nature. CRISPR-Cas systemsWith the advent of ZFNs and TALENs, introducing DSB...

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CRISPR specificity in tomato

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Dual activities of an X-family DNA polymerase regulate CRISPR-induced insertional mutagenesis across species

Weiss,

Kumar,

Chen

et al. 2024

Nat Commun

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The canonical non-homologous end joining (c-NHEJ) repair pathway, generally viewed as stochastic, has recently been shown to produce predictable outcomes in CRISPR-Cas9 mutagenesis. This predictability, mainly in 1-bp insertions and small deletions, has led to the development of in-silico prediction programs for various animal species. However, the predictability of CRISPR-induced mutation profiles across species remained elusive. Comparing CRISPR-Cas9 repair outcomes between human and plant species reveals significant differences in 1-bp insertion profiles. The high predictability observed in human cells links to the template-dependent activity of human Polλ. Yet plant Polλ exhibits dual activities, generating 1-bp insertions through both templated and non-templated manners. Polλ knockout in plants leads to deletion-only mutations, while its overexpression enhances 1-bp insertion rates. Two conserved motifs are identified to modulate plant Polλ‘s dual activities. These findings unveil the mechanism behind species-specific CRISPR-Cas9-induced insertion profiles and offer strategies for predictable, precise genome editing through c-NHEJ.

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Uncovering the Dynamics of Precise Repair at CRISPR/Cas9-induced Double-Strand Breaks

Cited by 2 publications

References 68 publications

CRISPR specificity in tomato

CRISPR specificity in tomato

Dual activities of an X-family DNA polymerase regulate CRISPR-induced insertional mutagenesis across species

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