Detailed mechanisms for unintended large DNA deletions with CRISPR, base editors, and prime editors
Hwang, G.-h.; Kim, S.-H.; Oh, M.; Kim, S.; Habib, O.; Jang, H.-K.; Kim, H. S.; Kim, C. H.; Kim, S.; Bae, S.
Show abstract
CRISPR-Cas9 nucleases are versatile tools for genetic engineering cells and function by producing targeted double-strand breaks (DSBs) in the DNA sequence. However, the unintended production of large deletions (>100 bp) represents a challenge to the effective application of this genome-editing system. We optimized a long-range amplicon sequencing system and developed a k-mer sequence-alignment algorithm to simultaneously detect small DNA alteration events and large DNA deletions. With this workflow, we determined that CRISPR-Cas9 induced large deletions at varying frequencies in cancer cell lines, stem cells, and primary T cells. With CRISPR interference screening, we determined that end resection and the subsequent TMEJ [DNA polymerase theta-mediated end joining] repair process produce most large deletions. Furthermore, base editors and prime editors also generated large deletions despite employing mutated Cas9 "nickases" that produce single-strand breaks. Our findings reveal an important limitation of current genome-editing tools and identify strategies for mitigating unwanted large deletion events.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Harnessing DSB repair to promote efficient homology-dependent and -independent prime editing 97%
- Engineered minimal type I CRISPR-Cas system for transcriptional activation and base editing in human cells 97%
- Chemically-inducible CRISPR/Cas9 circuits for ultra-high dynamic range gene perturbation 97%
Similar papers in this journal
- Interrogation of cancer gene dependencies reveals novel paralog interactions of autosome and sexchromosome encoded genes 96%
- High-throughput screens of PAM-flexible Cas9 variants for gene knock-out and transcriptional modulation 96%
- Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing 95%
Similar papers in this journal
- High throughput PRIME editing screens identify functional DNA variants in the human genome 96%
- Discovery of novel DNA cytosine deaminase activities enables a nondestructive single-enzyme methylation sequencing method for base resolution high-coverage methylome mapping of cell-free and ultra-low input DNA 95%
- Requirements for establishment and epigenetic stability of mammalian heterochromatin 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.