Written by Charlotte Harrison, Science Writer
A new paper in Nucleic Acid Research shows that it is possible to use CRISPR-based gene editing to induce global chromosome rearrangement (GCR) in human cells. The authors note that this is likely the first time that it has been possible to induce and hence study GCR in human cells.
Until now, large-scale chromosome rearrangement has been performed only in yeast. And although several studies have used CRISPR to generate chromosome rearrangements in mammalian cells, those were only individual rearrangements.
In the new study, the authors used single-guide gRNAs — with up to hundreds of thousands of matching sites — to target the endogenous retrotransposons LINE-1 or Alu in human embryonic kidney cells. Although the introduced double-strand breaks killed the majority of cells, karyotype analysis and whole genome sequencing showed that GCR occurred in the remaining cells.
The genomes of GCR cells showed patterns typically observed in tumour genomes. There were large numbers of inversions, translocations and copy-number variations.
The authors then performed transcriptomic analysis (using RNA sequencing) and epigenetic studies (using ATAC sequencing) to evaluate the effect of GCR on the cell. There were alterations in gene expression in pathways related to cell survival, such as the p53 pathway, DNA repair, the cell cycle and apoptosis.
Flexible and controllable
The authors note that their study provides a new application of CRISPR and an easy-to-use, practical method for inducing GCR in mammalian cells. Moreover, they note that the new method has advantages over the use of chemical or physical stimuli to induce large-scale chromosome rearrangements. The CRISPR method enables researchers to custom-design
the target-site sequences and the number of target sites. As such, the CRISPR method is flexible and controllable, unlike chemical or physical reagents that generate random breaks.
As a next step, the authors intend to use the method in pluripotent stem cells and study the 3D organization of chromatin after GCR.
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