Systematical Chromosome Rearrangement Reshapes the Landscape of Gene Expression in Human Cells (ATAC-seq)

Chromosome rearrangement plays an important role in development and cancerogenesis. At present, large-scale chromosome rearrangement has been performed in the simple eukaryote, wine yeast, but the relative research in mammalian cells remains at the level of individual chromosome rearrangement. In this study, we used CRISPR-Cas9 to target the highly repetitive human endogenous retrotransposons, LINE-1 (L1) and Alu, resulting in a large number of DNA double-strand breaks in the chromosomes. Karyotype analysis and genome re-sequencing confirmed that we have achieved systematic chromosome rearrangement (SCR) in human cells. The copy number variations (CNVs) and the chromosomal translocations of the rearranged genomes showed typical patterns observed in tumor cells. Transcriptome and ATAC sequencings further revealed that the epigenetic and the transcriptomic landscapes of the genomes were deeply reshaped by the systemic chromosome rearrangement. Gene expressions related to DNA repair, cell cycle and apoptosis were greatly altered to facilitate the cell survival under the severe stress induced by the large-scale chromosomal breaks. In addition, we found that the cells acquired CRISPR-Cas9 resistance after SCR by interfering with the Cas9 mRNA. Our study provided a new application of CRISPR-Cas9 and a practical approach for SCR for complex mammalian genomes.