Identification of chromosome-specific repeats

The Tandem Repeat Finder bioinformatics tools (45) was used to identify tandem repeats in the genome. The human reference genome hg19 was downloaded from the UCSC genome browser (genome.ucsc.edu) for analysis. Unique, highly conserved repeats (Percent matches > 70) with copy number >30 located in a defined site but <5 copies in all other places of the genome were selected as candidates. We further selected candidates with >10 targetable sequences and designed multiple sgRNAs in order to ensure high CRISPR imaging efficiency. The following regions were selected for CRISPR imaging in this study: Ch1R (chromosome 1:1011233–1014805); Ch2R (chromosome 2: 242744740–242749183); Ch3R (chromosome 3: 195502236–195504816); Ch7R (chromosome 7: 158122661–158135328); Ch15R (chromosome 15: 101094498–101098864); Ch17R (chromosome 17: 1642092–1645402); Ch19R (chromosome 19: 59050388–59054262); Ch22R (chromosome 22: 49661285–49662360). Details of all guide sequences for dSpCa9 or dSaCas9 targeting are listed in Supplementary Table S2.