Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line

被引:211
作者
Essletzbichler, Patrick [1 ]
Konopka, Tomasz [2 ]
Santoro, Federica [1 ]
Chen, Doris [2 ]
Gapp, Bianca V. [2 ]
Kralovics, Robert [2 ]
Brummelkamp, Thijn R. [2 ,3 ]
Nijman, Sebastian M. B. [1 ,2 ]
Buerckstuemmer, Tilmann [1 ]
机构
[1] Haplogen GmbH, A-7030 Vienna, Austria
[2] Austrian Acad Sci CeMM, Res Ctr Mol Med, A-7090 Vienna, Austria
[3] Netherlands Canc Inst, NL-7066 CX Amsterdam, Netherlands
关键词
EMBRYONIC STEM-CELLS; CHROMOSOMAL DELETIONS; GENETIC SCREENS; CAS9; INVERSIONS; NUCLEASES; CRISPR-CAS9; DERIVATION; LEUKEMIA;
D O I
10.1101/gr.177220.114
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Near-haploid human cell lines are instrumental for genetic screens and genome engineering as gene inactivation is greatly facilitated by the absence of a second gene copy. However, no completely haploid human cell line has been described, hampering the genetic accessibility of a subset of genes. The near-haploid human cell line HAP1 contains a single copy of all chromosomes except for a heterozygous 30-megabase fragment of Chromosome 15. This large fragment encompasses 330 genes and is integrated on the long arm of Chromosome 19. Here, we employ a CRISPR/Cas9-based genome engineering strategy to excise this sizeable chromosomal fragment and to efficiently and reproducibly derive clones that retain their haploid state. Importantly, spectral karyotyping and single-nucleotide polymorphism (SNP) genotyping revealed that engineered-HAPloid (eHAP) cells are fully haploid with no gross chromosomal aberrations induced by Cas9. Furthermore, whole-genome sequence and transcriptome analysis of the parental HAP1 and an eHAP cell line showed that transcriptional changes are limited to the excised Chromosome 15 fragment. Together, we demonstrate the feasibility of efficiently engineering megabase deletions with the CRISPR/Cas9 technology and report the first fully haploid human cell line.
引用
收藏
页码:2059 / 2065
页数:7
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