Computational prediction of CRISPR-impaired non-coding regulatory regions [article]

Nina Baumgarten, Florian Schmidt, Martin Wegner, Marie Hebel, Manuel Kaulich, Marcel H. Schulz
2020 bioRxiv   pre-print
Genome-wide CRISPR screens are becoming more widespread and allow the simultaneous interrogation of thousands of genomic regions. Although recent progress has been made in the analysis of CRISPR screens, it is still an open problem how to interpret CRISPR mutations in non-coding regions of the genome. Most of the tools concentrate on the interpretation of mutations introduced in gene coding regions. We introduce a computational pipeline that uses epigenomic information about regulatory elements
more » ... for the interpretation of CRISPR mutations in non-coding regions. We illustrate our approach on the analysis of a genome-wide CRISPR screen in hTERT-RPE-1 cells and reveal novel regulatory elements that mediate chemoresistance against doxorubicin in these cells. We infer links to established and to novel chemoresistance genes. Our approach is general and can be applied on any cell type and with different CRISPR enzymes.
doi:10.1101/2020.12.22.423923 fatcat:uccffnb5djddtaesvmtct7g52i