PT  - JOURNAL ARTICLE
AU  - Lindsey Montefiori
AU  - Liana Gonzales
AU  - Zijie Zhang
AU  - Yoav Gilad
AU  - Carole Ober
AU  - Gregory Crawford
AU  - Marcelo Nobrega
AU  - Noboru Jo Sakabe
TI  - Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9
AID  - 10.1101/087890
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 087890
4099  - http://biorxiv.org/content/early/2016/11/22/087890.short
4100  - http://biorxiv.org/content/early/2016/11/22/087890.full
AB  - ATAC-seq is a high-throughput sequencing technique that aims at identifying DNA sequences located in open chromatin. Depending on the cell type, ATAC-seq may yield a high number of mitochondrial sequencing reads (∽20-80% of the reads). As the regions of open chromatin of interest are usually located in the nuclear genome, mitochondrial reads are typically discarded from the analysis. To decrease wasted sequencing, we performed targeted cleavage of mitochondrial DNA using CRISPR/Cas9 and 100 mtDNA-specific guide RNAs. We also tested a modified ATAC-seq protocol that does not include detergent in the cell lysis buffer. Both treatments resulted in considerable reduction of mitochondrial reads (1.7 and 3-fold, respectively). The removal of detergent, however, resulted in increased background and fewer peaks identified. The highest number of peaks and highest quality data was obtained by preparing samples with the original ATAC-seq protocol (using detergent) and treating them with anti-mitochondrial guide RNAs and Cas9. This strategy could lead to considerable cost reduction and improved peak calling when performing ATAC-seq on a moderate to large number of samples and in cell types that contain a large amount of mitochondria.