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CRISPR

CRISPR

Genome editing technologies allow scientists to modify an organism’s DNA via the addition, removal, or rearrangement of genetic material at specific genomic locations. These types of techniques could potentially be used to cure genetic disorders such as hemophilia and sickle cell anemia. One popular and widely used DNA-editing research tool that could lead to safe and effective cures for genetic disorders is the CRISPR-Cas9 system. CRISPR-Cas9 stands for Clustered Regularly Interspaced...

CRISPR/Cas9 Genome Editing

CRISPR/Cas9 Genome Editing

The CRISPR-Cas system serves as a bacterial defense mechanism against invading genetic elements such as viruses and plasmids, forming the foundation for its adaptation as a powerful genome-editing tool. Originally discovered in prokaryotes, this system has been repurposed to revolutionize genetic engineering across a wide range of organisms, including plants, animals, and humans. The core component, Cas9, is an endonuclease derived from Streptococcus pyogenes, capable of introducing...

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Related Experiment Video

Updated: Mar 1, 2026

ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

ATAC-seq Assay with Low Mitochondrial DNA Contamination from Primary Human CD4+ T Lymphocytes

Published on: March 22, 2019

Reducing mitochondrial reads in ATAC-seq using CRISPR/Cas9.

Lindsey Montefiori¹, Liana Hernandez¹, Zijie Zhang¹

¹Department of Human Genetics, University of Chicago, 920 E 58th St Room 515, Chicago, IL, 60637, USA.

Scientific Reports

|May 28, 2017

Summary

This summary is machine-generated.

Targeted cleavage using CRISPR technology effectively reduces mitochondrial DNA in ATAC-seq libraries, minimizing wasted sequencing. Combining CRISPR with the original protocol yields the most usable data and highest quality chromatin accessibility peaks.

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ATAC-Seq Optimization for Cancer Epigenetics Research

ATAC-Seq Optimization for Cancer Epigenetics Research

Published on: June 30, 2022

Area of Science:

Genomics
Molecular Biology
Epigenetics

Background:

Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is crucial for identifying open chromatin regions.
Mitochondrial DNA reads often comprise a significant portion (20-80%) of ATAC-seq data, leading to wasted sequencing resources.
Nuclear genome-localized open chromatin regions are the primary focus, making mitochondrial reads typically irrelevant for analysis.

Purpose of the Study:

To investigate methods for reducing mitochondrial DNA contamination in ATAC-seq libraries.
To evaluate the efficacy of CRISPR-Cas9 targeted cleavage and detergent removal on sequencing efficiency and data quality.
To optimize ATAC-seq protocols for cell types with high mitochondrial content, aiming for cost reduction.

Main Methods:

Two primary methods were tested: targeted cleavage of mitochondrial DNA using CRISPR technology and removal of detergent from the cell lysis buffer.
ATAC-seq libraries were generated from lymphoblastoid cell lines using these modified protocols.
The impact of each treatment on usable read counts, peak number, and peak quality (including enhancer and transcription start site regions) was analyzed.

Main Results:

Both CRISPR treatment and detergent removal significantly reduced mitochondrial reads (1.7-fold and 3-fold, respectively).
Detergent removal led to increased background noise and a reduction in the number of identified peaks.
The combination of the original ATAC-seq protocol with CRISPR treatment yielded the highest number of peaks and superior data quality.

Conclusions:

CRISPR-mediated targeted cleavage of mitochondrial DNA is an effective strategy to reduce wasted sequencing in ATAC-seq.
While detergent removal also reduces mitochondrial reads, it negatively impacts data quality and peak detection.
Optimizing ATAC-seq by using CRISPR treatment alongside the standard protocol enhances data quality and reduces sequencing costs, particularly for samples with high mitochondrial content.