ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide

By Jason D. Buenrostro, Beijing Wu, Howard Y. Chang, W.J. Greenleaf. Current Protocols in Molecular Biology, 2015

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This unit describes Assay for Transposase‐Accessible Chromatin with high‐throughput sequencing (ATAC‐seq), a method for mapping chromatin accessibility genome‐wide. This method probes DNA accessibility with hyperactive Tn5 transposase, which inserts sequencing adapters into accessible regions of chromatin. Sequencing reads can then be used to infer regions of increased accessibility, as well as to map regions of transcription‐factor binding and nucleosome position. The method is a fast and sensitive alternative to DNase‐seq for assaying chromatin accessibility genome‐wide, or to MNase‐seq for assaying nucleosome positions in accessible regions of the genome. © 2015 by John Wiley & Sons, Inc.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/ad18b39be4b91ee0589b5a68e2f5ba9ed6f980cc

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Citations in the corpus

A major chromatin regulator determines resistance of tumor cells to T cell–mediated killing (2018, methodology): “ATAC-seq was performed on triplicates (200,000 cells) by the Center for Functional Cancer Epigenetics at DFCI as previously described (43, 44).”
Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine (2019, methodology): “Subsequently, in 2013, a new technology called ATAC-seq (assay for transposase-accessible chromatin using sequencing) was developed [65]; ATAC-seq could identify accessible (open) chromatin regions with hyperactive mutant Tn5 Transposase that inserts sequencing adaptors into open regions of the geno”
From reads to insight: a hitchhiker’s guide to ATAC-seq data analysis (2020, methodology): “These include Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) [9, 10], DNase I hypersensitive sites sequencing (DNase-seq) [11–13] and Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIREseq) [14], all of which interrogate chromatin accessibility; Chromatin Immuno”
Cistrome Data Browser: expanded datasets and new tools for gene regulatory analysis (2018, methodology): “Third, the Toolkit can determine the most similar ChIP-seq, DNase-seq, and ATAC-seq samples in terms of genomic interval overlaps with user-provided genomic interval sets.”
CD8 T Cell Exhaustion During Chronic Viral Infection and Cancer. (2019, background): “Recent technological advances in epigenetic profiling, including ATACseq (278), have allowed for epigenetic landscape analysis of Tex cells in chronic infections and cancer in bothmice and humans (42–44, 123, 279).”
Falco: high-speed FastQC emulation for quality control of sequencing data (2019, neutral): “…number variations in cancers 1 , assemble genomes of microbial organisms 2,3 , quantify gene expression 4 , identify cell populations from single-cell transcriptomes in a variety of tissues 5 and track epigenetic changes in developing organisms and diseases 6 , among numerous other applications.”
FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data (2017, methodology): “Other sources of open chromatin information, such as ATAC-seq [60] and FAIRE-seq [61], can also be used to replace or complement the existing DNase-seq data.”
Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation (2018, methodology): “In past work, we also used chromatin immunoprecipitation sequencing (ChIP-seq) data as annotations to explore chromatin accessibility differences in single-cell profiles (Buenrostro et al., 2015b).”
Mapping Transcriptomic Vector Fields of Single Cells (2022, positive): “To ensure high diversity in our libraries, multiple tagmentations were performed for the cDNA from each of the timepoints using the Nextera XT DNA Library Prep Kit (Illumina, FC-131-1096), and amplified in a second round of PCR (15 mL of Nextera PCR mix, 5 mL of 2 mM P5-TSO hybrid primer – AATGATACG”
Genome-wide enhancer maps link risk variants to disease genes (2021, methodology): “We applied ATAC-seq as previously described 43 , with modifications.”