Paper - Review

DOI: 10.1002/0471142727.mb2129s109.ATAC-seq

Abstract

ATAC-seq: Assay for Transpose Accessible Chromatin with high-throughput sequencing
→ a method for mapping chromatin accessibility genome-wide
→ probes (DNA accessibility) (← with hyper-active Tn5 transpose)
→ A (fast & sensitive) alternative to DNase-Seq

Introduction

DNA
→ packed with (biologically active regions) ← accessible to (transcription machinery)
→ (Physical compaction) → operates a (dynamic epigenetic code)

Cellular phenotypes
← is governed by (epigenetic mechanisms) ← (composition & compaction & nucleo-protein structure) of chromatin


MNase-seq & ChIP-seq & DNase-seq
→ 👍 (information-rich & genome-wide) analysis methods
→ 👎 require (hundreds of millions) of cells as input material
→ 👎 averaging out (hetero-geneity) in cellular populations

⭐ ATAC-seq
→ uses hyperactive Tn5 transposase → to (cut & ligate) adapters for high-throughput sequencing
→ is bioinformatically separated into reads → Different populations (← of reads) provide information (← about the positions of nucleosomes)

ATAC-seq
→ 👍: cell separation & isolation
→ work across many (cell types & species)

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