The major focus of this review is to discuss current resources for ATAC-seq analysis. However, this assumption has not been evaluated systematically. Analysis tools used in ChIP-seq and DNase-seq have been applied to ATAC-seq assuming similar data characteristics. ĭespite the simplicity and robustness of ATAC-seq, a major impediment exists as there are few bioinformatic analysis tools developed specifically for ATAC-seq data. ScATAC-seq can be applied in multiple situations including clinical specimens and developmental biology to study the heterogenous cell populations at single-cell resolution. Recently, single-cell ATAC-seq (scATAC-seq) has been described, using fluorescence-activated cell sorting (FACS), microfluidic, and nano-well-based approaches. Because ATAC-seq does not involve rigorous size selection during library preparation, it can also identify nucleosome positions using fragments representing nucleosome monomer and multi-mers. The sensitivity and specificity are comparable to DNase-seq but superior to FAIRE-seq where both methods require millions of cells as input material. The hyperactivity of Tn5 transposase makes the ATAC-seq protocol a simple, time-efficient method that requires 500–50,000 cells. Paired-end sequencing is then performed to facilitate higher unique alignment rates of these open regions. During this process, the nick is repaired, leaving a 9-bp duplication.
Briefly, ATAC-seq incorporates a genetically engineered hyperactive Tn5 transposase that simultaneously cuts open chromatin leaving a 9-bp staggered nick and ligates high-throughput sequencing adapters to these regions. A schematic diagram of this cutting-edge technology in fundamental and translational research is shown in Fig. 1a), such as depicting enhancer landscapes in healthy mammalian tissue and cell types, studying accessibility changes between normal hematopoiesis and leukemia, as well as the chromatin state within schizophrenia patients and the Cancer Genome Atlas (TCGA) pan-cancer cohort. An exponential increase of curated ATAC-seq datasets and publications indicates its value in a wide spectrum of biological questions (Fig. Īmong assays designed for detecting chromatin accessibility, ATAC-seq has gained particular popularity since first described in 2013. Detailed procedures of these assays are out of scope of this review and discussed in detail elsewhere. These include Assay of Transposase Accessible Chromatin sequencing (ATAC-seq), DNase I hypersensitive sites sequencing (DNase-seq) and Formaldehyde-Assisted Isolation of Regulatory Elements sequencing (FAIRE-seq), all of which interrogate chromatin accessibility Chromatin Immuno-Precipitation sequencing (ChIP-seq) which measures transcription factor (TF) binding and histone modifications and Micrococcal Nuclease sequencing (MNase-seq) which detects nucleosome positioning and occupancy. Recent gene regulation studies have focused on epigenetics, and through the advances of high-throughput sequencing technologies, various assays have been developed to decipher the epigenetic landscape. All three scales of DNA condensation and their interplay contribute to gene regulation. Chromatin can dynamically switch between transcriptionally active euchromatin and inactive heterochromatin. Mammalian DNA is highly condensed through three major hierarchical scales the first is the nucleosome which then wraps into chromatin leading to the third hierarchy, the chromosome.
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