Epigenomics Projects (ChIP-exo, ATAC-Seq, or ChIP-Seq)
ChIP-exo is a chromatin immunoprecipitation based method for mapping the locations at which a protein of interest (transcription factor) binds to the genome. It is a modification of the ChIP-seq protocol, improving the resolution of binding sites from hundreds of base pairs to almost one base pair. It employs the use of exonucleases to degrade strands of the protein-bound DNA in the 5′-3′ direction to within a small number of nucleotides of the protein binding site. The nucleotides of the exonuclease-treated ends are determined using some combination of DNA sequencing, microarrays, and PCR. These sequences are then mapped to the genome to identify the locations on the genome at which the protein binds.
ATAC-seq Assay for transposase-accessible chromatin sequencing (ATAC-seq) has been used extensively in a wide range of organisms to map functional elements using Tn5 transposase’s ability to enrich for open (actively regulated) chromatin regions irrespective of the unique aspects of the organism’s genome. ATAC-seq can identifyactive regulatory elements including but not limited to gene promoters, enhancer elements, and insulators. ATAC-seq operates on minimal cell input (<50K cells), is a simple assay (~2 hrs), and does not suffer from many of the issues present in other genome-wide epigenomic assays (RNA-degradation, target specific affinity reagents, etc.).
Chromatin ImmunoPrecipitation sequencing (ChIP-Seq) is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. Following ChIP protocols, DNA-bound protein is immunoprecipitated using a specific antibody. The bound DNA is then co-precipitated, purified, and sequenced.
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