AAT Bioquest

What are some common techniques to analyze chromatin activity?

Posted July 28, 2023


Common techniques to analyze chromatin activity include: ATAC-seq, DNase-Seq, MNase-seq, ChIP, single-cell techniques, and 3C-based. ATAC-seq works by inserting sequence adapters into accessible areas of DNA utilizing the transposase Tn5. ATAC-Seq displays an overview of all accessible chromatin regions in one snapshot. DNase-Seq uses DNAse to digest sequences into fragments for subsequent sequencing by NGS. MNase-seq uses micrococcal nuclease to digest regions of euchromatin, leaving the protected heterochromatin remaining for NGS analysis.    

ChIP-Seq is an antibody-based technology used to selectively enrich specific DNA-binding proteins and their DNA targets. Chip-Seq identifies the binding sites of DNA-associated proteins and can be utilized to mark binding sites for a specific protein. 

3C based techniques include Hi-C sequencing. Hi-C sequencing is a type of chromosome conformation capture technique that allows for the observation of chromatin organization in the cell. This capture allows for the analysis of long-range genomic interactions, such as those between enhancers and promoters. Hi-C data displays topologically associated domains and genomic compartments that indicate which genes are co-regulated or not. 

Additional resources

Chromatin Profiling Techniques: Exploring the Chromatin Environment and Its Contributions to Complex Traits

Chromatin Immunoprecipitation (ChIP)

Antibody & Protein Conjugation Service