Chromatin is made of a combination of proteins (histones) and DNA. Chromatin structure is shaped by histone modifications and transcription factors and influences gene expression. Moreover, chromatin remodeling occurs during development and as the result of treatments. The assays below are used to study chromatin structure.
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) allows researchers to examine the DNA sequences bound by various DNA binding proteins (i.e. transcription factors) or associated with histone modifications (e.g. H3K37ac, H3K4me3). The combination of different histone modifications can be used to define chromatin states (e.g. active promoters, active enhancers, repressed chromatin). The readout of this assay are "peaks" that indicate where the targeted protein is binding.
ATAC-seq stands for Assay for Transposase-Accessible Chromatin using sequencing. This method allows researchers to investigate genome-wide chromatin accessibility. The resulting sequencing data can be used to detect differential accessibility of DNA binding motifs between biological samples and infer differential regulation of gene networks in response to treatment.
Hi-C sequencing is a type of chromosome conformation capture that allows an examination of chromatin organization in the cell. This technique allows investigation of long-range genomic interactions, such as the ones between promotors and enhancers. Hi-C data processing yields genomic compartments and topologically associated domains (TADs), informing which genes might be co-regulated.
For Hi-C applications, see here: https://arimagenomics.com/publications