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Epigenomic methods profile chromatin state and regulatory activity across the genome. ChIP-seq (chromatin immunoprecipitation followed by sequencing) maps where specific proteins (transcription factors) or histone modifications (H3K4me3, H3K27ac) occur across the genome by using antibodies to pull down protein-DNA complexes. ATAC-seq (assay for transposase-accessible chromatin) identifies open chromatin regions by using a transposase that preferentially inserts into accessible DNA. Both methods produce genome-wide maps of regulatory activity, enabling identification of active promoters, enhancers, silencers, and transcription factor binding sites. Peak calling algorithms (MACS2) identify enriched regions above background.
Visualize ChIP-seq and ATAC-seq tracks alongside RNA-seq and gene annotation tracks in a genome browser (IGV or UCSC). Observe how H3K4me3 peaks mark active promoters, H3K27ac marks active enhancers, and ATAC-seq peaks coincide with both. Compare a gene that is expressed in the tissue to one that is silent and note the differences in epigenomic landscape.
The genome sequence is the same in nearly every cell of an organism, yet different cell types express radically different sets of genes. Epigenomic regulation — the system of chemical modifications to DNA and histones, chromatin accessibility, and three-dimensional genome organization — determines which genes are active in which cells. ChIP-seq and ATAC-seq are the primary tools for mapping this regulatory landscape genome-wide.
ChIP-seq works by cross-linking proteins to DNA in living cells (using formaldehyde), fragmenting the chromatin by sonication, using an antibody to immunoprecipitate the protein (and its associated DNA), and then sequencing the recovered DNA fragments. The resulting reads pile up at genomic locations where the target protein was bound. For transcription factors, the peaks are typically narrow (a few hundred base pairs centered on the binding site). For histone modifications, the peaks can be broad (spanning entire gene bodies for marks like H3K36me3) or narrow (at promoters for H3K4me3). The combination of multiple histone marks defines chromatin states: active promoters (H3K4me3 + H3K27ac), active enhancers (H3K4me1 + H3K27ac), repressed regions (H3K27me3), and heterochromatin (H3K9me3). Tools like ChromHMM learn these combinations and segment the genome into functional chromatin states.
ATAC-seq takes a complementary approach. Instead of asking where a specific factor is, it asks where the chromatin is accessible — where is the DNA physically open and available for regulatory proteins to bind? The Tn5 transposase preferentially inserts into accessible DNA, tagging those regions with sequencing adapters. After sequencing, reads pile up at open chromatin regions. ATAC-seq requires far fewer cells than ChIP-seq (thousands versus millions), works without antibodies (eliminating antibody quality issues), and captures the full landscape of regulatory potential in a single experiment. Fragment size analysis provides additional information: nucleosome-free fragments (~150 bp) come from accessible regulatory regions, while mono-nucleosomal fragments (~200 bp) reveal nucleosome positioning.
In practice, epigenomic experiments are most informative when integrated with each other and with gene expression data. An active enhancer should show: an ATAC-seq peak (accessible), H3K4me1 and H3K27ac ChIP-seq peaks (enhancer-specific marks), transcription factor ChIP-seq peaks (bound factors), and nearby gene expression (by RNA-seq). This convergent evidence approach, applied genome-wide across many cell types and conditions, has produced the comprehensive regulatory maps of projects like ENCODE and the Roadmap Epigenomics Project, fundamentally changing how we understand gene regulation and interpret disease-associated noncoding variants.