The epigenome is the complete description of all the chemical modifications to DNA and histone proteins that regulate the expression of genes within the genome. These modifications occur as a natural process of development and tissue differentiation, and can be altered in response to environmental exposures or disease. We offer three methods for epigenetic analysis; ATAC-Seq for examining the accessibility of chromatin, ChIP-Seq for profiling of DNA targets for histone modification, transcription factors, and other DNA-associated proteins, and WGBS for interrogating the methylation status of the genome. We also offer single cell ATAC-Seq. (services page)
ATACseq is a technique that detects open chromatin regions with enriched signals in Transcription Start Sites (TSS) and regulatory regions. ATACseq involves transposase cutting of exposed DNA while adding sequencing adaptors to see how chromatin compaction and DNA-binding proteins regulate gene expression at high resolution. ATACseq is a complementary technique to ChIPseq in order to take a first pass look at the epigenetics in your given cell type. Sample requirements can be found here.
ChIP is a method used for analyzing protein DNA interactions. ChIP-seq combines ChIP with massively parallel DNA sequencing to analyze the association of regulatory molecules to specific gene promoters and histone modifications. H3K27Ac is a broadly used epigenetic mark to identify active enhancers and promoters. H3K4me1 marks identify active or primed enhancers whereas H3K4me3 marks active promoters. CTCF mediated contacts identify longer range interactions thought to organize the genome into topologically active domains (TADs). Sample requirements can be found here.
(Whole Genome Bisufite Sequencing)
WGBS is a technology used to determine the DNA methylation status of a given cell type or tissue genome wide by bi-sulfite treating a sample and sequencing the conversion unmethylated cytosines to uracil. DNA methylation can act to repress gene transcription without changing the underlying DNA sequence. Identifying DMR (differential methylated regions) can identify hotspots of gene regulation throughout the genome. Sample requirements can be found here.