Chromatin compaction/accessibility, as well as histone post-translational modifications (PTMs) and the full repertoire of chromatin-associated proteins, define the chromatin state in any region of the genome. This Chromatin state is the primary driver of gene expression. Whether you are measuring chromatin compaction with ATAC-Seq, Histone PTMs, or other chromatin-associated proteins with ChIP-Seq, Cut&Run, or Cut&Tag, the UMGC can turn your enriched DNA samples into multiplexed libraries ready for Next Generation Sequencing.

Chromatin Profiling Options

ChIP-Seq: ChIP-Seq has historically been the most widely used method of localizing Histone PTMs and chromatin-associated proteins. After crosslinking proteins to the genome and releasing small fragments of DNA from the cell through sonication, factor specific immunoprecipitation is used to enrich for DNA fragments associated with your factor of interest. This workflow has been foundational in our understanding of chromatin structure and gene regulation.

ATAC-Seq: The assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) is a popular method for determining chromatin accessibility at the genome-wide level. The hyperactive Tn5 transposase inserts sequencing adapters into regions of open chromatin. By sequencing these regions, researchers can investigate areas of increased accessibility and correlate with gene expression. 

Single-cell ATAC-Seq: The Chromium Single Cell ATAC solution provides a robust and scalable approach to mapping the epigenetic landscape at single-cell resolution. By using a transposase enzyme to preferentially tag accessible DNA regions with sequencing adaptors, researchers can now generate sequencing-ready libraries and identify open chromatin regions. Contact single-cell@umn.edu. 

Cut&Run: Cut&Run can accurately map histone post-translational modifications (PTMs) as well as chromatin-associated proteins. Cut&Run relies on an MNase-proteinA/G fusion that can localize MNase DNA cleavage activity to an antibody bound to your factor of interest.  This workflow allows for a much lower background signal than ChIP-Seq because, unlike sonication, the tethered MNase will only release genomic loci physically associated with your factor of interest. Due to this “release specificity,” the cell number and sequence depth required are significantly reduced.

Cut&Tag: While less universally applicable than Cut&Run, Cut&Tag functions well for histone PTMs and feeds into a more streamlined sequencing library prep protocol. Cut&Tag utilizes a Tn5-proteinA/G fusion to tether the Tn5 transposase to an antibody bound to your histone PTM of interest. The tethered Tn5 then inserts a transposon containing sequencing adapters into the adjacent DNA. These resulting DNA fragments can be made into sequencing-ready libraries with a simple PCR.

Start a Project

Contact us a next-gen@umn.edu for project support or questions. If your project has unique requirements, higher complexity, or needs optimization, our Custom Services can do non-routine protocols not offered through our Standard Services.