Chromatin Profiling Analysis @ CRS

Workflow

Cleavage Under Targets & Tagmentation (CUT&Tag) A targeted chromatin profiling technique that maps protein-DNA interactions, including histone modifications and transcription factor binding, at high resolution. An antibody binds a chromatin-associated protein of interest, and a tethered transposase inserts sequencing adapters at nearby DNA sites, allowing precise mapping of the protein’s genomic locations. CUT&Tag is highly sensitive and works well with low-input or rare samples, providing a more efficient alternative to traditional ChIP-Seq. This workflow is from experiences in the Jessica Lang Lab at CPM, based on a protocol modified from the whole-cell CUT&Tag protocol described by Stephen Henikoff and colleagues (https://dx.doi.org/10.17504/protocols.io.x54v9mkmzg3e/v5). Potential Applications

• Profiling histone post-translational modifications
• Mapping transcription factor binding sites
• Studying chromatin accessibility at specific regulatory regions
• Epigenetic landscape characterization in low-input or single-cell samples
• Investigating dynamic chromatin changes during development or disease

 

Workflow

Assay of Transposase Accessible Chromatin (ATAC-Seq) Measures genome-wide chromatin accessibility, providing insights into regulatory regions such as promoters and enhancers. A hyperactive transposase inserts sequencing adapters into open chromatin regions, allowing direct sequencing of accessible DNA. This technique requires minimal input material and enables rapid profiling of chromatin states, making it a powerful tool for studying transcriptional regulation and epigenetic dynamics. This workflow is from experiences in the Jessica Lang Lab at CPM, based on a modified protocol from Corces et al. Nature Methods 2017 (https://www.nature.com/articles/nmeth.4396).   Potential Applications

• Mapping open chromatin regions genome-wide
• Identifying active promoters, enhancers, and regulatory elements
• Studying transcriptional regulation in different cell types or conditions
• Profiling chromatin accessibility in rare or low-input samples
• Integrating with other epigenomic assays to link accessibility with histone modifications or transcription factor binding

     

Schematic of the ATAC-seq transposition reaction and library preparation. Corces, et al. Nature Protocols 2022 https://www.nature.com/articles/s41596-022-00692-9