Lately, we’ve been faced with a veritable torrent of awesome single-cell epigenomics methods; thankfully, the development of a new technique – EpiDamID – promises to easily contain the floods of findings regarding histone modification and gene expression patterns coming from single cells!
Previously, a talented team from the lab of Jop Kind (Hubrecht Institute, Utrecht, the Netherlands) developed scDam&T-seq as a means to measure DNA-protein contacts and gene expression in single cells by combining DNA adenine methyltransferase identification (DamID) with CEL-Seq2 (a single-cell RNA-seq technique). The torrid rainfall of recently reported DamID-based techniques involve engineering a protein of interest fused to Dam methyltransferase, which then identifies protein binding locations by detecting proximity-induced adenine methylation; however, we can’t fuse Dam to modified proteins and, therefore, use DamID to profile histone modifications. This monsoon-like problem prompted the development of EpiDamID, which can contain the inundation of info on single-cell histone modification and gene expression profiles.
Let’s hear from Rang, De Luca, and colleagues on how EpiDamID can aid the study of the chromatin states underlying dynamic cellular processes:
- EpiDamID targets histone modifications (e.g., H3K9ac, H4K20me1, and H3K27me3) by fusing Dam to chromatin-binding proteins, engineered chromatin reader domains, or single-chain variable fragments of antibodies in straightforward workflow suitable for integration with other protocols to generate multi-modal measurements
- The incorporation of EpiDamID into scDam&T-seq supports the identification of genome-wide histone modification profiles and the measurement of gene expression from the same single-cell
- Profiling Polycomb-associated chromatin domains and transcriptomics in differentiating embryonic stem cells provides evidence for Polycomb-regulated and Polycomb-independent hierarchical transcription factor networks in vitro
- Mapping cell-type-specific patterns of H3K9me3 (using the injection of an mRNA construct for Mphosph8) during early zebrafish embryogenesis reveals broad domains of notochord-specific heterochromatin
- This approach demonstrates that EpiDamID can generate high-resolution single-cell information on the chromatin-associated mechanisms that underlie in vivo developmental processes
Overall, this veritable rainfall of results provides evidence for EpiDamID as an exciting means of understanding the chromatin states that underly dynamic cellular processes with more potential applications than drops in the ocean, given that EpiDamID can be applied to any currently existing DamID methodology.
For more information on how EpiDamID contains the flood of histone modification findings from single cells, see Molecular Cell, April 2022.