How do you double your fun? An extra scoop of ice cream, coffee and a cake, or the epigenetic delights of single-cell profiling of not one but two histone modifications? In the latter case, the scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing) integrated framework may represent a wise choice for those looking to indulge while still clinging to their New Year’s resolutions!
The dynamic duo of Jake Yeung and Alexander van Oudenaarden (Hubrecht Institute-KNAW, the Netherlands) have been working double-time to move past specific technological barriers and develop advanced histone modification profiling techniques. Their recently-reported sortChIC-seq protocol involves incubating cells with a modification-specific antibody that tethers protein A-MNase to generate targeted DNA fragments in single cells. In their latest, the team doubled down on sortChIC-seq to develop scChIX-seq, which doubles your epigenetic fun by deciphering the single-cell interplay of multiple histone modifications.
Let’s hear about this daily double of histone modification profiling from Yeung, Florescu, Zeller, and Colleagues:
- Profiling two histone modifications in single cells with scChIX-seq involves the generation of three genome-wide sortChIC-seq datasets
- Two target individual histone modifications, and a third targets both histone modifications in the same cell
- The deconvolution of multiplexed histone modifications uses the two single datasets as training data to define possible pairs of histone modification distributions that combine to generate a hypothetical double-incubated cell
- Each double-incubated cell becomes assigned to the most probable pair of cell states, one from each histone modification, and each pA-MNase cut is probabilistically assigned to their respective histone modification
- Label transfer allows joint analysis of two single-incubated sortChIC-seq datasets for distinct histone modifications, so that information from one modification links to another using double-incubated cells
- The application of scChIX-seq to study H3K36me3 and H3K9me3 dynamics during mouse organogenesis reveals joint transcriptional and heterochromatin relationships in single cells
- The technique identifies complex cell-type relationships between histone modifications, such as several cell types sharing a similar heterochromatin landscape
- Using scChIX-seq to evaluate two correlating active modifications during macrophage differentiation aids the description of the coordinated dynamics between H3K4me1 and H3K36me3
- The correlation structure between modifications becomes inferred from the model and does not require assumptions of specific features of the two modifications
Overall, scChIX-seq can enhance your epigenetic enjoyment significantly by unlocking the ability to systematically interrogate histone modification interplay in single cells; furthermore, this novel approach can reveal unique biological insights that may be obscured when analyzing each modality separately.