HENIKOFF LAB -- Epigenomic landscaping at base-pair resolution

Cell-type-specific epigenomic landscaping

Perhaps the most serious limitation of applying epigenomic technologies to developmental studies has been the need to obtain cell-type-specific chromatin of sufficient purity and abundance, and we recently introduced a simple and general method for doing this1. We express a nuclear envelope protein under control of a cell-type-specific promoter, and use in vivo biotinylation followed by affinity separation on magnetic beads to rapidly obtain large quantities of pure nuclei. We have applied our INTACT (for Isolation of Nuclei TAgged in specific Cell Types) method to measure gene expression and chromatin features of hair and non-hair cell types of the Arabidopsis root epidermis. We identified hundreds of genes that are preferentially expressed in each cell type and found that genes with the largest expression differences between hair and non-hair cells also show differences between cell types in H3K4me3 and H3K27me3. This method should be applicable to any organism that is amenable to transformation, and we have adapted it for our worm and fly epigenomic studies2

Recently, Jeremy Nathans, Joe Ecker and collaborators applied a version of INTACT3 to mouse brain, and obtained epigenomic profiles for specific neuronal sub-types that comprise only ~1-3% of the total. This revealed >200,000 epigenomic differences between neuronal sub-types4  similarly, Welcome Bender and colleagues used INTACT to determine chromatin profiles of single parasegments in Drosophila embryos that revealed sharp boundaries of H3K27me3 in the BX-C regulatory domains, implicating H3K27 domains in segment identity 5.

References

1              Deal, R.B. & Henikoff, S. A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell 18, 1030-1040 (2010).

2              Steiner, F.A., Talbert, P.B., Kasinathan, S., Deal, R. B. & Henikoff, S. Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res 22, 766-777 (2012).

3              Henry, G.L., Davis, F.P., Picard, S. & Eddy, S.R. Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res 40, 9691-9704 (2012).

4              Mo, A. et al. Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain. Neuron 86, 1369-1384 (2015).

5              Bowman, S.K. et al. H3K27 modifications define segmental regulatory domains in the Drosophila bithorax complex. eLife 3, e02833 (2014).