This is a high-throughput sequencing based method to map euchromatin and heterochromatin accessibility. The method is based on the sequential extraction of distinct nuclear fractions containing: soluble proteins (S1 fraction); the surnatant obtained after DNase treatment (S2 fraction); DNase-resistant chromatin extracted with high salt buffer (S3 fraction); and the most condensed and insoluble portion of chromatin, extracted with urea buffer that solubilizes the remaining proteins and membranes (S4 fraction). We further adapted the method to leverage high-throughput DNA sequencing for genome-wide mapping of the distinct chromatin fractions. The insoluble fractions are reproducibly enriched in lamina-associated heterochromatic regions (LADs), while the more soluble one correlates with euchromatin. Thus with a unique protocol we are able to describe the accessibility of euchromatin and heterochromatin.
Our protocol overcomes several major limitations of other methods for mapping lamina associated heterochromatic regions. First of all, the procedure can be applied on primary cells, as it doesn't require exogenous gene expression as in DamID-seq. Then, SAMMY-seq does not involve chemical modifications of chromatin, which might cause artifacts and biases in sequencing. Additionally, it does not rely on antibodies for enriching specific chromatin fractions, thus avoiding issues related to antibody specificity, production, lot-variability and cross reactivity. This is particularly important when studying epigenetic changes in cells where protein levels of chromatin associated factors could be altered, thus allowing more flexibility in terms of experimental design compared to antibody-based techniques. Finally, SAMMY-seq is robust, as it yields reproducible results even at lower sequencing depth or with a small number of starting cells (10K) and requires only about 3 hours of bench work, excluding DNA extraction and library preparation.