Mapping epigenetic features is essential for investigating chromatin regulation and gene expression control. We recently found that crosslinking- and sonication-based techniques preferentially exclude insoluble chromatin, restricting the investigation of large portions of eukaryotic genomes. Here, we present a protocol for overcoming this issue. We describe steps for chromatin fractionation, DNA extraction, and preparation of next-generation sequencing (NGS) libraries. This strategy can identify underrepresented heterochromatic regions, including repetitive elements and centromeres, permitting functional investigation of regions that are otherwise undetectable. For complete details on the use and execution of this protocol, please refer to Park et al.1.