Mapping Networks of Protein‐Mediated Physical Interactions Between Chromatin Elements

Abstract

Recent decade has witnessed an extensive advancement in our understanding of transcriptional regulation, in part due to a rapid progress in technologies which allow studying physical proximities between various chromatin regions at a resolution beyond that offered by conventional microscopy techniques. However, these methods do not specifically identify the protein component(s) that might mediate such interactions. Here we discusses the detailed protocol for Combined 3C-ChIP-Cloning (6C) technology which combines multiple techniques to simultaneously identify physical proximities between chromatin elements as well as the proteins that mediate these interactions. We further explore how the 6C assay can be incorporated with other techniques for a complete, cell-type-specific mapping of all inter and intrachromosomal interactions mediated by specific proteins. Thus, 6C assay provides an indispensable tool to address the role of specific proteins in nuclear organization and advances our understanding about the relation of chromatin higher order organization with transcriptional regulation to the next level.