Genome architecture and function are strictly related to nuclear structures, which contact chromatin at specific regions, regulating its compaction and three-dimensional higher-order structure, therefore contributing to specialized gene expression programs. Recently, growing evidence uncovers a dynamic role of nuclear structures in the plasticity of transcriptional programs. When the cellular microenvironment changes, external cues are transmitted to the nucleus through complex signalling cascades, finally resulting in a genome reorganization that allows the adjustment of the cell to a new condition. This process can be very rapid, especially in cells whose function is to contain sudden threats to the organism. Some examples are stem cells that switch from a quiescent to an activated state to replace damaged tissues or immune cells that, with a similar dynamic, identify and eliminate pathogens.Experimental treatments often require the isolation of cells from their physiological environment, exposing them to possible sudden changes in their nuclear architecture. Here we propose an early cross-linking on primary cells, a fixing method that can help to minimize the risk of nuclear structure alteration during the isolation process. We also bring some examples of downstream studies on early-fixed cells.
Keywords: Chromatin conformation; Chromatin immunoprecipitation; Cross-linking; FISH; Nuclear architecture.