smFISH of genes and enhancers during the LPS response of wild-type and cohesin-deficient macrophages

Transcription is an intermittent process that occurs in bursts. The frequency and the number of messenger RNA (mRNA) produced by these bursts determine expression levels and shape cell-to-cell variability. Productive encounters between enhancers and promoters control burst dynamics, which the cohesin complex can facilitate through loop extrusion. Cohesin is a ring-shaped complex involved in enhancer-promoter interactions. Without cohesin, bone-marrow-derived macrophages' transcriptional response to LPS is severely impaired. Here, we used bDNA smFISH to detect mature and nascent inducible gene mRNA, as well as enhancer transcripts.