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New Visualization Tool Suggests Refinement of Transcription Model

A Yale University-led team of researchers has developed an approach to visualize chromatin, transcription factors, and transcription in vivo, including during zygotic genome activation. The approach, dubbed chromatin expansion microscopy (ChromExM), combines pan-expansion microscopy with multimodal protein, RNA, and DNA labeling to visualize the nanoscale organization of chromatin. As they report in Science, the researchers applied ChromExM to examine interactions between Nanog, which is needed for genome reprogramming and transcription activation after fertilization, and nucleosomes and RNA polymerase II in zebrafish. They were able to visualize transcriptional elongation, finding string-like nanostructures some of which formed clusters and a portion of which also involved Nanog. Based on their visualizations, the researchers propose a refinement to the "kiss and kick" model of transcription in which enhancers and promoters are in transient contact. As researchers from Colorado State University and the Tokyo Institute of Technology note in a related commentary, the Yale team's version of the model "emphasize[s] the active role elongation seems to be playing in separating promoters and enhancers."