Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

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Science  02 Mar 2018:
Vol. 359, Issue 6379, pp. 1050-1055
DOI: 10.1126/science.aao3136

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Tracking regulatory DNA in action

Cis-regulatory DNA elements such as enhancers and promoters are critical for transcription regulation. Little is known about the relationship between these elements' transcriptional activity and their mobility within the nucleus in living cells. Gu et al. developed a strategy to deliver multiple RNAs to guide inactive Cas9 to label these elements. Quantitative measurement of their movement during stem cell differentiation revealed that increased DNA loci mobility correlated with transcriptional activation.

Science, this issue p. 1050


To achieve guide RNA (gRNA) multiplexing and an efficient delivery of tens of distinct gRNAs into single cells, we developed a molecular assembly strategy termed chimeric array of gRNA oligonucleotides (CARGO). We coupled CARGO with dCas9 (catalytically dead Cas9) imaging to quantitatively measure the movement of enhancers and promoters that undergo differentiation-associated activity changes in live embryonic stem cells. Whereas all examined functional elements exhibited subdiffusive behavior, their relative mobility increased concurrently with transcriptional activation. Furthermore, acute perturbation of RNA polymerase II activity can reverse these activity-linked increases in loci mobility. Through quantitative CARGO-dCas9 imaging, we provide direct measurements of cis-regulatory element dynamics in living cells and distinct cellular and activity states and uncover an intrinsic connection between cis-regulatory element mobility and transcription.

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