The dynamic 3D organization of DNA in the tiny nucleus of a cell plays a critical role in determining which genes are turned on in a cell (gene expression), which affects cell function. Determining the 3D organization of DNA in the nucleus of live cells has been extremely difficult. To overcome this obstacle, the NIH Common Fund 4D Nucleome (4DN) program is developing new tools to explore nuclear organization in relation to cell function and human health. 4DN-funded investigator Dr. Andrew Belmont and a team of researchers have developed a new technique called “TSA-seq” that can measure the positions of genes in the nucleus relative to nuclear landmarks such as the nuclear lamina (surrounds the nucleus) or nuclear speckles (found in the center of the nucleus). The technique works by targeting an enzyme called “horseradish peroxidase” to a specific nuclear structure. The enzyme generates reactive molecules that label the surrounding DNA, with DNA closer to the enzyme being more heavily labeled. The DNA is isolated and sequenced, and the amount of labeling at each gene can then be used to calculate how close each gene is to the tagged nuclear structure. This information can be used to build a genome-wide 3D picture of nuclear organization. Combining TSA-seq with measurements of gene expression showed that nuclear speckles tend to be “hot zones” of gene activity, with more of the genes close to the nuclear speckles being active. This finding suggests that even small changes in the position of a gene, that move the gene closer to or farther from a nuclear speckle, could have significant consequences on gene expression and cell function.

Reference

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler. Chen, Y, Zhang, Y, Wang, Y, Zhang, L, Brinkman, EK, Adam, SA, Goldman, R, van Steesel, B, Ma, J, and Belmont, A. Journal of Cell Biology. August 2018.

In the News

Researchers develop ‘cytological ruler’ to build 3D map of human genome, Science Daily