Scientists develop TSA-Seq technique for precise 3D mapping of human genome

Researchers from the University of Illinois at Urbana-Champaign have reported a new technique that can measure the position of every single gene in the nucleus to build a 3D picture of the genome’s layout, called tyramide signal amplification sequencing (TSA-Seq).

The location of genes – be they close to the edge or at the center of the nucleus, for example – may significantly affect their activity, and their position may change as a cell develops or becomes diseased. Researchers can examine the position of individual genes using a microscope, but determining the position of every gene simultaneously is impossible by this means.

Yu Chen, Andrew Belmont, and colleagues from the University of Illinois at Urbana-Champaign developed the TSA-Seq technique that allows the distance of every gene from specific nuclear landmarks to be measured simultaneously, in a collaborative study. The study was carried out with Jian Ma’s group at Carnegie Mellon University and with researchers at the Netherlands Cancer Institute and Northwestern University Feinberg School of Medicine.

The TSA-Seq technique involves targeting an enzyme – horseradish peroxidase – to particular nuclear structures, such as the nuclear lamina that surrounds the nucleus or protein-containing granules called nuclear speckles that tend to be found in the centre of the nucleus. The horseradish peroxidase then generates a highly reactive molecule called tyramide that can be used to label any DNA in the enzyme’s vicinity. The closer a gene is to the enzyme, the more it will be labelled. When researchers subsequently sequence the cells’ DNA, therefore, they can calculate how close each gene was to the nuclear structure tagged with horseradish peroxidase.

Commenting on the unique nature of their technique, Chen says: “TSA-Seq is the first genome-wide method capable of estimating actual distances of genes from particular nuclear subcompartments”.

Chen and colleagues tested their approach in leukaemia cells and found that genes closer to nuclear speckles tended to be more active than those closer to the nuclear lamina. Indeed, by examining the position of neighbouring genes, the researchers were able to trace whole sections of chromosomes that looped out from the nuclear periphery toward speckles in the centre of the nucleus. The function of nuclear speckles is unknown, but the regions of chromosomes close to speckles seem to be “hot zones” of gene activity.

A small shift in a gene’s position so that it lies close to a nuclear speckle could be sufficient to dramatically enhance the gene’s activity, for example.

The researchers say that the technique still needs to be improved, but they hope to use TSA-Seq to map the positions of genes in other cell types and examine how these positions change as cells develop or become diseased.

The paper was published in theJournal of Cell Biology