A standard gene-mapping slide can now also map chemical tags on DNA

EVERY CELL in a mouse's brain carries the same DNA, wound around proteins, but each type of cell uses a different set of its genes. Small chemical tags attached to those proteins help mark a stretch of DNA as in use or shut down. These tags are called histone modifications, after the proteins that carry them. Some sit at control regions that turn nearby genes on, and others cover stretches of DNA that are packed tight and silent.

In 2019 Steven Henikoff's group at the Fred Hutchinson Cancer Research Center described a method in which an antibody finds one tag and brings with it an enzyme that cuts the nearby DNA and labels each cut piece for sequencing. The method, called CUT&Tag, works on small numbers of cells and picks up very little stray signal.

Another method records where in a tissue each gene is in use. A thin slice is laid on a glass slide coated with short strands that catch RNA, the working copies made from active genes, by a tail at one end of each molecule. Each strand carries a code for its spot, so every RNA read can be traced to its place. This is spatial transcriptomics, and a widely used commercial slide is Visium, made by 10x Genomics.

Maps of the tags across a slice have been harder to make. One earlier method, described in 2022 by Rong Fan's group at Yale University and Gonçalo Castelo-Branco's group at the Karolinska Institute, labeled tissue through custom-made chips with tiny channels and reached a resolution of 20 micrometers. Such chips need specialized manufacture and cover small areas, the authors of a new preprint note.

The preprint, posted on bioRxiv on November 7th by Chao Yan, Ruiyang He, Sanja Vickovic and colleagues at the New York Genome Center and Columbia University, describes a method called SPACE-Tag that runs CUT&Tag on a Visium slide. The labels it attaches to the cut DNA carry a start signal for an enzyme that makes many RNA copies of each tagged piece, and the copies carry the tail that the slide catches. The copying increased the number of each targeted piece about 55-fold, and other changes to the procedure increased the number of distinct pieces read about eight-fold.

The team tested it on 16 brain sections from six mice, covering 63,437 spots, for three tags. The maps agreed closely with public reference maps from ENCODE, with a rank correlation above 0.88 for the two activating tags (1 would mean identical ordering). Without being told the anatomy, the maps of one activating tag, H3K27ac, picked out regions including the outer layer of the brain, known as the isocortex, and the fiber tracts, bundles of nerve fibers that make up the white matter.

The team then built an atlas of the aging brain from four mice, one each at 3, 12, 18 and 24 months of age, covering 24 sections and 95,442 spots. Five tags and gene activity were measured on neighboring slices, aligned by computer and analyzed at a resolution of 100 micrometers. The fiber tracts showed the largest change in gene activity at 24 months, mostly genes turned down, and most of those changes came without detectable shifts in nearby tags. In the isocortex, gene changes largely matched nearby tag changes, and a set of regions gained a tag found at control regions, H3K4me1, with age. These regions sat more often in clusters of control regions that govern many genes, called super-enhancers, than at ordinary ones. Nearby genes became more active with age, among them Egr3 and Egr4, which help nerve cells adjust their connections.

The authors hypothesize that proteins made from the EGR genes recruit the machinery that adds H3K4me1 at these sites, and suggest the pattern may reflect an adaptive program that supports nerve function in healthy aging. The paper does not test whether the tag changes cause the gene changes. With one mouse at each age, the atlas cannot show how typical these trends are, and the animals' sex is not stated. Each data point mixes many cells, a limit the authors list, and the work used only mice, not human brains.

Labs that already map gene activity on Visium slides could use SPACE-Tag to map five DNA tags in neighboring slices of the same tissue. Its first atlas suggests that brain regions age in different ways, though it rests on four mice, one at each age, in a preprint that has not been peer reviewed.