Building a 3D Map of the Genome
Posted on by Dr. Francis Collins
Researchers have learned a lot in recent years about how six-plus feet of human DNA gets carefully packed into a tiny cell nucleus that measures less than .00024 of an inch. Under those cramped conditions, we’ve been learning more and more about how DNA twists, turns, and spatially orients its thousands of genes within the nucleus and what this positioning might mean for health and disease.
Thanks to a new technique developed by an NIH-funded research team, there is now an even more refined view . The image above features the nucleus (blue) of a human leukemia cell. The diffuse orange-red clouds highlight chemically labeled DNA found in close proximity to the tiny nuclear speckles (green). You’ll need to look real carefully to see the nuclear speckles, but these structural landmarks in the nucleus have long been thought to serve as storage sites for important cellular machinery.
By sequencing that labeled DNA, the researchers found they could precisely measure the position of each and every gene in the genome relative to the nuclear speckles and other structures. That makes it possible to build remarkable 3D maps of the genome’s spatial arrangement within cells.
The work comes from the lab of Andrew Belmont at University of Illinois at Urbana-Champaign. Belmont and his team got interested in nuclear speckles a decade ago while studying how DNA was packaged into the strand-and-spool complex known as chromatin. They noticed that when a gene of interest was ready for transcription, its chromatin structure loosened but also appeared to wrap around something else . That something turned out to be a nuclear speckle, a structure first observed by the famed neuroscientist/pathologist Santiago Ramon y Cajal in 1910.
There are roughly 25 to 50 of them within the cell nucleus, and the researchers wondered whether some genes pre-position themselves near certain nuclear speckles. Belmont asked his graduate student Yu Chen to find out, noting it was an old idea that had fallen out of favor years before.
As described recently in the Journal of Cell Biology, Chen and her colleagues came up with a technique that worked better than Belmont had ever anticipated. Called tyramide signal amplification sequencing (TSA-Seq), the technique targets a special enzyme to the cell’s nuclear speckles. That enzyme generates a highly reactive molecule called a tyramide.
Tyramide then attaches to any nearby DNA, showing up as a fiery orange color when viewed through a microscope. In fact, the closer DNA is to a nuclear speckle, the more tyramide attaches. That makes it possible to estimate quantitatively how close DNA and the genes it encodes are to a tagged nuclear speckle.
What they didn’t expect is tyramide attaches to DNA so far and wide from the nuclear speckles to cover entire chromosomes. Their new technique therefore makes it possible to gauge the position of every single gene across the human genome relative to enzyme-tagged nuclear structures, including nuclear speckles and the outer layer, or lamina, of the nucleus.
The Illinois team and its collaborators already found in leukemia cells that genes closer to nuclear speckles tend to be more active than genes closer to the lamina. They’ve also observed whole sections of chromosomes that appear to loop outward from the lamina toward speckles, as might be expected in actively transcribed regions of the genome.
More work is needed, but it appears that nuclear speckles may indeed serve as important hubs for gene activity. The findings also suggest that a small shift in the position of a particular gene within the nucleus could have dramatic effects on that gene’s level of activity, with the potential perhaps to transform a healthy cell into a diseased one and vice versa..
 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 Steensel B, Ma J, Belmont AS. J Cell Biol. 2018 Aug 28. [Epub ahead of print]
 Large-scale chromatin structure of inducible genes: transcription on a condensed, linear template. Hu Y, Kireev I, Plutz M, Ashourian N, Belmont AS. J Cell Biol. 2009 Apr 6;185(1):87-100.
Deoxyribonucleic Acid (DNA) (National Human Genome Research Institute/NIH)
4D Nucleome (Common Fund/NIH)
Belmont Lab (University of Illinois, Urbana-Champaign)
NIH Support: National Institute of General Medical Sciences; National Human Genome Research Institute; National Institute of Diabetes and Digestive and Kidney Diseases; Common Fund