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Developmental biology - Genes|
3D Map of Genes in the Cell
The location of a gene, whether close to the edge or the center of a nucleus, may have significant effect on its activity. A gene's position may therefore change as a cell develops or becomes diseased. Researchers can examine the position of individual genes using a microscope, but determining the position of each gene at the same time is impossible.
Yu Chen, Andrew Belmont, and colleagues from the University of Illinois at Urbana-Champaign have now developed a technique called tyramide signal amplification sequencing (TSA-Seq) that allows the distance of every gene from specific nuclear landmarks to be measured simultaneously. The study was carried out in collaboration 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 the enzyme, horseradish peroxidase, to specific nuclear structures such as the nuclear lamina surrounding the nucleus or protein-containing granules called 'nuclear speckles' that tend to be found in the center 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 labeled. So, when researchers subsequently sequence the cells' DNA, they can calculate how close each gene was to the nuclear structure tagged with horseradish peroxidase.
"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 leukemia cells and found that genes closer to nuclear speckles tended to be more active than genes closer to the nuclear lamina. Indeed, by examining the position of neighboring genes, the researchers were able to trace whole sections of chromosomes that looped out from the nuclear periphery toward speckles in the center 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. Thus, sequencing DNA can produce a map of the genome's organization.
"Our model would suggest that chromosome movements of just a few hundred nanometers could have substantial functional significance."
Researchers know the technique still needs work, but hope to use TSA-Seq to map gene positions in other cell types and examine how positions change as cells develop or become diseased.
While nuclear compartmentalization is an essential feature of three-dimensional genome organization, no genomic method exists for measuring chromosome distances to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping method capable of providing a “cytological ruler” for estimating mean chromosomal distances from nuclear speckles genome-wide and for predicting several Mbp chromosome trajectories between nuclear compartments without sophisticated computational modeling. Ensemble-averaged results in K562 cells reveal a clear nuclear lamina to speckle axis correlated with a striking spatial gradient in genome activity. This gradient represents a convolution of multiple spatially separated nuclear domains including two types of transcription “hot zones.” Transcription hot zones protruding furthest into the nuclear interior and positioning deterministically very close to nuclear speckles have higher numbers of total genes, the most highly expressed genes, housekeeping genes, genes with low transcriptional pausing, and super-enhancers. Our results demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear structure and suggest a new model for spatial organization of transcription and gene expression.
Authors: Yu Chen, Yang Zhang, Yuchuan Wang, Liguo Zhang, Eva K. Brinkman, Stephen A. Adam, Robert Goldman, Bas van Steensel, Jian Ma, and Andrew S. Belmont.
The authors declare no competing financial interests.
Sequencing was done at the UIUC Biotechnology Center. We thank William Brieher, Lisa Stubbs, and Brian Freeman (UIUC, Urbana, IL) for helpful suggestions during the course of this research. We also thank Jiang Xu (University of Southern California, Los Angeles, CA) for reading our manuscript and providing helpful suggestions for revisions.
This work was supported by National Institutes of Health grant R01 GM58460 to A.S. Belmont, R01 HG007352 to J. Ma, and U54 DK107965 to A.S. Belmont, J. Ma, and B. van Steensel as well as a Netherlands Organization for Scientific Research ZonMW-TOP grant to B. van Steensel.
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Horseradish peroxidase adheres to nuclear speckles (GREEN) producing a diffuse cloud of tyramide containing molecules (RED) that label nearby DNA (BLUE). A small shift in a gene's position so that it lies close to a nuclear speckle could be sufficient to dramatically enhance that gene's activity.
Image credit: Chen et al., 2018.