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Developmental biology - Gene Organization

The 3D Nucleus

Creating 3D maps of DNA inside the nucleus of a cell...


Caltech researchers can now show how cells organize our seemingly immense genome in a clever and convenient manner. Understanding this delicate three-dimensional organization is crucial, particularly as alterations in DNA structure are linked to certain diseases such as cancer, as well as early aging. Mapping and pinpointing alterations in nuclear chromosomes helps us find solutions to disease.
The cartography of the nucleus creates a 3D map of DNA within the innermost part of the cell - the nucleus.

Nestled deep in each cell is what seems like a magic trick: Six feet of DNA packed into a tiny space 50 times smaller than the width of a human hair.

Like a long, thin string of genetic spaghetti, this DNA blueprint for our whole body is folded, twisted, and compacted to fit into the nucleus of each cell.

The work was done in the laboratory of Mitchell Guttman PhD, Assistant Professor of Biology and a Heritage Medical Research Institute Investigator. A paper describing the research appears in the June 7 online issue of the journal Cell.
Although the vast majority of cells in every human contain identical genomes (a genome being the pair of chromosomes in each cell nucleus), each cell type functions at unique levels and times, with each being able to be turned on or turned off.

For example, if a stem cell is developing into a nerve cell, a flurry of activity happens in the nucleus [a small dense sphere appearing during interphase] to turn up or down levels of gene function. Gene function differs according to cell type or whether a cell is deciding to self-destruct.

The nucleus also contains structures called nuclear bodies, miniature factories that work by turning on specific sets of genes, or by modifying RNA to make proteins. Nuclear Bodies efficiently search through the six feet of DNA - in mammals approximately 20,000 genes - to precisely locate and control specific DNA to be organized into a 3D structure.

In the new research, Guttman and his team describe a method to 3D map that DNA in order to find how chromosome regions interact with each other and with nuclear bodies. The technique, called SPRITE (Split-Pool Recognition of Interactions by Tag Extension), allows examination of clusters (called complexes) of molecules to see which molecules interact and where.
Each molecular complex in a nucleus was given a barcode, and that same barcode was given to each molecule within that complex. Complexes were then broken open and each molecule analyzed. Scientists can now verify when two or more molecules interact based on their barcodes.

Led by doctorual student Sofia Quinodoz, the team used SPRITE to discover which genes in chromosome clusters are turned off the nucleolus contains proteins that keep genes turned off. At the same time, looking for active genes grouped around another nuclear body called the speckle which turned molecules on.
"With SPRITE, we were able to see thousands of molecules - DNAs and RNAs - come together at various 'hubs' in the nucleus of a single cell.

Previously, researchers theorized each chromosome was on its own, occupying its own 'territory' in the nucleus. Now we can see that multiple genes of different chromosomes cluster around specific nuclear bodies.

We think these 'hubs' may help the cell keep DNA - whether turned on or turned off - neatly organized in the nucleus allowing other cell machinery easy access to specific genes."


Sofia A. Quinodoz, Post Doctorual student, Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA, and study first author.
SPRITE tags on chromosomes
SPRITE tags organize chromosome

Abstract
Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.

Authors: Sofia A. Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason M. Lai, Alexander A. Shishkin, Prashant Bhat, Yodai Takei, Vickie Trinh, Erik Aznauryan, Pamela Russell, Christine Cheng, Marko Jovanovic, Amy Chow, Long Cai, Patrick McDonel, Manuel Garber, Mitchell Guttman.


Acknowledgements
Funding was provided by the Howard Hughes Medical Institute Gilliam Fellowships for Advanced Study, the National Science Foundation, the National Institute of General Medical Sciences, the UCLA-Caltech Medical Scientist Training Program, the National Institutes of Health, the National Human Genome Research Institute, the New York Stem Cell Foundation, the Sontag Foundation, and Caltech.

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Jun 15, 2018   Fetal Timeline   Maternal Timeline   News   News Archive




3D model of a nucleus made using SPRITE reveals that DNA regions of an "inactive hub" on chromosome 15 (orange) and chromosome 18 (green) come together in the nucleus (blue) around the nucleolus (red). Image credit: Mitchell Guttman, Cell.


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