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Feature Story: The Genome Ball
Forget Those X-Shaped Chromosomes
A Genome Looks Like This
Visitors to the Genome exhibition are frequently intrigued by the Genome Ball, a three-dimensional model of the human genome that represents a creative synthesis of scientific knowledge and technical innovation. For students and adults raised on clinically produced karyotypes – those artificially arranged pairs of X-shaped chromosomes photographed during cell division – the Genome Ball will challenge all their previous (mis)conceptions and show the human genome in a new light.
How did we first begin to grasp the structure of the nucleus? It all began in 1682 when Anton van Leeuwenhoek, a fabric merchant in the Dutch city of Delft, examined blood cells of fish. Leeuwenhoek used a microscope with lenses he’d ground himself, and reported his observations in a letter to the Royal Society:
I came to observe the blood of a cod and of a salmon, which I also found to consist of hardly anything but oval figures … it seemed to me that some of them enclosed in a small space a little round body or globule …
If you’ve looked at human blood under a microscope, that description may sound odd: Mature red blood cells (RBCs) don’t contain nuclei – do they? You’re right! However, the RBCs of fish (and amphibians and reptiles) do indeed have nuclei, and Leeuwenhoek was the first to describe them. Nevertheless, the Royal Society wasn’t blown away by his letter (after all, how much could a business man with “little fortune and no formal education” know about science?). The “little round body or globule” remained nameless for the next 150 years.
Then, in 1831, the Scottish botanist Robert Brown was studying plant fertilization when he noticed that pollen moved in and out of “ovals” in the plant cells. He called each oval a “nucleus,” a Latin word meaning “nut” or “kernel” – a bit like a black walnut surrounded by its thick green hull. Not only did Brown’s name stick, but his 1833 paper even suggested that the nucleus was probably involved in fertilization and the development of embryos.
The next step in our nuclear narrative was taken by Friedrich Miescher, a Swiss physician who extracted and isolated a previously unknown substance from pus-soaked bandages at the hospital where he worked. White blood cells, a major constituent of pus, have very large nuclei, and Miescher correctly concluded that the substance came from those nuclei. He called it “nuclein.” Today we call it DNA.
How many chromosomes in a human cell?
Although the fine points of cell division were still unexplained, scientists in the early 1900s were eager to learn the number of chromosomes in human cells. However, counting the number of human chromosomes during cell division turned out to be quite a challenge. Even when chromosomes were lined up on the “midline” of a cell, scientists’ counts ranged from 16 to 36.
Evidently, Hans von Winiwarter got tired of these wide-ranging approximations. Using the best microscopes available to him in 1912, he produced early karyotypes by capturing and fixing human cells at the moment of cell division. Despite his best efforts, Winiwarter’s counts ranged from 46 to 49; and while noting correctly that women have two X chromosomes, he mistakenly concluded that males had only one X and no Y. For the next 40+ years, students were generally taught that human cells contained 48 chromosomes.
Finally, in 1956, the correct value of “46” was confirmed – 22 pairs of autosomes and 1 pair of sex chromosomes in human cells other than eggs or sperm. It’s surprising to learn that Watson & Crick had published their model of DNA’s structure, opening the world of modern genetics, several years before the number of human chromosomes was firmly established!
Good things come in small packages
By the end of the 20th century, knowledge of DNA structure and the mechanisms of cell division had advanced dramatically. Yet, based on their school textbooks, most people still tended to picture chromosomes as the condensed “X-shaped” bodies seen in karyotypes. DNA was known to uncoil between cell divisions, but it was hard to imagine how such long straggling threads (more than 2 meters, or 6 feet, per cell) could pack into a nucleus only 6/1,000,000 of a meter in diameter (smaller than the diameter of a human hair).
Eventually, studies showed that DNA decreases in length when regions of about 166 base pairs wrap like twine around small proteins to form complexes known as nucleosomes . A short stretch of non-wound DNA falls between each nucleosomal unit, the result looking a bit like a string of beads. In such a configuration, a 1-meter (3-foot) strand of DNA is reduced to 14 cm (about 6 inches). This shortened strand then coils even more, until an X-shaped chromosome in a dividing cell measures roughly 1/10,000 the length of the DNA strand it contains!
The “fractal globule” (aka ramen noodles)
So what does the 3-dimensional model of the nucleus, as seen in the Genome Ball, have to do with all this?
One of the most important discoveries in genome biology has been the demonstration that genomes are non-randomly organized in the nucleus.
Even though chromatin looks like long straggly threads, it is amazingly well organized: Thanks to the organized coiling of chromatin, genes are able to interact with the DNA regions that regulate them.
The genome is organized into “distinct regions of open and closed chromatin regulatory domains,” explains Dr. Laura Elnitski, senior investigator at the National Human Genome Research Institute (NHGRI) of the National Institutes of Health. Put more simply, chromatin that is less active in a given cell type, or chromosomes containing few genes, are located just inside the nuclear membrane; but more active chromatin (for example, a gene coding for insulin in healthy pancreatic cells), and chromosomes carrying many genes, occupy the center of the nucleus. Overall, the nuclear location of specific genes correlates with their activity in a given cell.
Erez Aiden (who spearheaded the Genome Ball project) also discussed chromatin organization in his prize-winning essay in Science: “Loci on the same chromosome – even at opposite ends – interact more than loci on different chromosomes.” And within individual chromosomes, “open [active] chromatin interacts more with open chromatin and closed with closed,” wrote Aiden. In short: Genes have more interactions with regions on their own chromosome; and within any given chromosome, active regions group together with other active regions, while quiet or gene-poor areas group with other quiet regions.
Aiden had found a paper theorizing that long polymers – DNA is a good example – are able to form very tight coils with no knots, “a configuration known as the fractal globule.” One of the most striking characteristics of the fractal globule is that it can be folded and refolded without disturbing the rest of the condensed polymer.
The fractal globule is easy to explain to graduate students because it closely resembles the only food we can afford: ramen, said Aiden.
Uncooked, the noodles don’t contain any knots. Even when partially cooked, they don’t get tangled in the cooking pan. However, ramen noodles do become tangled after cooking, whereas chromatin stably maintains its unknotted state throughout interphase – the period between cell divisions when chromatin in the nucleus uncoils. In that condensed but non-knotted configuration, sections of chromatin that are far apart on the long strands may be brought into proximity. Thus, interactions between chromatin on the same chromosome, or between sections with similar properties or functions, are made possible by the way chromatin is organized in the interphase nucleus.
These are but a few of the innovative and complex understandings that inspired the creators of the Genome Ball (for more information about the 3-D printing of the Genome Ball displayed at the exhibition, see the feature article “Super 3D Model: How the Genome Ball Was Created” on this website). Our knowledge of the nucleus has come a long way in the 332 years since Leeuwenhoek. But, as Aiden’s Science essay concluded: “at the fringes of our maps the world is full of surprises.”
The same is certainly true of the nucleus.
Source: Unlockinglifescode.org/the-genome-ball. Access November 19, 2017, Genome Project NIH
(2) “DNA packaging: Nucleosomes and Chromatin.” Nature Education 1 (2008):26.
(3) “Regulatory and Epigenetic Landscapes of Mammalian Genomes,” Current Topics in Genome Analysis 2014. March 26, 2014.
(4) “Leeuwenhoek Sees the Cell Nucleus.” Science of Aging: Timeline of Discoveries.
(5) Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science 326 (9 October 2009): 189-324.
Source: NIH (National Institute of Health) Genomic Project access and received for distribution 11/18/2017
Click on the link below:
We are all over this world in many countries, with differences, shades of color, opinions, thoughts. Make no mistake we are one, our ancestors came out of Africa. It’s in your DNA. I have found relatives in Brazil, India, Iran, Syria, Australia, Mexico, Boro Bora, Korea, China, and Japan. Never stop your journey finding your past. Gedmatch is a good place to start.
DNA collection, testing, and results are different for people of color and the algorithms used are not geared towards our DNA but can be very useful. It is Eurocentric, however, Helix, National Geo2, and 23andMe are moving towards a more inclusive model. Also, there are new projects in many countries to match DNA for people around the world.
Adult ADHD: An imbalance between the online and offline brain (https://www.genome.gov/27569602/2017-news-feature-adult-adhd-an-imbalance-between-the-online-and-offline-brain/?utm_source=NHGRI+Email+Updates&utm_campaign=5b96bdbf21-Skin+Pigmentation+publications&utm_medium=email&utm_term=0_3d227b0341-5b96bdbf21-118937769)
By Jeannine Mjoseth (mailto:Jeannine.Mjoseth@nih.gov)
November 7, 2017
A new study by researchers at the National Human Genome Institute (NHGRI) examined why some people grow out of childhood attention deficit hyperactivity disorder (ADHD), while others continue to have symptoms into adulthood. They discovered that adults with ADHD persisting from childhood partly lose the usual balance of connections between brain networks that control action and those that control daydreaming or introspecting. Researchers have argued that this imbalance – between the brain “online” and the brain “offline”- might account for the lapses of attention that are found in ADHD. By contrast, adults who had “grown out” of their childhood ADHD, did not show such a loss of balanced brain activity, according to findings published October 31, 2017, in The Proceedings of the National Academy of Science (PNAS).
“We hope to understand the mechanisms that explain why some people outgrow ADHD and other do not,” said Philip Shaw, B.M.B.Ch., Ph.D., senior author and an investigator in NHGRI’s Social and Behavioral Research Branch (https://www.genome.gov/11508935/Social-and-Behavioral-Research-Branch/Social-and-Behavioral-Research-Branch/Social-and-Behavioral-Research-Branch?utm_source=NHGRI+Email+Updates&utm_campaign=5b96bdbf21-Skin+Pigmentation+publications&utm_medium=email&utm_term=0_3d227b0341-5b96bdbf21-118937769) . “If we can understand why some people can recover from ADHD, we also might be able to apply this knowledge to other neuro-developmental conditions like learning disabilities or problems with social interaction.”
ADHD (https://www.nimh.nih.gov/health/topics/attention-deficit-hyperactivity-disorder-adhd/index.shtml?utm_source=NHGRI+Email+Updates&utm_campaign=5b96bdbf21-Skin+Pigmentation+publications&utm_medium=email&utm_term=0_3d227b0341-5b96bdbf21-118937769) is a heritable and treatable brain disorder marked by inattention and/or hyperactivity-impulsivity that can cause great difficulties with impulse control, attention span in school, social situations and the workplace. Around 20 to 30 percent of people with ADHD retain the full syndrome as young adults and about 50 percent show partial, though not complete remission.
The researchers looked at brain function in 205 adult participants: 101 participants had been diagnosed with childhood ADHD and 104 subjects never had ADHD. They looked at changes in the brain’s oxygen levels to determine the location of brain networks using functional magnetic resonance imaging (fMRI) (mailto:http://fmri.ucsd.edu/Research/whatisfmri.html) , and they studied the different levels of neuronal activity that by looking at the brain’s magnetic fields using magnetoencephalography (mailto:http://ilabs.washington.edu/what-magnetoencephalography-meg) .
Regardless of the type of brain imaging used, the researchers found that adults who had inattentive symptoms persisting from childhood lost the usual balance of connections between the online and offline brain networks. Specifically, a network that is prominent when a person is introspective is usually switched off when a person engages in tasks. This balance was partly lost in the adults with persistent inattention. By contrast, this pattern of connections between brain networks in adults who outgrew ADHD looked very similar to the adults who never had ADHD. These findings support the theory that among individuals who recover from ADHD, there is a childhood disruption to brain function that corrects itself by adulthood.
“Most adults have a balance between the online, task-oriented brain and the offline, day-dreaming brain, but we found that’s not the case for adults whose ADHD persists,” said Gustavo Sudre, Ph.D., study co-author and postdoctoral research fellow in Dr. Shaw’s lab. “We found that adults who recovered from ADHD had a very similar balance of online and offline brains to those who never had ADHD.”
NHGRI’s investment in this type of high impact, longitudinal research and the participants’ long-term commitment to ADHD research make studies like this possible.
“We first met these individuals at the National Institutes of Health Clinical Center when they were eight years old,” Dr. Shaw said. “They are so committed to ADHD research that they have kept coming back for 14 years. It’s great to see so many of the children who had severe ADHD grow into adults who are managing very well.”
In the next step of their research, Drs. Shaw and Gustavo will collaborate with an international ADHD research consortium to find genes associated with the disrupted brain networks.
Read the study
Sudre G, Szekely E, Sharp W, Kasparek S, Shaw P. Multimodal mapping of the brain’s functional connectivity and the adult outcome of attention deficit hyperactivity disorder (http://www.pnas.org/content/114/44/11787.full?utm_source=NHGRI+Email+Updates&utm_campaign=5b96bdbf21-Skin+Pigmentation+publications&utm_medium=email&utm_term=0_3d227b0341-5b96bdbf21-118937769) . PNAS, October 31, 2017.
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