DNA Densely Packed Without Knots

Biological Strategy

Humans

AskNature Team

Image: vitstudio / Shutterstock / Some rights reserved

Optimize Shape/Materials

Resources are limited and the simple act of retaining them requires resources, especially energy. Living systems must constantly balance the value of resources obtained with the costs of resources expended; failure to do so can result in death or prevent reproduction. Living systems therefore optimize, rather than maximize, resource use. Optimizing shape ultimately optimizes materials and energy. An example of such optimization can be seen in the dolphin’s body shape. It’s streamlined to reduce drag in the water due to an optimal ratio of length to diameter, as well as features on its surface that lie flat, reducing turbulence.

Search this Function

Modify Size/Shape/Mass/Volume

Many living systems alter their physical properties, such as size, shape, mass, or volume. These modifications occur in response to the living system’s needs and/or changing environmental conditions. For example, they may do this to move more efficiently, escape predators, recover from damage, or for many other reasons. These modifications require appropriate response rates and levels. Modifying any of these properties requires materials to enable such changes, cues to make the changes, and mechanisms to control them. An example is the porcupine fish, which protects itself from predators by taking sips of water or air to inflate its body and to erect spines embedded in its skin.

Search this Function

Physically Assemble Structure

Living systems use physical materials to create structures to serve as protection, insulation, and other purposes. These structures can be internal (within or attached to the system itself), such as cell membranes, shells, and fur. They can also be external (detached), such as nests, burrows, cocoons, or webs. Because physical materials are limited and the energy required to gather and create new structures is costly, living systems must use both conservatively. Therefore, they optimize the structures’ size, weight, and density. For example, weaver birds use two types of vegetation to create their nests: strong, a few stiff fibers and numerous thin fibers. Combined, they make a strong, yet flexible, nest. An example of an internal structure is a bird’s bone. The bone is comprised of a mineral matrix assembled to create strong cross-supports and a tubular outer surface filled with air to minimize weight.

Search this Function

Mammals

Class Mammalia (“breast”): Bats, cats, whales, horses, humans

Mammals make up less than 1% of all animals on earth, but they include some of the most well-known species. We know first-hand some of the characteristics that make mammals unique, like having hair, being able to sweat, and producing milk through mammary glands. Another critical shared feature is a set of highly-specialized teeth. Unlike sharks or alligators, for example, whose teeth are generally all the same size and shape, mammals have differently shaped teeth in different areas of the jaws to target specific foods or foraging strategies.

Search this Living System

The genomic DNA of humans is densely packed without knots into individual cells via fractal globule architecture.

Image: National Institutes of Health / Wikimedia commons /

Human karyotype with color added to distinguish chromosome pairs.

Image: Wikimedia commons /

“‘We’ve long known that on a small scale, DNA is a double …But if the double
helix didn’t fold further, the genome in each cell would be two meters
long. Scientists have not really understood how the double helix folds
to fit into the nucleus of a human cell, which is only about a hundredth
of a millimeter in diameter…’

“The researchers report two striking findings. First, the human genome is
organized into two separate compartments, keeping active genes separate
and accessible while sequestering unused DNA in a denser storage
compartment. Chromosomes snake in and out of the two compartments
repeatedly as their DNA alternates between active, gene-rich and
inactive, gene-poor stretches….

“Second, at a finer scale, the genome adopts an unusual organization
known in mathematics as a ‘fractal.’ The specific architecture the
scientists found, called a ‘fractal globule,’ enables the cell to pack
DNA incredibly tightly — the information density in the nucleus is
trillions of times higher than on a computer chip — while avoiding the
knots and tangles that might interfere with the cell’s ability to read
its own genome. Moreover, the DNA can easily unfold and refold during
gene activation, gene repression, and cell replication.” (EurekAlert! 2009)

“We identified an additional level of genome organization that is characterized by the spatial segregation of open and closed chromatin to form two genome-wide compartments. At the megabase scale, the chromatin conformation is consistent with a fractal globule, a knot-free, conformation that enables maximally dense packing while preserving the ability to easily fold and unfold any genomic locus. The fractal globule is distinct from the more commonly used globular equilibrium model.” (Lieberman-Aiden et al. 2009:289)

http://www.sciencemag.org/cgi/content/abstract/sci;326/5950/289
http://www.eurekalert.org/pub_releases/2009-10/hu-sdt100209.php

Last Updated September 14, 2016

References

Book

Scientists decipher the 3-D structure of the human genome

embedly preview

Reference

Journal article

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Science | 08/10/2009 | E. Lieberman-Aiden, N. L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B. R. Lajoie, P. J. Sabo, M. O. Dorschner, R. Sandstrom, B. Bernstein, M. A. Bender, M. Groudine, A. Gnirke, J. Stamatoyannopoulos, L. A. Mirny, E. S. Lander, J. Dekker

embedly preview

AskNature