The term “dark matter“ in biophysics and molecular biology

The term dark matter is used as a nickname for something we do not directly see, but infer from some observable effects. Best known is dark matter in astrophysics and cosmology, where it is hypothesized so it can keep results from measurements in harmony with current theory. Too far away, anyway? What about dark matter at the center of each cell in your human body and other evolving creatures? In a recent article on the dynamics and “densification” of chromatin, the complex of DNA and proteins (including histone) that form chromosomes, Gregory Babbitt refers to the dark matter of the human genome: the vast areas of noncoding regulatory DNA.

DNA contains blueprints (genetic instructions encoded in nucleotide sequences) for constructing other parts of the cell. Recent research suggests that the sequence of DNA also contains the information on how to fold and package itself into chromatin. A technique called chromosome conformation capture helps to shine some light into those “dark corners” of the DNA. Results provide evidence that the chromosome does not assemble itself as a disordered spaghetti globule, but as a globule mathematically organized in subglobules of subsubglobules. Evolution (of chromatin, at least) is becoming less a matter of darkness and more a subject of topology.

Reference
Gregory A. Babbitt: Chromatin Evolving. American Scientist January-February 2011, 99 (1), pp. 48-55.