Slashdot Mirror
Scientists Discover How DNA Is Folded Within the Nucleus
mikael writes "Sciencedaily.com is reporting that scientists have discovered how DNA is folded within the nucleus of a cell such that active genes remain accessible without becoming tangled. The first observation is that genes are actually stored in two locations. The first location acts as a cache where all active genes are kept. The second location is a denser storage area where inactive genes are kept. The second observation is that all genes are stored as fractal globules, which allows genes that are used together to be adjacent to each other when folded, even though they may be far apart when unfolded."
The first observation is that genes are actually stored in two locations. The first location acts as a cache where all active genes are kept. The second location is a denser storage area where inactive genes are kept. The second observation is that all genes are stored as fractal globules, which allows genes that are used together to be adjacent to each other when folded, even though they may be far apart when unfolded.
Well OBVIOUSLY.
All your base-pair are belong to us.
Knowledge is how to play a game, intelligence is how to win, wisdom is knowing what game to play.
Could all the "junk" DNA that we supposedly don't use maybe have some sort of structural stabilization function? It wouldn't actively code for any proteins but the coding structure itself might allow it to make these shapes and/or allow the globule to move without causing knots in the structure.
So, life figured out a form of a Hilbert Curve for storing data? Cool!
Now, if life could just figure out how to get the blinking numbers off of my VCR...
0 = 1 + e^(Alt something)
Anyone else wish they could read the actual publication? It's sad considering this is partly taxpayer funded and given the NIH's and Harvard's push toward open access that the authors didn't choose a more accessible journal for such a groundbreaking piece of work.
No it's not, as I understand the paper, the important work was in determining the structure of the folding of heterochromatin. All other theories still apply, we just know more about the folding itself. You can see using electron microscopy that there are discrete locations for heterochromatin and euchromatin inside the nucleus, that theory still apples as well.
The "beads (histones) on a string (DNA)" architecture is one step above the double helix organizational order, this is also the form of more highly transcribed or "active" DNA (called euchromatin). From there, that string is then wrapped into a much more complex structure which significantly reduces the transcription levels of the mRNAs that this DNA encodes for (called heterochromatin).
The who field of epigenetics deals with regulating expression of DNA to cause cellular differentiation and changes in cells throughout their lives. One of those ways of regulation is the cell controlling which genes are found in euchromatin and which are found in heterochromatin for certain types of cells at a certain point in their life cycles.
The post below me about the Hilbert curves is also accurate, thermodynamics is at the heart of all DNA and protein folding.
Actually, fractals generate arbitrarily complex structures with very simple rules (e.g. the Mandelbrot Set - take a complex number, square it, add the original number, repeat.) That's pretty much exactly the kind of structure you'd expect an evolutionary process to come up with. If I may say so myself.
PHEM - party like it's 1997-2003!
I would guess that the development of this sort of fractal packing was a watershed moment in the development of eukaryotic life, but the process itself can be logically seen as an extension of existing processes. Most bacteria, which lack a nucleus, arrange their DNA in a simple circle.
This has advantages: the entire genome is always accessible for transcription and replication, there aren't telomeres to deal with, and it requires less maintenance. There are disadvantages: if every gene is accessible to the cytoplasm, you have actively keep the 99% you aren't currently using shut off, which is why bacteria use the operon system, and a big circular strand floating around is liable to tie itself in an awful knot. Bacteria have the equipment to fix small topologically issues in their genome, but overall, bacterial genomes are limited in their potential size. Some more complex bacteria have found a partial solution: they draw folds of their circular genome around proteins, to make a single circle more manageable as a group of pinched off loops. So you can see that there's an intermediate stage between "circle" and "our DNA has Hausdorff dimension 3."
Of course, if you're going to head down the road of DNA folding, you would really benefit from a plan. The beauty of fractals, and a reason they are found so often in the natural world, is that very complex behavior can come from the repeated iteration of very simple rules. Your cells don't need to understand Hilbert curves; all they need is a protein complex that grabs a strand of DNA, then puts a short, specific sequence of folds in it. As that happens along the entire strand, you make a space filling curve that would impress a mathematician.
"FDA staff reviewers expressed concern about the number of patients who were left out of the study because they died."