Scientists at Leiden University have found evidence that a "second layer" of information in DNA can influence protein expression:
Leiden theoretical physicists have proven that not only the genetic information in DNA determines who we are, but also DNA's mechanics. Helmut Schiessel and his group simulated many DNA sequences and found a correlation between mechanical cues and the way DNA is folded.
[...] Now for the first time, Leiden physicist Helmut Schiessel and his research group provide strong evidence that this second layer of information indeed exists. With their computer code they have simulated the folding of DNA strands with randomly assigned mechanical cues. It turns out that these cues indeed determine how the DNA molecule is folded into so-called nucleosomes. Schiessel found correlations between the mechanics and the actual folding structure in the genome of two organisms—baker's yeast and fission yeast. With this finding we know that evolutionary changes in DNA—mutations—can have two very different effects: the letter sequence encoding for a specific protein can change or the mechanics of the DNA structure can change, resulting in a different packaging and accessibility of the DNA and therefore a different frequency of production of that protein.
Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach (open, DOI: 10.1371/journal.pone.0156905)
(Score: 0) by Anonymous Coward on Monday June 13 2016, @02:04AM
It's absolutely mind blowing that with so many combinations of DNA (and now a second layer), environmental factors, etc. that life has evolved to this point. It's almost too hard to believe, nevertheless the evidence is pretty convincing.
(Score: 2) by takyon on Monday June 13 2016, @04:15AM
I'm left wondering how much this "second layer" needs to be considered for bioengineering or gene therapy purposes (ignoring it could lead to a less efficient drug). And does sequencing a person's full genome capture this second layer or is more information required?
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(Score: 3, Interesting) by frojack on Monday June 13 2016, @06:33AM
It almost sounds to me that the second layer can only affect the EXPRESSIOM of some genes, delaying them or speeding them up by hiding (in folds) certain locations that trigger the manufacture of proteins (or what ever).
It doesn't appear from the article that sequencing the entire genome gathers any information about the folding.
Nor is it clear that the folding is passed down to offspring.
In fact it almost seems like the folding acts as a differentiation engine, allowing the same genome to generate different individual traits from sibling to sibling or even over the life of a single organism.
No, you are mistaken. I've always had this sig.
(Score: 2) by takyon on Monday June 13 2016, @07:07AM
I thought that the sequence of base pairs would have an effect on the DNA folding (because of varying bond strengths and forces between nearby atoms) which would in turn affect the gene expression (so you can't just insert a gene anywhere and get identical efficiency).
A small group of cells spreading a mutation that significantly altered the folding and gene expression could explain certain diseases.
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(Score: 0) by Anonymous Coward on Monday June 13 2016, @07:22AM
In fact it almost seems like the folding acts as a differentiation engine, allowing the same genome to generate different individual traits from sibling to sibling or even over the life of a single organism.
So do identical twins have similar folding in their cells? My guess is yes.
(Score: 0) by Anonymous Coward on Monday June 13 2016, @07:52PM
What can you accomplish with 5 billion years of experiments? It's only hard to believe if you can't grasp the timescale. Our current calendar only goes back 2000 years. That's only 0.0000004 of the age of the Earth. And remember most life got wiped out at least once. We could have been much further along than we are now.
(Score: 4, Informative) by maxwell demon on Monday June 13 2016, @09:07AM
Wouldn't that be a third layer?
First layer: The nucleotide sequence (genetics).
Second layer: Molecular attachments to the DNA like methylation (epigenetics)
Third layer: This folding layer
The Tao of math: The numbers you can count are not the real numbers.
(Score: 0) by Anonymous Coward on Monday June 13 2016, @12:05PM
Histone code and chromosomal location in the nucleus.
(Score: 0) by Anonymous Coward on Monday June 13 2016, @02:25PM
Their PR release reads like a breathless sales brochure.
(Score: 3, Informative) by gringer on Monday June 13 2016, @06:13PM
This isn't a discovery for the first time, Researchers have already worked out that 3D positioning of DNA plays a role in gene expression:
http://www.cell.com/cell/abstract/S0092-8674%2814%2901497-4 [cell.com]
Third, the presence of cell type-specific peaks is associated with changes in expression. When we examined RNA sequencing (RNA-seq) data produced by ENCODE, we found that the appearance of a loop in a cell type was frequently accompanied by the activation of a gene whose promoter overlapped one of the peak loci.
The map of genome-wide pairwise interactions (from which the 3D structure was derived) can be explored at Erez Lieberman Aiden's juicebox:
http://www.aidenlab.org/juicebox/ [aidenlab.org]
Ask me about Sequencing DNA in front of Linus Torvalds [youtube.com]