Second layer of information in DNA confirmed

June 8, 2016 by Erik Arends, Leiden Institute of Physics
The rigid base-pair model is forced, using 28 constraints (indicated by red spheres), into a lefthanded superhelical path that mimics the DNA conformation in the nucleosome. Credit: Leiden Institute of Physics

Leiden theoretical physicists have proven that DNA mechanics, in addition to genetic information in DNA, determines who we are. Helmut Schiessel and his group simulated many DNA sequences and found a correlation between mechanical cues and the way DNA is folded. They have published their results in PLoS One.

When James Watson and Francis Crick identified the structure of DNA molecules in 1953, they revealed that DNA information determines who we are. The sequence of the letters G, A, T and C in the famous double helix determines what proteins are made ny our cells. If you have brown eyes, for example, this is because a series of letters in your DNA encodes for proteins that build brown eyes. Each cell contains the exact same letter sequence, and yet every organ behaves differently. How is this possible?

Mechanical cues

Since the mid 1980s, it has been hypothesized that there is a second layer of information on top of the genetic code consisting of DNA mechanical properties. Each of our cells contains two meters of DNA molecules, and these molecules need to be wrapped up tightly to fit inside a single cell. The way in which DNA is folded determines how the letters are read out, and therefore which proteins are actually made. In each organ, only relevant parts of the genetic information are read. The theory suggests that mechanical cues within the DNA structures determine how preferentially DNA folds.

Simulation

For the first time, Leiden physicist Helmut Schiessel and his research group provide strong evidence that this second layer of 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. This finding reveals evolutionary changes in DNA—mutations—that 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 different packaging and levels of DNA accessibility, and therefore differing frequency of production of that protein.

Explore further: May repairs full of mistakes develop into cancer?

More information: Behrouz Eslami-Mossallam et al. Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach, PLOS ONE (2016). DOI: 10.1371/journal.pone.0156905

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22 comments

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caeman
3.3 / 5 (8) Jun 08, 2016
How is this different from epigentics?
Whydening Gyre
5 / 5 (12) Jun 08, 2016
Not different - It is inclusive of...

There is a second level of information/communication in ALL structures, be they physical or abstract.
usmdmark
2 / 5 (8) Jun 08, 2016
The second layer of information is defined by the 3D fixed (genetic) and mobile, flexible (epigenetic, adaptive) structures of DNA. There is also the 4D structure -preprogrammed time machine of DNA, keeping the third layer of archived information. And, at last, there is 5D super structure of DNA modern genetics even has no idea about.
FredJose
Jun 09, 2016
This comment has been removed by a moderator.
EnricM
5 / 5 (6) Jun 09, 2016
This finding reveals evolutionary changes in DNA—mutations—that have two very different effects:

The usual kow-tow just has to be made to the evolutionary god that designed all life on earth.
. r.

Yes, yes. Very interesting. Greeting to Big Gunga-Bunga!
torbjorn_b_g_larsson
5 / 5 (8) Jun 09, 2016
This is no different from other inherited control mechanisms for protein expression such as up and downstream regulators. Hence this is not 'a second layer of information' or 'codes' as the paper suggests. [How did this get pass peer review?] It is sensonalism.

@caeman: WG, usmdmark: Whether or not it is "epigenetics" depends on your stated definition. The original and often used definition is what regulates development and cell differentiation. [See e.g. the series of recent posts in Why Evolution Is True blog by biologist Coyne with many participating leading epigenetic scientists. It starts here: https://whyevolut...enetics/ ] This mechanism does not nothing of the kind.

[tbctd]
torbjorn_b_g_larsson
5 / 5 (9) Jun 09, 2016
[ctd]

@usmdmark: The genetic information in the DNA is a string. As a measure (of information) a string is zero dimensional, as a geometry a string is 1D. Your comment is nonsense, and that is likely why you don't provide references.

@Enric: Indeed, the ignorant troll believes in religious booga wooga magic. Put your hands together, or hit the forehead on a carpet and wiggle your ass, and mumble meaningless incantations, and - presto - all your wishes may become true! The chief magicians with pointy hats or long or square head scarfs says so!

The troll also doesn't know that the process of biological evolution is independent of the mostly geological/chemical process of emergence of life. [Wikipedia] Or that the latter is now a normal science, with both observation and theory, so highly useful now that astrobiology takes off with studying planets en masse.

But as always, trolls are best ignored, unless someone is actually reading their inflammatory nonsense.
torbjorn_b_g_larsson
5 / 5 (8) Jun 09, 2016
Oops. I meant "or round head scarfs", of course.

But it looks more like a small rug that they put on their, um, "rug". And some have small cube "hats". They all look and behave silly, anyway. It is a wonder anyone would believe in their patter.
Guy_Underbridge
4 / 5 (8) Jun 09, 2016
If there's no life, there's no Darwinian evolution either.
QED: We don't exist. That pretty much wraps up the discussion.
Whydening Gyre
5 / 5 (4) Jun 09, 2016
TBGL,
I believe what some might be overwhelmed by is the inter-relational aspect of the geometric configuration of said string (IE-histone wrapping, etc.)
And - how can biologic evolution be considered "independent of" the any geologic/chemical process that drives it? (And still does)
Examined independently, sure... but operationally independent?
Pooua
5 / 5 (3) Jun 09, 2016
How is this different from epigentics?

Epigenetics is chemical code that is part of the DNA, such as the attachment of methylation groups to certain segments. This article is discussing the mechanical properties of the DNA. The shape of molecules determines their function, so much so that it is possible to simulate one element's chemical activity by using another element that has its electron configuration forced into the first shape.
Frosted Flake
5 / 5 (3) Jun 09, 2016
I have the impression covalent bonds have a preferred alignment and act more like a hinge than a gimbal.

Am I mistaken? I mean, again?
Whydening Gyre
5 / 5 (3) Jun 09, 2016
I have the impression covalent bonds have a preferred alignment and act more like a hinge than a gimbal.

Am I mistaken? I mean, again?

Fair analogy, FF. But it's a "hinge" that works in multiple directions (axis).
Frosted Flake
5 / 5 (2) Jun 09, 2016
More flexible than I thought.

Thanks, W.G.
Averlorn
4.5 / 5 (8) Jun 10, 2016
@FredJose

Read the bottom of the article with the hyperlink that reads 'How proteins read meta DNA code.'
Pretty much makes your words pure nonintellectual religious spin. Which goes against the websites comments guidelines.
antialias_physorg
5 / 5 (7) Jun 10, 2016
I have the impression covalent bonds have a preferred alignment and act more like a hinge than a gimbal.

It's more of a gimbal. The way covalent bonds are often depicted (with the electrons in between the nuclei) does not imply a hinge movement. However, the degree of freedom of covalent bonds is also affected by how many other bonds are present (and whether these are single or double or triple bonds ...and also what kind of atom is bonded).

That it's more of a gimbal issue around the dihedral angles can be seen if you look at the image of the electron density plots
https://en.wikipe...geometry]https://en.wikipe...geometry[/url]
(images at thend of the page)

https://en.wikipe...geometry]https://en.wikipe...geometry[/url]
Whydening Gyre
5 / 5 (4) Jun 10, 2016
I have the impression covalent bonds have a preferred alignment and act more like a hinge than a gimbal.

It's more of a gimbal. The way covalent bonds are often depicted (with the electrons in between the nuclei) does not imply a hinge movement. However, the degree of freedom of covalent bonds is also affected by how many other bonds are present (and whether these are single or double or triple bonds ...and also what kind of atom is bonded).

That it's more of a gimbal issue around the dihedral angles can be seen if you look at the image of the electron density plots
http://https://en.wikipe...geometry

I defer to AAP's excellent definitions...:-)
I stand corrected...:-)
AGreatWhopper
2.6 / 5 (10) Jun 10, 2016
Averlorn 5 /5 (4) 4 hours ago
@FredJose
Pretty much makes your words pure nonintellectual religious spin. Which goes against the websites comments guidelines.


AND basic civility, but the sad truth is that the actual enforcement is very different. People posting a clearly right wing position- no evolution, no AGW, unrelated right wing political regurgitations- are protected by direct payments from the Koch and Heritage Foundations, among others.

I'm willing to be proven wrong. Based on what other (rational) posters have said, it's down more to the number of complaints received. I suggest we all report the canned "the creator made everything", "there is no evolution" tripe every time we see it and see which is the case.
They would not hesitate a moment to have one of us thrown out of a church if we interrupted and started yelling, "There is no God"; they deserve the same.
Captain Stumpy
5 / 5 (2) Jun 10, 2016
The usual kow-tow just has to be made to the evolutionary god that designed all life on earth
@fred
worse still, you've just committed the sins of blatant lie and heresy : GEN 1:21

ya can't have it both ways

.

.

are protected by direct payments from the Koch and Heritage Foundations, among others.

I'm willing to be proven wrong
@AGreatWhopper
I doubt you will be
we can demonstrate the complicity in a number of ways, like this:
http://www.drexel...nge.ashx

so the proof if you being wrong would have to be equivalent and i have yet to see a validated, published peer-reviewed study that demonstrates the point

xponen
3 / 5 (2) Jun 12, 2016
Proteins & enzymes already work based on physical shapes and binding sites, like a machine made of gears & clamp. Obviously, a protein folding is responsible for those shape, and the folding is based on sequence of molecule causing slightly differing polarity along the strand. So who is going to be hubris enough (fool enough) to say such folding won't be significant to DNA...
culkin
1 / 5 (1) Jun 13, 2016
@ torbjorn_b_g_larsson

This is no different from other inherited control mechanisms for protein expression such as up and downstream regulators. Hence this is not 'a second layer of information' or 'codes' as the paper suggests.


This is different from regulators... did you read and/or understand the paper? The paper is suggesting there has taken place a mechanical evolution alongside gene evolution. This is different from epigenetics, if that's what you're suggesting.

A key point is, due to the redundancy of the codon-amino acid code, most amino acids are coded for by multiple codons, e.g. alanine is coded by GCU, GCC, GCA, and GCG. This means the same protein can be coded by many different sequences. So the sequence can mutate such that chemical interactions are different, e.g. with nucleosomes and proteins, but the same genes are produced. These chemical interactions alter DNA organisation and expression, so the DNA may mechanically control its own expression.
ericpelser
1 / 5 (1) Jun 14, 2016
All I can say is WOW!, and thank you !

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