Dna Second Layer Of Information

[exit99]

Has anyone read about "DNA second level" (6/9/16) by Fiona MacDonald in scienceAlert.com?

http://www.sciencealert.com/scientists-confirm-a-second-layer-of-information-hiding-in-dna

 

She explains how genes are expressed or not depending on if they're on the inside or outside. 

My question is: on the inside or outside of what?

 

I sent an email to her but no reply yet. 

 

[exit99]

Here’s the part I don’t understand (Fiona MacDonald ScienceAlert 6/9/2016):

“But the mechanics of the DNA folding is the original control mechanism. That's because every single cell in our body contains around 2 metres of DNA, so to fit inside us, it has to be tightly wrapped up into a bundle called a nucleosome - like a thread around a spool.

And the way the DNA is wrapped up controls which genes are 'read' by the rest of the cell - genes that are all wrapped on the inside won't be expressed as proteins, but those on the outside will. This explains why different cells have the same DNA but different functions.”

 

Notice she says genes are on the inside or outside, after mentioning nucleosomes. But even a median size gene (23,329 bp) needs about 132 nucleosomes. So parts of this gene are on the inside and parts are on the outside of nucleosomes.

 

Perhaps she refers to the [smaller] genomic binding site being inside a nucleosome. but that leads to more questions.

 

Isn’t it true that during Interphase histones are not attached to DNA?

Especially in S phase when DNA is being replicated, it would be improbable for helicase and other parts of the DNA-polymerase group to work on DNA wound around histones.

 

But the article says gene expression is controlled by nucleosome positions. Wikipedia also says: “In general, genes that are active have less bound histone, while inactive genes are highly associated with histones during interphase.”

https://en.wikipedia.org/wiki/Histone

 

When are nucleosomes made and attached to DNA? I thought they were made to organize DNA [eventually] into chromosomes for mitosis in which gene expression is not done.

Edited June 15, 2016 by exit99

[exit99]

In all the tutorials about DNA replication or transcription, I’ve never seen or heard comments about “First the DNA must be separated from the histone.”

 

E.g. here, the impression is given that all the DNA is brought in as a “non-attached” format (no histone attachments).

Helicase is the first step.

http://www.hhmi.org/biointeractive/dna-replication-advanced-detail

 

My "old" understanding:

In Interphase, gene expression and replication require a normal string of DNA.

In Mitosis, chromosomes are formed (starting with histones) to enable diversity.

 

But there’s a need for each cell to identify itself (heart cell, nerve cell etc.); histones may play a role.

 

Wikipedia says: “In general, genes that are active have less bound histone, while inactive genes are highly associated with histones during interphase.”

https://en.wikipedia.org/wiki/Histone

 

Can you shed some light on this?

[GAHD]

That depends on which meaning "second layer" refers to: I'm bored with an hour or so to kill so I'll look into it.

Before I go digging, here's two bits that came to mind upon reading your post.
Eukaryotic cells have multiple genetic systems. There is the central nucleic DNA anyone with a 10th grade education knows a bit about, and then the secondary genetic systems of organelles, EG mitochondria. They MAY be referring to that and it got taken out of context. (betting this

Alternatively They may be referring to the second and third "loops" that form while the DNA is being split and read (which seem to be "another layer" of cryptography) for RNA transcription(2:55 onward, this particular animation is based on prokaryotic DNA and artisticly adapted AFAIK, and thus is missing the second and third loop-back observed in eukaryotes).
https://www.youtube.com/watch?v=f9ff4FQ39CE.:

I'll see if i can track down the ACTUAL PAPER the editorial you linked is based on, somehow I'm thinking it'll be here:
http://arxiv.org/find/all/1/all:+AND+Watson+Crick/0/1/0/all/0/1

BRB if I find something.

http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0156905

"We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model...This suggests that the exact positions of nucleosomes play crucial roles in chromatin function."

 

Edited June 22, 2016 by GAHD

[exit99]

"We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model...This suggests that the exact positions of nucleosomes play crucial roles in chromatin function."

Yes I read part of that article but couldn’t understand it. Why don’t they provide a model that’s easy to understand?

 

As I mentioned, an average gene with 23,329 bp needs about 132 nucleosomes, if each nucleosome has 147 bp on the core and 30 bp linker.

Are each of these 132 nucleosomes positioned in a unique way? Or only those on certain parts of the gene?

 

To explain the concept, say we have two genes A and B. Each one has 1,770 bp, so there are 10 nucleosomes in each gene.

 

We want to express gene A but not B.

How is DNA wrapped on the nucleosomes differently (in exact positions) on these genes, so that only gene A is expressed?

 

Are they saying the DNA content affects the wrapping? Wouldn’t DNA wrap in the least problematic (least energy) way?