
Second layer of information in DNA confirmed - GolDDranks
http://www.physics.leidenuniv.nl/index.php?id=11573&news=889&type=LION&ln=EN
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_of
PLOS ONE is a bit special in the PLOS family of journals. They publish
essentially _anything_, as long as it's scientifically correct, it doesn't
matter how interesting the science is. Usually scientists try to get their
paper published in other journals first (e.g. PLOS Biology), and if it is
rejected there they submit it to PLOS One.

~~~
sndean
> Usually scientists try to get their paper published in other journals first
> (e.g. PLOS Biology), and if it is rejected there they submit it to PLOS One.

In fact, the higher PLOS journals push this path. Here's part of a rejection
letter I got a few years ago:

"And while we cannot, unfortunately, proceed with your paper, we would like to
suggest our sister journal, PLOS ONE (www.plosone.org), as a potential forum
for the study. PLOS ONE aims to present the results of sound scientific
research from across disciplines and implements new tools to allow discussion
and commentary on your paper after publication. If you are interested in
submitting your paper to PLOS ONE, we can transfer your files directly to
their manuscript handling system."

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Aelinsaar
I don't understand how this is _evidence_ of anything; it seems almost
entirely speculative.

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aroch
Wait, what is this bullshit and what moron wrote this press release?

From the paper:

> Analysis of two high resolution nucleosome maps revealed

> strong signals that—even though they do not constitute a

> definite proof—are at least consistent with such a view.

Also, the premise of this paper is clearly something only a physicist would
think was interesting. And I'm not the least bit surprised this wound up in
PLoS.

This just in: Modeling DNA using what we already knew about DNA confirms what
we already knew about DNA.

\-----

Edit: OK, I've gone back and actually read the whole paper. I can't say I'm
particularly swayed by this paper and I'm not entirely sure the point. But, in
a pattern I'm seeing throughout biology, a non-biologist modeler just realized
that bio is cool and spent the weekend modeling something. Overall, I'm not
sure what this brings to the table that merits being published?

Here's my reading of the main points:

1\. Some DNA sequences are bendier than others [Not a finding of the paper,
already known]

2a. There are histone binding sites and "promoters" for nucleosome formation
[already known]

2b. Through modeling, Eslami-Mossallam et al., claim a major factor in
nucleosome binding is whether the DNA can (thermodynamically) easily bend
around the histone complex. OK, fine, the models are maybe more specific but
this preference (and the motifs that comprise the hotspots) were more or less
known.

3\. DNA sequence determines the physical and genetic properties... Yes, we
know.

4\. The degeneracy of the genetic code allows it to encode additional
information. We already knew this, in fact, we know the mechanical properties
of RNA encode functional roles (See, programmed ribosomal frameshifts and the
DNApol gmaa/tau subunits)

5\. [The real shocker] DNA in real life organisms encodes both genes and its
own structure.

~~~
WildUtah
The article says "second layer." Apparently someone hasn't heard of
methylation, introns and start and stop codons, and palindromic sequences. Or
any results from the last fifty years of DNA and RNA research.

If this is ever a thing, it will be way beyond the fifth or maybe tenth layer
of information in DNA.

~~~
dave2000
I'm almost entirely ignorant on this topic but it sounds like you're
suggesting this could be a thing, which is more than the other posters here
are currently saying (although it's early days yet, with only a handful of
comments).

The things you've just mentioned sound like properties of the sequences,
whereas the site sounds like it's describing something which modifies the
meaning of the sequences depending on how they're physically located. Ie if
gtta is resting next to tacg or whatever it'll have a different meaning to if
it was next to gata.

~~~
aroch
WildUtah is referring to chemical modifications (methylation, associated with
epigenetics: [http://www.whatisepigenetics.com/dna-
methylation/](http://www.whatisepigenetics.com/dna-methylation/)), the
structure of [eukaryotic] genes (intron/exon, start and stop; things many
elementary students know of -- and subsequently forget) and palindromic
elements.

Palindromic elements are most closely related to what the linked paper is
about. Basically, instead of existing as a normal double helix, the two
strands separate and bind with the palindrome on the same strand; like making
an X with DNA:
[https://en.wikipedia.org/wiki/Palindromic_sequence](https://en.wikipedia.org/wiki/Palindromic_sequence)
.

Ultimately, this is a crappy press release for a paper that, as _of points
out, is scientifically correct but otherwise dull. The paper is going back to
first principles, as it were, for DNA and looking at factors in DNA alone that
contribute to its function (well, 'normal', non-methylated, potentially
histone associated DNA).

