Second layer of information in DNA confirmed | Hacker News Reader

Second layer of information in DNA confirmed

physics.leidenuniv.nl

53 pointsGolDDranks7 comments

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.

> 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."

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

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.

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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.

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.

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.

WildUtah is referring to chemical modifications (methylation, associated with epigenetics: 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 .

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).

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