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(University of Washington)   Second code found in DNA. First reports have it as ↑↑↓↓←→←→ B A   (washington.edu) divider line 6
    More: Cool, First Report, DNA, genetic code, code, genes control, National Human Genome Research Institute  
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4602 clicks; posted to Geek » on 13 Dec 2013 at 7:56 AM (32 weeks ago)   |  Favorite    |   share:  Share on Twitter share via Email Share on Facebook   more»



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2013-12-13 08:01:02 AM
2 votes:
Just wait, we'll be seeing "DNA 2.0" show up on developer job listings, they'll also be wanting a decade of experience with it.
2013-12-13 01:45:18 PM
1 votes:
upload.wikimedia.org
2013-12-13 09:25:19 AM
1 votes:

mamoru: Based on my understanding from reading the abstract of the actual paper, this is not a new second code. That doesn't seem to be what the abstract is saying at all. Here is my take. If anyone does have access to the actual paper from Science, please feel free to correct me if I'm wrong.

1.) The idea of regulatory DNA is not new, nor is it really a secret code. I'm pretty sure just about everyone who has passed a reasonable high school biology class has been taught the basics of transcription regulation (even if you don't remember it), probably using the lac operon of E. coli as an example (it's the one in most textbooks).

2.) It is not surprising that some regulatory sequences which are binding sites for transcription factors (proteins which bind to DNA to affect gene expression) would also appear among the codons of coding sequences. Regulatory sequences tend to be short, and with only 4 DNA bases to work with, you would expect some to share sequences with coding sequences. Transcription factors, if they are present, will bind wherever they find the matching sequence.

3.) What the article really appears to be saying is that when this happens and you have a binding site for a transcription factor in the coding sequence of a gene (presumably to control a different gene, though it could act to repress the gene it is in, I guess) then sequence evolution is constrained because any mutation which changes that sequence will have multiple affects, possibly not only altering the amino acid sequence coded by that gene but the regulation of the other gene. That is what Dr John Stamatoyannopoulos is talking about in the quote, "Many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously."

At least that is what I gather from it. Please correct me if I'm wrong (and if anyone has access and would like to share the paper, I'd love to read it; EIP). :)


Here is a link to the paper  https://dl.dropboxusercontent.com/u/51521446/Science-2013-Stergachis- 1 367-72.pdf

TheMysteriousStranger: Wow.  Fifty-year-old news is so exciting.

Indeed a Nobel Prize was awarded in 1965 for it.   Whatever ENCODE found, it is not what was in the article.

This is not the first time for this project.  ENCODE has a history of extremely misleading press releases.  As if they care more about blowing their own horn then keeping the public informed about their work.


This is also true.  ENCODE is better at selling their science than anyone I have ever seen.

/now off to read the paper
2013-12-13 08:33:07 AM
1 votes:
Wow.  Fifty-year-old news is so exciting.

Indeed a Nobel Prize was awarded in 1965 for it.   Whatever ENCODE found, it is not what was in the article.

This is not the first time for this project.  ENCODE has a history of extremely misleading press releases.  As if they care more about blowing their own horn then keeping the public informed about their work.
2013-12-13 07:13:21 AM
1 votes:
Based on my understanding from reading the abstract of the actual paper, this is not a new second code. That doesn't seem to be what the abstract is saying at all. Here is my take. If anyone does have access to the actual paper from Science, please feel free to correct me if I'm wrong.

1.) The idea of regulatory DNA is not new, nor is it really a secret code. I'm pretty sure just about everyone who has passed a reasonable high school biology class has been taught the basics of transcription regulation (even if you don't remember it), probably using the lac operon of E. coli as an example (it's the one in most textbooks).

2.) It is not surprising that some regulatory sequences which are binding sites for transcription factors (proteins which bind to DNA to affect gene expression) would also appear among the codons of coding sequences. Regulatory sequences tend to be short, and with only 4 DNA bases to work with, you would expect some to share sequences with coding sequences. Transcription factors, if they are present, will bind wherever they find the matching sequence.

3.) What the article really appears to be saying is that when this happens and you have a binding site for a transcription factor in the coding sequence of a gene (presumably to control a different gene, though it could act to repress the gene it is in, I guess) then sequence evolution is constrained because any mutation which changes that sequence will have multiple affects, possibly not only altering the amino acid sequence coded by that gene but the regulation of the other gene. That is what Dr John Stamatoyannopoulos is talking about in the quote, "Many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously."

At least that is what I gather from it. Please correct me if I'm wrong (and if anyone has access and would like to share the paper, I'd love to read it; EIP). :)
2013-12-13 06:07:15 AM
1 votes:
One would be even further "stunned" to discover a blog writer who actually understands what he is talking about and can express it in plain language.
 
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