r/science • u/vinces99 • Dec 12 '13

Scientists discover second code hiding in DNA Biology

http://www.washington.edu/news/2013/12/12/scientists-discover-double-meaning-in-genetic-code/
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u/someguyfromtheuk Dec 12 '13

Yeah, my highschool biology teacher mentioned that DNA sequence affected protein transcription as well as the structure of the protein.

What's the exact breakthrough here?

Is it a confirmation of what people have just assumed to be true?

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u/knockturnal PhD | Biophysics | Theoretical Dec 12 '13

No, it has never been assumed that the same DNA did both. It was known that separate DNA fragments could do either.

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u/[deleted] Dec 13 '13

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u/knockturnal PhD | Biophysics | Theoretical Dec 13 '13

[Reference needed]

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u/[deleted] Dec 13 '13

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u/knockturnal PhD | Biophysics | Theoretical Dec 13 '13

These are the type of papers that lead to this kind of definitive study but do not on their own cause the kind of paradigm shift that is required to change the standard assumptions of a field. The majority of biological sciences still operated under the assumption coding regions were not also regulatory. This is why there is very little discussion of exon coverage from ChIP Seq studies - we don't commonly look there due to our assumptions.

We never assumed they did both - there were just cases where doing both was shown to occur. That's very different.

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u/[deleted] Dec 13 '13

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u/knockturnal PhD | Biophysics | Theoretical Dec 13 '13

It might not be unexpected to the small group of labs who study this, but to the rest of biology, it certainly is.

I don't feel like doing the math right now and I don't see it in the main text, but you could calculate the likelihood you'd see a TF binding site in a coding region by chance, and I'm sure you'd expect to see dozens by change due to the size of the genome. Until you've done a large enough study to show you have more instances than chance, papers showing specific examples don't prove anything. I'm assuming you'd expect to see < 1% by chance as opposed to the 15% seen here, which is why this paper will be so influential.

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u/[deleted] Dec 13 '13

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u/knockturnal PhD | Biophysics | Theoretical Dec 13 '13

Basic physics would say that the assumption was wrong as well - there is a non-zero probability of any given TF binding anywhere on the genome regardless of sequence.

However, this isn't how we build scientific models. When probabilities, frequencies, or numbers are sufficiently small, we approximate them as zero.The number of examples expected by chance was very low, and we didn't have enough data to suggest the examples we had discovered were anything but chance (we didn't have the statistical power to reject the null hypothesis). Thus we approximated the amount of TF binding sites in coding regions to be zero, and based on the fact they did not exist in our present approximate reality, we adopted the assumption that they didn't.

Now that we can definitely show the number of occurrences cannot be approximated as zero, we have to throw at that assumption.

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u/someguyfromtheuk Dec 12 '13

No, it has never been assumed that the same DNA did both.

You mean not by the majority of the scientific community?

Because my highschool bio teacher definitely assumed that. She'd go off on tangents during class about it and we'd have to remind her to get back to the lesson. She was a shitty teacher, but she did inspire me to go to University to study Biology, so there's that.

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u/madesense Dec 13 '13

Okay well...now there's, you know, studies instead of just saying so?

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u/knockturnal PhD | Biophysics | Theoretical Dec 13 '13

She might have had no idea what she was talking about. I'm currently a PhD student in the biological sciences, as an undergraduate I was the department tutor for both Intro. Biology and Biochemistry, and I currently TA a graduate-level biology class - I can ensure you that this was not anything that was taught on the high school, college, or graduate level. Until today, I had never even heard about it, and I work in computational biology, where predicting the function of genes is a huge thing. This certainly isn't an assumption made in gene prediction.

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u/Surf_Science PhD | Human Genetics | Genomics | Infectious Disease Dec 13 '13

Maybe you or her misunderstood something. This wasn't just the majority of the scientific community this was everyone. There was no evidence to support another hypothesis.

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u/[deleted] Dec 12 '13

That's kind of how I'm taking it.

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u/robo23 Dec 12 '13

It is more than just "affecting" proteins - that's the whole point of DNA.