Tuesday, May 24, 2016

University of Toronto press release distorts conclusions of RNA paper

My colleague, Ben Blencowe, just published a paper ...

Sharma, E., Sterne-Weiler, T., O’Hanlon, D., and Blencowe, B.J. (2016) Global Mapping of Human RNA-RNA Interactions. Molecular Cell, [doi: 10.1016/j.molcel.2016.04.030]

ABSTRACT (Summary)

The majority of the human genome is transcribed into non-coding (nc)RNAs that lack known biological functions or else are only partially characterized. Numerous characterized ncRNAs function via base pairing with target RNA sequences to direct their biological activities, which include critical roles in RNA processing, modification, turnover, and translation. To define roles for ncRNAs, we have developed a method enabling the global-scale mapping of RNA-RNA duplexes crosslinked in vivo, ‘‘LIGation of interacting RNA followed by high-throughput sequencing’’ (LIGR-seq). Applying this method in human cells reveals a remarkable landscape of RNA-RNA interactions involving all major classes of ncRNA and mRNA. LIGR-seq data reveal unexpected interactions between small nucleolar (sno) RNAs and mRNAs, including those involving the orphan C/D box snoRNA, SNORD83B, that control steady-state levels of its target mRNAs. LIGR-seq thus represents a powerful approach for illuminating the functions of the myriad of uncharacterized RNAs that act via base-pairing interactions.
The authors looked at RNA-RNA interactions (hybrid formation) by mapping different RNA molecules that bound to each other.

The idea is to map as many of these interactions as possible in order to get a handle on which of the RNAs have a significant biological function. The presence of an interaction does not prove that the RNA molecule(s) have a function since there are many cases where spurious transcripts could be complementary to an existing RNA. Only one of the RNAs might have a function or maybe neither has a function. However, it's one way of detecting possible functional RNAs.

The technique involves in vivo chemical crosslinking of the two interacting RNAs followed by sequencing. The authors tested the technique by showing that it detects known interactions between well-characterized RNA molecules. Then they applied it to all the interactions in human tissue culture cells.

A large fraction of the interactions involve associations between well-known functional RNA classes such as ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), spliceosomal RNAs (snRNAs), snoRNAs, and messenger RNAs (mRNAs). These interactions don't make a significant contribution to our understanding of which genes in the genome are functional since even if every interaction proved there was a function it would still only amount to a very tiny amount of the genome.

The authors did detect a few interactions involving long noncoding RNAs (lincRNAs) but this was only a small percentage of the total. There are thousands of lincRNAs but currently there are only about 200 that have known functions and not all of these are even human.

It's the lincRNAs and other noncharacterized RNAs that represent the biggest problem because if all of them have a function then there will be >50,000 genes in the human genome instead of the current estimates of about 25,000 (20,000 protein-coding genes and 5,000 genes for functional RNAs). If all of those RNAs were functional they would occupy about 1% of the genome so this has has very little to do with whether 90% of our genome is junk.

This paper does not make any significant contribution to our understanding of pervasive transcription and whether most of the transcripts are functional (hint: they aren't). It does not make a contribution to the debate over junk DNA since most of the RNAs that were detected were already in the functional category or strongly suspected of being functional.

The authors make no claims about junk DNA in the paper because the paper is not about junk DNA.

Now let's look at the press release from the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto. This building is attached to the building that houses my department and the authors of the study are colleagues in a sister department (Department of Molecular Genetics). The press release was written by Jovana Drinjakovic, a science writer with a Ph.D. in neurobiology.

Shedding light on the ‘dark matter’ of the genome

What used to be dismissed by many as “junk DNA” is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) – genome’s messages that do not code for proteins — in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions.
The actual paper shed almost no light on "dark matter" (whatever that is). The paper didn't mention junk DNA and it made no contribution whatsoever to the idea that 90% of our genome is junk. The paper was mostly concerned with interactions involving functional RNAs that have been known for decades. The press release grossly distorts the actual content of the paper in order to sensationalize the results and promote the Donnelly Centre.

This is unacceptable. It's time to put a stop to this nonsense. The actual paper was addressing the issue of how many of the noncoding RNAs are functional. It did not give us an answer. The press release makes it sound as though we are just learning about the existence of noncoding RNAs.
A plot of human RNA-RNA interactions detected by LIGR-Seq The new tool, called ‘LIGR-Seq’, captures interactions between different RNA molecules. When two RNA molecules have matching sequences – strings of letters copied from the DNA blueprint – they will stick together like Velcro. The paired RNA structures are then removed from cells and analyzed by state-of-the-art sequencing methods to precisely identify the RNAs that are stuck together.

“Most researchers in the life sciences agree that there’s an urgent need to understand what ncRNAs do. This technology will open the door to developing a new understanding of ncRNA function,” says Blencowe, who is also a professor in the Department of Molecular Genetics and Banbury Chair in Medical Research.
It's true that we would like to know how many of the RNAs are functional but it's not true that we are completely clueless. There's plenty of evidence supporting the idea that only 10% of our genome is functional. It's very likely that the vast majority of transcripts are spurious and nonfunctional. A good science reporter would put the study in proper context.

I send an email message to each one of the authors asking their opinion on how much of our genome is junk and whether they believe that their study contributes in any significant way to to the junk DNA debate. None of them replied.

I hope they're embarrassed about being misrepresented by Jovana Drinjakovic's press release. I suspect they're not embarrassed and that's a problem. Even if they actually believe that most of our DNA is functional, their peer-reviewed paper did not present any evidence one way or another. Press releases should not contain information and speculation that was not subjected to the peer review process that resulted in publication.

The press release was widely copied, e.g. Science Daily and EurekAlert (AAAS). The general public and other scientists are being give a totally false impression of the scientific consensus about junk DNA. Most knowledgeable scientists believe that the evidence supports the existence of large amounts of junk in our genome.

My colleagues Alex Pallazzo and his student Eliza Lee have addressed the issue of noncoding RNAs. They conclude that the default hypothesis has to be that most are nonfunctional unless there's solid evidence of function. Right now it looks like this evidence won't be found so most of these RNAs are spurious, they are junk RNA.
Palazzo, A.F. and Lee, E.S. (2015) Non-coding RNA: what is functional and what is junk? Frontiers in Genetics 6:1-11 [doi: 10.389/fgene/2015.00002]
The paper from the Blencowe lab didn't discuss these issues or reference the Palazzo and Lee paper.


19 comments :

  1. I can't help feeling annoyed by the implicit big science-envy in the use of terms like "dark matter". Physics and astronomy has their dark matter, large hadron colliders and gravitational waves so we must too. Meh.

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    1. I don't know. Large scale genomics projects certainly fulfill the criteria for "big science". I think "genomic dark matter" started of as a jokey line in a conference presentation and then started to get used for lack of a better term.

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  2. I agree that the press release is hype (redundant statement there) but I feel you're downplaying the importance of the method. It's very cool that they can detect RNA-RNA interactions experimentally.

    Of course some noncoding RNA actually does have a function that involves interacting with other RNA molecules, we don't know everything we need to know about that, so this experimental tool is very cool. Of course, percentage-wise it's probably not going to find function in more than a few % of the genome. But that few % could be very important medically and biologically. So the authors are to be congratulated.

    Junk DNA-wise, it certainly has not disproven Junk DNA, it is most likely not going to in the future, but this new tool could be used to shoot down anti-Junk speculation. If one speculates that a class of RNA transcripts has a function by interacting with other RNAs (a common speculation), and if this tool detects no such interactions with RNA, that would should down a lot of "It's all functional" speculation.

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  3. I agree that the press release is hype (redundant statement there) but I feel you're downplaying the importance of the method. It's very cool that they can detect RNA-RNA interactions experimentally.

    Downplaying??? Oxygen! Oxygen! I need some oxygen because I'm choking!!!

    Larry is bluntly ignoring the experimental evidence he has always claimed that was the foundation of science and my foundation was faith. This is one of the perfect examples what Larry thinks about experimental science; if it is not in accord with his beliefs, it not real science. It is a distortion of science.

    I'm glad that Diogenes said it rather than me trying to put in nicely so that Larry wouldn't remove it...

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    1. Larry is bluntly ignoring the experimental evidence

      Please do quote the experimental evidence from the paper (not the abstract) that Larry is ignoring.

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    2. Are you mentally retarded? Or are you just a Darwinists, that is trying to look good because I can't say anything positive about your group of people...

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    3. Yes Eric, we all know how morally and intellectually superior you are, now answer the question.

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    4. Are you mentally retarded?

      That's multiple times you've used mental disability as an insult in this comments section. If you had an sense or any morals, you would be ashamed of yourself.

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  4. "The Undo Comrades" are coming aboard just about now...lol

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  5. I guess the author of this blog himself trying make some fortune by criticizing a rather interesting paper. I didnt read anywhere in the paper that authors talked about junk DNA or anything of that sort,. "THE PAPER IS ABOUT THE METHOD TO STUDY RNA/RNA INTERACTIONS".
    What press release said, it has nothing to do with authors. Just criticize the press release rather than the actual work in the paper, loser

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    1. Make a fortune by criticizing a paper? Eric! Your alter-ego is more stupid than you.

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    2. Unknown, please tell us on the basis of your reading of the paper what "actual work" there Larry ought not to be criticizing.

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    3. I think that Larry was pretty fair to the paper, and had little to criticize. The paper is quite good in its ultimate assessments. As Larry points out

      "The authors make no claims about junk DNA in the paper because the paper is not about junk DNA."

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    4. Mikkel,

      You have just confirmed what I had told you you were; plus the paranoia... Tell me; how does it feel when your beliefs feel more and more insecure everyday (denying it doesn't help)?

      Give me a hint, so that at least I can try to understand what it feels like...

      I'm not going to try to offend you just because you had tried to offend me because you had not arguments to support your claims or beliefs.

      You see, I wouldn't even consider to lower myself to your level, or others trying to offend me instead of providing the evidence for their claims...

      Is the offencive language perhaps because your claims did not hold up in the first place?

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  6. I am fascinated by this much of the noncoding DNA genome being copied into RNA:

    Of the 3 billion letters in the human genome, only two per cent make up the protein-coding genes. The genes are copied, or transcribed, into messenger RNA (mRNA) molecules, which provide templates for building proteins that do most of the work in the cell. Much of the remaining 98 per cent of the genome was initially considered by some as lacking in functional importance. However, large swaths of the non coding genome -- between half and three quarters of it -- are also copied into RNA.

    Regardless of whether there is a known function or not: is there any reliable evidence against the 1/2 to 3/4 estimate?

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  7. Couldn't disagree more for the following reasons:

    You comment below (to be accurate) should read 'there is plenty of evidence supporting the idea that only 10% of our genome is known to be functional.

    The distinction is crucial. We are now only able to tease out function for 10% of our genome. This paper will attest to the work being done to tease out more. Our knowledge in this science is limited to the power of the technology being deployed to investigate the genome. We all agree that the genome is hugely complex. Therefore our technology must match the gargantuan nature of the task. I think the authors of this paper understand this quitely cleary and are making inroads in using this new technology.



    "It's true that we would like to know how many of the RNAs are functional but it's not true that we are completely clueless. There's plenty of evidence supporting the idea that only 10% of our genome is functional. "


    The idea (which Larry Moran seems to promote) that we should not be looking at RNAs that don't have any 'apparent' function is anti-science on the face of it. What does Larry Moran base his 'opinion' on? His 40 years of research and development experience? His unsurmountable lead in the race to scientific knowledge? His superior intellect?

    In fact, his arrogant stance on RNA function disses the hard work of authors such as those mentioned in this blogpost by insinuating that their work need not be taken seriously because they seemingly create hype in the direction of RNA function.

    Yet that is exactly what is required to acquire the huge amount of funds needed to continue this type of research.

    Scientific discovery would be dead if scientists thought like Larry Moran.

    "It's very likely that the vast majority of transcripts are spurious and nonfunctional."

    No, a good reporter would report the hard work that is being done to understand what is happening with the other 90% of RNA with currently unknown function.

    They need not kowtow to the evolutionary biologists who put all their eggs in the jDNA basket.

    Ironically, it is these same evolutionary biolgists that claim science is tentative and self-correcting. But folks like Larry Moran are loathe to allow that tentative and self-correcting process to work.

    If more function is found for RNA, more power to science. It is useless to continually emphasize that current consensus is 10% of RNA are functional. I mean, No shit shirlock! We f$%# know that already!

    But does that mean no grant funds for the remaining 90% which may (in constrast to Moranian thinking) very well have function??!! What is science for but to push the envelope, and rock the consensus!!

    "A good science reporter would put the study in proper context."

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    1. Steve,

      I believe you have missed the point of Dr. Moran's post.

      The techniques presented in the Sharma et al. paper represent an important advance in the ability to test the functionality of ncRNAs. Most of the RNA-RNA interactions identified in the paper were of already known RNA interactions. A number of new lincRNA interactions were identified. It is unlikely that all lincRNAs are functional, but even if they all were, this would only add another 1% or so to the functional total for the genome. Dr. Moran was trying to put this study into perspective, since it was not about the junk DNA issue. In contrast, this is part of the press release describing the paper:

      "What used to be dismissed by many as “junk DNA” is back with a vengeance as growing data points to the importance of non-coding RNAs (ncRNAs) – genome’s messages that do not code for proteins — in development and disease. But our progress in understanding these molecules has been slow because of the lack of technologies that allow the systematic mapping of their functions."

      This information is all in Dr. Moran's post. Do you see how this paper is not about what the press release says it is about?

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    2. "The idea (which Larry Moran seems to promote) that we should not be looking at RNAs that don't have any 'apparent' function"

      But he ISN'T promoting that idea. At all. Never did. Prove me wrong with a direct quote or retract the claim.

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  8. If I understood the post, the point was the execrable quality of the press release, not the content of the paper, which sounds interesting but not groundbreaking (but I am a layman). So discussing the technical value of the paper is really beside the point, and means one has actually not understood what Larry was discussing.

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