Friday, September 16, 2011

Transposon Insertions in the Human Genome

Transposons are mobile genetic elements that jump around in our genome (and the genomes of every species). They are known by various names such as "jumping genes" or mobile genetic elements.

Our genome has several different types of transposons [Transposons: Part I, Transposons: Part II, Retrotransposons/Endogenous Retroviruses]. Most of them are defective in one way or another so they can no longer "jump" to another location but some subfamilies have remained functional and these will spread to new locations. About 44% of our genome consists of active transposons and (mostly) defective transposons [What's in Your Genome?]. Most of these sequences have no function—they are junk DNA.

The development of new, cheap, sequencing technologies and the availability of an annotated standard human genome reference sequence has made it possible to look for new transposon insertions in a large number of individuals. The results can help confirm or refute the idea that most of our genome is junk.

A recently published article in PLoS Genetics describes the results of such an analysis (Stewart et al. 2011). It's part of the 1000 Genomes Project.

They detected a total of 7,310 insertions that were present in only a subset of the 179 genomes that were analyzed. About 85% of these were Alu elements, 12% were L1 LINES, and 3% were SVA's. This is consistent with earlier work that catalogued the number of active transposons in the human genome. As expected, very few of these insertions occurred in exons (39) and only 3 occurred in coding regions. This strongly suggests that there is strong selection against disruptions of coding regions. It implies that most of the detectable insertions occur in regions where disruption of the sequence has no effect on the viability of the the individual. In other words, insertions occur predominantly in junk DNA.

The authors examined the sequences of two families in order to assess the frequency of new transposon insertions. Earlier data indicated that a new insertion arises only once in every twenty births so it's not a surprise to find that the offspring in these two families showed no new insertions relative to their parents.

A data set of this size allows for an assessment of the rate of fixation of various new mobile element insertion (MEI) alleles in the population. The authors conclude,
MEI alleles propagate within population groups much like other predominantly neutral polymorphisms. MEI allele frequency spectra from the low coverage samples are in general agreement with expectations from the standard neutral model for allele drift in a population.
What this means is that most (perhaps all) of the insertion alleles are segregating as though they have no effect on the fitness of the individuals that carry them. This is further support for the idea that large parts of the genome are junk.


Stewart, C., Kural, D., Strömberg, M.P., Walker, J.A., Konkel, M.K., Stütz, A.M., Urban, A.E., Grubert, F., Lam, H.Y., Lee, W.P., Busby, M., Indap, A.R., Garrison, E., Huff, C., Xing, J., Snyder, M.P., Jorde, L.B., Batzer, M.A., Korbel, J.O., Marth, G.T. (2011) A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 2011 Aug;7(8):e1002236. Epub 2011 Aug 18. [doi:10.1371/journal.pgen.1002236]

22 comments :

  1. Unfortunately, all this is actively ingnored by a fraction of genome researchers. E.g., see the latest edition of "Lab Times":

    In conclusion, a great deal of the DNA previously described as junk DNA can be ascribed well-established functions today –
    there is hard evidence for it, at least. However, there are lots and lots of DNA stretches that still don’t seem to be of any function
    at all.
    Only time will tell if these sequences are, indeed, true junk or whether we are still too blind to see the real meaning of the
    “Dark Matter of the Genome”.


    (https://lh3.googleusercontent.com/-0cJmZLjSMVg/TnNkSyz8uiI/AAAAAAAAAdE/pvMaY3PlnjU/s800/UD.jpg)

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  2. except in coding regions where MEI are virtually absent, presumably due to strong negative selection


    Wouldn't this indicate that those regions are just less important in terms of fitness, but not necessarily junk?

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  3. I have to agree with Kara--I do not think our sample sizes are sufficiently large yet for anyone to say that the statistics of transposons indicate neutrality. They only show the effects on fitness are not large when they are inserted in "junk" regions of DNA.

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  4. ^
    If something in the genome doesn't appear to be selected for what would you say it is?

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  5. Devin, small samples simply can't lead to the conclusion that these are absolutely neutral when inserted into "junk" regions. The most we can infer is that selection is weak, and we can set bounds on the selection strength. As sample size increases we can make more precise statements about how close to zero the selection is. I don't think we can ever prove that it is exactly zero using these techniques. (That doesn't mean it isn't zero, either....I have no opinion one way or the other.)

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  6. @SPARC

    That Labtimes article annoyed me too. It was everything that the Nature/Science hype machines say, with little regard to the literature before 1990.

    Journalists need to realized that controversy is not the only way to sell a science story.

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  7. Just because many transposons are inactive - and thus can't jump around - does not mean they can later be reactivated by mutation (as can many pseudogenes that have not degenerated by too much).

    The inference that transposons don't affect fitness is a poor one because fitness only relates to immediate reproductive success. In the future, these insertions may turn out to be beneficial. Here is a paper on the subject which Larry would prefer not to read:

    Strong selective sweep associated with a transposon insertion in Drosophila simulans

    In summary, the localized reduction in heterozygosity around Cyp6g1 in California populations of both D. simulans and D. melanogaster, the existence of different transposable element insertions at high frequency in the 5′ regulatory region of Cyp6g1 in these species, and the associated transcriptional up-regulation of Cyp6g1 in both species provide a striking example of parallel evolution. The evidence that nucleotide variation linked to Cyp6g1 may be influenced by positive selection in D. simulans and D. melanogaster suggests that cytochrome P450s and other detoxification proteins may be hotspots for recent adaptive evolution in many insects.

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  8. Lou Jost says,

    Devin, small samples simply can't lead to the conclusion that these are absolutely neutral when inserted into "junk" regions.

    There's plenty of reason to suppose that most of our genome is junk. This paper proposed to test that hypothesis by checking to see whether new insertions (alleles) have the characteristics of neutral alleles or alleles that are being selected.

    The data is consistent with neutral alleles segregating in the population by random genetic drift. Does this absolutely prove that the DNA around the insertion sites is junk? No, it doesn't but it certainly lends no support to the proposition that it is functional.

    On balance, the results in this study are far more consistent with junk DNA than with functional DNA. That's not likely to stop the junk deniers because they can always make up excuses to cover their lack of evidence. However, at some point those excuses start to sound an awful lot like non-scientific arguments.

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  9. Atheistoclast says,

    The inference that transposons don't affect fitness is a poor one because fitness only relates to immediate reproductive success. In the future, these insertions may turn out to be beneficial.

    Wanna try and explain how that works? Do the members of a particular species get together for a meeting and discuss whether they should tolerate all that neutral junk DNA just because some small bit of it might possibly become useful a few million years from now?

    Evolution doesn't see into the future.

    Here is a paper on the subject which Larry would prefer not to read:

    I'm well aware of papers like that showing unique examples of beneficial transposon insertions that have occurred in particular species over the course of several million years of evolution.

    Are you claiming that all of those defective transposons in the Drosophila genome can't be junk because one of the active transposons might cause a beneficial mutation from time to time?

    Does that kind of reasoning really make sense to you?

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  10. I don't think we can ever prove that it is exactly zero

    No, but we can prove 2.Ne.s << 1.

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  11. Larry, I tend to agree with you, and if you stuck a gun to my head and made me support one side or the other right now, I would guess it's junk. However, this kind of study doesn't prove it, and you agree. Kara is right.

    Admittedly, it is almost impossible to prove that selection is exactly zero for these. A more honest approach would simply give the ever-narrowing range around zero as sample sizes get larger. Null hypothesis testing here, as elsewhere in science, is inappropriate; experiments like these should estimate the selection strength based on the data, with confidence intervals. (Maybe the study did this, I haven't checked.) The confidence interval in this case would include zero, but the important point is how narrow is the confidence interval. If sample size is small, the confidence interval could be very large, and the fact that it includes zero would have virtually no importance. Nobody can conclude anything scientific from a simple statement that an experiment failed to reject a null hypothesis.

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  12. Larry says:

    Wanna try and explain how that works? Do the members of a particular species get together for a meeting and discuss whether they should tolerate all that neutral junk DNA just because some small bit of it might possibly become useful a few million years from now? Evolution doesn't see into the future.

    It sure does. As long as the insertion doesn't cause an immediate fitness loss, it can just remain inactive and dormant until such a time as the environmental pressures change. When this happens, the insertion will be promoted by selection if it proves to be beneficial in some way.

    Are you claiming that all of those defective transposons in the Drosophila genome can't be junk because one of the active transposons might cause a beneficial mutation from time to time?

    As with pseudogenes, they may become active again. So, while degenerate, they have the potential to be useful in the future. By your reasoning, an arsenal of weapons is "junk" if it is not currently used. I would rather keep my defective transposons rather than have you surgically remove and bin them as you have repeatedly been threatening to do to the human genome.

    And maybe deleterious transposon insertions keep fitness levels in the population low enough for the sake of sustainability. You are missing the wider picture.

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  13. Whats kinda funny/coincidental here is that I've been reading Boudry 2011; Here be Dragons, which I only heard about from this blog. Therein Dr. Boudry discusses when 'excuses' for an idea overwhelm it.

    It sounds like the claim that the sample size here is to small to make the measured values particularly meaningful is not an 'ad hoc' assertion, and that it falls under what most of us, I think, would consider a reasonable 'defense' for 'junk-isn't-junky'.

    So at least the comments are still in the realm of science, or something.

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  14. @Shenck, I wouldn't consider my comment about statistical significance as a defense of "junk isn't junk". It is rather about the limitations of experimental evidence, and bad statistics (at least in this second-hand version of the paper's conclusion).

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  15. Here is another paper that claims that Alu retrotransposons (short sequences of around 300bp) are far more active in the human genome than was first thought:

    Active Alu retrotransposons in the human genome

    So perhaps Larry will care to revise his comments.

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  16. ^
    So they bounce around more? That's all you have to contribute?

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  17. It sure does. As long as the insertion doesn't cause an immediate fitness loss, it can just remain inactive and dormant until such a time as the environmental pressures change. When this happens, the insertion will be promoted by selection if it proves to be beneficial in some way


    So... transposons will be in the genome despite having no purpose simply because they don't cause an appreciable loss of fitness to their holder? That sounds a lot like junk DNA doesn't it?

    Yes, all sorts of elements may be co-opted into new genes in the future, but that can't be held in the genome for that purpose for the reason Larry set out.

    The idea that we have deleterious mutations to keep out populations size down (is that what you mean by 'sustainability'?) is confused in the same way. But I do like this:

    I would rather keep my defective transposons rather than have you surgically remove and bin them as you have repeatedly been threatening to do to the human genome.

    Has someone really threatened to genetically engineer future humans to be junk free?

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  18. @ David Winter,

    Humans - no. Mice? If they could afford it. There is an ~2.3 M bp deletion of mouse conserved nc-DNA, which showed no measurable phenotype.

    I think this is quite a fearful prospect for the ID crowd. If funding was not an issue, halving the mouse genome would be an intersting mega-project to set out on. All the technology is available to do it.

    http://www.nature.com/nature/journal/v431/n7011/abs/nature03022.html

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  19. The other Jim said...

    I think this is quite a fearful prospect for the ID crowd. If funding was not an issue, halving the mouse genome would be an intersting mega-project to set out on.

    While I agree that this is probably an interesting project I think the last thing needed is for the IDiots to have any sort of control over how funding is allocated, either directly or indirectly.

    Which begs the question, given how well funded the IDiot cabal is, why aren't they funding projects like this ?

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  20. @ steve oberski

    I hope I did not imply that the ID crowd should do this. They would try something like targeting the centromere regions, pretend that was junk DNA, and yell "see it's all there by design!". But yeah, they should start spending some money on experiments instead of ad campaigns if they want to be a legitimate scientific entity.

    But knocking out a single chrosome location in mouse runs about ~50,000€, if bought from a company. Up to 3 years of a student or postdoc salary, plus mouse space costs if done yourself. So add up the number of "gene deserts" required to take the genome size down by some appreciable size. I can't think of a funding agency will to fund the experiment.

    But compressing the genome of a non-mammal will not be taken as evidence, because mammals are special, right ;-)

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  21. I'm a researcher in one of the labs on the paper Larry is discussing in this post, and as a long-time Sandwalk reader, I just want to say how cool it is that a paper to which my labmates contributed was featured here. As to the discussion on the direction and magnitude of selection on the retrotransposon population of the genome goes, it sounds like some of the discussions/arguments that happen around the lunch table in the lab here periodically. :)

    My opinion as a researcher in the field of mobile elements for the last six years (I got my PhD studying these elements and am about to finish my finish my first year as a postdoc continuing to study them) is that the vast majority of mobile element insertions in the genome are neutral. A portion are deleterious when they hit exons, regulatory regions, or splice sites. And, there are a number of examples in the literature that make a case for a small portion of insertions being beneficial, too (e.g. band-aids, exon shuffling, etc.).

    But any discussion of the selection on these elements shouldn't stop only at insertions, because the high degree of homology between copies of elements of the same type allow for a tremendous amount of interaction (e.g. recombination-mediated deletions, recombination-mediated inversions) that appear to significantly contribute to genomic fluidity and dynamism. These interactions can be between elements separated by quite large stretches of other intervening sequence, and can therefore affect phenotypes should those stretches be coding or regulator in nature. As with the insertions, though, most INDELs and rearrangements of this type likely happen only within gene deserts, and are therefore mostly neutral. But, they can be both deleterious and beneficial in genic regions. Plus, it remains to be quantified whether the sequence variation produced through these interactions provides raw material on which selection may operate.

    It's a complex question without a single, clear answer. It's one of my favorites. My current opinion is that they're mostly neutral inhabitants, but there are instances and mechanisms that may give benefits in some cases, potentially offsetting to some small degree those instances in which they are deleterious.

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  22. One might come to the same conclusion examining the population genetics and fixation rate of single nucleotide polymorphisms (SNPs). To paraphrase Motoo Kimura, on the whole, the large majority of all genetic variants are neutral with respect to natural selection. The challenge is to identify the small minority of variants that do have a significant phenotypic effect on which natural selection can act.

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