One of the most common hypotheses that I hear with regard to possible non-coding DNA function is that it serves to protect genes against mutation. Junk DNA, according to this proposal, is there to provide a defensive shield against mutagens (usually this includes UV, ionizing radiation, chemical mutagens, viruses, and/or oxygen radicals). I am very skeptical of this explanation, but I am willing to take it seriously if it is studied seriously. In fact, one of my current graduate students first came to talk with me when he was an undergraduate and asked me about this possible function. For his undergraduate research project, we tried to test it using Drosophila species with different genome sizes exposed to chemical mutagens and screened for phenotypic effects (we learned a lot about how one might design such an experiment, but the results were inconclusive on the first attempt). That’s much more than most proponents of this hypothesis try to do, and I suspect that’s one reason that it has not really gained much ground in the genomics community.
Various visitors to this blog have brought up the hypothesis in one form or another, so even though little or no data is ever presented (and counter-examples are generally dismissed out of hand), I will once again treat the idea seriously.
Specifically, here is my overview of what proponents of the mutation protection hypothesis need to know and what they need to do if they want this to move out of the armchair and into the realm of science.
I. This is not a new idea.
If you have been following this blog, you will know that functions for non-coding DNA have been proposed regularly for decades. Not surprisingly, the notion that it protects genes from mutagens was one of them. This hypothesis dates back in a general form nearly 40 years to the paper in Nature by Yunis and Yasmineh (1971). As they wrote:
“Recent reports indicate that the DNA of constitutive heterochromatin is composed to a large extent of short repeated polynucleotide sequences, termed satellite DNA. This discovery has necessitated a critical review of current ideas concerning the origin and function of this portion of the genome of higher organisms (4-12). A careful appraisal of the information that has accumulated about heterochromatin since the time of Heitz [late 1920s, early 1930s] and on satellite DNA during the last decade suggests that these entities have vital structural functions: they maintain nuclear organization, protect vital regions of the genome, serve as an early pairing mechanism in meiosis, and aid in speciation.”
Yunis and Yasmineh (1971) focused primarily on structural roles for non-coding DNA, and I don’t think aiding in speciation can be considered a “function”, but they did also include the basic notion of genome defense.
True to the standard view of the 1970s (and, to a significant extent, of many authors today), they begin with an adaptationist assumption and build from there:
“With the assumption that a portion that comprises some 10 percent of the genomes in higher organisms cannot be without a raison d’etre, an extensive review led us to conclude that a certain amount of constitutive heterochromatin is essential in multicellular organisms at two levels of organization, chromosomal and nuclear. At the chromosomal level, constitutive heterochromatin is present around vital areas within the chromosomes. Around the centromeres, for example, heterochromatin is believed to confer protection and strength to the centromeric chromatin. Around secondary constrictions, heterochromatic blocks may ensure against evolutionary change of ribosomal cistrons by decreasing the frequency of crossing-over in these cistrons in meiosis and absorbing the effects of mutagenic agents. During meiosis heterochromatin may aid in the initial alignment of chromosomes prior to synapsis and may facilitate speciation by allowing chromosomal rearrangement and providing, through the species specificity of its DNA, barriers against cross-fertilization.”
A few years later — and three years after the rise of the term “junk DNA” (Ohno 1972; Comings 1972) — Hsu (1975) provided a much stronger argument for what he called the “bodyguard hypothesis”. To start, Hsu (1975) noted that many hypotheses had already been presented for the function of heterochromatin, of which he listed six. Importantly, he also noted the following, which seems to have been lost on most current authors:
“Some investigators consider the repeated DNA sequences as the equivalent of ‘appendices’ of gene evolution and therefore facetiously refer to them as ‘junk’. Actually few really think that ‘junk’ DNA is completely useless (cf. Ohno 1972; Comings 1972).”
Now, was Hsu saying that Ohno and Comings did or did not claim that junk DNA is completely useless? The “confer” is ambiguous (it can mean either “compare with” or “consult”), but Hsu was almost certainly aware that Comings was explicit in ascribing function to a large portion of junk DNA.
In any case, the “bodyguard hypothesis” was described as follows:
“The hypothesis proposed here is a simple-minded one: constitutive heterochromatin is used by the cell as a bodyguard to protect the vital euchromatin by forming a layer of dispensable shield on the outer surface of the nucleus. Mutagens, clastogens [inducing chromosome breakage] or even viruses attacking the nucleus must first make contact with the constitutive heterochromatin which absorbs the assault, thus sparing the euchromatic genes from damage, unless the detrimental agents are overpowering.”
Hsu did not apply this to all causes of mutation nor to all types of non-coding DNA — “Probably heterochromatin is ineffective in protecting euchromatic genes against penetrating ionizing radiations, but against chemicals (especially large molecules) and viruses, the layer of thick chromatin may be an excellent barrier” — but it has certainly been invoked more broadly by others since.
For example, the idea has been brought up with renewed vigour by some Russian geneticists (Patrushev 1997; Patrushev and Minkevitch 2006, 2007, 2008). In this case, the focus is on endogenous mutagens (i.e., free oxygen radicals generated through aerobic metabolism). They take this much farther than Hsu by applying it as a major explanation for genome size differences generally and by including transposable elements (which are much more abundant than satellite DNA). As they argued:
“Our data suggest the following molecular mechanism that controls the size of eukaryotic genome in phylogenesis. During the whole life, nuclear DNA of aerobic organisms is affected by a continuous flow of endogenous mutagens. Mutagens escaping the neutralizing effect of antimutagenesis system damage the nucleic bases of DNA, most of which are corrected by repair systems. This ensures a permissible genetically determined level of spontaneous mutagenesis. An increase in the intranuclear concentration of mutagens raises the mutation rate in genome-coding sequences,among which gene(s) of molecular sensor are present. Mutational alterations in the sensor mobilize retrotransposons, which results in a local growth in their copy number, enlargement of genome size, and a decrease inthe mutation in the corresponding coding sequences. As a result, the genome–endogenous mutagen system reaches a new steady-state level. A decrease in the intranuclear concentration of mutagens will be accompanied by a reduction of genome size as a result of spontaneous deletions in its now excessive (in view of accomplishing the protective functions) sequences.” (Patrushev and Minkevitch 2006)
Put more directly, and very much in line with Hsu’s depiction of a “bodyguard”,
“In such a situation, the noncoding DNA of eukaryotic genome behaves quite ‘altruistically’ by putting itself under injuries instead of coding DNA.” (Patrushev and Minkevitch 2008)
The model they propose is summarized in this figure from Patrushev and Minkevitch (2008):
From Patrushev and Minkevitch (2008). Click for larger image.
In another example, Vinogradov (1998) proposed that non-coding DNA serves in “buffering the effect of fluctuations in intra-cellular solute composition on chromatin condensation state in its condensed form and on binding of DNA-tropic proteins and other ligands in its decondensed form.” There are probably other examples, but these suffice to show that the idea has been in the literature for some time. In fact, non-experts who get excited about the idea when they first think of it should realize that it has been around for almost four decades, and that in all that time it has barely had any impact. I believe this is due in significant part to a chronic lack of supporting evidence and a number of counterexamples — but more on that later.
II. Specific predictions need to be made and tested.
There is nothing wrong with the mutation protection hypothesis on the face of it. As I said, at least one of my students first became interested in genome size because of it and we considered it worth testing experimentally. However, there is a crucial difference between thinking up the hypothesis and actually testing it. If anyone is serious about this idea, and doesn’t want to be just another person who holds on to the idea with an unjustified tenacity, then they need to present specific, testable predictions that derive from the hypothesis.
Hsu (1975) recognized the problem of speculating on functions for junk DNA without evidence or any clear means of empirical testing. Thus, he was careful to provide several specific predictions of his bodyguard hypothesis that are amenable to analysis:
- “the mutation rate induced by chemical mutagens should be inversely correlated with the number of B chromosomes”.
- heterochromatin should be “more concentrated at the periphery of the nucleus (and probably also at the nucleoli) than in the interior”.
- “organisms with more constitutive heterochromatin [should be] more resistant to induced mutations, at least by chemical mutagens”.
Again, let’s take the idea seriously and ask how Hsu’s original predictions have fared over the past 35 years.
Prediction 1: B chromosomes vs. mutation rate
B chromosomes (also called supernumerary chromosomes) are something of an odd choice in this context, because they are not found in all species and they vary in size and number within and among species. By definition, they are not important for survival. They do appear to have effects on recombination (i.e., they increase its frequency), and this has in the past been suggested as a functional role. On the other hand, in high numbers they appear to have deleterious effects on the organisms carrying them. Indeed, B chromosomes were described very early on as parasitic elements (Östergren 1945; one of the first clear expositions of the “selfish DNA” idea), and this remains the most common interpretation (Camacho 2005).
I am not aware of many tests of the prediction that more B chromosomes will provide greater protection against mutations (iperhaps because I don’t follow the B chromosome literature very closely), and in any case the other deleterious impacts and obvious parasitic properties of B chromosomes challenge a primarily adaptive explanation for their presence. However, there are a few experiments that are relevant to this prediction. For example, here is the abstract from a recent study by Weber et al. (2007) on B chromosomes and mutations in maize:
Two hypotheses (the Bodyguard hypothesis and the ABCW hypothesis) have been proposed that predict that the amount and type of chromatin in the nucleus will affect induced mutation rates. The Bodyguard hypothesis proposes that a function of constitutive heterochromatin may be to protect euchromatin from chemical mutagens. The ABCW hypothesis, states that the mutation rate per locus from ionizing radiation is directly proportional to the haploid DNA content of a species. We altered the total amount of genomic DNA and also the amount of heterochromatin by adding supernumerary B chromosomes (which are largely composed of heterochromatin) to maize (Zea mays L.) cells. We compared induced mutation frequencies at the yellow-green2 (yg2) locus in near-isogenic plants that contained 0 (diploid) or 4 supernumerary B chromosomes (diploid + 4 Bs) to evaluate these hypotheses. We found that the chemical mutagen, EMS, caused significantly higher mutation frequencies in plants that contained 4 B chromosomes (and therefore additional constitutive heterochromatin) than in diploid controls. The Bodyguard hypothesis predicts precisely the opposite result. We also found that ionizing radiation caused significantly higher mutation frequencies in plants with 4 B chromosomes than in diploid control plants. This type of change is predicted by the ABCW hypothesis; however, the extent of the increase observed in this study is much higher than the ABCW hypothesis would predict. The higher mutation frequencies from EMS and radiation in plants that contained 4 B chromosomes was unanticipated, and is the first observation that cells may be more susceptible to mutagenesis when B chromosomes are present. We also compared spontaneous mutation frequencies at the waxy1 (wx1) locus in plants containing 0 or 4-5 B chromosomes, and found that the presence of B chromosomes had no detectable impact. However, the pollen abortion frequency was significantly increased by the presence of 5 B chromosomes.
Prediction 2: Arrangement of chromatin
The idea that chromatin is arranged non-randomly in the nucleus is at least 100 years old. Theodor Boveri described chromatin “territories” in 1909, for example. According to Hsu’s hypothesis, heterochromatin should be localized on the outer region of the nucleus as a shield for the sensitive euchromatin in the interior. Again, I do not follow the literature on nuclear structure carefully, but there are some papers that deal with this issue of which I am aware. For example, Tanabe et al. (2002) concluded the following in their study of chromatin arrangement and mutational patterns:
“Evidence for evolutionary conservation argues for a still unknown functional significance of distinct radial higher-order chromatin arrangements. In 1975, T.C. Hsu proposed the ‘bodyguard’ hypothesis for a possible function of constitutive heterochromatin. He argued that constitutive heterochromatin localized in the nuclear periphery might protect the centrally localized euchromatin against mutagens, clastogens, and viruses. However, evidence for the existence of a protection shield has not been provided so far. The fact that later replicating, gene-poor chromatin is incorporated in the constitutive, gene free heterochromatin to form a chromatin shield in the nuclear periphery cannot be easily integrated into this hypothesis. While G-dark band chromatin contains tissue-specific genes, these genes are certainly not of minor importance as compared with the housekeeping genes that are localized in G-light band chromatin in the interior nuclear compartment. The finding in the human fibroblast nuclei that—in contrast to lymphocyte nuclei—both HSA18 and 19 territories are apparently in contact with the nuclear envelope and thus similarly exposed to mutagens, which will enter the nucleus, presents another difficulty. Why should gene dense HSA19 be better protected in lymphocyte nuclei than in fibroblast nuclei? Furthermore, in the light of the bodyguard hypothesis, we would expect to observe DNA damage preferentially in the peripheral chromatin shield. However, several reports indicate a non-random distribution of double strand breaks, as well as endonuclease- or radiation-induced chromosome aberration sites were preferentially observed in the gene-dense G-light bands.”
Again, there may be data out there that support the mutation protection idea, but so far it is not looking good for the hypothesis.
Prediction 3: Non-coding DNA content vs. mutation rate
It is an interesting bit of historical trivia that some early work on genome size diversity was funded by the US Atomic Energy Commission, much as the human genome sequencing initiative was supported by the Department of Energy. In the 1960s and 1970s, there was interest in patterns of sensitivity to radiation and their potential relation to genomic properties including genome size. In general, these studies reported a positive correlation between mutagenic sensitivity to radiation and DNA content (Sparrow and Evans 1961; Sparrow and Miksche 1961; Sparrow et al. 1965, 1968; Baetcke et al. 1967; Abrahamson et al. 1973; Wolff and Abrahamson 1974; Athanasiou and Heddle 1975; Heddle and Athanasiou 1975; Trujillo and Dugan 1975). That is to say, more DNA means more, not less, sensitivity to radiation-induced mutations on a per-locus basis.
From Abrahamson et al. (1973). Click for larger image
From Trujillo and Dugan (1975). Click for larger image.
From Heddle and Athanasiou (1975). Click for larger image.
From Heddle and Athanasiou (1975). Click for larger image.
Other possible predictions:
Hsu’s predictions do not seem to have stood up well to testing, but the important point is that he proposed them and allowed his hypothesis to face empirical scrutiny. Likewise, current proponents of the mutation protection hypothesis need to follow in this tradition.
III. Previous observations need to be explained.
One of the reasons that the mutation protection hypothesis does not have widespread acceptance is that there seem to be too many well-known phenomena that do not jive well with it. Consider the following patterns:
- Species exposed to intense UV (e.g., on land or in freshwater in the Arctic, pelagic plankton, etc.) do not appear to have large genomes. On the other hand, some very large genomes are found in deep-sea invertebrates.
- Among vertebrates, species with high metabolic rates, and presumably more free oxygen radicals, have smaller genomes than species with lower metabolic rates.
- There can be substantial differences in genome size among similar organisms, for example as in onion and its relatives or among salamanders.
- Despite claims to the contrary based on small and questionable analyses, there are no clear relationships between genome size and lifespan.
- Transposable elements, which are the primary contributor to genome size, can cause a range of mutations through insertion into genes or by causing large deletions by illegitimate recombination, the latter of which is especially likely with the long terminal repeat (LTR) elements that are common in plants.
- DNA content obviously can be amplified in somatic cells by endoreduplication, but this tends to be in cells involved in ion exchange, protein production, etc., and not ones exposed most to mutagens (such as the skin exposed to UV).
Conclusions
Overall, the mutation protection idea has intuitive appeal, which is why it was proposed so early and why it continues to pop up as an apparently independent invention among interested non-experts. As I said, I am happy to consider it as a legitimate hypothesis — but only if it moves well beyond the usual pattern in which it is proposed as though it were new, accepted without supporting evidence, and defended through dismissal of obvious counter-evidence. The null hypothesis, that much of the non-coding DNA in eukaryotic genomes does not have an organismal function, also has to be acknowledged as at least equally plausible in light of our understanding of genome biology.
References
Abrahamson, S., M.A. Bender, A.D. Conger, and S. Wolff (1973). Uniformity of radiation-induced mutation rates among different species. Nature 245: 460-462.
Athanasiou, K. and J.A. Heddle (1975). EMS induced mutation rates and their relation to genome size. Canadian Journal of Genetics and Cytology 17: 455.
Baetcke, K.P., A.H. Sparrow, C.H. Nauman, and S.S. Schwemmer (1967). The relationship of DNA content to nuclear and chromosome volumes and to radiosensitivity (LD50). Proceedings of the National Academy of Sciences of the USA 58: 533-540.
Camacho, J.P.M. (2005). B chromosomes. In: The Evolution of the Genome, ed. T.R. Gregory. Elsevier, San Diego, pp.223-286.
Comings, D. E. (1972). “The structure and function of chromatin.” Advances in Human Genetics 3: 237-431.
Heddle, J.A. and K. Athanasiou (1975). Mutation rate, genome size and their relation to the rec concept. Nature 258: 359-361.
Hsu, T.S. (1975). A possible function of constitutive heterochromatin: the bodyguard hypothesis. Genetics 79 (Suppl. 2): 137-150
Ohno, S. (1972). So much “junk” DNA in our genome. Evolution of Genetic Systems. H. H. Smith. New York, Gordon and Breach: 366-370.
Östergren, G. (1945). “Parasitic nature of extra fragment chromosomes.” Botaniska Notiser 2: 157-163.
Patrushev, L.I. (1997). Altruistic DNA: About protective functions of the abundant DNA in the eukaryotic genome and its role in stabilizing genetic information. Biochemistry and Molecular Biology International 41: 851-860
Patrushev, L.I. and I.G. Minkevich (2006). Eukaryotic non-coding DNA sequences provide genes with an additional protection against chemical mutagens. Russian Journal of Bioorganic Chemistry 32: 408-413
Patrushev, L.I. and I.G. Minkevich (2007).Genomic non-coding sequences and the size of eukaryotic cell nucleus as important factors of gene protection from chemical mutagens. Russian Journal of Bioorganic Chemistry 33: 474-477
Patrushev, L.I. and I.G. Minkevich (2008). The problem of eukaryotic genome size. Biochemistry 73: 1519-1552.
Sparrow, A.H. and H.J. Evans (1961). Nuclear factors affecting radiosensitivity. I. The influence of nuclear size and structure, chromosome complement, and DNA content. Brookhaven Symposia in Biology 14: 76-100.
Sparrow, A.H. and J.P. Miksche (1961). Correlation of nuclear volume and DNA content with higher plant tolerance to chronic radiation. Science 134: 282-283.
Tanabe, H., F.A. Habermann, I. Solovei, M. Cremer, and T. Cremer (2002). Non-random radial arrangements of interphase chromosome territories: evolutionary considerations and functional implications. Mutation Research 504: 37-45.
Sparrow, A.H., K.P. Baetcke, D.L. Shaver, and V. Pond (1968). The relationship of mutation rate per Roentgen to DNA content per chromosome and to interphase chromosome volume. Genetics 59: 65-78.
Trujillo, R. and V.L. Dugan 1975. Radiosensitivity and radiation-induced mutability: an empirical relationship. Rad. and Environm. Biophys. 12: 253-256.
Vinogradov, A.E. (1998). Buffering: a possible passive-homeostasis role for redundant DNA. Journal of Theoretical Biology 193: 197-199.
Weber, D.F., M.J. Plewa, and R. Feazel (2007). Effect of B chromosomes on induced and spontaneous mutation frequencies in maize. Maydica 52: 109-115.
Wolff, S., S. Abrahamson, M.A. Bender, and A.D. Conger (1974). The uniformity of normalized radiation-induced mutation rates among different species. Genetics 78: 133-134.
Yunis, J.J. and W.G. Yasmineh (1971). Heterochromatin, satellite DNA, and cell function. Science 174: 1200-1209.
Thank-you. That was a very nice summary.
My experience in discussion is that people simply use the probability argument (if 90% of the DNA is non coding, 90% of the mutations will be in non-coding). Not very satisfying, but a quite widespread argument. The other jim(Quote)
I have just noticed this so I suppose comments from the previous post (The junk DNA myth (or lack thereof), should move here.
TRG said: “As I said, I am happy to consider it as a legitimate hypothesis — but only if it moves well beyond the usual pattern in which it is proposed as though it were new, accepted without supporting evidence, and defended through dismissal of obvious counter-evidence. The null hypothesis, that much of the non-coding DNA in eukaryotic genomes does not have an organismal function, also has to be acknowledged as at least equally plausible in light of our understanding of genome biology.”
It’s not my intention to propode it as if it were new, never thought that because obviously it isn’t. I just mentioned it (sorry for mentioning it without listing all the evidence for and against) because i thought the idea of these blogs were for informal discussion, debate etc. I have often wondered why the “bodyguard” theory has never really been studied (maybe it is too difficult technically to test) in detail and why it is dismissed by many but without proper consideration. I am not saying that you are doing so but others, many others have. I have not had time to study what you write above, there is quite a lot of technical detail. The null hypothesis is the simplest – i.e. no real function, but the protective hypothesis (NOT MINE, just one i think could be possible) is the next simplest that needs to be explained away. I can attempt to answer your questions to your satisfaction (maybe more comments than detailed answers, so maybe not to youre satisfaction and so maybe I should keep quiet?) – in the end it’s not going to go away until it is properly tested and excluded, or else real evidence for some other function emerges Keith Grimaldi(Quote)
I’m fine with continuing to consider this as a viable hypothesis — my goal here is not to refute it but to move it forward and to point out what it will need in order to be accepted. However, I have an issue with your logic here. The simplest explanation is non-function. The second-simplest is bodyguard function. The latter is simple and therefore needs to be refuted with evidence. But the first, which is even simpler, apparently does not. Evidence for the bodyguard hypothesis would be evidence against the non-functional hypothesis, so you’re stuck with needing positive evidence for your idea before we worry about refuting it.
T. Ryan Gregory(Quote)
An interesting posting, and a useful reminder that just because something seems intuitive, does not make it true.
The difficulty as I see it is how do you test the hypothesis. For most organisms, irrespective of genome size, it is critical to minimise (manage?) the rate of mutation, either by perhaps reducing target size (under debate), or improving DNA repair mechanisms.
It is possible (testable) that organisms with smaller genomes have more efficient DNA repair.
I am interested in retrotransposition, and exaptation of retrotransposed elements. In most genomes the distribution is non-random, and indeed different elements may display different patterns of distibution.
Whilst not proving or disproving the hypothesis either way, anecdotally I have come across examples of repeats within repeats within repeats (like a russian doll), suggesting that the initial repeat was a target for a subsequent integration and so on.
One way of testing the relationship between genome size and mutation rate (without worrying about selection) would be to look at polyploid plants, by generating tetraploids. This would double the size of the genome, and allow for comparision of the mutation rate in parents and F1 David(Quote)
I’d be surprised if that had never been attempted, but I’ll let you search the botanical literature!
T. Ryan Gregory(Quote)
Yes I agree that I would be wrong to propose the 2nd less simplest as needing refutation without having refuted the simplest. I instinctively preferred the protective theory, but it was in preference to the more complex theories and the statements that it has to have complex function or nature would have discarded it (I don’t believe that nature is a perfectionist and that just because it – “junk” DNA- is there is has to have a purpose – it may have none). I accept that I am guilty of assuming that the protective theory was the simplest because I spontaneously concluded that there is too much DNA damage for a purely gene containing genome to sustain – the null is the simplest, even so, I am still inclined to the protective but also accept that the null needs to be dealt with, and I certainly can’t refute it without experimentation.
Positive evidence? I don’t know, I prefer the protective theory because of the fact of the background mutation rates of cells due to endogenous damage for which sophisticated processes have evolved to defend against. These processes are not 100% reliable and maybe they don’t need to be because of the presence of non-coding DNA, i.e. there is not a “purpose” or a “function” for non-coding DNA, but it just happens to be there which meant that repair mechanisms did not have to evolve to perfection without compromising life-span. This is speculating of course, but what is a fact is the level of endogenous damage and the rates of mutation caused by this damage (important to note that we are discussing here endogenous damage, not external artificially applied ionising radiation – for UV I need to come back to that). If these levels were concentrated to coding regions in the nuclear genome they would be too high for generational life spans (in humans at least). It doesn’t require development of specific chromosome structures, or molecular sensors, just the presence of a majority of non-coding DNA.
This does not mean that non-coding DNA needed to “evolve” to fulfil this function, but, as above, it is there so it meant that repair systems did not need to evolve to even higher levels of fidelity. So we are getting to a dependence on definitions. It has no “purpose” (what has?), it did not “evolve for a reason”, it just happens to be there… with maybe no function. The single question that differentiates the null hypothesis from the next level up (protective) is “does it need to be there, can we do without it”? I glibly and facetiously said in my first post that if it wasn’t there it would need to be invented – I meant it in this sense and that is the ultimate test or prediction: without it a cell would not survive. I would like to test it, unfortunately I don’t have the resources and I cannot think of a clever other way to test it, I don’t know if it is technologically possible to do so currently. On the other hand I don’t know either if it is worth dedicating too many resources to it because I’m not sure what benefit it would bring to know the answer apart from curiosity and the fact that it would be nice to resolve it, it’s giving me a bit of a headache…
Keith Grimaldi(Quote)
I think it is an interesting question, but my one caution would be that it’s not all or nothing. There may be a certain minimum amount of non-coding DNA that a complex genome really does need (this is a given, at least in terms of telomeres, centromeres, etc.), but the majority of it, and the differences in amount among species, may not be explained that way.
T. Ryan Gregory(Quote)
I have tried to answer your questions – nothing conclusive of course but maybe they still leave room for a protective property of DNA (i try to use neutral words – protective property rather than role or function. The latter suggest that non-coding DNA evolved to fulfil a particular role or function, i don’t believe that is necessary to propose).
1. Species exposed to intense UV (e.g., on land or in freshwater in the Arctic, pelagic plankton, etc.) do not appear to have large genomes. On the other hand, some very large genomes are found in deep-sea invertebrates.
I don’t think that either no-function or protective hypotheses need to explain very large genomes if it is accepted that they are there for no particular “reason” but that their existence may reduce the required fidelity of repair mechanisms (in the case of protective). What is the life cycle of plankton – a few days? Short enough perhaps to not be compromised by UV?
2. Among vertebrates, species with high metabolic rates, and presumably more free oxygen radicals, have smaller genomes than species with lower metabolic rates.
Even the smaller genomes are considerably non-coding (hummingbiord?) and would be sufficient to provide protection to allow survival long enough for reproduction in these short life-span animals. I’m trying not to dismiss out of hand…is there a proposed reason for smaller genomes linked to higher metabolic rates that would make the “cost” of genome size reduction worth it?
3. There can be substantial differences in genome size among similar organisms, for example as in onion and its relatives or among salamanders.
Again – I don’t think that either no-function or protective needs to explain vastly differing genome sizes. Neither propose that genome size evolved to fit specific needs, rather, the protective hypothesis would propose that the repair mechanisms evolved to the necessary fidelity required to cope with whatever circumstances existed. Both no-function and protective accept that the non-coding DNA happened by chance and was allowed to build up because there is not strong reason to get rid of it, since it is not such an energy consuming resource to replicate it etc (except maybe for high metabolic rates where some needs to be discarded?)
4. Despite claims to the contrary based on small and questionable analyses, there are no clear relationships between genome size and lifespan.
Ditto – except that obviously, for a protective role, there would need to be sufficient non-coding DNA to support a life-span long enough to reproduce. This does not predict though that genome size is tightly linked to lifespan – for protection, a genome with a majority of non-coding DNA would be necessary but not sufficient for an adequate life-span.
5. Transposable elements, which are the primary contributor to genome size, can cause a range of mutations through insertion into genes or by causing large deletions by illegitimate recombination, the latter of which is especially likely with the long terminal repeat (LTR) elements that are common in plants.
Mismatch detection and repair systems are very well developed and highly (not 100%) efficient – the greatest cause of DNA damage, by orders of magnitude, is endogenous, so problems related to transposable elements, copying long repeats, etc would presumably be coped with. Also not all mutation is bad even at the gene level, we are full of SNPs, insertions, deletions, CNVs, etc. Most damage is handled, if not the next protection is apoptosis if insertions corrupt crucial genes. Sometimes insertion into some crucial genes though may not be detected as aberrant and could lead to loss of cell growth control, or reduce damage repair fidelity, or anything that may lead eventually to transformed cells. But this could also be an argument for non-coding DNA being useful for protection – the presence of which makes it much less likely that insertions will happen in genes.
6. DNA content obviously can be amplified in somatic cells by endoreduplication, but this tends to be in cells involved in ion exchange, protein production, etc., and not ones exposed most to mutagens (such as the skin exposed to UV).
Not sure what the answer to this is, or if it needs one, given the “passive” role proposed for non-coding genome size regarding protection. For UV other protection mechanisms evolved (e.g. melanin)
Keith Grimaldi(Quote)
Dr. Gregory
This is a great blog, I’m just starting to sift through all the ideas presented here. I’ve also read a few of your papers. Although not about this post in particular, this comment is about non-coding DNA. How I learn, I hope you would forgive any naivety on my part in advance.
Let’s call this ncDNA for non-coding DNA. I don’t like the name “Junk DNA” because it implies “not worth sequencing.” Also, there is a semantic problem with “junk.” It doesn’t properly address the complexity of genomes and the evolutionary processes going on. Your analogy of genomes to gut bacteria is apt. Genomes are ecologies. An old ecology that could go back to a time before DNA. Variety is a key part. Even related species with the same genome size can have huge differences in the characteristics of their respective ncDNA. Parts of this ecology are host/associate processes that run the range from predator to parasite to a type of symbiosis. In response the genome has built defenses and through exaptation, has recruited various elements, especially new regulatory elements and sometimes new genes[3].
So I ask myself a question: Why is it that bacterial genomes don’t have ncDNA, especially:
introns
telemeres
centromeres
The null hypothesis would be they got there by accident, contingency.
Ten minutes on Google is a revelation. There are no structures on eukaryote genomes that doesn’t already exist in some form on bacterial genomes. Multiple chromosomes, linear chromosomes, group I and group II introns, retrotrasposons, precursors to centromeres[4]. The tell is that there are three ways bacteria solve the halting problem for linear chromosomes while eukaryote chromosomes only use one, telomere repeats[2]. So my bet would be contingency.
ncDNA as structure:
Seems like there is correlation between genome size and cell size. Also, that newer species tend to have smaller genomes (like the onions). I know that attempts to correlate different phenotypes and genome size in plants have not had very good results. Also, genome folding compartmentalizes gene rich and gene poor regions[1]. Seems the direct relationship is to physiology but I’m a little unclear as to what that means. I took the c-values of some of the various animal groups and did a frequency distribution. Large genomes are rare and small genomes common, the frequency of large genomes fall into a very long tail. Insects especially. If you look at the frequency of plant host families to Lepidoptera species you get a long-tailed graph. Specialists are common and generalists are rare. Frequency of gene introgression vs distance from cline center across a hybrid zone or seed dispersal vs distance, all long-tailed. This means that there is a barrier to larger genomes but the barrier is permeable. This would suggest that large genomes are being recruited for some function but it could be very different function depending on the group.
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome, Erez Lieberman-Aiden, Nynke L. van Berkum, Louise Williams, Maxim Imakaev, Tobias Ragoczy, Agnes Telling, Ido Amit, Bryan R. Lajoie, Peter J. Sabo, Michael O. Dorschner, Richard Sandstrom, Bradley Bernstein, M. A. Bender, Mark Groudine, Andreas Gnirke, John Stamatoyannopoulos, Leonid A. Mirny, Eric S. Lander, Job Dekker, Science Oct 2009.
Complete nucleotide sequence of the chlorarachniophyte nucleomorph: Nature’s smallest nucleus, Paul R. Gilson, Vanessa Su, Claudio H. Slamovits, Michael E. Reith, Patrick J. Keeling, Geoffrey I. McFadden, PNAS June 20, 2006.
DNA Transposons and the Evolution of Eukaryotic Genomes, Cédric Feschotte and Ellen J. Pritham, Annu Rev Genet. 2007.
Distribution of Centromere-Like parS Sites in Bacteria: Insights from Comparative Genomics, Jonathan Livny, Yoshiharu Yamaichi, and Matthew K. Waldor, J Bacteriol. 2007 December
Bill Beaver(Quote)