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Tag: DNA

Its not just SNPs

Another month, another paper (although this one is almost two weeks overdue – sorry!)

In my life in venture capital, I’ve started more seriously looking at new bioinformatics technologies so I decided to dig into a topic that is right up that alley. This month’s paper from Nature Biotechnology covers the use of next-generation DNA sequencing technologies to look into something which had been previously extremely difficult to study with past sequencing technologies.

As the vast majority of human DNA is the same from person to person, one would expect that the areas of our genetic code which tend to vary the most from person to person, locations which are commonly known as Single Nucleotide Polymorphisms, or SNPs, would be the biggest driver of the variation we see in the human race (at least the variations that we can attribute to genes). This paper from researchers at the Beijing Genomics Institute (now the world’s largest sequencing facility – yes, its in China) adds another dimension to this – its not just SNPs that make us different from one another: humans also appear to have a wide range of variations on an individual level in the “structure” of our DNA, what are called Structural Variations, or SVs.

Whereas SNPs represent changes at the individual DNA code level (for instance, turning a C into a T), SVs are examples where DNA is moved (i.e., between chromosomes), repeated, inverted (i.e., large stretches of DNA reversed in sequence), or subject to deletions/insertions (i.e., where a stretch of DNA is removed or inserted into the original code). Yes, at the end of the day, these are changes to the underlying genetic code, but because of the nature of these changes, they are more difficult to detect with “old school” sequencing technologies which rely on starting at one position in the DNA and “reading” a stretch of DNA from that point onward. Take the example of a stretch of DNA that is moved – unless you start your “reading” right before or right at the end of where the new DNA has been moved to, you’d never know as the DNA would read normally everywhere else and in the middle of the DNA fragment.

What the researchers figured out is that new sequencing technologies let you tackle the problem of detecting SVs in a very different way. Instead of approaching each SV separately (trying to structure your reading strategy to catch these modifications), why not use the fact that so-called “next generation sequencing” is far faster and cheaper to read an individual’s entire genome and then look at the overall structure that way?

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And that’s exactly what they did (see figures 1b and 1c above). They applied their sequencing technologies to the genomes of an African individual (1c) and an Asian individual (1b) and compared them to some of the genomes we have on file. The circles above map out the chromosomes for each of the individuals on the outer-most ring. On the inside, the lines show spots where DNA was moved or copied from place to place. The blue histogram shows where all the insertions are located, and the red histogram does the same thing with deletions. All in all: there looks to be a ton of structural variation between individuals. The two individuals had 80-90,000 insertions, 50-60,000 deletions, 20-30 inversions, and 500-800 copy/moves.

The key question that the authors don’t answer (mainly because the paper was about explaining how they did this approach, which I heavily glossed over here partly because I’m no expert, and how they know this approach is a valid one) is what sort of effect do these structural variations have on us biologically? The authors did a little hand-waving to show, with the limited data that they have, that humans seem to have more rare structural variations than we do rare SNPs – in other words, that you and I are more likely to have different SVs than different SNPs: a weak, but intriguing argument that structural variations drive a lot of the genetic-related individual variations between people. But that remains to be validated.

Suffice to say, this was an interesting technique with a very cool “million dollar figure” and I’m looking forward to seeing further research in this field as well as new uses that researchers and doctors dig up for the new DNA sequencing technology that is coming our way.

(All figures from paper)

Paper: Li et al., “Structural Variation in Two Human Genomes Mapped at Single-Nucleotide Resolution by Whole Genome Assembly.” Nature Biotechnology 29 (Jul 2011) — doi:10.1038/nbt.1904

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United States of Amoeba

Another month, another paper to read and blog about.

Most people know that viruses are notoriously tricky disease-causing pathogens to tackle. Unlike bacteria which are completely separate organisms, viruses are parasites which use a host cell’s own DNA-and-RNA-and-protein producing mechanisms to reproduce. As a result, most viruses are extremely small, as they need to find a way into a cell to hijack the cell’s  machinery, and, in fact, are oftentimes too small for light microscopes to see as beams of light have wavelengths that are too large to resolve them.

However, just because most viruses are small, doesn’t mean all viruses are. In fact, giant Mimiviruses, Mamaviruses, and Marseillesviruses have been found which are larger than many bacteria. The Mimivirus (pictured below), for instance, was so large it was actually identified incorrectly as a bacteria at first glance!

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Little concrete detail is known about these giant viruses, and there has been some debate about whether or not these viruses constitute a new “kingdom” of life (the way that bacteria and archaebacteria are), but one thing these megaviruses have in common is that they are all found within amoeba!

This month’s paper (HT: Anthony) looks into the genome of the Marseillesvirus to try to get a better understanding of the genetic origins of these giant viruses. The left-hand-side panel of picture below is an electron micrograph of an amoeba phagocytosing Marseillesvirus (amoeba, in the search for food, will engulf almost anything smaller than they are) and the right-hand-side panel shows the virus creating viral factories (“VF”, the very dark dots) within the amoeba’s cytoplasm. If you were to zoom in even further, you’d be able to see viral particles in different stages of viral assembly!

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Ok, so we can see them. But just what makes them so big? What the heck is inside? Well, because you asked so nicely:

    • ~368000-base pairs of DNA
        • This constitutes an estimated 457 genes
        • This is much larger than the ~5000 base pair genome of SV40, a popular lab virus, the ~10000 base pairs in HIV, the ~49000 in lambda phage (another scientifically famous lab virus), but is comparable to the genome sizes of some of the smaller bacterium
        • This is smaller than the ~1 million-base pair genome of the Mimivirus, the ~4.6 million of E. coli and the ~3.2 billion in humans
    • 49 proteins were identified in the viral particles, including:
        • Structural proteins
        • Transcription factors (helps regulate gene activity)
        • Protein kinases (primarily found in eukaryotic cells because they play a major role in cellular signaling networks)
        • Glutaredoxins and thioredoxins (usually only found in plant and bacterial cells to help fight off chemical stressors)
        • Ubiquitin system proteins (primarily in eukaryotic cells as they control which proteins are sent to a cell’s “garbage collector”)
        • Histone-like proteins (primarily in eukaryotic cells to pack a cell’s DNA into the nucelus)

As you can see, there are a whole lot of proteins which you would only expect to see in a “full-fledged” cell, not a virus. This begs the question, why do these giant viruses have so many extra genes and proteins that you wouldn’t have expected?

To answer this, the researchers ran a genetic analysis on the Marseillesvirus’s DNA, trying to identify not only which proteins were encoded in the DNA but also where those protein-encoding genes seem to come from (by identifying which species has the most similar gene structure). A high-level overview of the results of the analysis is shown in the circular map below:

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The outermost orange bands in the circle correspond to the proteins that were identified in the virus itself using mass spectrometry. The second row of red and blue bands represents protein-coding genes that are predicted to exist (but have yet to be detected in the virus; its possible they don’t make up the virus’s “body” and are only made while inside the amoeba, or even that they are not expressed at all). The gray ring with colored bands represents the researchers’ best guess as to what a predicted protein-coding gene codes for (based on seeing if the gene sequence is similar to other known proteins; the legend is below-right) whereas the colored bands just outside of the central pie chart represents a computer’s best determination of what species the gene seems to have come from (based on seeing if the gene sequence is similar to/the same as another specie’s; the legend is below-left).

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Of the 188 genes that a computational database identified as matching a previously characterized gene (~40% of all the predicted protein-coding genes), at least 108 come from sources outside of the giant viruses “evolutionary family”. The sources of these “misplaced” genes include bacteria, bacteria-infecting viruses called bacteriophages, amoeba, and even other eukaryotes! In other words, these giant viruses were genetic chimeras, mixed with DNA from all sorts of creatures in a way that you’d normally only expect in a genetically modified organism.

As many viruses are known to be able to “borrow” DNA from their hosts and from other viruses (a process called horizontal gene transfer), the researchers concluded that, like the immigrant’s conception of the United States of America, amoebas are giant genetic melting pots where genetic “immigrants” like bacteria and viruses comingle and share DNA (pictured below). In the case of the ancestors to the giant viruses, this resulted in viruses which kept gaining more and more genetic material from their amoeboid hosts and the abundance of bacterial and virus parasites living within.

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This finding is very interesting, as it suggests that amoeba may have played a crucial role in the early evolution of life. In the same way that a cultural “melting pot” like the US allows the combination of ideas from different cultures and walks of life, early amoeba “melting pots” may have helped kickstart evolutionary jumps by letting eukaryotes, bacteria, and viruses to co-exist and share DNA far more rapidly than “regular” natural selection could allow.

Of course, the flip side of this is that amoeba could also very well be allowing super-viruses and super-bacteria which could one day wipe out the human race to breed… but, maybe I’m just being paranoid. 🙂

Paper: Boyer, Mickael et al. “Giant Marseillevirus highlights the role of amoebae
as a melting pot in emergence of chimeric microorganisms.” PNAS 106, 21848-21853 (22 Dec 2009) – doi:10.1073/pnas.0911354106

(Image Credit – Mimivirus – Wikipedia) (Figures 1, 2, and 5 from paper)

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