ExperimentBank || TE evolution

Experiment Bank - The site for free exchange, review, and discussion of novel scientific experiments

Front Page ? Everything ? News ? Wish list ? Help ? FAQ

?TE evolution
By gbaute, Section Biology Posted on Thu Apr 29th, 2010 at 10:07:45 AM PST

Transposable elements play a large role in genome evolution. There are many unanswered questions about their evolution, where they go, how they proliferate, how much they effect gene expression, what kind of selection is acting on them and so on. There is also variation across different species with regards to what TE are found in their genome. The experiment outline is rather simple. Find a yeast strain that does not have any evidence of having a certain class of TE. Transfect the yeast line with it and confirm successful transformation. Separate into 10 parallel cultures. Sub culture to new media every day (week? what ever it takes to keep yeast in an exponential growth phase) and freeze remainder. Repeat for one or two decades (should only take a few minutes a day). By then genome sequencing will cost next to nothing and you can resequence all your lines and at time points all along their history from the frozen strains. Transcriptome work could also be interesting. It will then be up to some smart bio-informatics types (or just maybe just ask your computer nicely, who knows what will be going on in 2030) to tell you what happened.

< Let's cure leukemia - oncolytic virus at action again (8 comments) | Benign vs. Malignant Tumors (4 comments) >

TE evolution | 12 comments (8 topical, 4 editorial)

[new] Details? (none / 0) (#1)
by Bioinfkat on Fri Mar 26th, 2010 at 07:13:59 PM PST
(User Info)

I was wondering what type of TE you will be examining? For instance, Ty1, Ty2, Ty3, Ty4, and Ty5 elements are some examples of TE in yeast. And can you please provide some more details on how you would expect sequencing to answer some of the questions you outlined above? This might be difficult to answer though if the analysis is taking place in 20 years!

Kim et al. conducted a genome-wide survey of Saccharomyces cerevisiae retrotransposons and they have provided some evidence on the TE present in the genome and how they might have evolved (Genome Res.1998. 8:464-478). What do you expect to add to this existing body of literature?

[new] its all in the details. (none / 0) (#2)
by gbaute on Sun Mar 28th, 2010 at 01:31:38 PM PST
(User Info)

I haven't yet done a intense enough literature search to figure out the major types of TE in yeast and a strain which lacks it. I know there are many cases as such and thats all that really matters in the context of this proposal. There are lots of surveys that you can do and many which have already been done using available data. This is where i got this idea. You can only make inferences of ancestral states by looking at a genome, you cannot really know what happened. The core of this project is to figure that out. Take a simple case where there is a large expansion of TE's in a line which are wiped out of a population immediately. This may happen all the time but you would never guess that by looking at an organisms genomes even with including relatives. Where as with this experiment you can look the actual ancestors of the line in question. Not only that but you can assay their fitness.

Whole genome sequencing would be the easiest and most in depth way to assay and track TE activity.

[ Parent ]

[new] I might be wrong (none / 0) (#3)
by Earthworm Jim on Mon Mar 29th, 2010 at 01:18:55 PM PST
(User Info)

but i thought they have some insight on how TE like ALU repeats, SINEs, LINES, LTR etc replicate, transpose, get selected, and become integrated over time. Like SINEs are smaller, thed to be closer to genes and perhaps contribute to expression by providing alternative promoters. Whereas LINEs and LTRs were more intergenic in repeat sequences and for the most part epigenetically silenced by chromatin structure to prevent homologous recombination of their sequences. So in your experiment, are we looking at a specific TE and how it may propagate? and if so, what is the likelyhood of such an transposing event and if you'd be able to culture strains long enough to record multiple events and chart them?

[new] So might I (none / 0) (#4)
by gbaute on Tue Mar 30th, 2010 at 09:37:17 AM PST
(User Info)

We definitly do know quite a bit about how TEs replicate and transpose. Its the get selected and become integrated part that gets a little wobbly. With the exception of a few experiments looking at TE movement over one or two generations we know very little in this department. What is teh actual rate at which these elements insert into the spots we think they insert into? We see LINES and LTRs silenced in non-coding regions because of the detrimental effect of being in other areas.In this experiment I would like to just use one TE, although using many would be even better then you could make comparisons and ask some really neat questions. Its interesting you asked about the likelyhood of events happening,i dont think anyone can answer that. I would expect it to be a few orders of magnitude around one in a million per generation, which with millions of yeast individuals going through multiple generations daily it would add up quickly. Is the rate constant over time? How will the strains compare at the end? Will one to two be totally bloated by the new TE? will they all have rid themselves of it? If things like this pop up you can 'go back in tome' and find out what happened.Also, the immediate cost of this experiment is very little, and I do expect in 20 years time sequencing a yeast strain will be like doing pcr.

[ Parent ]

[new] Results interpretation (none / 0) (#5)
by timothy auyeung on Wed Mar 31st, 2010 at 10:32:13 AM PST
(User Info)

This is a very interesting proposal and the ideas are very novel :) I dont think anyone has studied TE extensively at this level.

I am wondering how you intend to generalize the results coming out from this experiment to how TE may behave in nature. The culturing of yeast is done in the lab (a very controlled environment), i.e. the yeast are grown on, say, Malt extract agar at certain temperature and are artificially innoculated onto new media plates etc. Will these artificial settings significantly affect the proliferation or removal of particular TE in the genome?

[new] good question (none / 0) (#8)
by gbaute on Wed Apr 7th, 2010 at 08:22:36 PM PST
(User Info)

Not sure if the growth conditions would bias TE gain or loss. Maybe another possible experiment you could include in this would be to grow some in a less favourable conditions (high or low temp, or both) to see how that might play a role. TEs can chance genome size which changes cell size which alters metabolic rates which could be favoured in different conditions.

[ Parent ]

[new] Time scale (none / 0) (#6)
by xerro five on Sun Apr 4th, 2010 at 09:46:58 PM PST
(User Info)

I was wondering if 20 years would truly be long enough to study the majority of the TE mechanisms? If we are relying on random insertion and mobilization events, then obviously whatever hotspots the TE "likes" will show up in this experiment (for example, the Drosophila P-element prefers to move to specific sequence regions over others), however, the more problematic events (and thus more inserting to study) may be exceptional cases in which a TE moves into a position where it causes deleterious effects. If these events are not in hotspots, then it could take a long time for them to occur. More importantly though, we generally talk about TE evolution on the scale of thousands to millions of years, so would this glimpse be sufficient? Perhaps if representative data could be obtained, an algorithm could extrapolate the rest of the evolution process?

[new] Hmm (none / 0) (#9)
by gbaute on Wed Apr 7th, 2010 at 08:27:23 PM PST
(User Info)

An projection based on what is found may be a good approach to find out what might happen on a very long time scale. That said, given the generation time of yeast I would expect to see quite a large difference after 20 years depending on how invasive the chosen TE is. I can imagine that a totally novel TE "species" could be very aggressive and it may take some time for the yeast to cope. In a nature paper last year "a burst of retrotranspostion reproduced in arabidopsis" researchers found a very large amount of TE movement after only 2 generations in a methylation mutant. So, it can happen very quickly.

[ Parent ]

Where is the selective pressure? none (#7)
by fongchun on Tue Apr 6th, 2010 at 01:30:07 PM PST
(User Info)

Cool idea! It will be interesting when you pay some lab tech to do the same experiment everyday for a decade. I can just imagine the job description =)

I am curious as to how you are going to test for selection considering that the yeast will be grown in an environment that theoretically won't change over a decade. If the TE are going to play any role in genome evolution, there should be some sort of selective pressure and I can't see that happening if the environment is consistently the same. I am not sure the results you will be getting after a decade will tell you anything other than the fact that they randomly transposed to different parts of the genome.

excellent concern none (#10)
by gbaute on Wed Apr 7th, 2010 at 08:32:51 PM PST
(User Info)

haha I was thinking it would be a great morning routine for a crazy professor. Your right in that it could easily become a question about random drift of TE activity. At the same time that is kind of they question I want to get at, all else the same how does a TE proliferate? This new 'species' appears and then what? I can imagine some very interesting possibilities, like some strains eliminating it and then others having it go totally out of control. A parallel experiment could involve growing the strains in different stresses.

[ Parent ]

Re: excellent concern none (#11)
by fongchun on Wed Apr 7th, 2010 at 08:54:11 PM PST
(User Info)

I think the different environment stresses on the TE evolution will definitely tell you a lot about how the TE evolves over time.

What will be an even interestingly experiment is to observe the evolution of the poor lab tech who does the same thing every day for a decade. How will they react under different pressures =) Just an idea.

Good idea of an experiment overall though

[ Parent ]

Re: excellent concerns none (#12)
by kjs86 on Thu Apr 29th, 2010 at 12:50:09 PM PST
(User Info)

Is it known for sure that the rate TEs jump around at is related to environmental stress? It would definitely be interesting to compare the stressed versus non-stressed and figure out more behind the cause of transposition.

[ Parent ]

TE evolution | 12 comments (8 topical, 4 editorial)

?+?Menu

? create account
? faq
? search

?+?Login

Make a new account

Username:

Password:

?+?Related Links

? More on cellular and molecular biology
? Also by gbaute

All trademarks and copyrights on this page are owned by their respective companies. Comments are owned by the Poster. The Rest ? 1999 The Management

create account | faq | search