Transposons, Browsers, and Annotation, oh my!

posted in: Science | 6

Friday was the first full day of the 51st Maize Genetics Conference, and it was filled with all kinds of genetic fun. When I saw the program, I knew I would be up for the first talks of the morning at 8 am, because they were about transposons. The rest of the day was filled with poster presentations, talks about online genetic resources, and a discussion of gene annotation. Anastasia was there with me, and she’ll have all sorts of good stuff to talk about as we give the 51st MGC the exposure it deserves!

Transposons are really neat. Also known as Mobile Genetic Elements, Transposable Elements, or just “jumping genes,” they are sequences of DNA that are capable of popping out of a chromosome and inserting themselves into another. The most well known kind of transposon contains a gene that encodes for an enzyme called Transposase, which physically chops the transposon out of the DNA strand it is in, and puts it in another. The result is a gene that does not remain in a fixed location, and ‘jumps’ around the genome from Chromosome to chromosome, turning other genes on and off if it inserts in them or near them. Transposons were first described in Maize, by the famous Cornell biologist Barbara McClintock, and are thought of as some of the source of genetic variations that fuel evolution. Sometimes they can incorporate bits of other genes and move them around, causing all sorts of genetic modifications.

The morning talks were full of transpositional goodness. We had one talk about using transposons to help in genetic studies where you try to connect genotypes to phenotypes, and one on studying the relationships between different transposons. One very interesting one described a pair of transposons near each other, that could actually pull an entire gene out (between them) to move them somewhere else. Titled Paired Transposons: Natural genetic engineers – it really makes you wonder what the difference is between genes moved around by the plants themselves or by people intending to move them around?

One transposon talk was truly the highlight of the day for me. It described a newer, quite interesting kind of transposon called a Helitron. It sounds cool, and it is. Helitrons are transposons that have sequence that complements part of itself near one of its ends. What this does is forms a couple “hairpin loops,” which look like little twisty knots that stick out of the DNA strand. Here is a picture of a Helitron (with an ear of corn behind it).

Helitron superimposed over an ear of maize
Helitron superimposed over an ear of maize

Helitrons are a little different from other transposons in how they operate. Rather than being snipped out of a chromosome by transposase and re-incorporated elsewhere, they actually “roll” into another strand, making a copy of themselves (Leaving a copy behind as well.) It’s called “Rolling Circle” replication, and here’s a picture of how it works.

Pretty neat, huh? Helitrons have been found with all sorts of pieces of genes inside them. Genes are made up of coding Exons and non-coding Introns that are spliced out of the mRNA before it is used to make a protein. Helitrons have been found carrying one or more Exons that they captured from other genes. We don’t know at this point whether they can contain entire large genes, but they demonstrate a clear mechanism by which parts of genes get shuffled around the genome, providing more mutational fuel for natural selection.

In Maize, Helitrons make up 1.4% of the genome. It’s already half transposon as it is, but just imagine that every 70th bite of sweet corn you’re eating a mouthful of helitron DNA. Mmm, delicious.

David Tribe has also talked about Helitrons before at the GMO Pundit.

It is clear that genomes engineer themselves. Not in a purposeful fashion, mind you, but the random moving and shuffling of genes that has constantly occurred in the evolution of our crops plants makes tweaking or adding one or two genes sound like nothing at all. The analogy between mobile genetic elements and human genetic engineers is not only getting stronger, but was also reflected in the titles of some of these talks.

After lunch, we had the first poster session, displaying grad student posters on topics everywhere from more transposons, to carotenoids (Vitamin A precursors) in maize, database resources, chromosomal variations, outreach efforts, and even a few on switchgrass. Unfortunately for you, the reader, we couldn’t take pictures of the cool posters, because it represents unpublished ongoing research being conducted by grad students, undergrads, and their research groups. But we have heard that poster presenters have the option of submitting their posters to be published online, and when that happens we’ll point out some of the good ones.

This year, I did not have a poster to present, as I already showed off my corn videos last year, and I didn’t have enough evidence in my research to submit an abstract by the deadline in January. (Oh, I will have a lot of sweet sugar enhanced evidence for next year’s conference!) So I had a lot of time to read other posters and get the zeitgeist of maize genetics research. A few techniques here, some strategies there, and I’ve got a few more ideas for my own research goals.

Anastasia, however, did have a poster at the conference, on her research with Maize Zein proteins. Here she is showing off her research… who is that posing with her in the picture? I’m sure she’ll be telling us all more about her project in the near future.

After the poster sessions, it was time to jump back into the lecture hall to learn about some new genetic resources on the web for scientists. One really cool one, called TARGeT, allows anyone to take the sequence of a gene, search for similar gene sequences to find related genes, and then also assemble an evolutionary tree from those sequences. I have been wondering (for years) where I could do this without buying a proprietary program, and rest assured I’ll be trying this out soon. It appears that TARGeT, (originally named TERT in the conference abstract book) was intended as a teaching tool for high schools and college classes, but has since morphed into a research platform as well. If you make it easy to assemble genes in a tree based on sequence similarity, you’ll find scientists flocking to it.

There were also some improvements to MaizeGDB, MaizeSequence.org, and some other resources that maize geneticists use to do their research.

After dinner, we listened to a talk by Pam Johnson, Chair of the Research and Business Development Action Team of the National Corn Growers Association. I will talk about her presentation in a separate post.

Finally, we come to the last event of the day, a panel discussion about Community Gene Annotation. Here’s the problem: We have the sequence of the corn genome in-hand, and there may be upwards of 50,000 genes in it. We have evidence of these genes through sequence analysis, expressed genes discovered through research, and more. But our computer gene-processing algorithms aren’t very good at annotating them, and well-assembled genes in the database will be very helpful for future research.

So the panel discussion set out to get input from the Maize Genetics community. They wanted to Wikify it, allowing researchers to log in, edit, and have their annotations proof-read by others. Bit by bit, with hundreds of people contributing a little, we could complete this task in a few years.

Well, that’s what the panel set out to do, but in my opinion, it was an unsuccessful exercise. The conversation happened between two panelists on the right side, and a member of the audience. More time was spent discussing minor details about how it would work in a technical sense, and those on the left hand side hardly had a chance to contribute. Maybe the one or two scientists in the audience who dominated the discussion should have been on the panel, and the panel should have had a little more direction.

When it came to how to encourage scientists to voluntarily contribute to the maize gene annotation semi-wiki, the emphasis was on the stick rather than the carrot. I felt like going to the microphone to suggest “fabulous prizes” or “fame and glory in the community” for top annotation editors, if I didn’t feel so bored and annoyed. It also went on too long.

Later, I talked to my roommate from Oregon about it and my experience with wikis such as the Davis Wiki. And in a tight-knit-enough community, the social incentive to be a [top] contributor was a pretty powerful motivator that built over 10,000 pages. The Maize Genetics community is pretty tight-knit, and that seems like a good starting point for a massively collaborative project like this. Perhaps with prizes, recognition at the meeting, or dangling other carrots (rather than thwacking potential annotators with sticks), it could get done. Wikis are a ground-up kind of community, and I don’t think top-down requirements will be as helpful. Truth be told, I think I had a better chat with my roommate about the issue than the panel did. There, I said it.

I’m looking forward to being able to contribute to the annotation process, as in my own research I have assembled a few candidate genes for my own gene, only to find out that they were excluded by my latest mapping data. That information is lost and would have to be re-done by someone else, so I plan to enter it in this system when it is ready. This kind of system will be good, because there’s nothing that a few hundred knowledgeable and experienced geneticists can’t do with the maize genome.

At 9:30, we broke for some casual socializing, poster viewing, with a few free drinks sprinkled in. Anastasia and I both had some good conversations with researchers, including one very fortuitous meeting, where we got a lot of good info about resources to look up. We also had a chance to promote the Biofortified blog and make plans for the next day at the Maize Genetics Conference. Stay tuned for more!

Follow Karl Haro von Mogel:
Karl earned his Ph.D. in Plant Breeding and Plant Genetics at UW-Madison, with a minor in Life Science Communication. His dissertation was on both the genetics of sweet corn and plant genetics outreach. He recently moved back to his home state of California. His favorite produce might just be squash.