Meet a Whitehead Postdoc: Satyaki Rajavasireddy

Satyaki Rajavasireddy is a postdoc in Whitehead Institute Member Mary Gehring’s lab investigating regulation of gene expression in plants. We sat down with Rajavasireddy to learn more about him and his experiences in and out of the lab.

Why is plant research important?

In recent history, a lot of money has been invested in medical research, which means people live longer, but what I feel we as a society have paid less attention to is improving agriculture at the same pace in order to keep feeding all those people. I also think work in plant biology will help us in the long term to address challenges related to climate change. Thinking more specifically about work we do in the Gehring Lab, one of the things we study is the endosperm, a placental tissue in seeds that surrounds the embryo. It supplies the vast majority of nutrients that we consume. A lot of the food we eat — like wheat, rice, maize, popcorn, even beer — originates in the endosperm. Even if you're eating meat, most cattle have been fed on nutrition derived from endosperm. Understanding how the endosperm develops and what its inner workings are will hopefully enable us to make bigger and better seeds, and so help agriculture keep pace with global nutritional needs.

What are you investigating?

I am trying to understand how gene expression is regulated in the endosperm. Most recently what I've been working on is an understanding of seed abortion (when seeds die before they reach maturity) in cases where the paternal plant has more genome copies than the maternal plant. In humans, both mother and father have two copies of every gene, and they each donate one copy to the embryo, so it ends up with two copies as well. Plants can have different numbers of genome copies, and the numbers don’t necessarily match between mother and father. Endosperm is a weird tissue and without going too much into detail, the ideal ratio of genome copies between mother and father in endosperm is 2:1. So if you cross parents with an equal number of genome copies, then the ratio of genomes inherited from mother to those inherited from the father is 2:1. In this case the seed will be fine. However, if it's less than that, the seed aborts. So, if you take a mother that has two copies of the genome and cross it to a father that has four copies of the genome, you get seed abortion. But the work I have done recently showed a way to get viable seeds with such a cross. My work provides insights into how genes are regulated in the endosperm and it is also of interest to plant breeders because breeders trying to improve crops may want to cross crop strains with different numbers of genome copies.

What I did was to look at a pathway called the RNA-dependent DNA methylation pathway. This pathway uses small fragments of RNA as a guide to laying down DNA methylation — essentially annotating the DNA in the genome with chemical groups. Our work suggests that the annotations left on DNA by this pathway in the father are then used in the endosperm of progeny seeds to decide whether certain genes should be switched on or off. I found that the role played by this pathway in the father was required for seed abortion, and that if you remove components of the pathway in the father, then you can change gene expression in the endosperm sufficiently so that the seeds that usually die now start surviving.

What’s your favorite part of your job?

Coming up with cool hypotheses — though they often turn out to be wrong. It's like a detective story; you have lots of data and you're trying to solve how a process is happening, so you have to come up with as many good hypotheses as you can and slowly get rid of them one by one. It's sort of grunt work, but to me that is the most appealing part of my job: the ability to explore a million possibilities and determine which of them is right. I also think it’s pretty cool to get to see something for the first time, and sometimes be surprised by the complexity or simplicity of what you find. 

What did you want to be as a kid?

A fighter pilot, when I was 6. Then I saw a plane crash and decided it wasn't for me.

What led to your interest in science?

I have always been fascinated with the many things we can engineer, like planes, but around 10th or 11th grade, I realized that my math and physics weren't that great, so I started exploring other things. I had a great botany teacher who introduced me to various aspects of biology, which I really enjoyed. That’s when I decided to be a scientist, but I wasn't completely set on which field in biology I would be interested in. My first year of undergrad, the C. elegans genome had been sequenced and there were a lot of publications on it coming out, and then the Human Genome Project really started to come out. So it was in the air that there was a genomics revolution coming, and that influenced me.

I did a master's degree studying mouse development, and for my PhD I studied speciation in flies and the function of a gene that was known to be involved in speciation in flies. I became aware of Mary’s work when I read a paper she had published that was somewhat related to what I was working on, but in the endosperm. I was interested in moving to plant biology because I see it as being important to solving some of the challenges facing this world, so when I had the opportunity I came to Mary's lab for my postdoc. It seemed like a happy overlap of things that interested me and things that could have a positive impact on the world.

What’s the biggest disaster you’ve ever had in the lab?

It's not a one-off incident so much as I spent three years during my PhD trying to ChIP a protein (identify the DNA regions that the protein interacts with), and it turned out the protein was essentially unchippable. I don't know if that counts as a disaster; I didn't set anything on fire.

How do you deal with spending so long on a project only to hit a dead end?

Lots of ice cream. That was years two, three, and four of my PhD. Eventually someone else tried it and couldn't ChIP it either, so we decided to give up on it, but it was a significant chunk of my life at that point. It would hurt a little when I would go to give talks, and the other speakers would come with a Cell paper while I had a bunch of failures to show. But it’s fine. It was a character-building experience, I would say. Everything turned out well in the end.

What are your hobbies?

I cook a lot. I read a lot of science fiction, and a lot of history. I sometimes think that my three favorite things outside of science are history, politics, and science fiction, so it's like the past, present, and future. I like to go hiking and New England is perfect for it. In the summer, I like to go see places in the countryside and amble over it.

What’s been your favorite hike in New England?

I really liked Mount Lafayette in New Hampshire. That's the tallest mountain I've climbed thus far; I usually go for the low-hanging fruit. The thing I found really interesting about it was the different zones — the changes in vegetation and animals — as you go up a mountain. At high elevation, you have the alpine zone and fell fields, where there are no trees but you have moss and other little plants colonizing the area. I had read a lot about this, but I had never seen it. Just seeing it was awe-inspiring in some ways. I grew up in a country that is very populated, India, and to see an untouched natural habitat was kind of hard. Mount Lafayette is not pristine, but you can still see enough of the original habitat that it inspires you. It makes you realize how much we've changed the world around us.

Do you collect anything?

Not recently, but I did my PhD at Cornell, and that place is really good for fossils, so a friend and I occasionally used to go fossil collecting. We found trilobites mostly, some fragments but some full sized. I still have them, although I think some broke over time because I kept handling them too much.

Where do you see yourself in ten years?

In the near future I want to break out of working on Arabidopsis to work on other species in plants. When we study a model system, like Arabidopsis, it’s like we're cracking the window open on plant biology and we get a tiny view of the room inside. If you want to get a broader understanding, or include every culture and prepare to face global challenges, you really need to look at more of plant biology. I want to use Arabidopsis as a gateway system and then see how the rules that we derive from Arabidopsis are applicable to different species.