Postdoctoral Fellow Greenberg Lab
Children's Hospital Boston/Harvard Medical School
In the lab of Michael Greenberg at Children's Hospital Boston and Harvard Medical School, Dr. Jesse Gray is working to discover how the environment can change brain development by altering gene expression. The lab's current work includes using the SOLiD™ System from Applied Biosystems to study neuronal activity and how it induces gene expression using chromatin IP and RNA sequencing, as well as to investigate how gene expression changes along the course of evolution.
We recently spoke with Dr. Gray about this work in the Greenberg lab, and how Applied Biosystems is helping scientists there as they start to unravel the mystery of how gene expression is controlled by external environmental factors while the brain develops.
Tell us a little about your area of expertise and what drew you to pursue this line of work.
Our lab focuses on the brain and how it develops in close concert with the environment. This relationship is very poorly understood and particularly interesting because we know there are a number of nervous system diseases in which the brain would normally be reaching a particular developmental stage and things start to fall apart right at the time when the environment is crucial. I wanted to take part in investigating the hypothesis of my advisor, Michael Greenberg, that the root causes of these diseases are related to how the environment controls gene expression through neuronal activity.
Why did you initially choose the SOLiD System for your research at the Greenberg Lab?
During the summer of 2007, we were looking for a new sequencer to buy. At the time there were almost no SOLD instruments in the field so the option was either to take a gamble on the very new, untested sequencing technology which the SOLID System represented or go with a more established but sort of mixed-reviewed technology from another provider.
Ultimately we chose the SOLiD System because of a number of factors, but the two most salient were the great relationship we had developed with AB over many years and the growth potential we saw in the platform. The throughput is already higher on the SOLiD System than it is on other systems and we believe that gap may very well increase in future years. We're very excited about that potential.
What research are you are currently conducting on the SOLiD System?
Right now we're undertaking two major studies on the SOLiD system, both involving an in vitro model for neuronal activation. In one study, we are doing RNA sequencing to examine how gene expression changes when neurons are activated by potassium depolarization. Using the same model, we're also using the SOLiD system to look at protein transcription factors binding to DNA using chromatin IP, or ChIP-seq sequencing. By combining the two data sets, we have already been able to uncover aspects of activity-induced gene expression that we never knew about before.
Can you give us an example of what you're learned so far?
By looking at the combination of transcription factors binding to DNA in response to neuronal activity and which RNAs are induced by neuronal activity, we've already seen that it's not enough to do a chromatin IP and say that a factor binds to a gene, and it's not enough to say that a gene is induced. In many cases, it's actually very crucial to show exactly where a transcription factor binds in the gene, whether it binds in an activity-dependent manner, and what transcript is induced by activity. This data is important because, in many case, we see factors binding in the middle of genes producing antisense transcripts and changing transcription in ways that are not as simple as a gene goes up or a gene goes down.
Are there any specific benefits or significant discoveries you can attribute to the SOLiD System?
All of my research is based entirely on SOLiD sequencing, so the fact that we're able to make progress by sequencing is 100% attributable to the SOLiD System. We're right in the middle of the guts of the work we're doing with SOLiD, but we can already see that we're able to pick out splice forms and antisense transcription. We have a sensitivity for detecting transcripts that we never had using microarrays, so it's clear that doing gene expression studies on SOLiD is an enormous step forward compared with previous technologies.
What do you think is most promising about the RNA sequencing you're doing with SOLiD?
Before RNA sequencing, assessing gene expression was based on microarrays that are extremely sensitive to the exact probe used in a probe set. When you change a probe set on a microarray, you can no longer compare one probe set with another. With RNA sequencing, we can compare the level of one gene to the level of another gene. More importantly, I believe we will also be able to compare RNA transcript levels from different species, which is something we could never do with microarrays.
That's what is really promising and exciting about next-generation sequencing-the potential to gain deeper insight into the evolution of genomes. Up until now, we've been able to study the evolution of genomes by looking at the conservation of sequence that tells us which parts of the genome are so important that they are under negative selection, or selection against change, throughout a broad range of phylogenies. What we'll be able to do going forward is to see what has actually changed throughout the course of evolution in the genome and how those changes alter the phenotypes of organisms.
Why is next-generation RNA sequencing important to the future of medicine?
Next-generation sequencing represents a potential revolution in medicine for many reasons. Number one, it's bringing down the cost of sequencing the human genome. We're not yet at the point that we will sequence everyone's genome as a routine part of medical care, but that day is not too far off in the future and the SOLiD platform brings us closer to that goal. Once we can achieve routine genome sequencing, it would mean that at some point early in your life your genome would be sequenced and that information would be used throughout your lifetime to help guide your healthcare through personalized medicine. But that's still a few years off.
Right now the research that's being done on the SOLiD platform spans a very broad area of biology. It is allowing us to see data sets that were simply not available and couldn't have been generated before. This next-generation sequencing is transforming our view of some of the fundamental questions about how cells work and how multi-cellular organisms are assembled, which is likely at some point down the line to lead to new drugs and treatments, or lead to an insight that later on will lead to another insight that will inform healthcare decisions.
Anything else you'd like to add about your research and your work with the SOLiD System and AB?
Just that I've had an absolutely outstanding relationship with AB. I am extremely appreciative of what they've done for my project and the kind of help they have extended above and beyond simply providing a machine and getting the machine up and running. It's really brought to mind the enormous contribution the industry makes to even very basic research, which I think a lot of us in academia often overlook. The impact of the SOLiD System on my research cannot be overstated. I couldn't do it without it.