In 2016, the PLOS Genetics Research Prize was awarded to Naranjo, Smith et al., for their work on a complex trait adaptation. Hunter Fraser, the corresponding author of the winning article and Associate Professor at Stanford University, tells us about the challenges he faced bringing the research to fruition and what winning the prize meant to him.
I was thrilled beyond words to start my job as an Assistant Professor in 2009. The previous two years had been tough—I had been fired from a postdoc position and then laid off from an industry job just 18 months later—so I was eager to turn things around. I was bursting with ideas for how to study the evolution of gene expression, but was missing just one ingredient: data.
During my ill-fated postdoc, I had devised an approach to use allele-specific gene expression data to identify lineage-specific selection on gene expression (see our paper’s Introduction for details). I wanted to use high-throughput sequencing of cDNA from inter-species hybrids for this, since sequence reads overlapping with heterozygous genetic variants (of which there are many in hybrids) could be used to measure the mRNA level of each allele. However, my advisor did not believe this would work, as this was before any publications of high-throughput cDNA sequencing (now known as RNA-seq). Without his support, I was unable to collect the data I so desperately wanted, and moved on to an industry position soon after that.
Fast forward to 2009: After being laid off in a “corporate restructuring,” I was chomping at the bit to start my faculty position. Things went slowly at first—I was busy buying equipment, writing grants, meeting new colleagues, and searching for my first lab hire, so those allele-specific expression (ASE) data I needed were still just a tantalizing mirage. However, I was overjoyed when I came across a paper (Tirosh et al., Science 2009) that generated exactly the type of ASE data that I wanted, from a hybrid between two species of budding yeast.
I immediately downloaded the paper’s supplemental information, and in a moment rivaling any Christmas morning, I eagerly opened the file. There I found over 17,000 glorious data points: ASE ratios for 4400 genes in four conditions. I sorted the genes by their ratios and copied them into an online functional enrichment calculator, which returned just one enriched annotation: toxin response. Remarkably, these gene annotations were all derived from a single paper that measured the transcriptional response to citrinin, a naturally occurring toxin produced by several species of fungi. And the enrichment was incredibly strong: 40-fold greater than expected among the 1% of genes with the strongest ASE biased towards one of the parental species (Saccharomyces paradoxus). This was clear evidence that natural selection had been acting on the expression levels of these citrinin-responsive genes—quite an exciting discovery, particularly since in 2009 polygenic gene expression adaptation was just a theoretical possibility, with no known empirical examples.
I had no idea that this discovery—which took all of six minutes to make—would take us the next six years to characterize. It was an exceptional undergraduate, Santiago Naranjo, who spearheaded the project during his three years in the lab. Santiago made a number of key observations, including characterizing the fitness of different strains in the presence of citrinin and performing precise allelic replacements (with laborious pre-CRISPR technology) to test the effects of specific transcriptional regulatory regions on the expression of our top candidate genes. After Santiago graduated, the torch was passed to an inventive graduate student, Justin Smith, who performed critical experiments measuring the fitness effects of Santiago’s promoter-swaps, as well as the effects of up-regulating our candidate genes. Along the way, several others made essential contributions as well—a true team effort. Altogether, their work implicated three specific genes involved in this complex adaptation (including a gene we named CIS1, ostensibly standing for CItrinin Sensitive, but which in fact was just an excuse to name a gene after my favorite scientific word), while also demonstrating an approach for investigating polygenic gene expression evolution more generally.
We were incredibly honored to be awarded the PLOS Genetics Research Prize for this work. It was especially inspiring to receive the award for this project, since out of all the work to come from my lab, this one was perhaps our hardest-won victory—at several points along the way it was not even clear if we could get the project to a publishable conclusion. But now we are more excited than ever about applying this framework to other inter-species hybrids from across the tree of life—including fruit flies, archaea, mice, cichlids, and zonkeys, my personal favorite model system to study the evolution of zebra stripes!
Nominations close on Friday, June 16, 2017 at 11.59 PM Eastern Time.
Competing Interests statement: Hunter Fraser is the corresponding author of PLOS Genetics Research Prize 2016’s winning article. The article is discussed in this blog.
Featured Image credit: May 2015 Issue Image. Post-transcriptional Regulation of Hair Cycling by miR-22. Image Credit: Yuan and colleagues