Assistant Professor, Weill Cornell Medical College
Recommended by George Grills, Cornell University
NEW YORK (GenomeWeb) – There's the epitranscriptome, the microbiome of the New York City subway, the multi-omic study of a pair of identical twins in conjunction with NASA, and more that Christopher Mason is working on.
But a lot of what he is studying has been enabled by the arrival of new technologies.
"You can never marry a technology because it always changes. You have to really be the constant connoisseur of molecular techniques, or try to be," Mason told GenomeWeb. "You have to always be thinking, 'What is a new enzyme or chemistry or sort of buffer or new sort of small molecule, some way that lets me look deeper into the cell or understand the context of some non-coding RNA?'"
For example, earlier in his career, Mason was placing probes on a Nimblegen array to examine DNA expression and alterative splicing in Drosophila and had leftover space on his array where he decided to add probes that matched up with intergenic areas. Rather than those probes acting as negative controls, Mason and his colleagues reported in Science that about half of the probes they placed in non-coding regions lit up, indicating that a good portion of non-coding genome was transcriptionally active.
"It really was a surprise," he said, adding, "that's an example of a new technology, in this case high-density arrays, that let us discover all kinds of new things."
Similarly, a few years ago, after a new antibody for methylated adenosine came out, he and his colleagues decided to see whether adenosine is methylated in both DNA and RNA, as some papers from the 1970s had suggested that RNA, too, could be methylated. Using a method called MeRIP-seq that's similar to ChIP-seq, they found that RNA itself does get methylated.
And lately his lab has been going around swabbing surfaces of the New York City subway to sequence the microbes living there.
At the same time Mason is also involved in a number of standards initiatives. Since he relies on new technologies, he noted that he has to be extra careful to ensure that what he is seeing is real. As a postdoc using RNA-seq in its early days, Mason said he had to convince his PI that what he was picking up was real, even though he couldn't validate his RNA-seq findings using another approach like RT-PCR because what he was finding was beyond its dynamic range.
"I became involved with standards so I could say, 'You know, we've done all the controls, the technology is good, the alignment is good, the informatics and the chemistry [is good],'" he said. "You have to make sure you've done everything you can so that when you're looking at results, people will know ... it is real. "
Mason said that the biggest challenge he faces is narrowing his focus. "I'm a geneticist living in the Candyland utopia of genetics right now. You can sequence anything you want for pretty cheap, and you can do long reads and short reads and go to the subway and sequence there," he said.
In addition to sequencing the microbes in the subway, Mason is also part of the NASA project that's sequencing and examining a range of data from a set of identical twins, one on Earth and one in space to study how being in space affects people.
Paper of note
Like his research, Mason's publications span a swath of biology. His 2012 papers in Cell and Genome Biology showed, for instance, that the transcriptome is highly modified and that small molecules can be used to study such RNA modifications.
But Mason said that he is also proud of the impact of a paper he wrote with Jeffrey Rosenfeld at the University of Medicine and Dentistry of New Jersey that appeared in Genome Medicine in 2013 on gene patenting.
In it, they reported on how they aligned sequences obtained from patent documents against the human genome to find that, depending on the stringency of the Blast parameters, some 41 percent of genes in the human genome could be covered by patent claims. This paper, Mason said, was alluded to in the Supreme Court's decision to prohibit gene patents in the Association for Molecular Pathology v. Myriad Genetics case.
The NASA astronaut twins project, Mason said, represents how he sees the field moving.
"Everyone says that we're doing systems biology, but if you think about things to really do systems biology, that means you need to know aspects of the entire system, which is an extraordinary thing for a scientist," he said. "That means you know everything about DNA to RNA to proteins to epigenetics."
He noted that it'll be nearly impossible for one researcher to be an expert in everything from DNA to RNA to proteins to epigenetics to the microbiome, but a project like the twins project brings together people who do know these disparate fields to do true systems biology.
And the Nobel goes to…
If Mason were to win the Nobel Prize, he'd like it to be for working on the transcriptome or for uncovering some aspect of RNA modification that affects humans in space.
This is the first in a series of Young Investigator Profiles for 2015 that will appear on GenomeWeb over the next few months.