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Modifying the message

Nicole Martinez is uncovering how small changes to the chemical structure of RNA affect which genes are expressed in our cells and when.
Nicole Martinez
Nicole Martinez studies how chemical modifications to RNA help cells regulate gene expression (Image credit: Nicole Martinez).

DNA is the cell’s permanent genetic material, contained in its entirety in every cell in our body and comprising the instructions for making all the proteins any cell could ever need. Basic cell biology classes teach us that the cell uses DNA to make messenger RNA, or mRNA, which in turn is used to make proteins. But the whole story turns out to be more complicated.

DNA first gets transcribed into precursor mRNA or pre-mRNA. That pre-mRNA is transformed into mRNA through a process called splicing. Pre-mRNA, like all types of RNA, is made up of four unique building blocks or bases, represented in shorthand by the letters A, C, U, and G, organized in one long sequence. Some, but not all of those letters will end up in the corresponding mRNA.

Any single piece of pre-mRNA contains one long string of letters. Through splicing, some segments, called exons, are stitched together, while other segments, called introns, are discarded. The exons are like words that can be pieced together in different ways to make unique sentences, and it’s those final mRNA sentences that determine which protein will be made. 

Any given pre-mRNA could make a number of different mRNAs, depending on how it is spliced. The different ways of splicing, plus the chemical modifications that are added to pre-mRNA and mRNA, are part of the cell’s complex process of gene regulation, the series of mechanisms that dictate what proteins get made, and when.

Nicole Martinez, who joined Stanford ChEM-H as an Institute Scholar in 2022, studies gene regulation at the level of RNA. She studies pseudouridine, a chemically modified cousin of uridine, which is the “U” of RNA sequences. During her postdoctoral studies, she discovered that pseudouridine, known to be present in pieces of mature mRNA, is actually found in pre-mRNA, but the role it could play so early in the gene regulation process is still largely unknown. Here, Martinez, who is an assistant professor of chemical and systems biology and of developmental biology, talks about how cells modify their genetic messages, her lab’s new home at Stanford ChEM-H, and the importance of strong mentors.

Did you always know that you wanted to be a professor?

I grew up in a small town in Puerto Rico where, if you went to college, you went to the University of Puerto Rico, so that was the only place I applied. I didn’t know any scientists or professors, so an academic research career wasn’t on my radar. But I liked science, so I studied industrial biotechnology, thinking I might work in the manufacturing sector of a pharmaceutical or biotech company. The solid foundational science education I received at the UPR was critical to get to where I am.

In college, I went to a recruitment fair featuring research institutions across the US. That was the first time I heard that you could get paid to do research, either for a PhD or summer research at a major research institution. I decided to do summer research at the Broad Institute, and I worked in a chemical biology lab trying to find new molecules that could be used as cancer therapeutics.

That was the first time I identified as a scientist. I had my own project, and I had mentors who reassured me that my contributions were valued even though I was an undergraduate with almost no research experience.

What was your transition to grad school like?

The mentors from my summer research experience really helped me navigate the grad school application process. They not only wrote letters of reference, but they also taught me about different schools. I really didn’t know what I was doing. I went to the University of Pennsylvania, and it was there that my fascination with RNA-based mechanisms of gene regulation began.

The first few years were a little challenging. I was coming from all Spanish classes to now being in English programs with lots of public speaking. I felt like I was different from everyone else, and I struggled in the beginning. There weren’t a lot of women in my class, or among the faculty.

Having supportive mentors was key to feeling like I belonged and that I had important contributions to make.

Tell me about your research. What did you study during grad school and your postdoc?

I worked on understanding alternative splicing, which is a method of gene regulation that can expand our genome’s protein-coding capacity. The process of splicing involves removing non-coding pieces of RNA and stitching together the coding regions, or exons, which can be joined together in different ways. That way, you can start with one gene, but you end up with multiple mRNA transcripts that are each a different message with different instructions for making different proteins. It’s a way to change what proteins are expressed at a given time, in response to things that are happening in or around the cell.

Scientists have learned that many mRNAs are modified with bases other than the four canonical ones--A, C, U and G. Since the expression of a cell’s mature mRNA is mediated by interactions between the RNA and proteins that bind to the mRNA, these modifications serve to influence what proteins are produced at different times by modulating those interactions.

One of the most abundant of these bases is called pseudouridine, a modified version of the canonical uridine. I found out that pseudouridine is added in the earliest stages of RNA synthesis, right when pre-mRNA is being made. So, the question is, why is it there? What purpose does it serve so long before a mature mRNA is created?

What do you hope to learn about pseudouridine and other modified RNA bases?

It turns out that pseudouridines are added in pretty important regions of pre-mRNA, in places that are near splice sites or that bind to important proteins. My postdoctoral research showed that this modification and the enzymes that converts uridine to pseudouridine guide the process of alternative splicing. It’s exciting because this a whole new method of gene regulation that we didn’t know about before.

I’m interested in answering a few questions. One is, what are the molecular mechanisms by which this modification affects alternative splicing and other mRNA processing steps. It could be that replacing a uridine with a pseudouridine changes how strongly a certain protein binds to the RNA, or what shape the RNA folds into.

Another question is, why do these modifications appear in certain locations on certain pre-mRNAs? And what conditions affect where they are added?

And the final question I’m interested in answering is, what role might pseudouridine play in health and disease? We know that the proteins responsible for installing pseudouridines are associated with cancer, autoimmune diseases, and neurodevelopmental disorders, but we don’t know why. I hope that by better understanding these mechanisms, we can identify new drug targets to be able to one day treat those diseases.

What made you decide to come to Stanford?

So much of what we do as scientists is influenced by our environment, and I can’t think of a better environment for my lab. There is so much exciting research happening at Stanford but, more than that, it’s also collaborative and interdisciplinary to a degree that I haven’t experienced. There are so many experts here that I feel like I can push my research in many different directions and be able to find collaborators and mentors along the way. I’m part of two departments and an institute—chemical and systems biology, developmental biology, and ChEM-H—and in a short time they have all become such a supportive community. There is an amazing culture of giving back and so many people, no matter how busy, have taken the time to meet with me and help me get started here.

I’m particularly excited to have my lab be part of ChEM-H because there is a lot of energy here. There’s an amazing diversity in the people here, in terms of their paths, their identities, and their research. There are many senior faculty who can serve as mentors, but there are also a lot of assistant professors who have just started their labs and are excited to do big things.

What is the best part about being a professor?

I’m really passionate about science and being able to solve unanswered questions, but another very important aspect of becoming a professor was being able to be a mentor. As a faculty mentor, your impact on science is not just in the new discoveries you make but in the students and postdocs that you train.

I think one quality of a good mentor is good communication and taking the time to understand the goals of your mentees. It’s also about finding a balance between lifting them up and letting them explore. It’s about allowing them to have their own journey but guiding them through it.

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