The future of genomics can be found in the Nuñez Lab

September 18, 2023

James Nuñez is a rising star in epigenetics, which studies how small chemical modifications on DNA are associated with human health and disease. Nuñez, an assistant professor in UC Berkeley’s Department of Molecular & Cell Biology, shows so much promise that the Howard Hughes Medical Institute and Chan Zuckerberg Biohub — two of the largest biomedical funders in the country — contributed to his lab’s launch.

Yet despite all his professional accomplishments, Nuñez is blown away by his students at UC Berkeley. Even his undergraduates have done amazing things by the time they arrive on campus.

“I could not have gotten into here as an undergraduate,” said Nuñez, laughing. “The talent pool among our students is unbelievable.”

Nuñez kindled his interest in biology at the University of Colorado, Denver and successfully applied to Berkeley as a Ph.D. candidate. He landed in Jennifer Doudna’s lab in 2012, months before she co-published her landmark paper on CRISPR that eventually earned her a Nobel Prize. Scientists can now make precise cuts in the DNA sequence using the gene-editing tool, leading to breakthrough treatments for diseases ranging from sickle-cell anemia to COVID-19.

Rather than directly modifying genes, epigeneticists like Nuñez alter the chemical environment to cause genes to react in specific ways, a safer strategy that is less likely to result in cell death, according to some researchers. As a postdoctoral scientist at UCSF, Nuñez co-invented CRISPRoff, a tool that can turn off genes causing health issues without needing to change a cell’s DNA sequence. If CRISPR is a pair of molecular scissors, CRISPRoff is a light switch.

A close-up shot of James Nuñez wearing a checkered shirt and smiling

Professor James Nuñez

Nuñez used CRISPRoff to demonstrate it is possible to reduce the potency of a gene associated with Alzheimer's. In addition, scientists are looking into epigenetic methods to lower cholesterol and reverse aging. One promising area Nuñez is monitoring would allow the immune system to prolong its fight against cancer by switching off genes that cause our T-cells to become tired during their fight against tumors.

Since joining Berkeley’s faculty in 2021, Nuñez has gained a new perspective on his admittance as a doctoral student.

“One of the best things about Berkeley is that the graduate students here are passionate about making an impact in our world,” said Nuñez. “Now that I've been on the admissions process for incoming Ph.D. students, I understand how hard it is to get into this place.”

Nowadays, Nuñez receives visits from established colleagues seeking advice. Nuñez understands the value of collaboration from his experience with group lab experiments. Rithu Pattali, a graduate student with a joint appointment in the Nuñez and Doudna labs, sees a lot of similarities between the two professors.

“They’ve achieved a lot in their careers, and they're both so humble and easy to talk to,” said Pattali. “Both of them care a lot about their students' development.”

A lot of people come to our lab; a lot of those people are people of color. It's a space where we feel really comfortable.
Izaiah Ornelas

The Nuñez Lab bucks the demographic trend of many scientific research labs in that it has achieved gender parity and a majority of its researchers are people of color. Nuñez credits these traits to deliberately recruiting people with different backgrounds and approaches.

“Part of why my lab has been so vibrant is because of our diversity,” said Nuñez. “It's become an open, safe space where people can ask what some people may consider dumb questions. We minimize any of that hesitation where people are learning. They're not going to be judged.”

Others have noticed. Pattali said the lab is an increasingly popular destination for graduate student rotations. Even students from other labs come to socialize and talk about science on the Nuñez Lab’s couches.

“A lot of people come to our lab; a lot of those people are people of color,” said Izaiah Ornelas, a graduate student whose interest in epigenetics was sparked by observing differences with his twin brother. “It's a space where we feel really comfortable.”

One of the best things about Berkeley is that the graduate students here are passionate about making an impact in our world.
James Nuñez
Izaiah Ornelas and Rithu Pattali wearing casual outgits in the lab

Izaiah Ornelas and Rithu Pattali, two graduate students in the Nuñez Lab

With his prominence in the CRISPR world, Nuñez had many options for faculty positions. Nuñez was on the job market during the height of the pandemic, which allowed him to think seriously about what he truly wanted out of academia.

“What it ended up being was community,” said Nuñez. “I really enjoyed my time at Berkeley as a student. I felt like people here were generally happy with the research they were doing and every lab here is a leader in their field.”

Nunez smiled as he considered his time as a faculty member.

“Everyone wants you to succeed. This is really an incredible place to be.”

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