Professor’s Research on Gene Regulation Awarded NSF CAREER Grant

03/23/2022
By Edwin L. Aguirre

Biology Asst. Prof. Frédéric Chain’s research on gene regulation has been recognized by the National Science Foundation (NSF) with a prestigious national faculty early-career development award. 

Called the CAREER award, the highly competitive annual program selects the nation’s best young university faculty-scholars who, according to the NSF, “most effectively integrate research and education within the context of the mission of their organization.”

Chain, who obtained his Ph.D. in biology from McMaster University in Ontario, Canada, in 2009, joined UMass Lowell in 2017. He will use his CAREER award, worth $1.35 million spread over a period of five years, to support his research.

“My research focuses mainly on studying the molecular mechanisms that allow newly emerged genes to generate new biological functions,” says Chain, who is an expert on bioinformatics as well as evolutionary and environmental genomics.

According to Chain, genetic mutations naturally occur at random in all organisms due to errors in DNA replication and repair. A portion of these mutations gets passed down from generation to generation, which scientists can use to trace evolutionary lineages, as is being done with the variants of the coronavirus that causes COVID-19.

Chain says some types of mutations can create entirely new gene copies by duplicating long stretches of DNA. Many (if not most) genes are created in this way, allowing the evolution of a diversity of biological functions and adaptations. 

“For example, recent duplications of a gene in human populations and domesticated dogs help us better digest starchy foods by increasing activity of an enzyme that breaks down starches,” he explains. “But because mutations are in large part random, most new genes are not helpful but either harmless or harmful, causing imbalances associated with a wide range of health conditions and disorders such as cancer, cardiovascular disease and diabetes as well as autoimmune, neurodevelopmental and metabolic disorders. Most new genes will be eliminated over evolutionary time by natural selection.”

In his NSF-funded project, entitled “Epigenetic Dynamics Shaping the Early Evolution of Duplicate Genes,” Chain is studying gene-regulation mechanisms. He is focusing on epigenetic processes, which can prevent such imbalances and help new genes evade death by extending the window of opportunity to evolve new functions. (Epigenetic processes refer to modifications to DNA that control gene activity without changing the DNA sequence.)

Chain notes that this is the first time such a study is being conducted.

“We do not know the evolutionary impact of epigenetic modifications on newly emerged genes. We will be able to answer this question using recent technological advances in gene sequencing, including ‘long-read sequencing’ and ‘epigenomic profiling,’” he says.

The generation and maintenance of mutations are important for predicting and assessing population health as well as adaptation. Just as mutations in a gene can cause disease, so can the duplication or addition of a gene if it leads to protein overactivity, Chain says. 

“This project will help advance our understanding of the molecular mechanisms of regulation during a critical period of establishment of newly emerged genes,” he says.

Chain’s project uses sticklebacks, a group of coastal fish species with diversified populations that have quickly adapted to numerous marine and freshwater environments.

“This natural system allows us to track recently emerged genes and their adaptive potential in different habitats and species, and to evaluate the evolutionary fates of genes depending on their environment and regulation status,” he says.

Chain is collaborating with other faculty members in the Department of Biological Sciences to provide guidance on different aspects of the project. Asst. Prof. Natalie Steinel, who also studies sticklebacks from an immunological perspective, is assisting with technical and sampling procedures; Asst. Prof. Teresa Lee, who studies epigenetics of longevity, is helping with data interpretation; and Assoc. Prof. Jessica Garb is helping with the development of genomics protocols.

“For my own research team, I plan to enlist students of all levels, including Immersive Scholars and research students from the Urban Massachusetts Louis Stokes Alliance for Minority Participation, as well as senior research/thesis students and master’s and Ph.D. students, mainly biology majors,” Chain says.

Community Educational Outreach

Chain is also getting help from the Tsongas Industrial History Center in recruiting and organizing genomics and bioinformatics curriculum workshops for local high school teachers. 

“The aim is to help establish strengths in genome literacy and coding in teens while forming new partnerships with local educators,” he says.

Biology Assoc. Teaching Prof. Naomi Wernick will help Chain with recruiting and co-advising students in UTeach and in the department’s master’s degree option in education, communication and outreach for the delivery of educational workshop materials.

“With the help of UMass Lowell undergraduate and graduate students, we will use the data generated from this study to produce publicly available bioinformatics tutorials and run workshops for high school educators to develop genomics curricula to strengthen students’ coding and analytical skills,” says Chain.

“We will also recruit and train local high school interns from underrepresented groups in STEM to participate in this research and gain foundational and transferable knowledge in genomics and bioinformatics.”