Researchers shared between the University of Minnesota Medical School and the College of Biological Sciences have helped catalogue — for the very first time — nearly one million functional elements in the human genome as part of a worldwide research network.

Juan Carlos Rivera-Mulia, PhD, an assistant professor in the Department of Biochemistry, Molecular Biology and Biophysics, is one of the scientists contributing to the Encyclopedia of DNA Elements (ENCODE) Project, which began in 2003 and is funded by the National Human Genome Research Institute. 

According to a release from the National Institutes of Health, “Significant progress has been made in characterizing protein-coding genes, which comprise less than 2% of the human genome. Researchers know much less about the remaining 98% of the genome, including how much and which parts of it perform other functions. ENCODE is helping to fill in this significant knowledge gap.”

ENCODE’s latest project, ENCODE Phase III, which was published in the journal “Nature,” identified functional elements that cover 7.9% of the human genome. That information, including research by Dr. Rivera-Mulia’s lab, helped establish a web-based tool, called SCREEN, that details the different kinds of DNA regions and their corresponding candidate functions.

“Our research specifically provided a comprehensive characterization of the temporal order of DNA replication and transcriptomes of multiple human cell types,” said Dr. Rivera-Mulia, who is also a member of the U of M Masonic Cancer Center. “We contributed by mapping the DNA replication timing programs of cell types, representing multiple stages of human development, and established bioinformatic tools to identify the normal cells from which distinct type of cancer cells derive.” 

Dr. Rivera-Mulia’s lab also collaborated with ENCODE to develop novel tools for the identification of alterations in the human genome in cancer. This work was published in “Nature Communications” as a companion publication to the ENCODE Phase III article. 

“Since only a small fraction of the human genome codes for proteins, these findings constitute a great progress in our understanding of how the non-coding part of the genome regulates gene function,” he said.

Dr. Rivera-Mulia continues his research, supported by the National Institute of Health (R35GM137950), by investigating the regulatory elements in the human genome, dissecting the mechanisms of DNA replication timing control and constructing cell type-specific regulatory networks to understand how gene interactions are established during human development.