The last common ancestor of humans and rodents lived more than 80 million years ago, and billions of changes in their respective DNA sequences have occurred over this vast timespan. Yet, intriguingly, there are a few hundred stretches of DNA in our genome that are still identical to the corresponding sequences in mice and rats. Generally, sequence conservation between distantly related species is an indication that the function the DNA serves is vitally important and highly sensitive to mutations. For example, most DNA sequences that encode proteins show at least moderate conservation in evolution. However, more than two-thirds of the “ultraconserved” sequences shared by humans and rodents are outside of protein-coding genes, raising the question of what led to their extreme level of conservation.
The American Association for the Advancement of Science (AAAS), which was founded in 1848 and is the world’s largest general scientific society, announced that 489 of its members—among them nine scientists at Berkeley Lab—have been named Fellows. This lifetime honor, which follows a nomination and review process, recognizes scientists, engineers, and innovators for their distinguished achievements toward the advancement or applications of science.
The three newly named Fellows from the Biosciences Area are: Sanjay Kumar, a faculty scientist in the Biological Systems and Engineering (BSE) Division; Mary Maxon, the Associate Laboratory Director for the Biosciences Area; and Len Pennacchio, a senior scientist in the Environmental Genomics and Systems Biology (EGSB) Division and the Deputy of Genomic Technologies at the DOE Joint Genome Institute (JGI).
The Encyclopedia of DNA Elements (ENCODE) collaboration was launched 17 years ago by the National Human Genome Research Institute with the goal of developing the tools and expertise needed to shed light on the 98% of our genome that does not code for proteins. Now in its final year, ENCODE has made huge advances thanks to the combined scientific and technological prowess of several hundred researchers at dozens of institutions. Leading the project for Berkeley Lab are Diane Dickel, Len Pennacchio, and Axel Visel, co-PIs of the Mammalian Functional Genomics Laboratory in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division. They are co-authors on 4 of the 15 new ENCODE papers published this week as part of a special collection in Nature.
The Mammalian Functional Genomics Laboratory in Biosciences’ Environmental Genomics and Systems Biology (EGSB) Division has developed a higher-throughput transgenic mouse assay to evaluate the disease-causing potential of human variants in enhancers that turn on gene expression during development. The new approach leverages the CRISPR-Cas9 genome editing technology to create transgenic mice that carry an enhancer-reporter construct at a specific “safe harbor” location in the mouse genome. Because the transgenes are integrated in the same location in the genome there are no position effects, so fewer mice are needed to get reproducible results. To demonstrate proof of principle, the researchers used the new method—which they dubbed enSERT (enhancer inSERTion)—to examine nearly a thousand variants of one of the most well-characterized human enhancers that is associated with polydactyly (extra fingers or toes).
Several Biosciences Area personnel are among the 2019 Berkeley Lab Director’s Awards honorees. This annual program recognizes outstanding contributions by employees to all facets of Lab activities. A complete list of winners can be found here. The Director’s Achievement Awards ceremony will take place on November 15 at 4 PM in the Building 50 Auditorium. All staff are invited and the event will be streamed live.