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.
JGI Leads Large-Scale Effort to Develop a Genomic Catalog of Earth’s Microbiomes
Microorganisms play key roles in regulating global nutrient cycles but only a small fraction has been identified and an even smaller number has been successfully cultured in a lab for study. In Nature Biotechnology, the known diversity of bacteria and archaea has now expanded by 44% through a publicly available collection of more than 52,000 microbial genomes from environmental samples. Of that number, 70% of the novel genome sequences were previously unknown, not yet cultured in the lab. The work results from a JGI-led collaboration involving more than 200 scientists around the world, KBase and NERSC. Read more about the genomic catalog of Earth’s microbiomes on the JGI website.
Plant Single-cell Solutions for Energy and the Environment Workshop Report Released
On January 23, 2020, Berkeley Lab hosted a workshop on opportunities afforded by single-cell technologies for energy and environmental science, as well as conceptual and technological grand challenges that must be tackled to apply these powerful approaches to plants, fungi and algae. This event, which was spearheaded by Diane Dickel in the Environmental Genomics and Systems Biology Division, brought together a diverse group of leaders in functional genomics technologies from academia, the National Laboratories, and local research institutions.
Interpreting the Human Genome’s Instruction Manual
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.
Deciphering the Impact of Non-coding Mutations in the Human Genome
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).
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