Genetics Department News
The human genome includes millions of "enhancer" sequences that turn genes on and off—but it has been unclear which enhancers can regulate which genes. A new study led by researchers from the Engreitz Lab finds that two types of genes respond differently to enhancers, and that these responses are controlled by specific sequences in gene promoters. Link to article: https://rdcu.be/cNZxa
2022 Winners of the FNIH Lurie Prize in Biomedical Sciences Provide Powerful Contributions to Our Understanding of the Aging Process
The Foundation for the National Institutes of Health (FNIH) has named Anne Brunet, Ph.D., and Andrew Dillin, Ph.D., co-winners of the 2022 Lurie Prize in Biomedical Sciences
Transcriptional neighborhoods regulate transcript isoform lengths and expression levels
Authors: Aaron N. Brooks1†‡, Amanda L. Hughes1†, Sandra Clauder-Münster1, Leslie A. Mitchell2, Jef D. Boeke2,3, Lars M. Steinmetz1,4,5 *
1European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
2Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.
3Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY 11201, USA
4Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94304, USA 5Department of Genetics, School of Medicine, Stanford University, Stanford, CA 94305, USA *Correspondence to: firstname.lastname@example.org
Abstract: Sequence features of genes and their flanking regulatory regions are determinants of RNA transcript isoform expression and have been used as context-independent, plug-and-play modules in synthetic biology. However, genetic context, including the adjacent transcriptional environment, also influences transcript isoform expression levels and boundaries. We used synthetic yeast strains with stochastically repositioned genes to systematically disentangle sequence from contextual effects. Profiling 120 million full-length transcript molecules across 612 genomic perturbations, we observed sequence-independent alterations to gene expression levels and transcript isoform boundaries that were influenced by neighboring transcription. We identified features of transcriptional context that could predict these alterations and used these features to engineer a synthetic circuit where neighboring transcription controlled transcript length. This demonstrates how positional context can be leveraged in synthetic genome engineering.
“90 Seconds with Lisa Kim”: Genome sequencing sets Guinness World Record
A new ultra-rapid genome sequencing approach developed by Stanford Medicine scientists sets the first Guinness World Record for the fastest DNA sequencing technique, producing results for one study participant in just over five hours. See the video on StanfordMed TODAY.
Genome-wide association studies (GWAS) have identified thousands of noncoding loci that are associated with human diseases and complex traits, each of which could reveal insights into the mechanisms of disease1. Many of the underlying causal variants may affect enhancers2,3, but we lack accurate maps of enhancers and their target genes to interpret such variants. Read more...
Image credit: Zayna Sheikh
Stanford Medicine scientists hope to use data from wearable devices to predict illness, including COVID-19
Researchers from Stanford Medicine and their collaborators aim to predict the onset of viral infection through data provided by wearable technology. What they need now are participants.
We are all exposed to a vast and dynamic cloud of microbes, chemicals and particulates that, if visible, might make us look something like Pig-Pen from Peanuts.
A new approach that distills deluges of genetic data and patient health records has identified a set of telltale patterns that can predict a person’s risk for a common, and often fatal, cardiovascular disease, according to a new study from the Stanford University School of Medicine.
A study out of Stanford in which blood sugar levels were continuously monitored reveals that even people who think they’re “healthy” should pay attention to what they eat.
At the Precision Health and Integrated Diagnostics Center, scientists turn the norms of disease research on their head, searching not for treatments but for ways to prevent disease entirely.
It’s not often that world-class scientists band together to investigate disease with no intention of curing it. Yet upward of 55 scientists at Stanford’s Precision Health and Integrated Diagnostics Center are doing just that in a push to get researchers and physicians off their heels and onto their toes in the battle against disease..
In a proof-of-principle study, Stanford scientists and their colleagues used the CRISPR-Cas9 gene-editing system to modify genes in coral, suggesting that the tool could one day aid conservation efforts.
Coral reefs on the precipice of collapse may get a conservation boost from the gene-editing tool known as CRISPR, according to researchers at the Stanford University School of Medicine and their collaborators.
Stanford scientists have found links between changes in a person’s weight and shifts in their microbiome, immune system and cardiovascular system.
A paper describing the work was published online Jan. 17 in Cell Systems. The lead authors are Stanford postdoctoral scholars Wenyu Zhou, PhD, and Hannes Röst, PhD; staff scientist Kévin Contrepois, PhD; and former postdoctoral scholar Brian Piening, PhD. Senior authorship is shared by Michael Snyder, PhD, professor of genetics at Stanford; Tracey McLaughlin, MD, professor of medicine at Stanford; and George Weinstock, PhD, professor and director of microbial genomics at the Jackson Laboratory, an independent, nonprofit biomedical research institution.
Cancer researchers have long hailed p53, a tumor-suppressor protein, for its ability to keep unruly cells from forming tumors. But for such a highly studied protein, p53 has hidden its tactics well.
Now, researchers at the Stanford University School of Medicine have tapped into what makes p53 tick, delineating a clear pathway that shows how the protein mediates anti-tumor activity in pancreatic cancer. The team’s research also revealed something unexpected: A particular mutation in the p53 gene amplified the protein’s tumor-fighting capabilities, creating a “super tumor suppressor.”
Understanding how a person’s DNA sequence affects gene expression in various tissues reveals the molecular mechanisms of disease. Stanford scientists involved in the National Institutes Health’s GTEx project have published some of their insights.
Three Stanford researchers are among the 84 newly elected members of the National Academy of Sciences.
The new members from Stanford are Dominique Bergmann, PhD, professor of biology; John Pringle, PhD, professor of genetics; and Anne Villeneuve, PhD, professor of developmental biology and of genetics. Full story..
Stanford’s William Greenleaf, Michael Bassik, Michael Snyder, Jonathan Pritchard and Michael Cherry have won grants to work on the federally funded Encyclopedia of DNA Elements. Full story..
New research from Stanford shows that fitness monitors and other wearable biosensors can tell when an individual’s heart rate, skin temperature and other measures are abnormal, suggesting possible illness. Full story..
"Genetics and genomics are undergoing an unparalleled revolution: our mission is to continue to lead this revolution for a better understanding of biology and human health."
Michael Snyder, Ph.D.
Stanford W. Ascherman Professor and Chair, Department of Genetics
Director, Center for Genomics and Personalized Medicine
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