Genome analysis tools took center stage at the annual NIEHS Genomics Day May 12. Scientists from across the institute attended presentations on research tools available through the NIEHS Molecular Genomics Core, Epigenomics Core, and Integrative Bioinformatics Support Group.
“We want to raise awareness and promote the different types of genomics experiments that are being performed here,” said Kevin Gerrish, Ph.D., acting director of the Molecular Genomics Core and event organizer. He and others updated the audience on available technologies, and tips to get the most out of the services.
Scientists, ranging from trainees to lead researchers, who have used the various resources to advance their studies gave talks on their findings (see text box). An afternoon session featured more than 60 posters by scientists from NIEHS, the National Toxicology Program (NTP), and the U.S. Environmental Protection Agency, as well as vendors.
Core strengths
Gerrish described the technologies his core makes available, as the team strives to keep up with scientific advances and meet the developing needs of institute researchers. “We’ve only been using NanoString for about a year and a half and there have already been four publications containing the data,” Gerrish said, underscoring the importance of offering cutting-edge services.
Greg Solomon, manager of both the Epigenomics and DNA Sequencing Cores, said his team performs hundreds of millions of reads every day, and works with contractors who provide many more. Solomon stressed the steps researchers can take to achieve high quality results from the more than a dozen techniques they provide. “Plan ahead — that is the key,” he said. “Besides a core lab, we like to think of ourselves as a teaching lab,” he continued, describing some of the training they provide.
Sara Grimm, Ph.D., deputy director of the Integrative Bioinformatics Support Group, discussed the key services her group offers, including bioinformatics support, managing sequencing data, and training. Their bioinformatics instruction takes the form of courses, vendor-sponsored classes, and individually tailored training.
Stem cell research advanced through genomics
The keynote presentation, “Cnot3-dependent mRNA Deadenylation Safeguards the Pluripotent State,” was presented by Guang Hu, Ph.D., head of the NIEHS Stem Cell Biology Group. He described his team’s recent findings on the role of the Ccr4-Not protein complex in maintaining the pluripotent state of stem cells. Pluripotency is a state in which the cells can be maintained as stem cells in culture and still retain the ability to differentiate into all the cell types found in the body.
“Pluripotent stem cells hold great promise for both basic and translational research,” Hu said, pointing out that NTP and outside labs use stem cells to develop tools for studying the impact of environmental compounds on early development. Hu’s team aims to help such researchers, by building knowledge of how the developmental potential of stem cells is regulated.
Hu thanked all the core facilities for support of his group’s research. “We’ve used a variety of genomic tools to try and answer the questions we are interested in,” he said. “We’ve benefitted greatly from the core facility, which is readily available to [researchers] at the institute.”
In his talk, Solomon, center, said his core is now able to sequence a human genome in about 27 hours.
Nicol described how the use of transcriptome profiles shed new light on the role of certain proteins in gonadal differentiation, and helped identify new sets of genes associated with testis differentiation.
From left, Stephanie London, Ph.D., deputy chief of the Epidemiology Branch, and Andy Shapiro, NTP data scientist, listened as Chris Lavender, Ph.D., from the Integrative Bioinformatics Support Group, demonstrated a resource for analyzing and visualizing high-dimensional, whole-genomic data.
Quinn presented data suggesting that targeting estrogen signaling may help combat inflammation and cell death in autoimmune liver diseases.
Nicole Reeves, biologist in the Epigenomics Core, discussed analyses the group performs on RNA and DNA samples supplied by institute scientists and provided tips on how to avoid common problems that arise.
Shannon Farris, Ph.D., left, IRTA fellow in the NIEHS Synaptic and Developmental Plasticity Group, discussed her poster on gene expression in the hippocampus with Yu Wang, contractor in the NTP Special Techniques Group.
Kang’s talk described how his team used gene profiling analysis to help them clarify the role of GLIS3 in several important thyroid functions.
Yin Li, right, biologist in the NIEHS Receptor Biology group, and Ken Korach, Ph.D., group leader and head of the Reproductive and Developmental Biology Laboratory, discussed Li’s poster on using gene expression profiling to analyze reproductive effects of an endocrine disrupting chemical.
Jenny Zhang represented Partek, a genomic data analysis software vendor. They were one of 16 vendors at the event displaying the latest advances in genomics technology.
From thyroids to mitochondria
Research findings aided by resources featured at Genomics Day were presented by six scientists from four NIEHS laboratories.
Hong Soon Kang, Ph.D., staff scientist in the Cell Biology Group, led by Anton Jetten, Ph.D., discussed findings showing that “The Kruppel-like Zinc Finger Transcription Factor, GLIS3, Is a Critical Regulator of Several Thyroid Functions.”
Intramural Research and Training Award (IRTA) fellow Scott Lujan, Ph.D., from the DNA Replication Fidelity Group, led by Tom Kunkel, Ph.D., discussed “Polymerase Fidelity and Mismatch Repair Bias Genome Variation and Composition.”
“Insights Into the Genetics of Sex Determination in Mouse Embryos,” was presented by Barbara Nicol, Ph.D., visiting fellow in the Reproductive Developmental Biology Group, led by Humphrey Yao, Ph.D.
Matt Quinn, Ph.D., IRTA fellow in the Molecular Endocrinology Group, led by John Cidlowski, Ph.D., described findings that “Endogenous Glucocorticoids Regulate Hepatic Inflammation and Apoptosis in a Sexually Dimorphic Manner.”
“Mutation Load in a Human Somatic Cell-derived Clonal Lineage Reveals Genetic Changes Accumulated Over the Lifetime of an Individual” was discussed by Natalie Saini, Ph.D., visiting fellow in the Mechanisms of Genome Dynamics Group, led by Dmitry Gordenin, Ph.D.
“Inter-Strain Variation in Mouse Mitochondrial Genome and Effects of Oxidative Stress,” was presented by Kirsten Verhein, Ph.D., IRTA fellow in the Environmental Genetics Group, led by Steve Kleeberger, Ph.D.
