Environmental Factor

Environmental Factor

Your Online Source for NIEHS News

June 2017

Genomics Day showcases NIEHS resources

NIEHS scientists were treated to a day-long showcase featuring in-house resources for the increasingly vital study of genomes and epigenomes. Epigenetics refers to changes to DNA that do not affect the underlying genes, but do affect their activity. Anchored by a keynote presentation from NIEHS Acting Deputy Scientific Director Paul Wade, Ph.D., the May 11 event offered a wealth of scientific findings and technology updates.

Complementing the presentations were nearly 70 posters displayed by researchers and trainees in the NIEHS Division of Intramural Research and Clinical Research Branch, the National Toxicology Program, and vendors.

Cores offer cutting-edge technology and services

Lead organizer Kevin Gerrish, Ph.D., acting director of the NIEHS Molecular Genomics Core Laboratory, kicked off the day with a welcome and thanks for the staff of the core. "They do the real work," he said.

Greg Solomon, manager of the Epigenomics Core Laboratory, and Jason Li, Ph.D., director of the Integrative Bioinformatics Support Group, described the analyses and support their groups provide, recent growth in operations, and how to best use their resources.

The Epigenomics Core offers several high-throughput DNA sequencing technologies, and Solomon noted the increase of requests in recent years (see graph, right). This is undoubtedly due to the changing nature of biomedical research, but his service-oriented attitude is at least partially responsible. "If there’s a technique you’d like to do, let us know, and we’ll learn how to do it," he told the audience.

Li, who stepped into his director role in 2016, explained that his group provides support to researchers as needed, and for long-term projects, includes informaticians within the research groups. The team consults on research design, analytical strategies, data analysis, training, and outreach. Scientists in the core also develop software and tools needed by environmental health scientists, such as the recently released Online Resource for Integrative Omics (ORIO) software package (see summary).

ORIO, published in April, was discussed in more detail by Christopher "Andy" Lavender, Ph.D., from Li’s group. Other talks (see text box) by trainees and researchers, despite their wide-ranging topics and techniques, all featured research that relied on the services of NIEHS core laboratories.

DNA methylation in parents and offspring

Patterns of DNA methylation, which is one form of epigenetic change, can provide information about the individual being studied, as well as their parents, Wade explained in his talk. Ongoing research in his lab, the Eukaryotic Transcriptional Regulation Group, examines how methylation patterns in parents influence those of offspring and whether those patterns provide a record of environmental exposures, such as endocrine disrupting chemicals and obesity.

"DNA methylation has rules about how it is inherited from parent to progeny, it is stable under controlled circumstances, and it does provide a long-lasting record of major life events, including obesity and diet," Wade concluded, thanking by name the individuals who helped design the experiments and analyze the data, with much of the sequencing done in-house at NIEHS.

Postdoctoral fellow Kerry Dorr, Ph.D., center, from the Cell Biology Group, discussed her findings on the mechanism by which the JAZF1 gene regulates energy balance and development of obesity in mice. Postdoctoral fellow Kerry Dorr, Ph.D., center, from the Cell Biology Group, discussed her findings on the mechanism by which the JAZF1 gene regulates energy balance and development of obesity in mice. (Photo courtesy of Steve McCaw)
NIEHS clinical researcher Natalie Shaw, M.D., right, used whole genome, whole exome, and gene-targeted sequencing, as well as advanced computational methods in the research presented in her poster. NIEHS clinical researcher Natalie Shaw, M.D., right, used whole genome, whole exome, and gene-targeted sequencing, as well as advanced computational methods in the research presented in her poster. (Photo courtesy of Steve McCaw)
Even the library got into the act — Victoria Patterson, right, and Nora Weston described library support for researchers navigating the process of journal selection, internal review, and status tracking. Even the library got into the act — Victoria Patterson, right, and Nora Weston described library support for researchers navigating the process of journal selection, internal review, and status tracking. (Photo courtesy of Steve McCaw)

Genomics Day talks

Visiting fellow Sara Andres, Ph.D., from the Genome Stability Structural Biology Group shared her research on DNA repair during her talk, "Mediating Genomic Integrity Through Ctp1 Bridging Filaments."

"Transcription at Intragenic Enhancers Attenuates Gene Expression," was the focus of visiting fellow Senthilkumar Cinghu, Ph.D., from the Systems Biology group. He explored the notion that one regulatory element can be involved in both enhancing gene transcription from a distance and fine-tuning transcription of the host gene.

From the Reproductive Medicine Group, biologist Wendy Jefferson, Ph.D., shared research on how mechanisms of gene expression are affected by the timing of diethylstilbestrol (DES) exposure, in "Alterations in the Epigenetic Landscape of the Neonatal Mouse Uterus Following DES Exposure."

Ashutosh Kumar, Ph.D., a visiting fellow in the Free Radical Metabolism Group, discussed his studies of the role of environmental factors in Parkinson’s disease, in "Formation and Implications of an alpha-Synuclein Radical in an Animal Model of Pesticide-induced Parkinson's Disease."

Lavender took the audience through a dry run of the new bioinformatics tool, with "ORIO (Online Resource for Integrative Omics): A Web-based Platform for Rapid Integration of Next Generation Sequencing Data."

Discovery of a novel regulatory mechanism for metabolizing the nutrient methionine was explained in "Methionine Metabolism Is Essential for SIRT1-Regulated mESC Maintenance and Embryonic Development" by visiting fellow Shuang Tang, M.D., Ph.D., from the Metabolism, Genes, and Environment Group.

Wade's keynote talk was titled, "DNA Methylation: Inheritance and the Environment."

Back To Top