American Society of Human Genetics 2016: 3D Genome Organization and Chromatin Interaction

Tuesday October 18, 2016, 2:30PM

Vancouver, British Columbia

Workshop Agenda

Improvements in DNA sequencing technologies have resulted in an exponential increase in the amount of genomic and epigenomic data available. Some of these data have been generated as part of large-scale, focused mapping efforts aimed at understanding how genes are regulated, such as the NIH Roadmap Epigenomics Program, and ENCODE (Encyclopedia of DNA Elements). Efforts such as these can be extremely valuable for hypothesis generation and data mining, but can only be useful if one knows what is available and how to use it.

The three dimensional (3D) organization of mammalian genomes is tightly linked to gene regulation, as it reveals the physical interactions between distal regulatory elements and their target genes, and further orchestrate spatial- and temporal-specific gene expression. Several recent high-throughput technologies based on Chromatin Conformation Capture (3C) have emerged (such as 4C, 5C, Hi-C and ChIA-PET) and given us an unprecedented opportunity to study the higher-order genome organization. However, genome-wide chromatin interaction data analysis and visualization are complicated and even in tissue/cell types where the data are published, it is still difficult for the scientific community to visualize and use them for their own research. This interactive workshop will showcase three online tools to illustrate how to query gene expression, candidate cis-elements (such as promoters and enhancers), chromatin interaction loops, and 3D genome organization. All the presenters are experienced investigators from the ENCODE, Roadmap/Epigenomics and newly founded 4D Nuclesome consortia. This workshop will integrate the data generated through the aforementioned large projects, with a focus gene regulation through chromatin interaction. We will use case studies to show the audience how disease-related genetic variants can lead to altered gene expression and eventually disease pathogenesis.


All slides and materials from the workshop are on this page.

For questions or more information contact:
Daniel Gilchrist, Ph.D.,
ENCODE Help Desk:


Presentation Title



Additional materials

1 Overview of 4D Nucleome program Lisa Chadwick, Ph.D. NIEHS Presentation
2 Overview of ENCODE Daniel Gilchrist, Ph.D. ENCODE, NHGRI Presentation

Review and Background Information of techniques involved in 3D Genome organization, such as Hi-C, Capture-C

Dave Gorkin, Ph.D.




ENCODE element browser and 3D genome browser

Feng Yue, Ph.D.

ENCODE, Penn State



WashU Epigenome Browser

Tim Wang, Ph.D.

Washington University in St. Louis