3D Genome Organization and Chromatin Interaction Workshop at 2016 ASHG meeting


2016 ASHG 3D Genome Organization and Chromatin Interaction workshop


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.


Lisa Chadwick (NIEHS)

Daniel Gilchrist (NHGRI)

Dave Gorkin (UCSD)


Ting Wang (WUSTL)

When and Where

October 18, 2016 | 2:30 – 4:00 p.m.
Convention Centre, Ballroom A, East Building
Vancouver, Canada

Browser Booklet

  • Download a PDF version.

Tutorial Book

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  1. 10 minutes: Lisa Chadwick - Overview of 4DN
    Download presentation: PDF
  2. 10 minutes: Dan Gilchrist - Overview of ENCODE
    Download presentation: PDF, PPT
  3. 20 minutes: Dave Gorkin - Review/background info of techniques involved in 3D Genome organization, such as Hi-C, Capture-C ...
    Download presentation: PDF, PPT
  4. 25 minutes: Feng Yue - ENCODE element browser and 3D genome browser
    Download presentation: PDF
  5. 25 minutes: Ting Wang - WashU Epigenome Browser
    Download presentation: PDF

Heart Gene Set


Roadmap EpiGenome Browser

Roadmap SNP list
chr1 10353111 10353112
chr1 85772008 85772009
chr1 93303602 93303603
chr1 101331535 101331536
chr1 101407518 101407519
chr1 117038286 117038287
chr1 117100956 117100957
chr1 117104214 117104215
chr1 179469313 179469314
chr10 6099044 6099045
chr10 6102011 6102012
chr10 6110828 6110829
chr10 43814048 43814049
chr10 81036006 81036007

Past Workshops

2016 Keystone Workshop

Workshop at 2016 Keystone Symposia.

2016 SOT Workshop

Workshop at SOT 2016 Satellite Meeting.

2016 Epigenomics Workshop

Workshop at EPIGENOMICS 2016.

2015 Roadmap Epigenomic Workshop

Workshop at The First International Epigenomics Conference.

Keystone joint meeting on Epigenomics and DNA methylation 2015

Workshop at 2015 Keystone: Epigenomic Annotation of Transposable Elements Using The Washington University Epigenome Browser.

American Society of Human Genetics 2014

Workshop at 2014 ASHG: Epigenomic Annotation of Genetic Variants Using The Washington University Epigenome Browser.