Uncovering the interplay between regulatory regions and gene coding regions is essential for understanding the mechanisms governing gene regulation in health and disease. Chromatin Interaction Analysis Using Paired-End Tag Sequencing (ChIA-PET) offers a new strategy for mapping chromatin interaction networks on a global scale with high resolution and specificity. Data generated from ChIA-PET analysis can be used to map protein-factor binding sites, as well as to construct genome-wide chromatin interactome maps associated with a specific protein factor of interest. The proposed Workshop on Chromatin Interaction Analysis by Paired End- Tag Sequencing, will train young scientists (graduate students, post-doctoral trainees, new investigators) in the use of ChIA-PET as a tool for asking questions about chromatin interactions, 3D genome organization and genome regulation in human health and disease. Our five-day ChIA-PET workshop provides a balance of didactic and laboratory-based instruction with ample opportunities for interactions among participants and course faculty. Participants will conduct a ChIA-PET experiment from the chromatin immunoprecipitation (ChIP) step to high throughput sequencing and through the bioinformatics analysis and data processing phases. In 2014 JAX successfully piloted the ChIA-PET workshop and a registration waitlist demonstrated significant demand for this technical training. The 4D Nucleome project initiated by the NIH Common Fund in 2015 will further increase research activity within this field and will likely generate significant additional interet in ChIA-PET and related technologies. The proposed course will be held annually during the late fall at The Jackson Laboratory for Genomic Medicine in Farmington, Connecticut. Lectures, discussions, and laboratory work will be held morning, afternoon, and evening for a total of approximately 50 hours of didactic and hands-on training. The Jackson Laboratory is an NCI-designated Basic Research Cancer Center and has a long history of hosting advanced courses and workshops.

Public Health Relevance

ChIA-PET represents a unique technology that will play a profound role in understanding aspects of human biology and disease associated with higher order gene regulation and genome organization, and may eventually be used to inform new and existing clinical strategies. Training courses such as these are, and will continue to be, criticalto develop the cadre of highly skilled young investigators that will be needed to transform basic research findings into positive clinical outcomes.

Agency
National Institute of Health (NIH)
Institute
National Human Genome Research Institute (NHGRI)
Type
Education Projects (R25)
Project #
5R25HG007631-02
Application #
9134829
Study Section
National Human Genome Research Institute Initial Review Group (GNOM)
Program Officer
Pazin, Michael J
Project Start
2015-09-01
Project End
2018-06-30
Budget Start
2016-07-01
Budget End
2017-06-30
Support Year
2
Fiscal Year
2016
Total Cost
Indirect Cost
Name
Jackson Laboratory
Department
Type
DUNS #
042140483
City
Bar Harbor
State
ME
Country
United States
Zip Code
Li, Xingwang; Luo, Oscar Junhong; Wang, Ping et al. (2017) Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions. Nat Protoc 12:899-915
Thibodeau, Asa; Márquez, Eladio J; Luo, Oscar et al. (2016) QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PLoS Comput Biol 12:e1004809
Hnisz, Denes; Weintraub, Abraham S; Day, Daniel S et al. (2016) Activation of proto-oncogenes by disruption of chromosome neighborhoods. Science 351:1454-1458
Sza?aj, Przemys?aw; Tang, Zhonghui; Michalski, Paul et al. (2016) An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization. Genome Res 26:1697-1709
Ji, Xiong; Dadon, Daniel B; Powell, Benjamin E et al. (2016) 3D Chromosome Regulatory Landscape of Human Pluripotent Cells. Cell Stem Cell 18:262-75
Tang, Zhonghui; Luo, Oscar Junhong; Li, Xingwang et al. (2015) CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell 163:1611-27
Zhang, Jingyao; Poh, Huay Mei; Peh, Su Qin et al. (2012) ChIA-PET analysis of transcriptional chromatin interactions. Methods 58:289-99