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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Endemic Poultry Viral Diseases Research » Research » Research Project #431140

Research Project: Genomic Screens to Identify Regulatory Elements with Causative Polymorphisms Accounting for Marek's Disease Genetic Resistance in Chicken

Location: Endemic Poultry Viral Diseases Research

Project Number: 6040-31320-010-008-A
Project Type: Cooperative Agreement

Start Date: Jul 1, 2018
End Date: May 30, 2021

Objective:
The Cooperator is a recognized expert for his contributions to molecular genetics and computational analysis. For this specific project, the Cooperator will generation Hi-C data from the submitted samples (3 treatments x 3 biological replicates/treatment) and aid in the integrated analyses of all the genomic datasets.

Approach:
The Cooperator will utilize their improved in situ Hi-C method to analyze splenic-derived lymphocytes from defined chicken lines that have or have not been challenged with Marek's disease virus. Specifically, proximity DNA ligation will be conducted with materials from ~1-5 million cells and sequenced to produce 100K-1M reads from each sample. Analysis of Hi-C data will use HiCCUPS, an unbiased algorithm for identifying chromatin loops quickly and accurately from Hi-C contact maps. The Cooperator will help to integrate all the resulting datasets to identify chromatin loops that connect promoters with distal regulatory elements. In brief, after using HiCCUPS to annotate chromatin loops genome-wide, the Cooperator will integrate these chromatin loop annotations with ChIP seq data sets to identify loop anchors contain promoters as well as distal anchor regions that may exert some regulatory influence.