1a.Objectives (from AD-416):
(1) Measure DNA methylation patterns and chromatin modifications to determine the influence of MDV effects on epigenetic factors. (2) Evaluate the changes in gene expression and biopathway, which result from the DNA methylation and chromatin alterations. (3) Analyze epimutations that lead to epigenetic changes by computational epigenetics and advanced statistical analysis.
1b.Approach (from AD-416):
Epigenomics is an emerging area which encompasses a genome-wide analysis of a continually growing list of epigenetic phenomena. Recent studies show that environmental factors (i.e. virus exposure and diet) can have systemic influences on genome structure, which are then heritable (epigenetics). These genome-level changes in DNA structure alter gene expression and subsequently phenotype characteristics. Our long-term goal is to identify such heritable epigenetic modification induced by the Marek’s disease virus (MDV) exposure in chickens. Our initial studies in the last three years have unveiled the importance of partial methylation changes and chromatin modifications induced by MDV exposure, thus documenting a series of publications. Now, we are ready to design an in-depth crossing exploratory study that will significantly extend our current research in genetics and epigenetics of Marek’s Disease (MD) resistance. For the first time the potential influence of MDV exposure on genome-wide epigenetics will be studied in relation to MD incidences and resistance. In the present application, we propose to test whether MDV exposure results in changes in DNA methylation patterns and chromatin alterations, which in turn lead to MD incidences and disease resistance changes. We hypothesize that: (1) MDV exposure induces epigenetic variations; and (2) such variations significantly contribute to the risk of Marek’s Disease (MD) and results in different signatures of MD incidence and resistance between MD resistant and susceptible lines of chickens. We will test the working hypotheses through genome-wide epigenetic analysis and computational epigenetic methods using data from MD viral challenging experiment to be conducted in the unique and highly inbred SPF chicken lines 63 and 72 developed and maintained at the USDA-ARS Avian Disease and Oncology Lab (ADOL) at East Lansing, Michigan. The line 63 chickens are resistant to MD tumors, whereas the line 72 is highly susceptible to MD tumors. This proposal has selected an important agricultural disease (MD) that has significant impact in the poultry industry and animal health. It will primarily address the issue of Agricultural and Food Security and secondarily the issue of Genomics and Future Food Source. If supported, the proposed study would have profound implications for understanding the role of environmental changes in disease prevention and production performance for poultry industry.
This project is directly linked to Specific Cooperative Agreement 3635-31320-008-40S titled “Genetic and Epigenetic Resistance to Marek’s Disease.” A third challenge trial was conducted this year using birds from two reciprocal crosses, a line 6 by line 7 cross and a line 7 by line 6 cross. CD4 cells were isolated from blood samples. Challenged chickens will be euthanized 8 weeks post infection to determine Marek’s disease status and survival time. DNA methylation patterns and histone modifications will be examined by University of Maryland.