Epigenome Dynamics During DNA Replication

01 Mar 2011 28 Feb 2018

Linda Hanley-Bowdoin (PI) , George C Allen (CoPI), William F Thompson (CoPI), Robert Martienssen (CoPI), Linda K Hanley-Bowdoin (CoPI), Matthew W Vaughn (CoPI)


PI: William F. Thompson (North Carolina State University)

CoPIs: George C. Allen and Linda Hanley-Bowdoin (North Carolina State University), Robert Martienssen (Cold Spring Harbor Laboratory) and Matthew W. Vaughn (University of Texas at Austin, the Texas Advanced Computing Center).

Senior Personnel: Pete E. Pascuzzi (North Carolina State University) and David A. Micklos (Cold Spring Harbor Laboratory)

Epigenetics, the study of structural or chemical modifications of chromosomes that affect how genetic traits are expressed, is an exciting new area of biology. However, very little is yet known about the processes that transmit these structural or chemical modifications - known as "epigenetic marks" - through the multiple rounds of DNA replication and cell division that are required to make a plant or animal. Understanding this cell-to-cell transmission requires understanding events occurring only during the small part of the cell cycle in which DNA is synthesized ("S-phase"). In this project, the tools and knowledge from a previous NSF-supported project will be used to study transmission of epigenetic marks through S phase in two important model systems - maize and Arabidopsis. The results are expected to be relevant to most plants and animals. Millions of plant cell nuclei will be isolated and then sorted into groups depending on how much DNA they contain using a technique called flow cytometry . This sorting technique will provide material for a genome-wide analysis of epigenetic marks at each of several stages in the DNA replication process. Studying the sequence of events through the replication cycle will help to understand the molecular mechanisms that lead to formation active or inactive structures at different places along a chromosome. Similar techniques applied to mutant plants with known defects in chromosome structure or function may help highlight even more subtle control mechanisms. The results are expected to provide a better understanding of how genes are affected by structural and chemical modifications of DNA and the chromosomes in which it is housed. Understanding these epigenetic influences will have a profound impact on both basic and applied plant biology. For example, many crops are propagated clonally, and the occasional occurrence of "sports" (epigenetic variants) can impact both yield and quality. Another example involves crops engineered by gene transfer, which often experience unexpected inactivation, or "silencing", of the transferred gene. Silencing greatly complicates the process of obtaining commercially viable plant lines. This project will contribute to the ability to predict, and perhaps to control, gene silencing, which will be of considerable value for a wide variety of applications.

The project will bring together investigators with expertise in biochemistry, molecular biology, genetics, genomics and bioinformatics, and support a productive collaboration between two major research institutions. An excellent training environment for graduate and postdoctoral students will be provided, and selected undergraduates will participate in various aspects of the research. There will be two principal outreach efforts. A successful "Science in a Suitcase" unit on Genetics for middle schools, created during a previous PGRP project, will be updated, and teacher workshops will be extended to include many more teachers and students. In addition, a program in epigenetics will be inaugurated at the Dolan DNA Learning Center. This program will target advanced high school students and faculty at two year and agricultural colleges, and will provide valuable resources for teaching about epigenetics. A combination of web materials and podcasts, as well as resources for experiments, will be created. Public access to information about this project, including links to primary data, will be provided through the project website (www.plantreplication.net), GEO (http://www.ncbi.nlm.nih.gov/geo/), the NCBI's SRA (http://www.ncbi.nlm.nih.gov/sra), Gramene (http://www.gramene.org/), MaizeGDB (http://www.maizegdb.org/), and TAIR (http://www.arabidopsis.org/).