Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Epigenomics of Development in Populus

2008 Awardee

Investigators: Steven H. Strauss, Todd Mockler, and Michael Freitag

Institution: Oregon State University

Non-Technical Summary: Epigenetics is defined by long-lasting or heritable changes in gene expression that are not associated with changes in DNA sequence. It is mainly reflected in methylation of DNA and chemical changes in DNA-associated chromosomal proteins such as histones. Recognition of its importance as a means for control of plant development has increased significantly in recent years, however, little is known about epigenetic controls in the life of trees and other woody plants. Many traits important to biomass growth and adaptability in trees may be under epigenetic control, thus may be useful for their breeding and biotechnology. This includes timing of flowering and flower structure; dormancy induction and release; shoot and leaf architecture; amenability to organ regeneration; stress tolerance; and phase-associated changes in wood structure. We will use poplar (genus Populus, including aspens and cottonwoods), because it has been designated as a model woody biomass species for genomic studies, and is a major source of wood, energy, and environmental services in the USA and throughout the world. We will characterize epigenetic changes in DNA methylation and two kinds of histone modification via a combination of antibody-based chromatin immunoprecipitation and DNA sequencing (“ChIP-sequencing”).

Objectives: We will study changes in epigenetics in relation to three major aspects of tree development: 1) among the major differentiated tissues of poplar trees such as roots, leaves, and stems; 2) during de- and redifferentiation in tissue culture (stem tissues and callus); and 3) during entry and release from seasonal vegetative bud dormancy. We will also generate genetically modified poplars with reduced DNA methylation, and assess its consequences for modification of tree growth and epigenetic state. By reference to the whole genome expression arrays (“gene chips”) already produced in our laboratory and by collaborators, we will study the relationship of gene expression to epigenetic states.


  1. Produce and characterize DNA methylation-deficient poplars via transformation (RNA interference against the methylation-enzyme encoding gene DDM1).
  2. Prepare genomic DNA from tissues of the sequenced Populus trichocarpa clone and use (a) commercially available antibodies against 5-methyl-cytidine, (b) tagged methyl-C DNA binding proteins, and (c) bisulfite sequencing to isolate methylated DNA segments.
  3. Prepare chromatin from tissues of the sequenced P. trichocarpa clone and use commercially available antibodies to methylated histone H3 K9 and H3 K27 to produce enriched DNA fractions.
  4. Sequence the methylated and enriched DNA on an Ilumina/Solexa 1G sequence analyzer at OSU and conduct statistical studies to determine the extent to which DNA methylation and/or histone modification differs between differentiation states and are associated with RNA transcription levels, and whether suppression of DNA methylation disturbs vegetative development and dormancy.

Project Contact
Name: Steven H. Strauss
Phone: (541) 737-6578
Fax: (541) 737-1393
Email: [email protected]