Epigenomics of Development in Populus

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Epigenomics of Development in Populus
INVESTIGATORS: Steven H. Strauss, Todd Mockler, Michael Freitag
INSTITUTION: Oregon State University
NON-TECHNICAL SUMMARY: Epigenetics is defined by longlasting 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 deand 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.
APPROACH:
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
dtermine 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: Strauss, Steven H.
Phone: 541 737 6578
Fax: 541 737 1393
Email: [email protected]
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