New Technologies Facilitate Investigation of Wood Formation

The Science

Woody plants are an important source of renewable biomass for bioenergy feedstocks. Wood formation is a complex, highly regulated process generating key sources of material for bioenergy and bioproducts. Understanding the gene regulatory networks underlying wood formation would facilitate efforts to develop higher biomass yielding, sustainable trees as bioenergy feedstocks. However, the nature of woody material makes it recalcitrant to genetic manipulation, presenting a significant challenge. Researchers funded by the Department of Energy’s Genomic Science program report the development of two new methods optimized for woody material and expediting molecular genetic approaches for investigating wood formation in Populus trichocarpa, a model woody plant and bioenergy feedstock. They detail systematic and extensive modification of the chromatin immunoprecipitation (ChIP) procedure, widely used to identify chromatin-associated DNA-protein interactions in nonwoody plants and animals, making it usable for the first time with wood-forming tissues. Using this new protocol, the researchers identified genome-wide specific transcription factor-DNA interactions associated with the regulation of wood formation. They also describe a new higher-yielding and faster method for the isolation and transfection of high-quality protoplasts from P. trichocarpa wood-forming tissue. Protoplasts are useful for transient transgene expression-based studies, particularly for woody plants that are difficult to genetically transform and for which mutants are unavailable.

The Impact

Both methods should be broadly applicable to other woody species, enabling comparative analyses of the evolution of the genetic regulation and epigenetic modifications of wood formation. These advances will facilitate essential genome-wide studies of wood formation and biomass productivity in woody feedstocks.

BER Program Manager

Kari Perez

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
[email protected]


Li, W., Y.-C. Lin, Q. Li, R. Shi, C.-Y. Lin, H. Chen, L. Chuang, G.-Z. Qu, R. R. Sederoff, and V. L. Chiang. 2014. “A Robust Chromatin Immunoprecipitation Protocol for Studying Transcription Factor-DNA Interactions and Histone Modifications in Wood-Forming Tissue,” Nature Protocols 9(9), 2180-93. DOI:10.1038/nprot.2014.146.

Lin, Y.-C., W. Li, H. Chen, Q. Li, Y.-H. Sun, R. Shi, C.-Y. Lin, J. P. Wang, H.-C. Chen, L. Chuang, G.-Z. Qu, R. R. Sederoff, and V. L. Chiang. 2014. “A Simple Improved-Throughput Xylem Protoplast System for Studying Wood Formation,” Nature Protocols 9(9), 2194-2205. DOI:10.1038/nprot.2014.147. ]