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Plant Physiology 138:80-91 (2005)
© 2005 American Society of Plant Biologists

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GENOME ANALYSIS

Organ-Specific Expression of Arabidopsis Genome during Development1,[w]

Ligeng Ma, Ning Sun, Xigang Liu, Yuling Jiao, Hongyu Zhao and Xing Wang Deng*

Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China (L.M., X.W.D.); Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520–8104 (L.M., Y.J., X.W.D.); Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, Connecticut 06520 (N.S., H.Z.); and Laboratory of Molecular Cell Biology, Hebei Normal University, Shijiazhuang, Hebei 050016, People's Republic of China (X.L.)

The development of complex eukaryotic organisms can be viewed as the selective expression of distinct fractions of the genome in different organs or tissue types in response to developmental and environmental cues. Here, we generated a genome expression atlas of 18 organ or tissue types representing the life cycle of Arabidopsis (Arabidopsis thaliana). We showed that each organ or tissue type had a defining genome expression pattern and that the degree to which organs share expression profiles is highly correlated with the biological relationship of organ types. Further, distinct fractions of the genome exhibited expression changes in response to environmental light among the three seedling organs, despite the fact that they share the same photoperception and transduction systems. A significant fraction of the genes in the Arabidopsis genome is organized into chromatin domains exhibiting coregulated expression patterns in response to developmental or environmental signals. The knowledge of organ-specific expression patterns and their response to the changing environment provides a foundation for dissecting the molecular processes underlying development.

1 This work was supported by the National Science Foundation of China (strategic international corporation project grant no. 30221120261), by the National Institutes of Health (grant nos. GM–47850 to X.W.D. and GM59507 to H.Z.), and by the National Science Foundation (grant no. DMS 0241160). L.M. is a long-term postdoctoral fellow of the Human Frontier Science Program.

[w] The online version of this article contains Web-only data.

www.plantphysiol.org/cgi/doi/10.1104/pp.104.054783.

* Corresponding author; e-mail xingwang.deng{at}yale.edu; fax 203–432–3854.

Received October 12, 2004; returned for revision February 14, 2005; accepted February 14, 2005.


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