Genome-wide transposon tagging reveals location-dependent effects on transcription and chromatin organization in Arabidopsis

Faye M. Rosin, Naohide Watanabe, Jean Luc Cacas, Naohiro Kato, Juana M. Arroyo, Yuda Fang, Bruce May, Matthew Vaughn, Joseph Simorowski, Umamaheswari Ramu, Richard W. McCombie, David L. Spector, Robert A. Martienssen, Eric Lam

Research output: Contribution to journalArticle

37 Scopus citations

Abstract

The interphase nucleus exists as a highly dynamic system, the physical properties of which have functional importance in gene regulation. Not only can gene expression be influenced by the local sequence context, but also by the architecture of the nucleus in three-dimensions (3D), and by the interactions between these levels via chromatin modifications. A challenging task is to resolve the complex interplay between sequence- and genome structure-based control mechanisms. Here, we created a collection of 277 Arabidopsis lines that allow the visual tracking of individual loci in living plants while comparing gene expression potential at these locations, via an identical reporter cassette. Our studies revealed regional gene silencing near a heterochromatin island, via DNA methylation, that is correlated with mobility constraint and nucleolar association. We also found an example of nucleolar association that does not correlate with gene suppression, suggesting that distinct mechanisms exist that can mediate interactions between chromatin and the nucleolus. These studies demonstrate the utility of this novel resource in unifying structural and functional studies towards a more comprehensive model of how global chromatin organization may coordinate gene expression over large scales.

Original languageEnglish (US)
Pages (from-to)514-525
Number of pages12
JournalPlant Journal
Volume55
Issue number3
DOIs
StatePublished - Aug 1 2008

All Science Journal Classification (ASJC) codes

  • Genetics
  • Plant Science
  • Cell Biology

Keywords

  • Chromatin
  • Gene regulation
  • Nuclear organisation
  • Position effects

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    Rosin, F. M., Watanabe, N., Cacas, J. L., Kato, N., Arroyo, J. M., Fang, Y., May, B., Vaughn, M., Simorowski, J., Ramu, U., McCombie, R. W., Spector, D. L., Martienssen, R. A., & Lam, E. (2008). Genome-wide transposon tagging reveals location-dependent effects on transcription and chromatin organization in Arabidopsis. Plant Journal, 55(3), 514-525. https://doi.org/10.1111/j.1365-313X.2008.03517.x