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

Rosin, F. M., Watanabe, N., Cacas, Jean-Luc, Kato, N., Arroyo, J. M., Fang, Y., May, B., Vaughn, M., Simorowski, J., Ramu, U., McCombie, R., 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). pp. 514-525. ISSN 0960-7412

URL: http://www.ncbi.nlm.nih.gov/pubmed/18410481
DOI: 10.1111/j.1365-313X.2008.03517.x

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.

Item Type: Paper
Uncontrolled Keywords: Arabidopsis Cell Nucleolus Chromatin Chromatin Assembly and Disassembly Chromosome Mapping Chromosomes, Plant DNA Methylation DNA Transposable Elements Gene Expression Regulation, Plant Gene Silencing Genome, Plant Transcription, Genetic
Subjects: organism description > plant > Arabidopsis
bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > Chromatin dynamics
CSHL Authors:
Communities: CSHL labs > Martienssen lab
CSHL labs > McCombie lab
CSHL labs > Spector lab
Depositing User: Matt Covey
Date Deposited: 10 Dec 2012 20:02
Last Modified: 28 Jan 2015 21:01
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26363

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