The goals of the project are:

  1) to obtain a global view of "position effects" in the Arabidopsis chromosomes.

  2) to identify the three dimensional (3-D) positions of genes of interest in interphase nuclei.

In the phenomenon known as position effect, sites of integration affect the expression levels of transgenes. For instance, a transgene that is highly expressed when integrated into euchromatic regions may be poorly expressed when inserted into heterochromatic regions. Recent studies suggest that chromosomes in interphase nuclei are highly organized, and that the 3-D positions of genes in the interphase nuclei may influence their expression.

In the project scheme we are generating over 15,000 Ds-tagged lines of Arabidopsis. The Ds-tagging cassette contains a CAMV35S::luciferase which allows monitoring of position effects, and a lac operator repeat (array) which allows the tagged loci to be visualized by expressing fusions of fluorescent-proteins with lacI within the nuclei of live plants. We are mapping the tagged loci with the goal of selecting 3,000 lines in which tagged loci occur on average once every 40 kbp. The selected lines will be used to evaluate the position effects. We are also generating a set of anchoring lines comprising transgenic Arabidopsis lines which would contain two tagged loci that can be visualized with autofluorescent proteins of distinct spectral properties. These "anchoring lines" will be crossed to the Ds-tagged lines in order to compare the organization and dynamic properties of these Ds-tagged loci in interphase nuclei using a three-color system. More information is available at the Rutgers University website.

These materials should be useful for the characterization of mutations and corresponding genes that influence gene expression through altering chromatin architecture.

• To browse luciferase expression patterns across chromosomal regions, click on Browser above.
• To search for markers at particular genomic loci using keywords (e.g. "kinase"), click on Annotations above.
• To search for loci using direct DNA sequence comparison, click on BLAST above.
• To search for expression levels at loci, click on Expression above.
• To search for loci at particular positions in the nucleus, click on Position above.
• For further information on how to use the website and how the lines are generated and analyzed, click on Help above.

NEW FEATURES

• View some preliminary nuclear position data [Position Data]
• Browse gus staining data for these lines [Gus Staining]

Chromosome 1

Chromosome 2

Chromosome 3

Chromosome 4

Chromosome 5
Distrbution of Luciferase expression vs chromosomal position