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Trapper Welcome to the Arabidopsis Genetrap Website at Cold Spring Harbor Lab

This website describes a collection of transposon insertions and their flanking sequences from the Martienssen lab at Cold Spring Harbor Laboratory. Most of the lines carry a unique insertion of a genetrap (GT) or enhancer trap (ET) transposable Ds element somewhere in the Arabidopsis genome. These elements simultaneously disrupt gene function and monitor gene expression (Sundaresan et al., 1995; Martienssen, 1998).

  • A major goal of the NSF Arabidopsis 2010 project is to characterize the roles and functions of unknown and hypothetical genes. The TRAPPER collection currently contains putative insertions in over 1500 of these undescribed genes. Here is a listing of these genes.
  • The transposon launch-pad constructs can be accessed at NCBI: Enhancer trap construct,   Gene trap construct.
  • Launch pads, protocols for mutagenesis, reversion and construction of mosaics can be found in Springer and Martienssen.
  • View the current progress for the project.
  • Get the genomic locations of the starting launch pads.
  • View the chromosomal distribution of insertions.

Insertion sites were amplified by TAIL PCR (Liu et al., 1995; Tsukegi et al., 1996) and sequenced in the McCombie lab (CSHWU Sequencing Consortium, 2000). These sequence tags were validated and annotated according to the sequence of the Arabidopsis genome (see sequence annotation). Many of the lines have been stained and about 20% of these have reporter gene expression. Photographs of positive lines are included as links with each entry.

Searches can be performed by keyword or by sequence similarity (BLAST). Seed from individual lines are available on request and many have been deposited at the Nottingham Arabidopsis Stock Center and the Ohio Arabidopsis Biological Resource Center.

WARNING The sequence annotation is intended as a guide to additional database searching only. Multiple sequence reads are listed together on each entry page and may reflect multiple elements in some lines. However, while every effort has been made to remove tracking and other errors, the data is preliminary and is mostly unpublished. Many of the sequences have been deposited in Genbank.

To begin:
Click on Annotations above to search the sequence annotations.
Click on Phenotypes above to search observed phenotypes.
Click on BLAST above to perform a BLAST search on transposant sequence data using your own query sequence.
Click on Expression above to search expression patterns.
Click on Multiple Categories above to search combinations of the above types of data.
Click on Help above for more information on using the database and the arabidopsis lines.

Links to WWW Arabidopsis Genome resources:
Arabidopsis Genome Analysis at Cold Spring Harbor Laboratory
Arabidopsis thaliana database (TAIR)
MIPS
TIGR

Requests:
Seeds from individual lines are available for research purposes on request. Due to the increased volume, these requests are now subject to a handling fee. Please send requests by email to Joe Simorowski (simorows@cshl.edu). A Material Transfer Agreement (MTA) is required for all seed requests.

Queries and helpful comments should be sent to:
Joe Simorowski (simorows@cshl.edu) for questions about the data.

References:

Underwood, C. J., Choi, K., Lambing, C., Zhao, X., Serra, H., Borges, F., Simorowski, J., Ernst, E., Jacob, Y., Henderson, I.R. and Martienssen, R. A. (2018). Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation. Genome research, 28(4), 519-531. [PubMed]

Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815. [PubMed]

Cold Spring Harbor Laboratory, Washington University Genome Sequencing Center and ABI Arabidopsis Sequencing Consortium (2000) The complete sequence of a heterochromatic island from a higher eukaryote. Cell 100, 377-386. [PubMed]

Gu Q., Ferrandiz C. , Yanofsky M. and R. Martienssen (1998) FRUITFULL encodes a MADS-box gene and mediates cell differentiation during fruit development in Arabidopsis. Development 125, 1509-1517. [PubMed]

Liu Y.G., Mitsukawa N., Oosumi T. and Whittier R.F. (1995) Efficient isolation and mapping of Arabidopsis thaliana T-DNA insert junctions by thermal asymmetic interlaced PCR. Plant J. 8, 457-463. [PubMed]

Martienssen R. (1998) Functional genomics: probing plant gene function and expression with transposons. Proc. Natl. Acad. Sci. 95, 2021-2026. [PubMed]

Martienssen R. (2000) Weeding out the genes: The Arabidopis Genome Project. Functional and Integrative Genomics, 1: 2-20.i [PubMed]

Martienssen R. and McCombie W.R. (2001) The First Plant Genome. Cell 105(5) 571-574. [PubMed]

Springer, P. and Martienssen, R.A. (2000). Enhancer and Gene Trap Transposon Mutagenesis in Arabidopsis. [genetrap.cshl.edu]

Springer, P., McCombie, W.R., Sundaresan, V. and Martienssen, R.A. (1995). Gene trap tagging of PROLIFERA, an essential MCM2-3-5 like gene in Arabidopsis. Science 268, 877-880. [PubMed]

Sundaresan, V., Springer, P., Volpe, T., Haward, S., Jones, J.D.G., Dean, C., Ma, H. and R.A. Martienssen (1995). Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements. Genes Dev. 9, 1797-1810. [PubMed]

Tsugeki R., Kochieva E.Z. and Fedoroff N. (1996) A transposon insertion in the Arabidopsis SSR16 gene causes an embryo-defective lethal mutation. Plant J. 10, 479-489. [PubMed]

Credits:
Genetraps: Cristy Yordan, Joe Simorowski, Juana-Maria Arroyo, Rulan Shen, Dick McCombie
Sequence Database: Bruce May, Matt Vaughn, Neilay Dedhia, Lincoln Stein
Collaborators: Hong Ma, Dan Bush, Liam Dolan, Joe Ecker, Patty Springer, Albrecht
vonArnim, Vivian Irish

Supported by Cold Spring Harbor Laboratory Plant Research Fund

 

First posted 23 June 2000, Last updated 11 February 2021