ARABIDOPSIS CHROMOSOME IV

¹ Lita Annenberg Hazen Genome Center, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA

² M. Beven, et. al., John Innes Centre, Colney Lane, Norwich NR4 7UH, UK

³ Genome Sequencing Center, Washington University, School of Medicine, 4444 Forest Park Blvd., St. Louis, MO 63108 USA

⁴ Applied Biosystems, 850 Lincoln Centre Drive, Foster City, CA 94494 USA

⁵ Cold Spring Harbor Plant Biology Group, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724 USA

The Arabidopsis Genome Initiative is an international collaboration to determine the complete sequence of the Arabidopsis thaliana genome. Two consortia, one European, the other American, have been collaborating to sequence and analyze Arabidopsis chromosome IV. This task is now essentially complete. Using a map-based approach, the chromosome arms have been completely sequenced and over 2MB of the predicted 4MB pericentromeric heterochromatin has been sequenced. The chromosome contains approximately 3800 genes. We will describe the analysis of the centromeric region and a region of heterochromatin at the sequence level. As part of this effort, we have sequenced and analyzed a 2MB contiguous region of Arabidopsis thaliana (ecotype Columbia) which contains an isolated region of heterochromatin, or a heterochromatic knob. Heterochromatic knobs in higher plant genomes were first discovered in the early part of this century by Barbara McClintock. We show that the region of condensed heterochromatin on Arabidopsis chromosome IV is characterized by a low density of expressed genes, low levels of recombination and a low incidence of insertion of the maize transposon Ac/Ds. An analysis of repeats found in this region indicates that knobs are characterized by methylated long tandem repeats that are unique to this region of the genome, as well as transposons common pericentromeric domains. The sequence thus shows a fascinating relationship between chromosome structures and biological activity.