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Nucleic Acids Research, 1990, Vol. 18, No. 11 3135-3145
© 1990

MOLECULAR BIOLOGY

Structural analysis of the short length ribosomal DNA variant from Pisum sativum L cv. Alaska

Kenneth J. Piller, Scott R. Baerson, Neil O. Polans1 and Lon S. Kaufman*

Laboratory for Cell, Molecular and Developmental Biology, Department of Biological Sciences, University of Illinois at Chicago Chicago, IL 60680 1department of Biological Sciences, Northern Illinois University DeKalb, IL 60115-2861, USA

*To whom correspondence should be addressed al University of Illinois at Chicago, PO Box 4348, M/C 067, Chicago, IL 60680, USA

Received March 27, 1990. Accepted April 17, 1990.

The genomic clone, RRNpssl, representing the short ribosomal DNA length variant in Pisum sativum L. cv. Alaska, has been Isolated and the 2859 bp intergenic spacer, along with the 25S rRNA 3' border and 18S rRNA 5' border, has been sequenced. The intergenic spacer contains nine tandem repeats, approximately 180 bp in length, which show greater than 80% sequence homology to each other. The RNA polymerase I transcription start site and a processing site, located 776 bp and 536 bp upstream of the 5' end of 18S rRNA, respectively, have been determined using S1 analysis. The region surrounding the +1 site shows strong homology between the positions –6 to +10 to the rONA sites of initiation in radish, maize, and wheat. The sequence CATGCAAA is located 19 bp upstream of the site of initiation, and appears once within each subrepeat and twice more between the end of the subrepeat array and the site of initiation. A previously characterized HpaW site which shows developmental regulation of methylation is located 31 bp downstream of the site of initiation. Using RFLP linkage analysis, the short rDNA length variant of cv. Alaska is assigned to Chromosome 4 where it is genetically independent of the long rDNA length variant which is putatively assigned to Chromosome 7.


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