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Nucleic Acids Research, 1994, Vol. 22, No. 10 1785-1796
© 1994

SURVEY AND SUMMARY

Conservation of sequence in recombination signal sequence spacers

Dale A. Ramsden+, Kristin Baetz and Gillian E. Wu*

Department of Immunology, University of Toronto, Toronto Ontario M5S 1A8 and The Wellesley Hospital Research Institute 160 Wellesley Street East, Toronto, Ontario M4Y 1J3, Canada

*To whom correspondence should be addressed

Received October 21, 1993. Revised April 13, 1994. Accepted April 13, 1994.

The variable domains of immunoglobulins and T cell receptors are assembled through the somatic, site specific recombination of multiple germline segments (V, D, and J segments) or V(D)J rearrangement. The recombination signal sequence (RSS) is necessary and sufficient for cell type specific targeting of the V(D)J rearrangement machinery to these germline segments. Previously, the RSS has been described as possessing both a conserved heptamer and a conserved nonamer motif. The heptamer and nonamer motifs are separated by a ‘spacer’ that was not thought to possess significant sequence conservation, however the length of the spacer could be either 12 +/– 1 bp or 23 +/– 1 bp long. In this report we have assembled and analyzed an extensive data base of published RSS. We have derived, through extensive consensus comparison, a more detailed description of the RSS than has previously been reported. Our analysis indicates that RSS spacers possess significant conservation of sequence, and that the conserved sequence in 12 bp spacers is similar to the conserved sequence in the first half of 23 bp spacers.

+Present address: National Institutes of Health, NIDDK, Room 312, Building 5, Bethesda, MD 20892, USA


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