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Assembly and analysis of the mouse immunoglobulin kappa gene sequence

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Abstract

The mechanisms regulating V gene usage leading to the immunoglobulin (Ig) repertoire have been of interest for many years but are only partially defined. To gain insight into these processes, we have assembled the nucleotide sequence of the Mus musculus Igκ locus using data recently made available from genome-wide sequencing efforts. We found the locus to be 3.21 Mb in length and mapped all known functional, pseudo- and relic V gene segments onto the sequence, along with known regulatory elements. We corrected errors in former gene assignments, positions and orientations and identified a novel V κ4 gene segment. This assembly allowed the establishment of a unified nomenclature for the V genes based on their relative positions similar to the nomenclature system adopted for the human Ig loci. The 5′ boundary of the locus is defined by the presence of the tumor-associated calcium-signal transducer-2 gene located 19 kb upstream of V κ24-140 , the most distal V gene. No non-V κ genes were found in the sequence of the locus. Detailed analysis of the sequences 0.5 kb upstream, within, and 0.5 kb downstream of each potentially functional V gene revealed interesting patterns of statistically significant clustering of transcription factor consensus binding sites, generally specific to a particular family. We found E boxes were clustered not only in promoter regions, but also nearby recombination signal sequences. Family members of V κ4/5 genes exhibit a conserved pattern of octamer sites in their downstream regions, as well as Ebf sites in their introns, and Lef-1 sites in their upstream regions. We discuss potential functional implications of these findings in the context of possible combinatorial mechanisms for targeting V genes for rearrangement. The assembled sequence and its analyses are available as a resource to the scientific community.

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Acknowledgements

This data was generated through use of the Celera Discovery System. The authors would like to thank Christopher Antos for critical review of the manuscript, Monty Brekke for assistance in computer programming, and William Frawley for assistance with statistical analysis. This investigation was supported by Grants GM29935 and GM59809 from the National Institutes of Health and Grant I-823 from the Robert A. Welch Foundation (to W.T.G.). All experiments in this work comply with the laws of the United States of America.

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  1. Department of Molecular Biology, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd., Dallas, TX 75390-9148, USA

    Katherine M. Brekke & William T. Garrard

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  1. Katherine M. Brekke
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  2. William T. Garrard
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Correspondence to William T. Garrard.

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The assembled nucleotide sequence of the Igκ locus of the mouse will be provided upon request from the authors.

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Brekke, K.M., Garrard, W.T. Assembly and analysis of the mouse immunoglobulin kappa gene sequence. Immunogenetics 56, 490–505 (2004). https://doi.org/10.1007/s00251-004-0659-0

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