, Volume 56, Issue 7, pp 490–505 | Cite as

Assembly and analysis of the mouse immunoglobulin kappa gene sequence

  • Katherine M. Brekke
  • William T. GarrardEmail author
Original Paper


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.


Immunoglobulin Transcription factors V(D)J recombination Promoters Igκ 



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.

Supplementary material

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  1. Allen E, Horvath S, Tong F, Kraft P, Spiteri E, Riggs AD, Marahrens Y (2003) High concentrations of long interspersed nuclear element sequence distinguish monoallelically expressed genes. Proc Natl Acad Sci USA 100:9940–5994CrossRefPubMedGoogle Scholar
  2. Apel TW, Scherer A, Adachi T, Auch D, Ayane M, Reth M (1995) The ribose 5-phosphate isomerase encoding gene is located immediately downstream from that encoding murine immunoglobulin kappa. Gene 156:191–197CrossRefPubMedGoogle Scholar
  3. Aranburu A, Carlsson R, Persson C, Leanderson T (2001) Transcription factor AP-4 is a ligand for immunoglobulin-κ promoter E-box elements. Biochem J 353:431–438CrossRefGoogle Scholar
  4. Barberis A, Widenhorn K, Vitelli L, Busslinger M (1990) A novel B-cell lineage-specific transcription factor present at early but not late stages of differentiation. Genes Dev 4:849–859PubMedGoogle Scholar
  5. Bemark M, Liberg D, Leanderson T (1998) Conserved sequence elements in K promoters from mice and humans: implications for transcriptional regulation and repertoire expression. Immunogenetics 47:183–195CrossRefPubMedGoogle Scholar
  6. Blackwell TK, Weintraub H (1990) Differences of similarities in DNA-binding preferences of MyoD and E2A protein complexes revealed by binding site selection. Science 250:1104–1110Google Scholar
  7. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268:78–94CrossRefPubMedGoogle Scholar
  8. Casellas R, Shih T-AY, Kleinewietfeld M, Rakonjac J, Nemanzee D, Rajewsky K, Nussenweig MC (2001) Contribution of receptor editing to the antibody repertoire. Science 291:1541–1544Google Scholar
  9. Casellas R, Jankovic M, Meyer G, Gazumyan A, Luo Y, Roeder RG, Nussenzweig MC (2002) OcaB is required for normal transcription and V(D)J recombination of a subset of immunoglobulin κ genes. Cell 110:575–585CrossRefPubMedGoogle Scholar
  10. Cirillo LA, Zaret KS (1999) An early developmental transcription factor complex that is more stable on nucleosome core particles than on free DNA. Mol Cell 4:961–969CrossRefPubMedGoogle Scholar
  11. Durdik J, Moore MW, Selsing E (1984) Novel kappa light-chain gene rearrangements in mouse lambda light chain-producing B lymphocytes. Nature 307:749–752PubMedGoogle Scholar
  12. Eisenbeis CF, Singh H, Storb U (1995) Pip, a novel IRF family member, is a lymphoid-specific, PU.1-dependent transcriptional activator. Genes Dev 9:1377–1387PubMedGoogle Scholar
  13. Ephrussi A, Church GM, Tonegawa S, Gilbert W (1985) B lineage-specific interactions of an immunoglobulin enhancer with cellular factors in vivo. Science 227:134–140Google Scholar
  14. Falkner FG, Zachau HG (1984) Correct transcription of an immunoglobulin κ gene requires an upstream fragment containing conserved sequence elements. Nature 310:71–74PubMedGoogle Scholar
  15. Felsenfeld G, Groudine M (2003) Controlling the double helix. Nature 421:448–453CrossRefPubMedGoogle Scholar
  16. Gellert M (2002) V(D)J recombination: RAG proteins, repair factors, and regulation. Annu Rev Biochem 71:101–132CrossRefPubMedGoogle Scholar
  17. George JB, Li S, Garrard WT (1995) Yeast artificial chromosome contigs reveal that distal variable-region genes reside at least 3 megabases from the joining regions in the murine immunoglobulin κ locus. Proc Natl Acad Sci USA 92: 12421–12425PubMedGoogle Scholar
  18. George JB, Li S, Garrard WT (1997) The murine immunogloublin kappa locus: new insights into genome organization and expression. In: Capra JD, Zanetti M (eds) The antibodies. Gordon and Breach/Harwood Academic, San Diego, pp 41–62Google Scholar
  19. Georgopoulos K, Moore D, Derfler B (1992) Ikaros, an early lymphoid-specific transcription factor and a putative mediator for T cell commitment. Science 258:808–812Google Scholar
  20. Georgopoulos K, Bigby M, Wang J-H, Molnar A, Wu P, Winandy S, Sharpe A (1994) The Ikaros gene is required for the development of all lymphoid lineages. Cell 79:143–156CrossRefPubMedGoogle Scholar
  21. Goebel P, Janney N, Valenzuela JR, Romanow WJ, Murre C, Feeney AJ (2001) Localized gene specific induction of accessibility to V(D)J recombination induced by E2A and early B cell factor in nonlymphoid cells. J Exp Med 194:645–656CrossRefPubMedGoogle Scholar
  22. Hagman J, Travis A, Grosschedl R (1991) A novel lineage-specific nuclear factor regulates mb-1 gene transcription at the early stages of B cell differentiation. EMBO J 10:3409–3417PubMedGoogle Scholar
  23. Hampsey M, Reinberg D (2003) Tails of intrigue: phosphorylation of RNA polymerase II mediates histone methylation. Cell 113:429–432CrossRefPubMedGoogle Scholar
  24. Kadesch T (1992) Helix-loop-helix proteins in the regulation of immunoglobulin gene transcription. Immunol Today 13:31–36CrossRefPubMedGoogle Scholar
  25. Kalled SL, Brodeur PH (1990) Preferential rearrangement of Vκ4 gene segments in pre-B cell lines. J Exp Med 172:559–566CrossRefPubMedGoogle Scholar
  26. Kaushik A, Schulze DH, Bona C, Kelsoe G (1989) Murine Vκ gene expression does not follow the VH paradigm. J Exp Med 169:1859–1864CrossRefPubMedGoogle Scholar
  27. Kelley DE, Coleclough C, Perry RP (1982) Functional significance and evolutionary development of the 5′-terminal regions of immunoglobulin variable-region genes. Cell 29:681–689CrossRefPubMedGoogle Scholar
  28. Kirschbaum T, Pourrajabi S, Zöcher I, Schwendinger J, Heim V, Röschenthaler F, Kirschbaum V, Zachau HG (1998) The 3′ part of the immunoglobulin κ locus of the mouse. Eur J Immunol 28:1458–1466PubMedGoogle Scholar
  29. Kirschbaum T, Röschenthaler F, Bensch A, Hölscher B, Lautner-Rieske A, Ohnrich M, Pourrajabi S, Schwendinger J, Zöcher I, Zachau HG (1999) The central part of the mouse immunoglobulin κ locus. Eur J Immunol 29:2057–2064CrossRefPubMedGoogle Scholar
  30. Klemsz M, McKercher S, Celada A, VanBeveren C, Maki R (1990) The macrophage and B cell-specific transcription factor PU.1 is related to the ets oncogene. Cell 61:113–124CrossRefPubMedGoogle Scholar
  31. Lefranc MP (2001a) Nomenclature of the human immunoglobulin heavy (IGH) genes. Exp Clin Immunogenet 18:100–116CrossRefPubMedGoogle Scholar
  32. Lefranc M P (2001b) Nomenclature of the human immunoglobulin kappa (IGK) genes. Exp Clin Immunogenet 18:161–174CrossRefPubMedGoogle Scholar
  33. Li S, Garrard WT (2003) The kinetics of V-J joining throughout 3.5 megabases of the mouse Ig kappa locus fit a constrained diffusion model of nuclear organization. FEBS Lett 536:125–129CrossRefPubMedGoogle Scholar
  34. Lin H, Grosschedl R (1995) Failure of B-cell differentiation in mice lacking the transcription factor EBF. Nature 376:263–267CrossRefPubMedGoogle Scholar
  35. Liu X, Robinson GW, Gouilleux F, Groner B, Hennighausen L (1995) Cloning and expression of Stat5 and an additional homologue (Stat5b) involved in prolactin signal transduction in mouse mammary tissue. Proc Natl Acad Sci USA 92:8831–8835PubMedGoogle Scholar
  36. Liu Z-M, George-Raizen JB, Li S, Meyers KC, Chang MY, Garrard WT (2002) Chromatin structural analyses of the mouse Igκ gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer. J Biol Chem 277:32640–32649CrossRefPubMedGoogle Scholar
  37. Max EE, Maizel JV Jr, Leder P (1981) The nucleotide sequence of a 5.5-kilobase DNA segment containing the mouse kappa immunoglobulin J and C region genes. J Biol Chem 256:5116–120PubMedGoogle Scholar
  38. McMurry MT, Krangel MS (2000) A role for histone acetylation in the developmental regulation of VDJ recombination. Science 287:495–498Google Scholar
  39. Medina CA, Teale JM (1993) Restricted κ chain expression in early ontogeny: biased utilization of Vκ exons and preferential Vκ−Jκ recombination. J Exp Med 177:1317–1330CrossRefPubMedGoogle Scholar
  40. Myers EW, Sutton GG, Delcher AL, Dew IM, Fasulo DP, Flanigan MJ, Kravitz SA, Mobarry CM, Reinert KH, Remington KA, Anson EL, Bolanos RA, Chou HH, Jordan CM, Halpern AL, Lonardi S, Beasley EM, Brandon RC, Chen L, Dunn PJ, Lai Z, Liang Y, Nusskern DR, Zhan M, Zhang Q, Zheng X, Rubin GM, Adams MD, Venter JC (2000) A whole-genome assembly of Drosophila. Science 287:2196–204Google Scholar
  41. Ng KH, Lavigueur A, Ricard L, Boivrette M, Maclean S, Cloutier D, Gibson DM (1989) Characterization of allelic Vk1 region genes in inbred strains of mice. J Immunol 143:638–648PubMedGoogle Scholar
  42. Ng HH, Ciccone DN, Morshead KB, Oettinger MA, Struhl K (2003) Lysine-79 of histone H3 is hypomethylated at silenced loci in yeast and mammalian cells: a potential mechanism for position-effect variegation. Proc Natl Acad Sci USA 100:1820–1825CrossRefPubMedGoogle Scholar
  43. Pongubala JMR, Nagulapalli S, Klemsz MJ, McKercher SR, Maki RA, Atchison ML (1992) PU.1 recruits a second nuclear factor to a site important for immunoglobulin k 3′ enhancer activity. Mol Cell Biol 12:368–378PubMedGoogle Scholar
  44. Ramsden DA, Paige CJ, Wu GE (1994) κ light chain rearrangement in mouse fetal liver. J Immunol 153:1150–1160PubMedGoogle Scholar
  45. Ren Z, Lin P, Klintworth G, Iwata F, Munier F, Schorderet D, El-Matri L, Theenkadara V, Basti S, Reddy M, Hejtmancik J (2002) Allelic and locus heterogeneity in autosomal recessive gelatinous drop-like corneal dystrophy. Hum Genet 110:568–577CrossRefPubMedGoogle Scholar
  46. Reya T, Grosschedl R (1998) Transcriptional regulation of B-cell differentiation. Curr Opin Immunol 10:158–165CrossRefPubMedGoogle Scholar
  47. Romanow WJ, Langerak AW, Goebel P, Wolvers-Tettero ILM, van Dongen JJM, Feeney AJ, Murre C (2000) E2A and EBF act in synergy with the V(D)J recombinase to generate a diverse immunoglobulin repertoire in nonlymphoid cells. Mol Cell 5:343–353CrossRefPubMedGoogle Scholar
  48. Röschenthaler F, Hameister H, Zachau HG (2000) The 5′ part of the mouse immunoglobulin κ locus as a continuously cloned structure. Eur J Immunol 30:3349–3354CrossRefPubMedGoogle Scholar
  49. Schable KF, Thiebe R, Bench A, Brensing-Kuppers J, Heim V, Kirschbaum T, Mitlöhner H, Ohnrich M, Pourrajabi S, Röschenthaler F, Zachau HG (1999) Characteristics of the immunoglobulin Vκ genes, pseudogenes, relics and orphons in the mouse genome. Eur J Immunol 29:2082CrossRefPubMedGoogle Scholar
  50. Schebesta M, Heavey B, Busslinger M (2002) Transcriptional control of B cell development. Curr Opin Immunol 14:216–223CrossRefPubMedGoogle Scholar
  51. Schilham MW, Clevers H (1998) HMG box containing transcription factors in lymphocyte differentiation. Semin Immunol 10:127–132CrossRefPubMedGoogle Scholar
  52. Schlissel MS, Baltimore D (1989) Activation of immunoglobulin kappa gene rearrangement correlates with induction of germline kappa gene transcription. Cell 58:1001–1007CrossRefPubMedGoogle Scholar
  53. Schlissel MS, Corcoran LM, Baltimore D (1991) Virus-transformed pre-B cells show ordered activation but not inactivation of immunoglobulin gene rearrangement and transcription. J Exp Med 173:711–720CrossRefPubMedGoogle Scholar
  54. Schwarzenback H, Newell JW, Matthias P (1995) Involvement of the Ets family factor PU.1 in the activation of immunoglobulin promoters. J Biol Chem 270:898–907CrossRefPubMedGoogle Scholar
  55. Sen R, Baltimore D (1986a) Inducibility of kappa immunoglobulin enhancer-binding protein Nf-kappa B by a posttranslational mechanism. Cell 47:921–928CrossRefPubMedGoogle Scholar
  56. Sen R, Baltimore D (1986b) Multiple nuclear factors interact with the immunoglobulin enhancer sequences. Cell 46:705–716CrossRefPubMedGoogle Scholar
  57. Sigvardsson M, Bemark M, Leanderson T (1995) Stimulation of kappa transcription by a decamer-dependent, synergistic mechanism. Eur J Immunol 25:298–301PubMedGoogle Scholar
  58. Sigvardsson M, Akerblad P, Leanderson T (1996) Early B cell factor interacts with a subset of κ promoters. J Immunol 156:3788–3796PubMedGoogle Scholar
  59. Sleckman BP, Gorman JR, Alt FW (1996) Accessibility control of antigen-receptor variable-region gene assembly: role of cis-acting elements. Annu Rev Immunol 14:459–481CrossRefPubMedGoogle Scholar
  60. Thiebe R, Schable KF, Bensch A, Brensing-Kupers J, Heim V, Kirchbaum T, Mitlohner H, Ohnrich M, Pourrajabi S, Roschenthaler F, Schwendinger J, Wichelhaus D, Zocher I, Zachau HG (1999) The variable genes and gene families of the mouse immunoglobulin κ locus. Eur J Immunol 29:2072–2081CrossRefPubMedGoogle Scholar
  61. Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, Levine AJ, Roberts RJ, Simon M, Slayman C, Hunkapiller M, Bolanos R, Delcher A, Dew I, Fasulo D, Flanigan M, Florea L, Halpern A, Hannenhalli S, Kravitz S, Levy S, Mobarry C, Reinert K, Remington K, Abu-Threideh J, Beasley E, Biddick K, Bonazzi V, Brandon R, Cargill M, Chandramouliswaran I, Charlab R, Chaturvedi K, Deng Z, Di Francesco V, Dunn P, Eilbeck K, Evangelista C, Gabrielian AE, Gan W, Ge W, Gong F, Gu Z, Guan P, Heiman TJ, Higgins ME, Ji RR, Ke Z, Ketchum KA, Lai Z, Lei Y, Li Z, Li J, Liang Y, Lin X, Lu F, Merkulov GV, Milshina N, Moore HM, Naik AK, Narayan VA, Neelam B, Nusskern D, Rusch DB, Salzberg S, Shao W, Shue B, Sun J, Wang Z, Wang A, Wang X, Wang J, Wei M, Wides R, Xiao C, Yan C, et al (2001) The sequence of the human genome. Science 291:1304–1351CrossRefPubMedGoogle Scholar
  62. Wirth T, Baltimore D (1988) Nuclear factor NF-kappa B can interact functionally with its cognate binding site to provide lymphoid-specific promoter function. EMBO J 7:3109–3113PubMedGoogle Scholar
  63. Wirth T, Staudt L, Baltimore D (1987) An octamer oligonucleotide upstream of a TATA motif is sufficient for lymphoid-specific promoter activity. Nature 329:174–178CrossRefPubMedGoogle Scholar
  64. Yancopoulos GD, Alt FW (1985) Developmentally controlled and tissue-specific expression of unrearranged Vh gene segments. Cell 40:271–281CrossRefPubMedGoogle Scholar
  65. Zachau HG (2004) Immunoglobulin κ genes of human and mouse. In: Alt FW, Honjo T, Neuberger M (eds) Molecular biology of B cells. Elsevier, London, pp 27–36Google Scholar

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© Springer-Verlag 2004

Authors and Affiliations

  1. 1.Department of Molecular BiologyUniversity of Texas Southwestern Medical Center at DallasDallasUSA

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