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Comparative genomics of the keratin-associated protein (KAP) gene clusters in human, chimpanzee, and baboon

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Abstract

We have previously identified a cluster of 16 genes that encode hair-specific proteins, called keratin-associated proteins (KAPs), located on human Chromosome (Chr) 21q22.3. Here, we have identified similar KAP gene clusters in two primates, chimpanzee and baboon. DNA sequence comparison revealed the common cluster structure consisting of 16 KAP genes for these three primates, but a significant difference was found in the baboon. Baboon possesses a new KAP gene not found in human and chimpanzee, whereas one KAP gene (KRTAP18.12) that exists in human and chimpanzee was lost in baboon, making no change in the total number of KAP genes. Interestingly, the sequence for coding regions are highly variable among species owing to insertions and deletions, resulting in variation of gene size. On the contrary, the sequences for the 5′ upstream region are highly conserved among species. These findings suggest that the ancestral KAP gene cluster was composed of 17 genes before the divergence of Old World monkeys (baboon) to the anthropoid (human and chimpanzee).

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References

  1. SF Altschul W Gish W Miller EW Myers DJ Lipman (1990) ArticleTitleBasic local alignment search tool. J Mol Biol 215 403–410 Occurrence Handle10.1006/jmbi.1990.9999 Occurrence Handle1:CAS:528:DyaK3MXitVGmsA%3D%3D Occurrence Handle2231712

    Article  CAS  PubMed  Google Scholar 

  2. N Aoki K Ito M Ito (1998) ArticleTitleHair follicle has a novel anagen-specific protein, mKAP13. J Invest Dermatol 111 804–809 Occurrence Handle10.1046/j.1523-1747.1998.00387.x Occurrence Handle1:CAS:528:DyaK1cXnt1OhsL4%3D Occurrence Handle9804342

    Article  CAS  PubMed  Google Scholar 

  3. N Ceratto C Dobkin M Carter E Jenkins XL Yao et al. (1997) ArticleTitleHuman type I cytokeratin genes are a compact cluster. Cytogenet Cell Genet 77 169–174 Occurrence Handle1:CAS:528:DyaK2sXmtVGnsL8%3D Occurrence Handle9284906

    CAS  PubMed  Google Scholar 

  4. SE Cole RH Reeves (1998) ArticleTitleA cluster of keratin-associated proteins on mouse chromosome 10 in the region of conserved linkage with human chromosome 21. Genomics 54 437–442 Occurrence Handle10.1006/geno.1998.5590 Occurrence Handle1:CAS:528:DyaK1MXmsFKqtg%3D%3D Occurrence Handle9878246

    Article  CAS  PubMed  Google Scholar 

  5. B Ewing P Green (1998) ArticleTitleBase-calling of automated sequencer traces using phred II, error probabilities. Genome Res 8 186–194 Occurrence Handle1:CAS:528:DyaK1cXitlWlu7g%3D Occurrence Handle9521922

    CAS  PubMed  Google Scholar 

  6. B Ewing L Hillier MC Wendl P Green (1998) ArticleTitleBase-calling of automated sequencer traces using phred I Accuracy assessment. Genome Res 8 175–185 Occurrence Handle1:CAS:528:DyaK1cXitlWlu78%3D Occurrence Handle9521921

    CAS  PubMed  Google Scholar 

  7. D Gordon C Abajian P Green (1998) ArticleTitleConsed: a graphical tool for sequence finishing. Genome Res 8 195–202 Occurrence Handle1:CAS:528:DyaK1cXitlWksr0%3D Occurrence Handle9521923

    CAS  PubMed  Google Scholar 

  8. K Kawasaki S Minoshima E Nakato K Shibuya A Shintani et al. (1997) ArticleTitleOne-megabase sequence analysis of the human immunoglobulin lambda gene locus. Genome Res 7 250–261 Occurrence Handle1:CAS:528:DyaK2sXhvFamt7o%3D Occurrence Handle9074928

    CAS  PubMed  Google Scholar 

  9. J Kudoh K Nagamine S Asakawa I Abe K Kawasaki et al. (1997) ArticleTitleLocalization of 16 exons to a 450-kb region involved in the autoimmune polyglandular disease type I (APECED) on human chromosome 21q22.3. DNA Res 4 45–52 Occurrence Handle1:CAS:528:DyaK2sXisVWhtbw%3D Occurrence Handle9179495

    CAS  PubMed  Google Scholar 

  10. F Kuhn C Lassing A Range M Mueller T Hunziker et al. (1999) ArticleTitlePmg-1 and pmg-2 constitute a novel family of KAP genes differentially expressed during skin and mammary gland development. Mech Dev 86 193–196 Occurrence Handle10.1016/S0925-4773(99)00115-X Occurrence Handle1:CAS:528:DyaK1MXlt1Sgs7o%3D Occurrence Handle10446281

    Article  CAS  PubMed  Google Scholar 

  11. MD Lalioti HS Scott C Buresi C Rossier A Bottani et al. (1997) ArticleTitleDodecamer repeat expansion in cystatin B gene in progressive myoclonus epilepsy. Nature 386 847–851 Occurrence Handle1:CAS:528:DyaK2sXivVGiu7s%3D Occurrence Handle9126745

    CAS  PubMed  Google Scholar 

  12. CE Lawrence SF Altschul MS Boguski JS Liu AF Neuwald et al. (1993) ArticleTitleDetecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science 262 208–214 Occurrence Handle1:CAS:528:DyaK3sXms1Gjsrk%3D Occurrence Handle8211139

    CAS  PubMed  Google Scholar 

  13. PJ MacKinnon BC Powell GE Rogers (1990) ArticleTitleStructure and expression of genes for a class of cysteine-rich proteins of the cuticle layers of differentiating wool and hair follicles. J Cell Biol 111 2587–2600 Occurrence Handle1:CAS:528:DyaK3MXjs12ntg%3D%3D Occurrence Handle1703541

    CAS  PubMed  Google Scholar 

  14. PJ MacKinnon BC Powell GE Rogers EG Baker RN MacKinnon et al. (1991) ArticleTitleAn ultrahigh-sulphur keratin gene of the human hair cuticle is located at 11q13 and cross-hybridizes with sequences at 11p15. Mamm Genome 1 53–56 Occurrence Handle1:CAS:528:DyaK3MXktVahtr4%3D Occurrence Handle1724400

    CAS  PubMed  Google Scholar 

  15. AF Neuwald JS Liu CE Lawrence (1995) ArticleTitleGibbs motif sampling: detection of bacterial outer membrane protein repeats. Protein Sci 4 1618–1632 Occurrence Handle1:CAS:528:DyaK2MXnvVyjsLg%3D Occurrence Handle8520488

    CAS  PubMed  Google Scholar 

  16. NC Popescu PE Bowden JA DiPaolo (1989) ArticleTitleTwo type II keratin genes are localized on human chromosome 12. Hum Genet 82 109–112 Occurrence Handle1:STN:280:BiaB2MzksFw%3D Occurrence Handle2470667

    CAS  PubMed  Google Scholar 

  17. BC Powell GE Rogers (1997) The role of keratin proteins and their genes in the growth, structure and properties of hair. P Jollès H Zahn H Höcker (Eds) Formation and structure of human hair. Birkhauser Verlag Basel 59–148

    Google Scholar 

  18. BC Powell A Nesci GE Rogers (1991) ArticleTitleRegulation of keratin gene expression in hair follicle differentiation. Ann N Y Acad Sci 642 1–20 Occurrence Handle1:CAS:528:DyaK38XkvVOhurc%3D

    CAS  Google Scholar 

  19. MA Rogers R Nischt B Korge T Krieg TM Fink et al. (1995) ArticleTitleSequence data and chromosomal localization of human type I and type II hair keratin genes. Exp Cell Res 220 357–362 Occurrence Handle10.1006/excr.1995.1326 Occurrence Handle1:CAS:528:DyaK2MXosVOrtLY%3D Occurrence Handle7556444

    Article  CAS  PubMed  Google Scholar 

  20. MA Rogers L Langbein H Winter C Ehmann S Praetzel et al. (2001) ArticleTitleCharacterization of a cluster of human high/ultrahigh sulfur keratin-associated protein genes embedded in the type I keratin gene domain on chromosome 17q12-21. J Biol Chem 276 19440–19451 Occurrence Handle10.1074/jbc.M100657200 Occurrence Handle1:CAS:528:DC%2BD3MXkt12rtrY%3D Occurrence Handle11279113

    Article  CAS  PubMed  Google Scholar 

  21. MA Rogers L Langbein H Winter C Ehmann S Praetzel et al. (2002) ArticleTitleCharacterization of a first domain of human high glycine-tyrosine and high sulfur keratin-associated protein (KAP) genes on chromosome 21q221. J Biol Chem 277 48993–49002 Occurrence Handle10.1074/jbc.M206422200 Occurrence Handle1:CAS:528:DC%2BD38Xptlenu78%3D Occurrence Handle12359730

    Article  CAS  PubMed  Google Scholar 

  22. V Romano P Bosco M Rocchi G Costa RE Leube et al. (1988) ArticleTitleChromosomal assignments of human type I and type II cytokeratin genes to different chromosomes. Cytogenet Cell Genet 48 148–151

    Google Scholar 

  23. M Rosenberg A RayChaudhury TB Shows MM Le Beau E Fuchs (1988) ArticleTitleA group of type I keratin genes on human chromosome 17: characterization and expression. Mol Cell Biol 8 722–736 Occurrence Handle1:CAS:528:DyaL1cXksV2gt7k%3D Occurrence Handle2451124

    CAS  PubMed  Google Scholar 

  24. M Rosenberg E Fuchs MM Le Beau RL Eddy TB Shows (1991) ArticleTitleThree epidermal and one simple epithelial type II keratin genes map to human chromosome 12. Cytogenet Cell Genet 57 33–38 Occurrence Handle1:CAS:528:DyaK3MXmsV2htLk%3D Occurrence Handle1713141

    CAS  PubMed  Google Scholar 

  25. H Scheel S Tomiuk K Hofmann (2002) ArticleTitleA common protein interaction domain links two recently identified epilepsy genes. Hum Mol Genet 11 1757–1762 Occurrence Handle10.1093/hmg/11.15.1757 Occurrence Handle1:CAS:528:DC%2BD38XlsFCku7g%3D Occurrence Handle12095917

    Article  CAS  PubMed  Google Scholar 

  26. K Shibuya I Obayashi S Asakawa S Minoshima J Kudoh et al. (2004) ArticleTitleA cluster of 21 keratin-associated protein (KAP) genes within introns of another gene on human chromosome 21q22.3. Genomics . .

    Google Scholar 

  27. ELL Sonnhammer R Durbin (1995) ArticleTitleA dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167 GC1–GC10 Occurrence Handle1:STN:280:BymC2cvjtVA%3D Occurrence Handle8566757

    CAS  PubMed  Google Scholar 

  28. M Takaishi Y Takata T Kuroki N Huh (1998) ArticleTitleIsolation and characterization of a putative keratin-associated protein gene expressed in embryonic skin of mice. J Invest Dermatol 111 128–132 Occurrence Handle10.1046/j.1523-1747.1998.00241.x Occurrence Handle1:CAS:528:DyaK1cXks1emtbo%3D Occurrence Handle9665399

    Article  CAS  PubMed  Google Scholar 

  29. InstitutionalAuthorNameThe chromosome 21 mapping and sequencing consortium (2000) ArticleTitleThe DNA sequence of human chromosome 21. Nature 405 311–319 Occurrence Handle1:CAS:528:DC%2BD3cXjs1KlsL8%3D Occurrence Handle10830953

    CAS  PubMed  Google Scholar 

  30. JD Thompson DG Higgins TJ Gibson (1994) ArticleTitleCLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22 4673–4680 Occurrence Handle7984417

    PubMed  Google Scholar 

  31. AV Tkatchenko RP Visconti L Shang T Papenbrock ND Pruett (2001) ArticleTitleOverexpression of Hoxc13 in differentiating keratinocytes results in downregulation of a novel hair keratin gene cluster and alopecia. Development 128 1547–1558 Occurrence Handle1:CAS:528:DC%2BD3MXktVWlsLs%3D Occurrence Handle11290294

    CAS  PubMed  Google Scholar 

  32. NR Watts LN Jones N Cheng JS Wall DA Parry (2002) ArticleTitleCryo-electron microscopy of trichocyte (hard alpha-keratin) intermediate filaments reveals a low-density core. J Struct Biol 137 109–118 Occurrence Handle10.1006/jsbi.2002.4469 Occurrence Handle1:CAS:528:DC%2BD38XksVygsLk%3D Occurrence Handle12064938

    Article  CAS  PubMed  Google Scholar 

  33. SJ Yoon J LeBlanc-Straceski D Ward K Krauter R Kucherlapati (1994) ArticleTitleOrganization of the human keratin type II gene cluster at 12q13. Genomics 24 502–508 Occurrence Handle10.1006/geno.1994.1659 Occurrence Handle1:CAS:528:DyaK2MXjtVemu78%3D Occurrence Handle7536183

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan

    Kazunori Shibuya, Jun Kudoh, Izumi Obayashi, Atsushi Shimizu, Takashi Sasaki, Shinsei Minoshima & Nobuyoshi Shimizu

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  1. Kazunori Shibuya
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  2. Jun Kudoh
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  3. Izumi Obayashi
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  4. Atsushi Shimizu
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  5. Takashi Sasaki
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  6. Shinsei Minoshima
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  7. Nobuyoshi Shimizu
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Correspondence to Nobuyoshi Shimizu.

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Shibuya, K., Kudoh, J., Obayashi, I. et al. Comparative genomics of the keratin-associated protein (KAP) gene clusters in human, chimpanzee, and baboon . Mamm Genome 15, 179–192 (2004). https://doi.org/10.1007/s00335-003-2313-9

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  • DOI: https://doi.org/10.1007/s00335-003-2313-9

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