Aitchison Lab at ISB
Publications

  1. Nuttley, W. M., Aitchison, J. D., and Rachubinski, R. A. (1988) cDNA cloning and primary structure determination of the peroxisomal trifunctional enzyme hydratase-dehydrogenase-epimerase from the yeast Candida tropicalis pK233, Gene 69, 171-180
  2. Aitchison, J. D., and Rachubinski, R. A. (1990) In vivo import of Candida tropicalis hydratase-dehydrogenase-epimerase into peroxisomes of Candida albicans, Curr Genet 17, 481-486
  3. Aitchison, J. D., Murray, W. W., and Rachubinski, R. A. (1991) The carboxyl-terminal tripeptide Ala-Lys-Ile is essential for targeting Candida tropicalis trifunctional enzyme to yeast peroxisomes, J Biol Chem 266, 23197-23203
  4. Aitchison, J. D., Sloots, J. A., Nuttley, W. M., and Rachubinski, R. A. (1991) Sequence of the gene encoding Candida tropicalis peroxisomal trifunctional enzyme, Gene 105, 135-136
  5. Sloots, J. A., Aitchison, J. D., and Rachubinski, R. A. (1991) Glucose-responsive and oleic acid-responsive elements in the gene encoding the peroxisomal trifunctional enzyme of Candida tropicalis, Gene 105, 129-134
  6. Aitchison, J. D., Nuttley, W. M., Szilard, R. K., Brade, A. M., Glover, J. R., and Rachubinski, R. A. (1992) Peroxisome biogenesis in yeast, Mol Microbiol 6, 3455-3460
  7. Aitchison, J. D., Szilard, R. K., Nuttley, W. M., and Rachubinski, R. A. (1992) Antibodies directed against a yeast carboxyl-terminal peroxisomal targeting signal specifically recognize peroxisomal proteins from various yeasts, Yeast 8, 721-734
  8. Nuttley, W. M., Brade, A.M., Gaillardin, C., Eitzen, G.A., Glover, J.R., Aitchison, J.D., Rachubinski, R.A. (1993) Rapid identification and characterization of peroxisomal assembly mutants in Yarrowia lipolytica, Yeast 9, 507-517
  9. Nuttley, W. M., Brade, A. M., Eitzen, G. A., Veenhuis, M., Aitchison, J. D., Szilard, R. K., Glover, J. R., and Rachubinski, R. A. (1994) PAY4, a gene required for peroxisome assembly in the yeast Yarrowia lipolytica, encodes a novel member of a family of putative ATPases, J Biol Chem 269, 556-566
  10. Aitchison, J. D., Blobel, G., and Rout, M. P. (1995) Nup120p: a yeast nucleoporin required for NPC distribution and mRNA transport, J Cell Biol 131, 1659-1675
  11. Aitchison, J. D., Rout, M. P., Marelli, M., Blobel, G., and Wozniak, R. W. (1995) Two novel related yeast nucleoporins Nup170p and Nup157p: complementation with the vertebrate homologue Nup155p and functional interactions with the yeast nuclear pore-membrane protein Pom152p, J Cell Biol 131, 1133-1148
  12. Eitzen, G. A., Aitchison, J. D., Szilard, R. K., Veenhuis, M., Nuttley, W. M., and Rachubinski, R. A. (1995) The Yarrowia lipolytica gene PAY2 encodes a 42-kDa peroxisomal integral membrane protein essential for matrix protein import and peroxisome enlargement but not for peroxisome membrane proliferation, J Biol Chem 270, 1429-1436
  13. Aitchison, J. D., Blobel, G., and Rout, M. P. (1996) Kap104p: a karyopherin involved in the nuclear transport of messenger RNA binding proteins, Science 274, 624-627
  14. Rout, M. P., Blobel, G., and Aitchison, J. D. (1997) A distinct nuclear import pathway used by ribosomal proteins, Cell 89, 715-725
  15. Marelli, M., Aitchison, J. D., and Wozniak, R. W. (1998) Specific binding of the karyopherin Kap121p to a subunit of the nuclear pore complex containing Nup53p, Nup59p, and Nup170p, J Cell Biol 143, 1813-1830
  16. Mitchell, D. M., Zhou, M., Pariyarath, R., Wang, H., Aitchison, J. D., Ginsberg, H. N., and Fisher, E. A. (1998) Apoprotein B100 has a prolonged interaction with the translocon during which its lipidation and translocation change from dependence on the microsomal triglyceride transfer protein to independence, Proc Natl Acad Sci U S A 95, 14733-14738
  17. Wozniak, R. W., Rout, M. P., and Aitchison, J. D. (1998) Karyopherins and kissing cousins, Trends Cell Biol 8, 184-188
  18. Lee, D. C., and Aitchison, J. D. (1999) Kap104p-mediated nuclear import. Nuclear localization signals in mRNA-binding proteins and the role of Ran and Rna, J Biol Chem 274, 29031-29037
  19. Wylie, D. R., Glover, R. G., and Aitchison, J. D. (1999) Optic flow input to the hippocampal formation from the accessory optic system, J Neurosci 19, 5514-5527
  20. Aitchison, J. D., and Rout, M. P. (2000) The road to ribosomes. Filling potholes in the export pathway, J Cell Biol 151, F23-26
  21. Rout, M. P., and Aitchison, J. D. (2000) Pore relations: nuclear pore complexes and nucleocytoplasmic exchange, Essays Biochem 36, 75-88
  22. Rout, M. P., Aitchison, J. D., Suprapto, A., Hjertaas, K., Zhao, Y., and Chait, B. T. (2000) The yeast nuclear pore complex: composition, architecture, and transport mechanism, J Cell Biol 148, 635-651
  23. Aitchison, J. D., and Rout, M. P., (2001) The Encyclopedia of Genetics Brenner, S., and Miller, J. H., Ed., Academic Press, pp. 1352-1356.
  24. Dilworth, D. J., Suprapto, A., Padovan, J. C., Chait, B. T., Wozniak, R. W., Rout, M. P., and Aitchison, J. D. (2001) Nup2p dynamically associates with the distal regions of the yeast nuclear pore complex, J Cell Biol 153, 1465-1478
  25. Iouk, T. L., Aitchison, J. D., Maguire, S., and Wozniak, R. W. (2001) Rrb1p, a yeast nuclear WD-repeat protein involved in the regulation of ribosome biosynthesis, Mol Cell Biol 21, 1260-1271
  26. Marelli, M., Dilworth, D. J., Wozniak, R. W., and Aitchison, J. D. (2001) The dynamics of karyopherin-mediated nuclear transport, Biochem Cell Biol 79, 603-612
  27. Marelli, M., Lusk, C. P., Chan, H., Aitchison, J. D., and Wozniak, R. W. (2001) A link between the synthesis of nucleoporins and the biogenesis of the nuclear envelope, J Cell Biol 153, 709-724
  28. Pariyarath, R., Wang, H., Aitchison, J. D., Ginsberg, H. N., Welch, W. J., Johnson, A. E., and Fisher, E. A. (2001) Co-translational interactions of apoprotein B with the ribosome and translocon during lipoprotein assembly or targeting to the proteasome, J Biol Chem 276, 541-550
  29. Rout, M. P., and Aitchison, J. D. (2001) The nuclear pore complex as a transport machine, J Biol Chem 276, 16593-16596
  30. Aitchison, J. D., and Rout, M. P. (2002) A tense time for the nuclear envelope, Cell 108, 301-304
  31. Leslie, D. M., Grill, B., Rout, M. P., Wozniak, R. W., and Aitchison, J. D. (2002) Kap121p-mediated nuclear import is required for mating and cellular differentiation in yeast, Mol Cell Biol 22, 2544-2555
  32. Lusk, C. P., Makhnevych, T., Marelli, M., Aitchison, J. D., and Wozniak, R. W. (2002) Karyopherins in nuclear pore biogenesis: a role for Kap121p in the assembly of Nup53p into nuclear pore complexes, J Cell Biol 159, 267-278
  33. Smith, J. J., Marelli, M., Christmas, R. H., Vizeacoumar, F. J., Dilworth, D. J., Ideker, T., Galitski, T., Dimitrov, K., Rachubinski, R. A., and Aitchison, J. D. (2002) Transcriptome profiling to identify genes involved in peroxisome assembly and function, J Cell Biol 158, 259-271
  34. Yi, E. C., Marelli, M., Lee, H., Purvine, S. O., Aebersold, R., Aitchison, J. D., and Goodlett, D. R. (2002) Approaching complete peroxisome characterization by gas-phase fractionation, Electrophoresis 23, 3205-3216
  35. Aitchison, J., and Schwikowski, B (2003) Systems biology and elephants, Nature Cell Biology 5, 285
  36. Aitchison, J. D., and Galitski, T. (2003) Inventories to insights, J Cell Biol 161, 465-469
  37. Makhnevych, T., Lusk, C. P., Anderson, A. M., *Aitchison, J. D., and *Wozniak, R. W. (2003) Cell cycle regulated transport controlled by alterations in the nuclear pore complex, Cell 115, 813-823
  38. Rout, M. P., Aitchison, J. D., Magnasco, M. O., and Chait, B. T. (2003) Virtual gating and nuclear transport: the hole picture, Trends Cell Biol 13, 622-628
  39. Steiner-Mosonyi, M., Leslie, D. M., Dehghani, H., Aitchison, J. D., and Mangroo, D. (2003) Utp8p is an essential intranuclear component of the nuclear Trna export machinery of Saccharomyces cerevisiae, J Biol Chem 278, 32236-32245
  40. Sydorskyy, Y., Dilworth, D. J., Yi, E. C., Goodlett, D. R., Wozniak, R. W., and Aitchison, J. D. (2003) Intersection of the Kap123p-mediated nuclear import and ribosome export pathways, Mol Cell Biol 23, 2042-2054
  41. Tam, Y. Y., Torres-Guzman, J. C., Vizeacoumar, F. J., Smith, J. J., Marelli, M., Aitchison, J. D., and Rachubinski, R. A. (2003) Pex11-related proteins in peroxisome dynamics: a role for the novel peroxin Pex27p in controlling peroxisome size and number in Saccharomyces cerevisiae, Mol Biol Cell 14, 4089-4102
  42. Vizeacoumar, F. J., Torres-Guzman, J. C., Tam, Y. Y., Aitchison, J. D., and Rachubinski, R. A. (2003) YHR150w and YDR479c encode peroxisomal integral membrane proteins involved in the regulation of peroxisome number, size, and distribution in Saccharomyces cerevisiae, J Cell Biol 161, 321-332
  43. Lausted, C., Dahl, T., Warren, C., King, K., Smith, K., Johnson, M., Saleem, R., Aitchison, J., Hood, L., and Lasky, S. R (2004) POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer, Genome Biology 5, R58
  44. Leslie, D. M., Zhang, W., Timney, B. L., Chait, B. T., Rout, M. P., Wozniak, R. W., and Aitchison, J. D. (2004) Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import, Mol Cell Biol 24, 8487-8503
  45. Marelli, M., Smith, J. J., Jung, S., Yi, E., Nesvizhskii, A. I., Christmas, R. H., Saleem, R. A., Tam, Y. Y., Fagarasanu, A., Goodlett, D. R., Aebersold, R., Rachubinski, R. A., and Aitchison, J. D. (2004) Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane, J Cell Biol 167, 1099-1112
  46. Vizeacoumar, F. J., Torres-Guzman, J. C., Bouard, D., Aitchison, J. D., and Rachubinski, R. A. (2004) Pex30p, Pex31p, and Pex32p form a family of peroxisomal integral membrane proteins regulating peroxisome size and number in Saccharomyces cerevisiae, Mol Biol Cell 15, 665-677
  47. Dilworth, D. J., Tackett, A. J., Rogers, R. S., Yi, E. C., Christmas, R. H., Smith, J. J., Siegel, A. F., Chait, B. T., Wozniak, R. W., and Aitchison, J. D. (2005) The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control, J Cell Biol 171, 955-965
  48. Fagarasanu, M., Fagarasanu, A., Tam, Y. Y., Aitchison, J. D., and Rachubinski, R. A. (2005) Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae, J Cell Biol 169, 765-775
  49. Hwang, D., Rust, A. G., Ramsey, S., Smith, J. J., Leslie, D. M., Weston, A. D., de Atauri, P., Aitchison, J. D., Hood, L., Siegel, A. F., and Bolouri, H. (2005) A data integration methodology for systems biology, Proc Natl Acad Sci U S A 102, 17296-17301
  50. Hwang, D., Smith, J. J., Leslie, D. M., Weston, A. D., Rust, A. G., Ramsey, S., de Atauri, P., Siegel, A. F., Bolouri, H., Aitchison, J. D., and Hood, L. (2005) A data integration methodology for systems biology: experimental verification, Proc Natl Acad Sci U S A 102, 17302-17307
  51. Scott, R. J., Lusk, C. P., Dilworth, D. J., Aitchison, J. D., and Wozniak, R. W. (2005) Interactions between Mad1p and the nuclear transport machinery in the yeast Saccharomyces cerevisiae, Mol Biol Cell 16, 4362-4374
  52. Sydorskyy, Y., Dilworth, D. J., Halloran, B., Yi, E. C., Makhnevych, T., Wozniak, R. W., and Aitchison, J. D. (2005) Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein, Biochem J 388, 819-826
  53. Tackett, A. J., Dilworth, D. J., Davey, M. J., O'Donnell, M., Aitchison, J. D., Rout, M. P., and Chait, B. T. (2005) Proteomic and genomic characterization of chromatin complexes at a boundary, J Cell Biol 169, 35-47
  54. Fagarasanu, A., Fagarasanu, M., Eitzen, G. A., Aitchison, J. D., and Rachubinski, R. A. (2006) The peroxisomal membrane protein Inp2p is the peroxisome-specific receptor for the myosin V motor Myo2p of Saccharomyces cerevisiae, Dev Cell 10, 587-600
  55. Leslie, D. M., Timney, B., Rout, M. P., and Aitchison, J. D. (2006) Studying nuclear protein import in yeast, Methods 39, 291-308
  56. Niemistro, A., Selinummi, J., Saleem, R.., Shmulevich, I., Aitchison, J.D., Yli-Harja, O., (2006) Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis, in 28th IEEE EMBS Annual International Conference, New York, NY.
  57. Orrell, D., Ramsey, S., Marelli, M., Smith, J.J., Petersen, T.W., de Atauri, P., Aitchison, J.D., Bolouri, H. (2006) Feedback control of stochastic noise in the yeast galactose utilization pathway, Physica D 217, 64-76
  58. Pedrioli, P. G., Raught, B., Zhang, X.D., Rogers, R., Aitchison, J.D., Matunis, M., Aebersold, R. (2006) Automated identification of SUMOylation sites using mass spectrometry and SUMmOn pattern recognition software, Nature Methods 3, 533-539
  59. Ramsey, S. A., Smith, J. J., Orrell, D., Marelli, M., Petersen, T. W., de Atauri, P., Bolouri, H., and Aitchison, J. D. (2006) Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast, Nat Genet 38, 1082-1087
  60. Saleem, R. A., Smith, J. J., and Aitchison, J. D. (2006) Proteomics of the peroxisome, Biochim Biophys Acta 1763, 1541-1551
  61. Smith, J. J., Sydorskyy, Y., Marelli, M., Hwang, D., Bolouri, H., Rachubinski, R. A., and Aitchison, J. D. (2006) Expression and functional profiling reveal distinct gene classes involved in fatty acid metabolism, Mol Syst Biol 2, 2006 0009
  62. Taverna, S. D., Ilin, S., Rogers, R. S., Tanny, J. C., Lavender, H., Li, H., Baker, L., Boyle, J., Blair, L. P., Chait, B. T., Patel, D. J., Aitchison, J. D., Tackett, A. J., and Allis, C. D. (2006) Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs, Mol Cell 24, 785-796
  63. Vizeacoumar, F. J., Vreden, W. N., Aitchison, J. D., and Rachubinski, R. A. (2006) Pex19p binds Pex30p and Pex32p at regions required for their peroxisomal localization but separate from their peroxisomal targeting signals, J Biol Chem 281, 14805-14812
  64. Vizeacoumar, F. J., Vreden, W. N., Fagarasanu, M., Eitzen, G. A., Aitchison, J. D., and Rachubinski, R. A. (2006) The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner, J Biol Chem 281, 12817-12823
  65. Makhnevych, T., Ptak, C., Lusk, C. P., *Aitchison, J. D., and *Wozniak, R. W. (2007) The role of karyopherins in the regulated sumoylation of septins, J Cell Biol 177, 39-49
  66. Niemistö, A., Korpelainen, T., Saleem, R., Yli-Haja, O., Aitchison, J.D., Shmulevich, I., (2007) A K-Means Segmentation Method for Finding 2-D Object Areas Based on 3-D Image Stacks Obtained by Confocal Microscopy, in 29th International Conference of the IEEE Engineering in Medicine and Biology Society in conjunction with the Biennial Conference of the French Society of Biological and Medical Engineering, Lyon, France.
  67. Oeffinger, M., Wei, K. E., Rogers, R., Degrasse, J. A., Chait, B. T., Aitchison, J. D., and Rout, M. P. (2007) Comprehensive analysis of diverse ribonucleoprotein complexes, Nat Methods 4, 951-956
  68. Smith, J. J., Ramsey, S. A., Marelli, M., Marzolf, B., Hwang, D., Saleem, R. A., Rachubinski, R. A., and Aitchison, J. D. (2007) Transcriptional responses to fatty acid are coordinated by combinatorial control, Mol Syst Biol 3, 115
  69. Aitchison, J. D., and Wozniak, R. W. (2007) Cell biology: Pore puzzle, Nature 450, 621-622
  70. Gradolatto, A., Rogers, R., Lavender, H., Taverna, S.D., Allis, C.D., Aitchison, J.D., Tackett, A.J. (2008) Saccaromyces cerevisiae Yta7 regulates histone gene expression, Genetics 179(1): 291-304
  71. Saleem, R.A., Knoblach, B., Mast, F.D., Smith, J.J., Boyle, J., Dobson, C.M., Long-O'Donnell, R., Rachubinski, R.A., Aitchison, J.D. (2008) Genome-wide analysis of signalling networks regulating fatty acid induced gene expression and organelle biogenesis, J Cell Biol 2: 281-292

* Co-corresponding Authors

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