Human Genetics Unit: Staff Papers 2004

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1. Aijaz, S.; Clark, B.J.; Williamson, K.; van Heyningen, V.; Morrison, D.; Fitzpatrick, D.; Collin, R.; Ragge, N.; Christoforou, A.; Brown, A. and Hanson, I. Absence of SIX6 mutations in microphthalmia, anophthalmia, and coloboma. Investigative Ophthalmology & Visual Science 45:3871-3876, 2004

2. Auwerx, J.; Avner, P.; Baldock, R.; Ballabio, A.; Balling, R.; Barbacid, M.; Berns, A.; Bradley, A.; Brown, S.; Carmeliet, P.; Chambon, P.; Cox, R.; Davidson, D.; Davies, K.; Duboule, D.; Forejt, J.; Granucci, F.; Hastie, N.; de Angelis, M.H.; Jackson, I.; Kioussis, D.; Kollias, G.; Lathrop, M.; Lendahl, U.; Malumbres, M.; von Melchner, H.; Muller, W.; Partanen, J.; Ricciardi-Castagnoli, P.; Rigby, P.; Rosen, B.; Rosenthal, N.; Skarnes, B.; Stewart, A.F.; Thornton, J.; Tocchini-Valentini, G.; Wagner, E.; Wahli, W. and Wurst, W. The European dimension for the mouse genome mutagenesis program. Nat Genet 36:925-927, 2004

3. Bamiou DE, Musiek FE, Sisodiya SM, Free SL, Davies RA, Moore A, van Heyningen V, Luxon LM. Deficient auditory interhemispheric transfer in patients with PAX6 mutations. Ann Neurol. Oct;56(4):503-9. 2004

4. Beaujean,N.; Taylor,J.E.; McGarry,M.; Gardner,J.O.; Wilmut,I.; Loi,P.; Ptask,G.; Galli,C.; Lazzari,G.; Bird,A.; Ypung,L.E. and Meehan,R.R. The effect of interspecific oocytes on demethylation of sperm DNA. PNAS 101(20):7636-7640, 2004

5. Beaujean,N.; Taylor,J.; Gardner,J.; Wilmut,I.; Meehan,R. and Young,L. Effect of Limited DNA Methylation Reprogramming in the Normal Sheep Embryo on Somatic Cell Nuclear Transfer. Biology of Reproduction 71:185-193, 2004

6. Bickmore, W.A.; Mahy, N.I. and Chambeyron, S. Do Higher-order Chromatin Structure and Nuclear Reorganization Play a Role in regulating Hox Gene Expression during Development. Cold Spring Harbor Symposia on Quantitative Biology 69:1-7, 2004

7. Burger,A.; Davidson,D. and Baldock,R. Bioinformatics Formalization of mouse embryo anatomy Bioinformatics 20(2):259-267, 2004

8. Bryson-Richardson,R.J.; Logan,D.; Currie,P.D. and Jackson,I.J. Large-scale analysis of gene structure in rhodopsin-like GPCRs; evidence for widespread loss of an ancient intron. Gene: 338 15-23, 2004

9. Campopiano, D.J; Clarke, D.J.; Polfer,N.C.; Barran, P.E.; Langley, R.J.; Govan,J.R.W.; Maxwell, A.; Dorin, J.R. Structure-activity relationships in defensin dimers. JBC 279:48671-9, 2004

10. Chambeyron,S. and Bickmore,W.A. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Genes and Development 18:1119-1130, 2004

11. Chambeyron,S. and Bickmore,W.A. Does looping and clustering in the nucleus regulate gene expression. Current Opinion Cell Biology 16:256-262, 2004

12. Charizopoulou, N.; Jansen, S.; Dorsch, M.; Stanke, F.; Dorin, J.; Hedrich, H.J. and Burkhard, T. Instablilty of the insertional mutation in Cftr TgH(neoim)Hgu cystic fibrosis mouse model. BMC Genetics 5:2004

13. Clark, A.J.; Stockton, D.; Elder, A.; Wilson, R.G. and Dunlop, M.G. Assessment of outcomes after colorectal cance resection in the elderly as a rationale for screening and early detection. British Journal of Surgery 91:1345-1351, 2004

14. Collinson,M.J.; Chanas,S.A.; Hill,R.E. and West,J.D. Corneal Development Limbal Stem Cell Function, and Corneal Epithelial Cell Migration in the Pax6+/- Mouse. Investigative Ophthalmology and Visual Science 45(4):1101-1108, 2004

15. Collinson, M.J.; Hill,R.E. and West, J.D. Analysis of mouse development with chimeras and mosaics. Int J Dev Biol 48:793-804, 2004

16. Cooke,H.J Silence of the centromeres - not. Trends in Biotechnology 22(7):319-321, 2004

17. Cross,S.H.; Morgan,J.E.; Pattyn,A.; West,K.; McKie,L.; Hart,A.; Thuang,C.; Brunet,J-F. and Jackson,I.J. Haploinsufficiency for Phox2b in mice causes dilated pupils and atrophy of the ciliary ganglion: mechanistic insights into human congenital central hypoventilation syndrome. Human Molecular Genetics 13(14):1433-1439, 2004

18. Daggett, D.F.; Boyd, C.A.; Gautier, P.; Bryson-Roibertson,R.J.; Thisse, C.; Thisse, B.; Amacher,S.L. and Currie, P.D. Developmentally restricted actin-regulatory molecules control morphogenetic cell movements in the zebrafish gastrula. Current Biology 14:1632-1638, 2004

19. Davidson, D.J.; Webb, S.; Teague, P.; Govan, J.R. and Dorin, J.R. Lung pathology in response to repeated exposure to Staphylococcus aureus in congenic residual function cystic fibrosis mice does not increase in response to decreased CFTR levels or increased bacterial load. Pathobiology 71:152-158, 2004

20. Davies JA, Ladomery M, Hohenstein P, Michael L, Shafe A, Spraggon L, Hastie N. Development of an siRNA-based method for repressing specific genes in renal organ culture and its use to show that the Wt1 tumour suppressor is required for nephron differentiation. Hum Mol Genet. 13(2):23546, 2004

21. De las Haras,J.I.; D'Aiuto,L. and Cooke,H. Mammalian Artificial Chromosome Formation in Human Cells After Lipofection of a Precursor. In:Methods in Molecular Biology Vol.240: 187-206, 2004

22. Deary,I.J.; Whiteman,M.C.; Pattie,A.; Starr,J.M.; Hayward,C.; Wright,A.F.; Visscher,P.M.; Tynan,M.C.; Whalley,L.J. Apolipoprotein e gene variability and cognitive functions at age 79: a follow-up of the Scottish mental survey of 1932. Psychology and Aging 19(2):367-371, 2004

23. Deary,I.J.; Wright, A.F.; Harris, S.E.; Whalley, L.J. and Starr, J.M. Searching for genetic influences on normal cognitive ageing. Trends Cogn Sci 8:178-184, 2004

24. Din, F.V.; Dunlop,M.G.; Stark,L.A. Evidence for colorectal cancer cell specificity of aspirin effects on NF kappa B signalling and apoptosis. Br J Cancer 91(2):381-8, 2004

25. European Mouse Mutagenesis Consortium (Baldock, R.; Davidson, D., Hastie, N. and Jackson, I.J.) The European dimension for the mouse genome mutagenesis program. Nature Genetics 36(9):925-927, 2004

26. Farrington, S.M. and Dunlop, M.G. Familial colon cancer syndromes and their genetics. In: Genetic Predisposition to Cancer. Eeles, R. et al. (Eds.), London, Hodder Arnold. 2004, 315-330

27. Forster,T.; Costa,Y.; Roy,D.; Cooke,H.J. and Maratou,K Triple-target microarray experiments: a novel experimental strategy. BMC Genomics 5:13, 2004

28. Gilbert, N.; Boyle, S.; Fiegler, H.; Woodfine, K., Carter, N.P. and Bickmore, W.A. Chromatin architecture of the human genome; gene-rich domains are enriched in open chromatin fibers. Cell 118:555-566, 2004

29. Gilchrist,S.; Gilbert,N.; Perry,P. and Bickmore,W.A. Nuclear organization of centromeric domains is not perturbed by inhibition of histone deacetylases. Chromosome Research 12:505-516, 2004

30. Gilchrist, S.; Gilbert,N.; Perry, P.; Ostlund, C.; Worman, H.J. and Bickmore, W.A. Altered protein dynamics of disease-associated lamin A mutants. BMC Cell Biology 5:46, 2004

31. Gkoutos, G.V.; Green, E.C.J.; Mallon, A.M.; Hancock, J.M. and Davidson, D. Building Mouse Phenotype Ontologies. Pac Symp Biocomput 178-189, 2004

32. Gkoutos, G.V.; Green, E.C.J; Mallon, A-M.; Hancock, J.M. and Davidson, D. Using ontologies to describe mouse phenotypes. Genome Biology 6:R8, 2004

33. Gorgoni,B. and Gray,N.K. The roles of cytoplasmic poly(A)-binding proteins in regulating gene expression: A developmental perspective. Briefings in Functional Genomics and Proteomics 3(2):125-141, 2004

34. Haines,L.; Neyt,C.; Gautier,P.; Keenan,D.G.; Bryson-Richardson,R.J.; Hollway,G.E.; Cole,N.J. and Currie,P.D. Met and Hgf signaling controls hypaxial muscle and lateral line development in the zebrafish. Development 131:4857-4869, 2004

35. Hanks, S.; Coleman, K.; Reid, S.; Plaja, A.; Firth, H.; Fitzpatrick, D.; Kidd, A.; Mehes, K.; Nash, R.; Robin, N.; Shannon, N.; Tolme, J.; Swansbury, J.; Irrthum, A.; Douglas, J. and Rahman, N. Constitutional aneuploidy and cancer predisposition caused by biallelic mutations in /BUB1B. /Nature Genetics 36(11):1159-1161, 2004

36. Hartmann-Petersen, R. and Gordon,C. Integral UBL domain proteins: a family of proteasome interacting proteins. Seminars in Cell & Developmental Biology 15:247-259, 2004

37. Hartmann-Petersen, R. and Gordon, C. Protein degradation: recognition of ubiquitinylated substrates. Current Biology 14:R754-756, 2004

38. Hartmann-Petersen, R. and Gordon,C. Proteins interacting with the 26S proteasome. Cellular and Molecular Life Sciences 61:1589-1595, 2004

39. Hartmann-Petersen,R.; Wallace,M.; Hofmann,K.; Koch,G.; Johnsen,A.H.; Hendil,K.B.; and Gordon,C. The Ubx2 and Ubx3 Cofactors Direct Cdc48 Activity to Proteolytic and Nonproteolytic Ubiquitin-Dependent Processes. Current Biology 14:824-828, 2004

40. Hecksher-Sorensen, J.; Watson, R.P.; Lettice, L.A. Serup, P. Eley, L.; De Angelis, C.; Ahlgren, U. and Hill, R.E. The splanchnic mesodermal plate directs spleen and pancreatic laterality, and is regulated by Bapx1/Nkx3.2. Development 131:4665-4675, 2004

    
    

41. Hohenstein,P. Tumour Suppressor Genes - One Hit Can Be Enough. PloS Biology 2(2):0165-0166, 2004

42. Jackson,I. The G-netics of dark skin. Nature Genetics 36(9):935-936, 2004

43. Jackson, M.; Krassowska, A.; Gilbert, N.; Chevassut, T.; Forrester, L.; Ansell, J. and Ramsahoye, B. Severe Clobal DNA Hypomethylation Blocks Differentiation and Induces Histone Hyperacetylation in Embryonic Stem Cells. Mollecular and Cellular Biology 24:8862-8871, 2004

44. Jacobson, S.G.; Sumaroka, A.; Aleman, T.S.; Cideciyan, A.V.; Schwartz, S.B.; Roman, A.J.; McInnes, R.R.; Sheffield, V.C.; Stone, E.M., Swaroop and A., Wright, A.F. Nuclear receptor NR2E3 gene mutations distort human retinal laminar architecture and cause an unusual degeneration. Hum.Mol Genet. 13:1893-1902, 2004

45. Karasavvas,K.A.; Baldock,R. and Burger,A. Bioinformatics integration and agent technology. Journal of Biomedical Informatics 37:205-219, 2004

46. Keegan,L.P.; Leroy,A.; Sproul,D. and O'Connell,M.A. Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes Genome Biology 5(2):209, 2004

47. Kerwin J, Scott M, Sharpe J, Puelles L, Robson SC, Martinez-de-la-Torre M, Ferran JL, Feng G, Baldock R, Strachan T, Davidson D, Lindsay S. 3 dimensional modelling of early human brain development using optical projection tomography. BMC Neurosci. 5(1):27, 2004

48. Kleinjan,D.A.; Seawright,A.; Childs,A.J. and van Heyningen,V. Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription. Developmental Biology 265(2):462-477, 2004

49. Lee,D.; Cross,S.H.; Strunk,K.E.; Morgan,J.E.; Bailey,C.L.; Jackson,I.J. and Treadgill,D.W. Wa5 is a novel ENU-induced antimorphic allele of the epidermal growth factor receptor. Mammalian Genome 15:525-536, 2004

50. Liakos, K.; Burger, A. and Baldock, R. A Scalable Mediator Approach to Process Large Biomedical 3D Images. IEEE Transactions on Information Technology in Biomedicine 8:354-259, 2004

51. Magin-Lachmann C, Kotzamanis G, D'Aiuto L, Cooke H, Huxley C, Wagner E. In vitro and in vivo delivery of intact BAC DNA -- comparison of different methods. J Gene Med. Feb;6(2):195-209, 2004

52. Marotou,K.; Forster,T.; Costa,Y.; Taggart,M.; Speed,R.M.; Ireland,J.; Teague,P.; Roy,D. and Cooke,H.J. Expression Profiling of the Developing Testis in Wild-Type and Dazl Knockout Mice. Molecular Reproduction and Development 67:26-54, 2004

53. McBride DJ and Kleinjan DA. Rounding up active cis-elements in the triple C corral: combining conservation, cleavage and conformation capture for the analysis of regulatory gene domains. Brief Funct Genomic Proteomic. 3(3):267-79, 2004

54. Meilhac,S.M.; Esner,M.; Kerszberg,M.; Moss,J.E. and Buckingham, M.E. Oriented clonal cell growth in the developing mouse mycardium underlies cardiac morphogenesis. Journal Cell Biology 164(1):97-109, 2004

55. Mitchell, R.J.; Brewster, D.H.; Campbell, H.; Porteous, M.E.; Wyllie, A.H.; Bird, C.C. and Dunlop, M. Accuracy of reporting of family history of colorectal cancer. Gut 53:291-295, 2004

56. Niksic,M.; Slight,J.; Sanford,J.R.; Caceres,J.F. and Hastie,N.D. The Wilms' tumour protein (WT1) shuttles between nucleus and cytoplasm and is present in functional polysomes Human Molecular Genetics 13(4):463-471, 2004

57. Pall, G.S.; Wallis, J.; Axton, R.; Brownstein, D.; Gautier, P.; Buerger, K.; Mulford, C.; Mullins, J.J. and Forrester, L.M. A novel transmembrane MSP-containing protein that plays a role in right ventricle development. Genomics 84:1051-1059, 2004

58. Ramuirez, A.; Page, A.; Grandarillas, A.; Zanet, J.; Pibre, S.; Vidal, M.; Tusell, L.; Genesca, A.; Whitaker, D.A.; Melton, D.W. and Jorcano, J.L. A Keratin K5Cre Transgenic Line Appropriate for Tissue-Specific or Generalized Cre-Mediated Recombination. Genesis 39:52-57, 2004

59. Rollman, E.; Arnheim, L.; Collier, B.; Oberg, D.; Hall, H.; Klingstrom, J.; Dillner, J.; Pastrana, D.V.; Buck, C.B.; Hinkula, J.; Wahren, B. and Schwartz, S. HPV-16 L1 genes with inactivated negative RNA elements induce potent immune responses. Virology 322:182-189, 2004

60. Rovio, A.T.; Abel, J.; Ahola, A.L.; Andres, A.M.; Bertranpetit, J.; Blancher, A.; Bontrop, R.E.; Chemnick, L.G.; Cooke, H.J.; Cummins, J.M.; Davis, H.A.; Elliott, D.J.; Fritsche, E.; Hargreave, T.B.; Hoffman, S.M.; Jequier, A.M.; Kao, S.H.; Kim, H.S.; Marchington, D.R.; Mehmet, D.; Otting, N.; Poulton, J.; Ryder, O.A.; Schuppe, H.C.; Takenaka, O.; Wei, Y.H.; Wichmann, L. and Jacobs, H.T. A prevalent POLG CAG microsatellite length allele in humans and African great apes. Mamm Genome 15:492-502, 2004

61. Rudan I, Stevanovic R, Vitart V, Vuletic G, Sibbett L, Vuletic S, Ivankovic D, Szirovicza L, Stanic A, Hayward C, Campbell H, Cvjetanovic B. Lost in transition--The Island of Susak (1951-2001). Coll Antropol. 2004 Jun;28(1):403-21.

62. Ruzov, A.; Dunican, D.S.*; Prokhortchouk, A.; Pennings, S.; Stancheva, I.; Prockhortchouk, E. and *Meehan, R.R.* Kaiso is a genome-wide repressor of transcription that is essential for amphibian development. Development 131:6185-6194, 2004

63. Sanford, J.R. and Caceres, J.F. Pre-mRNA splicing: life at the centre of the central dogma. Journal of Cell Science 117:6261-6263, 2004

64. Sanford,J.R.; Gray,N.K.; Beckmann,K. and Caceres,J.F. A novel role for shuttling SR proteins in mRNA translation. Genes & Development 18:755-768, 2004

65. Semple CA. Deep genomics in shallow times: the finished sequence of human chromosomes 13 and 19. Eur J Hum Genet. 12(11):875-6, 2004

66. Sharpe, J. Optical Projection Tomography. Annu Rev Biomed Eng 6:209-28, 2004

67. Shen,M-H. Mammalian Artificial Chromosomes: Methods and Protocols. (Book Review) Chromome Research 12:415-416, 2004

68. Smyth,I.; Du,X.; Taylor,M.S; Justice,M.J; Beutler,B. and Jackson,I.J. The extracellular matrix gene Frem 1 is essential for the normal adhesion of the embryonic epidermis. PNAS 101(37):13560-5, 2004

69. Smyth, I.; Ellis, T.; Hetherington, R.; Riley, E.; Narang, M.; Mahony, D.; Wicking, C.; Rothenagel, J.A. and Wainwright, B.J. Krt6a-Cre Transgenic Mice Direct Loxp-Mediated Recombination to the Companion Cell Layer of the Hair Follicle and Following Induction by Retinoic Acid to the Interfollicular Epidermis. Journal of Investigative Dermatology 122:232-234, 2004

70. Sutherland,H.G.E.; Lam,Y.W.; Briers,S.; Lamond,A.I. and Bickmore,W.A. 3D3/lyric: a novel transmembrane protein of the endoplasmic reticulum and nuclear envelope, which is also present in the nucleolus. Experimental Cell Research 294:94-105, 2004

71. Stone, M.; Hartmann-Petersen, R.; Seeger, S.; Bech-Otschir, D.; Wallace, M. and Gordon, C. Uch2/Uch37 is the Major Deubiquitinating Enzyme Associated with the 26 S Proteasome in Fission Yeast. Jounal of Molecular Biology 344:697-706, 2004

72. Thomson,I.; Gilchrist,S.; Bickmore,W.A. and Chubb,J.R. The Radial Positioning of Chromatin Is Not Inherited through Mitosis but Is Established De Novo in Early G1. Current Biology 14:166-172, 2004

73. Tenesa,A.; Wright,A.F.; Knott,S.A.; Carothers,A.D.; Hayward,C.; Angius,A.; Persico,I.; Maestrale,G.; Hastie,N.D.; Pirastu,M. and Visscher PM. Extent of linkage disequilibrium in a Sardinian sub-isolate: sampling and methodological considerations. Hum Mol Genet. 13(1):25-33. 2004

74. Thomson, I., Gilchrist, S., Bickmore, W.A., Chubb, J.R. The radial positioning of chromatin is not inherited through mitosis but is established de novo in early G1. Curr Biol 14:166-172, 2004

75. Thomson,P.J.; Mitchell,T.N.; Free,S.L.; Williamson,K.A.; Hanson,I.M.; van Heyningen,V. ; Moore,A.T. and Sisodiya,S.M. Cognitive functioning in humans with mutations of the PAX6 gene. Neurology 62:1216-1218, 2004

76. Tucker,A.S.; Watson,R.P.; Lettice,L.A.; Yamada,G. and Hill,R.E. Bapx1 regulates patterning in the middle ear: altered regulatory role in the transition from the proximal jaw during vertebrate evolution. Development 131:1235-1245, 2004

77. van Heyningen,V. and Williamson,K. PAX6 and Aniridia and related Phenotypes. In:Inborn Errors of Development:the molecular basis of clinical disorders of morphogenesis. Epstein, C. et al. (Eds.), 649-657, 2004

78. van Heyningen,V. and Yeyati, P.L. Mechanisms of non-Mendelian inheritance in genetic disease. Human Molecular Genetics 13(Review Issue 2):R225-R233, 2004

79. Wilkie,A.L.; Jordan,S.A.; Sharpe,J.A.; Price,D.J.and Jackson,I.J. Widespread tangential dispersion and extensive cell death during early neurogenesis in the mouse neocortex. Developmental Biology 267(1):109-118, 2004

80. Wright, A.F.: Jacobson, S.G.; Cideciya, A.V.; Roman, A.J.; Shu, X.; Vlachantoni, D.; McInnes, R.R and Riemersma, R.A. Lifespan and mitochondrial control of neurodegeneration. Nature Genetics 36(11), 1153-1158, 2005

81. Zeng,K; de las Heras, J.I.; Ross,A.; Yang,J.; Cooke,H. and Shen, M-H. Localisation of centromeric proteins to a fraction of mouse minor satellite DNA on a mini-chromosome in human, mouse and chicken cells. Chromosoma 113:84-91, 2004