Genomes and Genes
Affiliation: Wellcome Trust Genome Campus
- Immunogenomics: molecular hide and seekMarcos M Miretti
Immunogenomics Laboratory, The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Hum Genomics 2:244-51. 2006..The discussion will focus on data available for the major histocompatibility complex and the leukocyte receptor complex, the two most polymorphic regions of the human immune sub-genome...
- DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome projectVardhman K Rakyan
The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
PLoS Biol 2:e405. 2004..e., the vast majority of the analysed regions were either hypo- or hypermethylated), tissue specificity, inter-individual variation, and correlation with independent gene expression data...
- A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafishJennifer G Sambrook
Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 ISA, UK
BMC Genomics 6:152. 2005..Here we report a survey of MHC genes and their paralogues in the zebrafish genome...
- Evolution and comparative analysis of the MHC Class III inflammatory regionJanine E Deakin
ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia
BMC Genomics 7:281. 2006..We also discuss the extent of sequence conservation across the entire region and identify elements conserved in evolution...
- Identification of the ancestral killer immunoglobulin-like receptor gene in primatesJennifer G Sambrook
Immunogenomics Laboratory, Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 ISA, UK
BMC Genomics 7:209. 2006..Since few KIR remain orthologous between species, with only one of them, KIR2DL4, shown to be common to human, apes and monkeys, the evolution of the KIR gene family in primates remains unclear...
- The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancerYing Liu
Cancer Research UK Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
BMC Genet 3:20. 2002..To accelerate the identification of genes, we sequenced the entire contig of approximately 1.1 Mb. Seven genes were identified within the region of allele loss between D6S264 and D6S149...
- The human major histocompatability complex: lessons from the DNA sequenceS Beck
The Sanger Centre, Wellcome Trust Genome Campus, University of Cambridge, Cambridge CB10 1SA United Kindgom
Annu Rev Genomics Hum Genet 1:117-37. 2000..We suggest some ways in which the sequence may be exploited in the future to explore the relationship between the extraordinary polymorphism of the region and its association with both autoimmune and infectious diseases...
- Sequence organisation of the class II region of the human MHCS Beck
Sanger Centre, Cambridge, UK
Immunol Rev 167:201-10. 1999....
- The DNA sequence and comparative analysis of human chromosome 10P Deloukas
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
Nature 429:375-81. 2004..Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence...
- The cluster of BTN genes in the extended major histocompatibility complexD A Rhodes
Department of Immunology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, United Kingdom
Genomics 71:351-62. 2001..Most transcripts of BTN2 subfamily genes contained this domain, whereas BTN3 genes did not. Using immunofluorescence, we showed surface expression of BTN-green fluorescent protein fusions in mammalian cell transfectants...
- BTL-II: a polymorphic locus with homology to the butyrophilin gene family, located at the border of the major histocompatibility complex class II and class III regions in human and mouseM Stammers
Sanger Centre, Wellcome Trust Genome Campus, Cambridge, UK
Immunogenetics 51:373-82. 2000..In the light of the newly discovered locus, we revisit and discuss the possible origin of the butyrophilin gene family...
- DNA sequence and analysis of human chromosome 9S J Humphray
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 429:369-74. 2004..We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection...
- The DNA sequence and biological annotation of human chromosome 1S G Gregory
The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK
Nature 441:315-21. 2006....
- The genomic context of natural killer receptor extended gene familiesJ Trowsdale
Department of Pathology, University of Cambridge, UK
Immunol Rev 181:20-38. 2001..The picture that emerges from both complexes is of eternal evolutionary restlessness, presumably in response to resistance to disease...
- The DNA sequence and comparative analysis of human chromosome 20P Deloukas
The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
Nature 414:865-71. 2001....
- Characterization of clustered MHC-linked olfactory receptor genes in human and mouseR M Younger
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, CB10 1SA, UK
Genome Res 11:519-30. 2001..Taken together with our previous finding that ORs are also polymorphic, the presented data indicate that the expression, function, and evolution of these interesting genes might be more complex than previously thought...
- Gene organisation, sequence variation and isochore structure at the centromeric boundary of the human MHCR Stephens
Immunology, Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
J Mol Biol 291:789-99. 1999..By comparative analysis, we have precisely identified the mouse/human synteny breakpoint at the centromeric end of the extended MHC class II region between the genes HSET and PHF1...
- The DNA sequence and analysis of human chromosome 13A Dunham
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
Nature 428:522-8. 2004..Chromosome 13 has one of the lowest gene densities (6.5 genes per Mb) among human chromosomes, and contains a central region of 38 Mb where the gene density drops to only 3.1 genes per Mb...
- The MHC haplotype project: a resource for HLA-linked association studiesR J N Allcock
University of Cambridge, UK
Tissue Antigens 59:520-1. 2002
- The DNA sequence and analysis of human chromosome 6A J Mungall
The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Nature 425:805-11. 2003..Within the essential immune loci of the major histocompatibility complex, we find HLA-B to be the most polymorphic gene on chromosome 6 and in the human genome...
- Epigenomics: genome-wide study of methylation phenomenaK L Novik
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
Curr Issues Mol Biol 4:111-28. 2002..Here, we review the current and future potential of this field and introduce the pilot study towards the Human Epigenome Project (HEP)...
- The LRC haplotype project: a resource for killer immunoglobulin-like receptor-linked association studiesR Horton
Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Tissue Antigens 68:450-2. 2006..The LRC haplotype project aims to provide this knowledge by sequencing common LRC haplotypes...
- Chromosomal localization, gene structure and transcription pattern of the ORFX gene, a homologue of the MHC-linked RING3 geneK L Thorpe
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Gene 200:177-83. 1997..RING3 and ORFX are found to be ubiquitously expressed in human adult and foetal tissues. Evidence suggests that the two genes may have arisen from an ancient duplication in a common ancestral chromosome...
- DNA sequence and structure of the mouse RING3 gene: identification of variant RING3 transcriptsK L Thorpe
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, England
Immunogenetics 48:82-6. 1998
- The genomic structure and promoter region of the human parkin geneS Asakawa
Department of Molecular Biology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku ku, Tokyo, 160 8582, Japan
Biochem Biophys Res Commun 286:863-8. 2001..Furthermore, we located a neighboring novel gene in a head-to-head direction with Parkin with only a 198-bp interval...
- Applying whole-genome studies of epigenetic regulation to study human diseaseJ D Lieb
Department of Biology, Carolina Center for Genome Sciences, The University of North Carolina, Chapel Hill, NC, USA
Cytogenet Genome Res 114:1-15. 2006
- Small GTPase Rac1: structure, localization, and expression of the human geneP Matos
Centre for Human Genetics, National Institute of Health Dr Ricardo Jorge, Lisbon, 1649 016, Portugal
Biochem Biophys Res Commun 277:741-51. 2000..These data indicate that the RAC1 gene encodes two signaling GTPases. The gene structure reported here will enable studies on the regulation of RAC1 expression during tumorigenesis and development...
- Evolutionary dynamics of non-coding sequences within the class II region of the human MHCS Beck
DNA Sequencing Laboratory, Imperial Cancer Research Fund, London, England
J Mol Biol 255:1-13. 1996..We also report the finding of a class I-related pseudogene (HLA-ZI) in the middle of the class II region, which provides the first direct evidence for DNA exchange between these two related regions in man...
- Cloning and characterization of human phosphatase inhibitor-2 (IPP-2) sequencesP Sanseau
ICRF, Human Immunogenetics, London, UK
Mamm Genome 5:490-6. 1994..We sequenced one gene located in the major histocompatibility complex (MHC) on Chromosome (Chr) 6 that contained the entire coding region of IPP-2...
- The major and a minor class II beta-chain (B-LB ) gene flank the Tapasin gene in the B-F /B-L region of the chicken major histocompatibility complexJ P Jacob
Institute of Animal Health, Compton, Berkshire, RG20 7NN, UK
Immunogenetics 51:138-47. 2000....
- Human trefoil peptides: genomic structure in 21q22.3 and coordinated expressionP Gott
Department of Anthropology and Human Genetics, University of Tubingen, Germany
Eur J Hum Genet 4:308-15. 1996..Using RT-PCR, a change in the pattern of trefoil gene expression is detected in tissue samples from normal gastric mucosa, hyperplastic polyps, gastric cancer, and gastric cancer cell lines, respectively...
- Genomic structure and domain organisation of the human Bak geneJ A Herberg
Imperial Cancer Research Fund Laboratories, 44 Lincoln s Inn Fields, London, UK
Gene 211:87-94. 1998..The position of a single intron was conserved in comparison to other members of the Bcl-2 family, namely Bax, CED-9, Bcl-X and Bcl-2, but all other introns were displaced, consistent with a divergent phylogeny...
- Polymorphism in a second ABC transporter gene located within the class II region of the human major histocompatibility complexS H Powis
Imperial Cancer Research Fund Laboratories, Lincoln s Inn Fields, London, United Kingdom
Proc Natl Acad Sci U S A 89:1463-7. 1992..We have identified two RING11 alleles, which differ in the length of their derived protein sequence by 17 amino acids. The more common of these alleles is present in a Caucasoid population at a frequency of 79%...
- Sequences encoded in the class II region of the MHC related to the 'ABC' superfamily of transportersJ Trowsdale
Imperial Cancer Research Fund, Lincolns Inn Fields, London, UK
Nature 348:741-4. 1990..This superfamily includes the human multidrug-resistance protein, and a series of transporters from bacteria and eukaryotic cells capable of transporting a range of substrates, including peptides...
- The genomic sequence and analysis of the swine major histocompatibility complexC Renard
LREG INRA CEA, Jouy en Josas, France
Genomics 88:96-110. 2006..We show that the centromere insertion has occurred within a cluster of BTNL genes located at the boundary of the class II and III regions, which might have resulted in the loss of an orthologue to human C6orf10 from this region...
- A proteasome-related gene between the two ABC transporter loci in the class II region of the human MHCR Glynne
Human Immunogenetics Laboratory, Imperial Cancer Research Fund, Lincoln s Inn Fields, London, UK
Nature 353:357-60. 1991..We have now identified a human gene with sequence homology to proteasome components. Remarkably, this gene maps between the two putative peptide transporter genes...
- Genomic organization of HLA-DMA and HLA-DMB. Comparison of the gene organization of all six class II families in the human major histocompatibility complexE Radley
Imperial Cancer Research Fund, London, United Kingdom
J Biol Chem 269:18834-8. 1994..One of these events seems to have partially replaced exon 1 in DPA2. The possibility of this event causing DPA2 to become a pseudogene is discussed...
- RPS6KA2, a putative tumour suppressor gene at 6q27 in sporadic epithelial ovarian cancerP A Bignone
Cancer Research UK, Molecular Oncology Laboratories, Ovarian Cancer Group, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, UK
Oncogene 26:683-700. 2007..In contrast, small interfering RNA against RPS6KA2 showed the opposite effect in 41M cells. The above results suggest that RPS6KA2 is a putative tumour suppressor gene to explain allele loss at 6q27...
- Amino acid sequence of mouse tenascin and differential expression of two tenascin isoforms during embryogenesisA Weller
Friedrich Miescher Laboratorium der Max Planck Gesellschaft, Tubingen, Germany
J Cell Biol 112:355-62. 1991..and P. Ekblom. 1988. J. Cell Biol. 107:2341-2349)...
- New autoantibodies in pediatric opsoclonus myoclonus syndromeA Kirsten
Institute of Biochemistry, Faculty of Medicine, Friedrichstrasse 24, Justus Liebig University, D 35392 Giessen, Germany
Ann N Y Acad Sci 1110:256-60. 2007..Antiproliferative and proapoptotic effects of these autoantibodies on neuroblastoma cell lines were noted as well. These results support the concept of a humoral autoimmune process in the pathogenesis of OMS...
- Analysis of the genomic region containing the tammar wallaby (Macropus eugenii) orthologues of MHC class III genesJ G R Cross
Comparative Genomics Unit, ARC Centre for Kangaroo Genomics, Research School of Biological Sciences, Australian National University, Canberra, Australia
Cytogenet Genome Res 111:110-7. 2005..Full length sequencing of BACs containing the three genes has been partially completed, and reveals the presence of a number of other tammar MHC III orthologues in this region...
- The major histocompatibility complex-encoded proteasome component LMP7: alternative first exons and post-translational processingR Glynne
Human Immunogenetics Laboratory, Imperial Cancer Research Fund, London
Eur J Immunol 23:860-6. 1993..To our knowledge, LMP7 provides the first biochemical evidence for such processing of proteasome components...
- Plasticity in the organization and sequences of human KIR/ILT gene familiesM J Wilson
Immunology Division, Department of Pathology, Tennis Court Road, Cambridge CB2 1QP, United Kingdom
Proc Natl Acad Sci U S A 97:4778-83. 2000..KIR genesis was followed by extensive duplication/deletion as well as intergenic sequence exchange, reminiscent of MHC class I genes, which provide KIR ligands...
- Large-scale chromatin organization of the major histocompatibility complex and other regions of human chromosome 6 and its response to interferon in interphase nucleiE V Volpi
Human Cytogenetics Laboratory, Imperial Cancer Research Fund, London WC2A 3PX, UK
J Cell Sci 113:1565-76. 2000..Our data are consistent with an association between large-scale chromatin organization of specific genomic regions and their transcriptional status...
- Genomic organization of the HSET locus and the possible association of HLA-linked genes with immotile cilia syndrome (ICS)K Janitz
Institut für Immungenetik, Universitatsklinikum Charite, Humboldt Universitat zu Berlin, Spandauer Damm 130, 14050 Berlin, Germany
Immunogenetics 49:644-52. 1999..Four single base substitutions were detected in the HSET gene, and none in the TUBB gene. On the basis of these data, a role of the HSET and TUBB products in the pathogenesis of ICS in the two families is unlikely...
- 5'-flanking motifs control cell-specific expression of trefoil factor genes (TFF)S Beck
Division of Molecular Genetics, Institute of Anthropology and Human Genetics, University of Tubingen, Germany
Int J Mol Med 2:353-61. 1998..Thus such specific DNA-protein interaction may explain the TFF peptides' cell specific expression pattern and altered levels in pathological conditions...
- The chicken B locus is a minimal essential major histocompatibility complexJ Kaufman
Institute for Animal Health, Compton, UK
Nature 401:923-5. 1999....
- Genomic analysis of the Tapasin gene, located close to the TAP loci in the MHCJ A Herberg
Imperial Cancer Research Fund Laboratories, London, GB
Eur J Immunol 28:459-67. 1998..The IgC domain was encoded by a separate exon. However, the positions of the other introns were not characteristic of other Ig superfamily genes, indicating that Tapasin has a distinct phylogeny...
- A homologue of the Drosophila female sterile homeotic (fsh) gene in the class II region of the human MHCS Beck
Imperial Cancer Research Fund, London, England
DNA Seq 2:203-10. 1992..This highly conserved gene may play an important role in human development. In addition, its location in the MHC class II region may be related to some HLA-associated diseases...
- Transcript analysis of the cystic fibrosis splicing mutation 1525-1G>A shows use of multiple alternative splicing sites and suggests a putative role of exonic splicing enhancersA S Ramalho
Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisboa, Portugal
J Med Genet 40:e88. 2003
- Phylogeny and structure of the RING3 geneK L Thorpe
DNA Sequencing Laboratory, Imperial Cancer Research Fund, PO Box 123, London WC2A 3PX, UK
Immunogenetics 44:391-6. 1996
- Divergent intron arrangement in the MB1/LMP7 proteasome gene pairS Abdulla
Imperial Cancer Research Fund, 44 Lincolns Inn Fields, Holborn, London WC2A 3PX, UK
Immunogenetics 44:254-8. 1996..The unique structure of MB1 implies a separate origin or different selection pressures acting at this particular locus. DNA repeat analysis provides information on the minimum time of separation of the MB1/LMP7 pair of genes...
- A third P-domain peptide gene (TFF3), human intestinal trefoil factor, maps to 21q22.3H Schmitt
Department of Anthropology and Human Genetics, University of Tubingen, Germany
Cytogenet Cell Genet 72:299-302. 1996..3 suggesting a physical linkage of all three trefoil peptide genes...
- The history of Seasonally Dry Tropical Forests in eastern South America: inferences from the genetic structure of the tree Astronium urundeuva (Anacardiaceae)S Caetano
Laboratoire de Systématique et de Biodiversité, Unité de Phylogénie et Génétique Moléculaires, Conservatoire et Jardin Botaniques, 1 Chemin de l Impératrice, CP 60, CH 1292 Chambésy, Geneve, Switzerland
Mol Ecol 17:3147-59. 2008..This study provides arguments that favour the existence of a previously more continuous formation of SDTF in eastern South America...