Genomes and Genes
Affiliation: National Institute for Medical Research
- Highly conserved non-coding sequences are associated with vertebrate developmentAdam Woolfe
Medical Research Council Rosalind Franklin Centre for Genomics Research Hinxton, Cambridge, United Kingdom
PLoS Biol 3:e7. 2005..These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development...
- Identification and analysis of cis-regulatory elements in development using comparative genomics with the pufferfish, Fugu rubripesGreg Elgar
MRC Rosalind Franklin Centre for Genomics Research, Genome Campus, Hinxton, Cambridgeshire CB10 1SB, UK
Semin Cell Dev Biol 15:715-9. 2004..This review describes progress made in this kind of comparison, from small regions of individual genes, to whole genome alignments...
- Functional analysis of conserved non-coding regions around the short stature hox gene (shox) in whole zebrafish embryosEmma J Kenyon
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, Cambridgeshire, United Kingdom
PLoS ONE 6:e21498. 2011..As this gene is not found in rodents, we used zebrafish as a model to characterise the expression pattern of the shox gene across the whole embryo and characterise the enhancer domains of different CNEs associated with this gene...
- Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humansTanya Vavouri
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
Genome Biol 8:R15. 2007..Despite their extreme sequence conservation in vertebrates, sequences homologous to CNEs have not been identified in invertebrates...
- Comparative analysis of vertebrate Shh genes identifies novel conserved non-coding sequenceDebbie K Goode
Comparative Genomics Group, HGMP Resource Centre, Hinxton, Cambridge, CB10 1SB, UK
Mamm Genome 14:192-201. 2003..This work demonstrates the value of using Fugu in comparative genomics, which has allowed identification of new putative regulatory elements, as well as corroborating enhancers identified by the more traditional deletion mapping method...
- Molecular characterisation of the SAND protein family: a study based on comparative genomics, structural bioinformatics and phylogenyAmanda Cottage
MRC Rosalind Franklin Centre for Genomic Research, Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Cell Mol Biol Lett 9:739-53. 2004..A comprehensive evaluation of yeast and human functional studies in conjunction with our in silico analysis has identified potential roles for some of these motifs...
- Prediction of cis-regulatory elements using binding site matrices--the successes, the failures and the reasons for bothTanya Vavouri
Comparative Genomics Group, MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Curr Opin Genet Dev 15:395-402. 2005..Nonetheless, a combination of experimental, computational and comparative data is likely to reveal aspects of complex regulatory networks in vertebrates, just as it has already done for simple eukaryotic genomes...
- Fugu ESTs: new resources for transcription analysis and genome annotationMelody S Clark
MRC Rosalind Franklin Centre for Genomics Research, formerly known as the MRC UK HGMP Resource Centre, Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Genome Res 13:2747-53. 2003..This is particularly timely with the increasing availability of draft genome sequence from different organisms and the mounting emphasis on gene function and regulation...
- Isolation and characterisation of the corticotropin releasing factor receptor 1 (CRFR1) gene in a teleost fish, Fugu rubripesJoão C Cardoso
Comparative Genomics Group, MRC HGMP Resource Centre, Genome Campus, Hinxton, Cambridge CB10 1SB, UK
DNA Seq 14:215-8. 2003..In vertebrates this receptor appears to have a different tissue distribution and its presence in the gills may indicate a new role in osmoregulatory processes...
- AP1 genes in Fugu indicate a divergent transcriptional control to that of mammalsAmanda J Cottage
Medical Research Council, UK Human Genome Mapping Project Resource Centre, Hinxton, Cambridge, CB 10 1SB, UK
Mamm Genome 14:514-25. 2003..We have determined that Fugu has more Jun and Fos genes than mammals, and if each proves to have a separate function, then addressing the roles of the individual AP1 proteins in Fugu may be simpler than in human...
- Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the keyTanya Vavouri
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, CB10 1SA
Trends Genet 22:5-10. 2006..This enables us to provide the first systematic estimate of the genomic range for distal cis-regulatory interactions in the human genome: half of CNEs are >250 kb away from their associated gene...
- Minor change, major difference: divergent functions of highly conserved cis-regulatory elements subsequent to whole genome duplication eventsDebbie K Goode
Department of Physiology Development and Neuroscience, Anatomy Building, Downing Street, Cambridge, UK
Development 138:879-84. 2011..Therefore, if CNEs are to be used as candidate enhancers for transgenic studies or for multi-species comparative analyses, it is paramount that the CNEs are accurately delineated...
- Fugu orthologues of human major histocompatibility complex genes: a genome surveyJennifer G Sambrook
Fugu Genomics, HGMP Resource Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Immunogenetics 54:367-80. 2002..Comparison with zebrafish substantiates previously observed linkages between class III region orthologues and hints at an ancient conserved class III region...
- Plenty more fish in the sea: comparative and functional genomics using teleost modelsGreg Elgar
MRC Rosalind Franklin Centre for Genomics Research, Genome Campus, Hinxton Hinxton, Cambridge, CB10 1SB, UK
Brief Funct Genomic Proteomic 3:15-25. 2004..In this review, the relationship between fish species is examined along with the role of different fish models in a wide range of biological disciplines...
- Genomic characterisation of putative growth hormone releasing hormone (GHRH) receptor genes in the teleost fish Fugu rubripesJoão C Cardoso
Fugu Genomics Group, MRC HGMP Resource Centre, Genome Campus, Hinxton, Cambridge, UK
DNA Seq 14:129-33. 2003..This is the first time that the genomic organisation of a GHRH receptor gene has been characterised from a nonmammalian vertebrate...
- Characterization of a novel gene adjacent to PAX6, revealing synteny conservation with functional significanceDirk A Kleinjan
MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
Mamm Genome 13:102-7. 2002..The possible role of PAXNEB in aniridia was assessed. Using a transgenic mouse model, we show that the aniridia phenotype of the chromosomal rearrangement cases is not due to the heterozygous loss of PAXNEB function...
- Analyses of the extent of shared synteny and conserved gene orders between the genome of Fugu rubripes and human 20qSarah F Smith
Fugu Genomics, United Kingdom Human Genome Mapping Project Resource Centre, Wellcome Genome Campus, Hinxton Hall, Hinxton, Cambridgeshire, CB10 1SB, United Kingdom
Genome Res 12:776-84. 2002....
- Highly conserved regulatory elements around the SHH gene may contribute to the maintenance of conserved synteny across human chromosome 7q36.3Debbie K Goode
Comparative Genomics Group, MRC Rosalind Franklin Centre for Genomics Research, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
Genomics 86:172-81. 2005....
- Characterisation of a gene cluster in Fugu rubripes containing the complement component C4 geneJennifer G Sambrook
Comparative Genomics, MRC UK HGMP Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK
Gene 312:73-83. 2003..All of the six identified Fugu MHC-related genes have been characterised at the genomic level...
- Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequencesKlaudia Walter
MRC Rosalind Franklin Centre for Genomics Research, Hinxton, Cambridge CB10 1SB, UK
Trends Genet 21:436-40. 2005..The analysis reveals a novel, sharp and distinct signal of nucleotide frequency bias precisely at the border between CNEs and flanking regions...
- Theatre: A software tool for detailed comparative analysis and visualization of genomic sequenceYvonne J K Edwards
Comparative Genomics Group, Research Division, MRC UK Human Genome Mapping Project Resource Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SB, UK
Nucleic Acids Res 31:3510-7. 2003..Theatre can be accessed at http://www.hgmp.mrc.ac.uk/Registered/Webapp/theatre/...
- Capturing the regulatory interactions of eukaryote genomesDebbie K Goode
Cambridge Institute for Medical Research, Deptartment of Haematology, Addenbrooke s Hospital, Hills Road, Cambridge, UK
Brief Funct Genomics 12:142-60. 2013..While we are only at the advent of making these discoveries, the next decade promises to be a very exciting and rewarding time for genome researchers...
- Persistence of duplicated PAC1 receptors in the teleost, Sparus auratusJoão C R Cardoso
CCMAR, Molecular and Comparative Endocrinology, University of Algarve, 8005 139 Faro, Portugal
BMC Evol Biol 7:221. 2007..These receptors belong to family 2 GPCRs and most of their members are duplicated in teleosts although the reason why both persist in the genome is unknown...
- Whole-genome shotgun assembly and analysis of the genome of Fugu rubripesSamuel Aparicio
Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609
Science 297:1301-10. 2002..Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order...
- Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common featureUberto Pozzoli
IRCCS E Medea, Associazione La Nostra Famiglia, 23842 Bosisio Parini LC, Italy
Genome Res 13:764-72. 2003..The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes...
- Organization of conserved elements near key developmental regulators in vertebrate genomesAdam Woolfe
School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
Adv Genet 61:307-38. 2008..This chapter describes the identification and characterization of these elements, with particular reference to their composition and organization...
- Molecular evolution of the vertebrate blood coagulation networkColin J Davidson
Haemostasis Group, MRC Clinical Sciences Centre, The Faculty of Medicine, Imperial College, Hammersmith Hospital Campus, London, UK
Thromb Haemost 89:420-8. 2003..Comparative sequence analyses of amino acid residues in the active site region suggest these additional sequences have evolved new and as yet unknown functions...
- Divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysisDaisuke Ikeda
Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
Physiol Genomics 32:1-15. 2007..Phylogenetic analysis suggests that fast skeletal MYHs evolved independently in teleosts and tetrapods after fast skeletal MYHs had diverged from four ancestral MYHs...
- CONDOR: a database resource of developmentally associated conserved non-coding elementsAdam Woolfe
School of Biological Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
BMC Dev Biol 7:100. 2007..Despite this, there remains little in the way of user-friendly access to a large dataset of such elements in conjunction with the analysis and the visualization tools needed to study them...
- Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expressionZissis Paparidis
Institute of Human Genetics, Philipps University, Bahnhofstrasse 7, D35037 Marburg, Germany
Dev Growth Differ 49:543-53. 2007..Time, location, and quantity of reporter gene expression are congruent with part of the pattern previously reported for endogenous GLI3 transcription...
- Comparative genomics using Fugu reveals insights into regulatory subfunctionalizationAdam Woolfe
School of Biological Sciences, Queen Mary, University of London, London, UK
Genome Biol 8:R53. 2007..We have exploited fish-mammal genomic alignments to identify and compare more than 800 conserved non-coding elements (CNEs) that associate with genes that have undergone fish-specific duplication and retention...
- Faithful expression of a tagged Fugu WT1 protein from a genomic transgene in zebrafish: efficient splicing of pufferfish genes in zebrafish but not miceColin G Miles
Medical Research Council Human Genetics Unit, Western General Hospital, Creve Road, Edinburgh EH4 2XU, UK
Nucleic Acids Res 31:2795-802. 2003..These data demonstrate that the zebrafish:Fugu system is a powerful and convenient tool for dissecting both vertebrate gene regulation and gene function in vivo...
- Different words, same meaning: understanding the languages of the genomeGreg Elgar
School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
Trends Genet 22:639-41. 2006..It is as yet unclear whether these sequences are 'below the radar' of current sequence alignment tools or whether their functional homology is not sequence based...
- A genomic approach to reveal novel genes associated with myotube formation in the model teleost, Takifugu rubripesJorge M O Fernandes
Gatty Marine Laboratory, School of Biology, University of St Andrews, St Andrews, Fife, United Kingdom
Physiol Genomics 22:327-38. 2005..The novel genes identified, which are also present in other vertebrate genomes, may play a role in inhibiting myotube formation in vertebrate muscle...
- A Fugu-Human Genome Synteny Viewer: web software for graphical display and annotation reports of synteny between Fugu genomic sequence and human genesMark Halling-Brown
School of Crystallography, Birkbeck College, University of London, Malet Street, London WC1E 7HX, UK
Nucleic Acids Res 32:2618-22. 2004..The Fugu-human genome synteny views are available for each Fugu scaffold through the clonesearch web page located at the Fugu Genomics website (http://fugu.rfcgr.mrc.ac.uk/)...
- The nicotinic acetylcholine receptor gene family of the pufferfish, Fugu rubripesAndrew K Jones
MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
Genomics 82:441-51. 2003..We show, using RT-PCR, that the Fugu nAChR subunits are expressed in a variety of tissues...
- Xena, a full-length basal retroelement from tetraodontid fishDamian E Dalle Nogare
Department of Biochemistry, University of Otago, Dunedin, New Zealand
Mol Biol Evol 19:247-55. 2002..The Penelope-Xena lineage is apparently a basal group within the retrotransposons and therefore represents an evolutionarily important class of retroelement...
- Ancient duplicated conserved noncoding elements in vertebrates: a genomic and functional analysisGayle K McEwen
School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
Genome Res 16:451-65. 2006..We propose a model whereby gene duplication and the evolution of cis-regulatory elements can be considered in the context of increased morphological diversity and the emergence of the modern vertebrate body plan...
- A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactylyLaura A Lettice
MRC Human Genetics Unit, Western General Hospital, Crewe Rd, Edinburgh EH4 2XU, Scotland, UK
Hum Mol Genet 12:1725-35. 2003..Thus point mutations residing in long-range regulatory elements are capable of causing congenital abnormalities, and possess the capacity to modify gene activity such that a novel gamut of abnormalities is detected...
- What is systems biology?Greg Elgar
Brief Funct Genomic Proteomic 7:237-8. 2008
- Effect of cryopreservation on mitochondrial DNA of zebrafish (Danio rerio) blastomere cellsJulia Kopeika
Luton Institute of Research in the Applied Natural Sciences, University of Luton, The Spires, 2 Adelaide Street, Luton LU1 5DU, UK
Mutat Res 570:49-61. 2005..Meanwhile, it is important to be cautious in making judgements of the effect of cryopreservation technique in assisted reproduction. This is the first report on the effect of cryopreservation on mtDNA...
- Data handling and dissemination in proteomics and genomicsGreg Elgar
Brief Funct Genomic Proteomic 1:324-5. 2003