Genomes and Genes
Affiliation: Queen Mary
- 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...
- 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...
- 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...
- Pan-vertebrate conserved non-coding sequences associated with developmental regulationGreg Elgar
School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Rd, London E1 4NS, UK
Brief Funct Genomic Proteomic 8:256-65. 2009..I will also discuss the evolution of these elements, and examine their emerging and likely roles in disease. Together these analyses are starting to unravel how conserved non-coding regions function at the molecular level...
- Tuning in to the signals: noncoding sequence conservation in vertebrate genomesGreg Elgar
School of Biological and Chemical Sciences, Queen Mary, University of London, London, UK
Trends Genet 24:344-52. 2008....
- 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...
- 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...
- 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...
- Early evolution of conserved regulatory sequences associated with development in vertebratesGayle K McEwen
School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
PLoS Genet 5:e1000762. 2009....
- Parallel evolution of chordate cis-regulatory code for developmentLaura Doglio
Systems Biology, MRC National Institute for Medical Research, Mill Hill, London, United Kingdom
PLoS Genet 9:e1003904. 2013..However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations. ..
- 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 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 PAX258 gene subfamily: a comparative perspectiveDebbie K Goode
Queen Mary, University of London, School of Biological and Chemical Sciences, London, United Kingdom
Dev Dyn 238:2951-74. 2009..We also discuss their fundamental place within gene regulatory networks and the likely influence of cis-regulatory elements over their differential roles during early animal development...
- Complete re-sequencing of a 2Mb topological domain encompassing the FTO/IRXB genes identifies a novel obesity-associated region upstream of IRX5Lilian E Hunt
The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, UK
Genome Med 7:126. 2015..Consequently, at least three genes in this interval have been implicated in the aetiology of obesity...
- A reporter assay in lamprey embryos reveals both functional conservation and elaboration of vertebrate enhancersHugo J Parker
Division of Systems Biology, Medical Research Council National Institute for Medical Research, London, United Kingdom
PLoS ONE 9:e85492. 2014..We find instances of both functional conservation and lineage-specific functional evolution of CNEs across vertebrates, emphasising the utility of functionally testing homologous CNEs in their host species. ..
- 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...
- 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...
- 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....
- 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...
- 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...
- 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....
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...
- 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...