Research Topics
Genomes and Genes
| Byrappa VenkateshSummaryCountry: Singapore Publications
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Detail Information
Publications
Basal vertebrates clarify the evolutionary history of ciliopathy-associated genes Tmem138 and Tmem216Byrappa Venkatesh
Comparative Genomics Lab, Institute of Molecular and Cell Biology, A STAR, Biopolis, Singapore
Mol Biol Evol 30:62-5. 2013..Analyses of the coelacanth and lamprey genomes support this hypothesis. Our study highlights the importance of basal vertebrates as critical reference genomes...
Emergence and evolution of the glycoprotein hormone and neurotrophin gene families in vertebratesSandra Dos Santos
Universite Paris Diderot, Sorbonne Paris Cité, Unité Biologie Fonctionnelle et Adaptative BFA, EAC4413 CNRS, Paris, France
BMC Evol Biol 11:332. 2011..To have a better insight into this process we used new genomic resources and tools to characterize the ancestral environment before the duplication occurred...- Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii ) in zebrafish and miceRyan B MacDonald
Center for Advanced Research in Environmental Genomics, Department of Biology, University of Ottawa, Ottawa, ON, K1N 6N5, Canada
BMC Evol Biol 10:157. 2010..We then conducted a comparative study of the sequence and enhancer activity of CmURE2 with that of orthologous regulatory sequences from zebrafish and mouse... 
Sequencing and comparative analysis of fugu protocadherin clusters reveal diversity of protocadherin genes among teleostsWei Ping Yu
Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng 308433, Singapore
BMC Evol Biol 7:49. 2007..To gain further insight into the evolutionary history of protocadherin clusters, we have sequenced and analyzed protocadherin clusters from the compact genome of the pufferfish, Fugu rubripes...- Early vertebrate chromosome duplications and the evolution of the neuropeptide Y receptor gene regionsTomas A Larsson
Department of Neuroscience, Uppsala University, Box 593, 75124 Uppsala, Sweden
BMC Evol Biol 8:184. 2008..These correspond to Homo sapiens chromosomes 4, 5, 8 and 10... 
Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elementsByrappa Venkatesh
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
Bioessays 27:100-7. 2005..The functions of these conserved vertebrate elements can be rapidly assayed in mammalian cell lines or in transgenic systems such as zebrafish/medaka and Xenopus, followed by validation of crucial elements in transgenic rodents...- Fugu genome does not contain mitochondrial pseudogenesByrappa Venkatesh
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
Genomics 87:307-10. 2006..Shotgun sequences of whole genomes often include some mitochondrial sequences. Therefore, any Numts identified in shotgun-sequence assemblies should be verified by Southern hybridization or PCR amplification... - Ancient noncoding elements conserved in the human genomeByrappa Venkatesh
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
Science 314:1892. 2006..The ancient vertebrate-specific CNEs in the elephant shark and human genomes are likely to play key regulatory roles in vertebrate gene expression... - Survey sequencing and comparative analysis of the elephant shark (Callorhinchus milii) genomeByrappa Venkatesh
Institute of Molecular and Cell Biology, Singapore
PLoS Biol 5:e101. 2007..This study also demonstrates that a survey-sequencing approach can be applied productively for comparative analysis of distantly related vertebrate genomes... - Characterization of the neurohypophysial hormone gene loci in elephant shark and the Japanese lamprey: origin of the vertebrate neurohypophysial hormone genesPai Chung Gwee
Institute of Molecular and Cell Biology, A STAR Agency for Science, Technology and Research, Biopolis, 138673 Singapore
BMC Evol Biol 9:47. 2009..We have also analyzed the neurohypophysial hormone gene locus in an invertebrate chordate, the amphioxus (Branchiostoma floridae)... - Elephant shark (Callorhinchus milii) provides insights into the evolution of Hox gene clusters in gnathostomesVydianathan Ravi
Institute of Molecular and Cell Biology, ASTAR, Biopolis, Singapore 138673
Proc Natl Acad Sci U S A 106:16327-32. 2009.... - Evolution of the Cdk-activator Speedy/RINGO in vertebratesSangeeta Chauhan
Institute of Molecular and Cell Biology IMCB, A STAR Agency for Science, Technology and Research, 61 Biopolis Drive, Singapore, 138673, Republic of Singapore
Cell Mol Life Sci 69:3835-50. 2012..Despite the interspecies variation, Speedy is conserved among most species examined. Our results provide a complete picture of the Speedy gene family and its evolution... - Rapidly evolving fish genomes and teleost diversityVydianathan Ravi
Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Biopolis, Singapore, Singapore
Curr Opin Genet Dev 18:544-50. 2008..The divergence of CNEs seems to have been initiated in basal ray-finned fishes before the WGD. The fast evolving singleton and duplicated genes as well as the divergent CNEs might have contributed to the diversity of teleost fishes... - STAT4 is a target of the hematopoietic zinc-finger transcription factor Ikaros in T cellsWai Ho Yap
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
FEBS Lett 579:4470-8. 2005..Transactivation, electrophoretic mobility shift assay and RNA interference-mediated gene knockdown experiments revealed that Ik is involved in the regulation of STAT4 in human T cells... - Identification and comparative analysis of the protocadherin cluster in a reptile, the green anole lizardXiao Juan Jiang
Gene Regulation Laboratory, National Neuroscience Institute, Singapore, Singapore
PLoS ONE 4:e7614. 2009..In this study, we report the identification and comparative analysis of the protocadherin cluster in a reptile, the green anole lizard (Anolis carolinensis)... - Investigation of loss and gain of introns in the compact genomes of pufferfishes (Fugu and Tetraodon)Yong Hwee Loh
Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research, Biopolis, Singapore
Mol Biol Evol 25:526-35. 2008..Our findings indicate that overall very little intron turnover has occurred in pufferfishes and mammals during recent evolution and that intron gain is an extremely rare event in vertebrate evolution... - Highly conserved syntenic blocks at the vertebrate Hox loci and conserved regulatory elements within and outside Hox gene clustersAlison P Lee
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673
Proc Natl Acad Sci U S A 103:6994-9. 2006..We propose that the regulatory elements spread across large regions on either side of Hox clusters are a major evolutionary constraint that has maintained the exceptionally long syntenic blocks at the HoxA and HoxD loci... - Characterization of a hypoxia-response element in the Epo locus of the pufferfish, Takifugu rubripesRashmi P Kulkarni
Institute of Molecular and Cell Biology, A STAR, Biopolis, 138673, Singapore
Mar Genomics 3:63-70. 2010..Our investigations also revealed that the Epo locus has experienced extensive rearrangements during vertebrate evolution... - Mouse transgenesis identifies conserved functional enhancers and cis-regulatory motif in the vertebrate LIM homeobox gene Lhx2 locusAlison P Lee
Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore
PLoS ONE 6:e20088. 2011..Other approaches such as sequence comparison between multiple mammals are required to identify and characterize such enhancers... - Ancient vertebrate conserved noncoding elements have been evolving rapidly in teleost fishesAlison P Lee
Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, A STAR Agency for Science, Technology and Research, Biopolis, Singapore
Mol Biol Evol 28:1205-15. 2011..Transgenic zebrafish assay of some human CNE enhancers that have been lost in teleosts has indicated instances of conservation or changes in trans-acting factors between mammals and fishes... - Genetic basis of tetrodotoxin resistance in pufferfishesByrappa Venkatesh
Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
Curr Biol 15:2069-72. 2005..4b is similar to that in the saxitoxin- and TTX-resistant Na+ channels of softshell clams . Besides helping to deter predators, TTX resistance enables pufferfishes to selectively feed on TTX-bearing organisms... - Phylogenetic and evolutionary relationships and developmental expression patterns of the zebrafish twist gene familyGare Hoon Yeo
Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
Dev Genes Evol 219:289-300. 2009..We also observed minimal expression overlap among the four twist genes, suggesting that despite their significant peptide similarity, their regulatory controls have diverged considerably, with minimal functional redundancy between them... - Duplication, degeneration and subfunctionalization of the nested synapsin-Timp genes in FuguWei-ping Yu
Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore, 117609 Singapore
Trends Genet 19:180-3. 2003.... - TFCONES: a database of vertebrate transcription factor-encoding genes and their associated conserved noncoding elementsAlison P Lee
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
BMC Genomics 8:441. 2007..To this end, we have used a comparative genomics approach to identify putative cis-regulatory elements associated with TF-encoding genes in vertebrates... - Characterization of the platelet-derived growth factor receptor alpha and c-kit genes in the pufferfish Fugu rubripesHawys Williams
Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore, Singapore 117609
DNA Seq 13:263-70. 2002..The Fugu PDGFR alpha gene is transcribed from two promoters giving rise to alternate transcripts... - Identification and analysis of additional copies of the platelet-derived growth factor receptor and colony stimulating factor 1 receptor genes in fuguHawys Williams
Institute of Molecular and Cell Biology, 30 Medical Drive, 117609, Singapore
Gene 295:255-64. 2002..These results are discussed in the context of the proposed teleost lineage-specific whole genome duplication hypothesis... - Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishesAlan Christoffels
Institute of Molecular and Cell Biology, Singapore
Mol Biol Evol 21:1146-51. 2004..These data strongly suggest a whole-genome duplication event early during the evolution of ray-finned fishes, probably before the origin of teleosts... - Sequencing and analysis of full-length cDNAs, 5'-ESTs and 3'-ESTs from a cartilaginous fish, the elephant shark (Callorhinchus milii)Yue Ying Tan
Comparative Genomics Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore
PLoS ONE 7:e47174. 2012..These resources will also be useful for annotating genes in other cartilaginous fishes whose genomes have been targeted for whole genome sequencing... - Sequence and organization of coelacanth neurohypophysial hormone genes: evolutionary history of the vertebrate neurohypophysial hormone gene locusPai Chung Gwee
Institute of Molecular and Cell Biology, A STAR Agency for Science, Technology and Research, Biopolis, 138673, Singapore
BMC Evol Biol 8:93. 2008..The coelacanths occupy a unique phylogenetic position close to the divergence of the mammalian and ray-finned fish lineages... - The regulation of retina specific expression of rhodopsin gene in vertebratesTao Zhang
Institute of Molecular and Cell Biology, 117609 Singapore, Singapore
Gene 313:189-200. 2003..Our investigation suggests that the regulation of retinal specific expression is conserved in the pufferfish, frog and mouse and that the ancestral intron-containing rhodopsin gene has been displaced by an intronless copy in teleosts... - Sequencing of pax6 Loci from the elephant shark reveals a family of pax6 genes in vertebrate genomes, forged by ancient duplications and divergencesVydianathan Ravi
Institute of Molecular and Cell Biology, Agency for Science Technology and Research ASTAR, Biopolis, Singapore, Singapore
PLoS Genet 9:e1003177. 2013..In summary, our study reveals that the pleiotropic functions of Pax6 in vertebrates are served by a divergent family of Pax6 genes, forged by ancient duplication events and by independent, lineage-specific gene losses... - Cloning and expression of the reverse transcriptase component of pufferfish (Fugu rubripes) telomeraseWai Ho Yap
Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673, Singapore
Gene 353:207-17. 2005..The level of expression was found to be higher in actively dividing cells and reduced at quiescence, suggesting cell cycle regulation of TERT and possibly telomerase activity, in this cell line... - Fugu and human sequence comparison identifies novel human genes and conserved non-coding sequencesPatrick Gilligan
Institute of Molecular and Cell Biology, 30 Medical Drive, 117609, Singapore
Gene 294:35-44. 2002..This study confirms the utility of the Fugu as a supplementary tool to uncover and confirm novel genes and putative gene regulatory regions in the human genome... - cDNA cloning of Runx family genes from the pufferfish (Fugu rubripes)Cherry Ee Lin Ng
Institute of Molecular and Cell Biology, 61 Biopolis Drive, 138673, Singapore
Gene 399:162-73. 2007..The similarities and differences between the Runx family genes of fugu and mammals will improve our understanding of the functions of these proteins... - Genetic alterations in the tyrosine kinase transcriptome of human cancer cell linesJens E Ruhe
Institute of Medical Biology, Singapore, Singapore
Cancer Res 67:11368-76. 2007..Our data therefore provide extensive system information for the design and interpretation of cell line-based cancer research, and may stimulate further investigations into broader clinical applications of current cancer therapeutics... - Variation in sequence and organization of splicing regulatory elements in vertebrate genesGene Yeo
Departments of Biology and Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue 68-223, Cambridge, MA 02139-4307, USA
Proc Natl Acad Sci U S A 101:15700-5. 2004.... - Comparative genomics of the Hlx homeobox gene and protein: conservation of structure and expression from fish to mammalsMichael D Bates
Division of Gastroenterology, Hepatology and Nutrition, Cincinnati Children s Hospital Medical Center, Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA
Gene 352:45-56. 2005..These results suggest that the function of Hlx and the mechanisms regulating its expression are highly conserved in mammals, birds, amphibians and fish... - Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebratesHenner Brinkmann
Department of Biology, University of Konstanz, 78457 Konstanz, Germany
Proc Natl Acad Sci U S A 101:4900-5. 2004..These results are supported by high bootstrap values, Bayesian posterior probabilities, and likelihood ratio tests... - A genetic linkage map for the tiger pufferfish, Takifugu rubripesWataru Kai
Fisheries Laboratory, The University of Tokyo, Maisaka, Shizuoka, Japan
Genetics 171:227-38. 2005.... - Hox gene clusters in the Indonesian coelacanth, Latimeria menadoensisEsther G L Koh
Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609
Proc Natl Acad Sci U S A 100:1084-8. 2003.... - A compact cartilaginous fish model genomeByrappa Venkatesh
Curr Biol 15:R82-3. 2005 - Novel vertebrate genes and putative regulatory elements identified at kidney disease and NR2E1/fierce lociBrett S Abrahams
Centre for Molecular Medicine and Therapeutics, British Columbia Research Institute for Children s and Women s Health, and Department of Medical Genetics, University of British Columbia, 980 West 28 th Avenue, Vancouver, British Columbia, V5Z 4H4, Canada
Genomics 80:45-53. 2002..A high degree of conservation across NR2E1 combined with a lack of interspersed repeats suggests that an array of regulatory elements embedded within the gene is required for proper gene expression... - Evolution and diversity of fish genomesByrappa Venkatesh
Institute of Molecular and Cell Biology 30, Medical Drive, Singapore 117609, Singapore
Curr Opin Genet Dev 13:588-92. 2003..Fish genomes seem to be 'plastic' in comparison with other vertebrate genomes because genetic changes, such as polyploidization, gene duplications, gain of spliceosomal introns and speciation, are more frequent in fishes... - Comparative genomics of the human and Fugu voltage-gated calcium channel alpha1-subunit gene family reveals greater diversity in FuguEsther Wong
Ion Channel and Transporter Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng, S308433, Singapore
Gene 366:117-27. 2006..These results indicate that Fugu, a lower vertebrate, has more extensive channel heterogeneity compared to human... - Extensive expansion of the claudin gene family in the teleost fish, Fugu rubripesYong Hwee Loh
Institute of Molecular and Cell Biology, Singapore 117609
Genome Res 14:1248-57. 2004.... - The mitochondrial genome of Indonesian coelacanth Latimeria menadoensis (Sarcopterygii: Coelacanthiformes) and divergence time estimation between the two coelacanthsJun G Inoue
Ocean Research Institute, The University of Tokyo, 1 15 1 Minamidai, Nakano Ku, Tokyo 164 8639, Japan
Gene 349:227-35. 2005.... - Evolution of the neuropeptide Y family: new genes by chromosome duplications in early vertebrates and in teleost fishesGorel Sundstrom
Department of Neuroscience, Uppsala University, Box 593, 75124 Uppsala, Sweden
Gen Comp Endocrinol 155:705-16. 2008..Our study shows that when sequence comparisons give ambiguous results, chromosomal location can serve as a useful criterion to identify orthologs. This strategy may help to resolve relationships in several families of short peptides... - 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... - Application of comparative genomics to the analysis of vertebrate regulatory elementsPatrick Gilligan
Institute of Molecular and Cell Biology, 30, Medical Drive, Singapore 117609
Brief Funct Genomic Proteomic 3:7-11. 2004..There is need for high throughput assay systems to analyse the function of predicted vertebrate gene regulatory regions... - Origin and diversity of the SOX transcription factor gene family: genome-wide analysis in Fugu rubripesPeter Koopman
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
Gene 328:177-86. 2004.... - Elephant shark sequence reveals unique insights into the evolutionary history of vertebrate genes: A comparative analysis of the protocadherin clusterWei Ping Yu
Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore
Proc Natl Acad Sci U S A 105:3819-24. 2008..The small and "stable" genome of the elephant shark is a valuable reference for understanding the evolution of vertebrate genomes... - Pufferfish and zebrafish have five distinct NPY receptor subtypes, but have lost appetite receptors Y1 and Y5Tomas A Larsson
Department of Neuroscience, Uppsala University, Sweden
Ann N Y Acad Sci 1040:375-7. 2005..These results reveal interesting differences in the NPY system of teleosts and mammals that may have arisen in the genetic turmoil involving the basal ray-fin fish tetraploidization... - Biochemical implications of sequence comparisons of the cystic fibrosis transmembrane conductance regulatorAgnes L C Tan
Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609, Republic of Singapore
Arch Biochem Biophys 401:215-22. 2002..Major adaptations in fishes include variations in the postulated ion sensor (111)PDNKE, and the absence of a proline residue in the R domain with consequent higher chloride efflux... - Ray-fin fish tetraploidization gave rise to pufferfish duplicates of NPY and PYY, but zebrafish NPY duplicate was lostGorel Sundstrom
Department of Neuroscience, Uppsala University, Sweden
Ann N Y Acad Sci 1040:476-8. 2005..The two fugu NPY genes are predominantly expressed in brain. The two PYY genes are expressed in a broad range of tissues including brain and gonads. Thus, the NPY system appears to be more complex in teleosts than in tetrapods... - Conserved regulation of the lymphocyte-specific expression of lck in the Fugu and mammalsSydney Brenner
Institute of Molecular and Cell Biology, 30 Medical Drive, Singapore 117609, USA
Proc Natl Acad Sci U S A 99:2936-41. 2002..The short promoter of the Fugu lck isolated by us offers a powerful tool for labeling T cells, targeting expression, and manipulating T cell activity in fishes as well as in mammals... - Compact intergenic regions of the pufferfish genome facilitate isolation of gene promoters: characterization of Fugu 3'-phosphoadenosine 5'-phosphosulfate synthase 2 (fPapss2) gene promoter function in transgenic XenopusTara Stapleton
Department of Biochemistry and Molecular Biology, University of Calgary, 3330 Hospital Drive N.W, T2N 4N1, Calgary, AB, Canada
FEBS Lett 556:59-63. 2004.... - The RIN family of Ras effectorsJoanne M Bliss
Department of Biological Chemistry, University of California Los Angeles School of Medicine, Los Angeles, California, USA
Methods Enzymol 407:335-44. 2006..In this chapter, we summarize our assays and approaches for evaluating the biochemistry and biology of RIN1... - Erythropoietin gene from a teleost fish, Fugu rubripesChih-Fong Chou
Institute of Molecular and Cell Biology, 30 Medical Dr, Singapore 117609
Blood 104:1498-503. 2004..Transient transfection studies in a fish hepatoma cell line (PLHC-1) and a human hepatoma cell line (HepG2) suggest that although the Fugu Epo promoter many not be hypoxia inducible, the gene may be regulated by hypoxia... - The 350-fold compacted Fugu parkin gene is structurally and functionally similar to human ParkinWei-ping Yu
Gene Regulation Laboratory, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore
Gene 346:97-104. 2005..Conceivably, the compact locus of fuparkin could serve as a useful model to understand the transcriptional regulation of huParkin...