101
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Reichwald K, Lauber C, Nanda I, Kirschner J, Hartmann N, Schories S, Gausmann U, Taudien S, Schilhabel MB, Szafranski K, Glöckner G, Schmid M, Cellerino A, Schartl M, Englert C, Platzer M. High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research. Genome Biol 2009; 10:R16. [PMID: 19210790 PMCID: PMC2688266 DOI: 10.1186/gb-2009-10-2-r16] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2008] [Revised: 01/26/2009] [Accepted: 02/11/2009] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The annual fish Nothobranchius furzeri is the vertebrate with the shortest known life span in captivity. Fish of the GRZ strain live only three to four months under optimal laboratory conditions, show explosive growth, early sexual maturation and age-dependent physiological and behavioral decline, and express aging related biomarkers. Treatment with resveratrol and low temperature significantly extends the maximum life span. These features make N. furzeri a promising new vertebrate model for age research. RESULTS To contribute to establishing N. furzeri as a new model organism, we provide a first insight into its genome and a comparison to medaka, stickleback, tetraodon and zebrafish. The N. furzeri genome contains 19 chromosomes (2n = 38). Its genome of between 1.6 and 1.9 Gb is the largest among the analyzed fish species and has, at 45%, the highest repeat content. Remarkably, tandem repeats comprise 21%, which is 4-12 times more than in the other four fish species. In addition, G+C-rich tandem repeats preferentially localize to centromeric regions. Phylogenetic analysis based on coding sequences identifies medaka as the closest relative. Genotyping of an initial set of 27 markers and multi-locus fingerprinting of one microsatellite provides the first molecular evidence that the GRZ strain is highly inbred. CONCLUSIONS Our work presents a first basis for systematic genomic and genetic analyses aimed at understanding the mechanisms of life span determination in N. furzeri.
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Affiliation(s)
- Kathrin Reichwald
- Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr,, 07745 Jena, Germany.
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102
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Novikova OS, Blinov AG. Origin, evolution, and distribution of different groups of non-LTR retrotransposons among eukaryotes. RUSS J GENET+ 2009. [DOI: 10.1134/s102279540902001x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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103
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Yasuoka A, Abe K. Gustation in fish: search for prototype of taste perception. Results Probl Cell Differ 2009; 47:239-55. [PMID: 19145412 DOI: 10.1007/400_2008_6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Fish perceive water-soluble chemicals at the taste buds that are distributed on oropharyngeal and trunk epithelia. Recent progress in molecular analyses has revealed that teleosts and mammals share pivotal signaling components to transduce taste stimuli. The fish orthologs of taste receptors, fT1R and fT2R, show mutually exclusive expression in taste buds, and both are coexpressed with phospholipase C-beta2 and the transient receptor potential M5 channel as common downstream components of taste receptor signals. Interestingly, fT1R heteromers are activated by various L-amino acids but not by sugars. This may reflects that in fish the energy metabolism depends primarily on gluconeogenesis from amino acids. fT2Rs are activated by denatonium benzoate, which is a bitter substance for mammals. It is thus likely that the preferable and aversive tastes for vertebrates, though their taste modalities somewhat vary, are transduced by the sensory conserved pathways. The comparative molecular biology of the fish taste system would lead to understanding a general logic of encoding taste modalities in vertebrates.
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Affiliation(s)
- A Yasuoka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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104
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Li M, Li Y, Lu L, Wang X, Gong Q, Duan C. Structural, gene expression, and functional analysis of the fugu (Takifugu rubripes) insulin-like growth factor binding protein-4 gene. Am J Physiol Regul Integr Comp Physiol 2008; 296:R558-66. [PMID: 19091910 DOI: 10.1152/ajpregu.90439.2008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The insulin-like growth factor (IGF) signaling pathway is a conserved pathway that regulates animal development, growth, metabolism, reproduction, and aging. The biological actions of IGFs are modulated by IGF-binding proteins (IGFBPs). Although the structure and function of fish IGFBP-1, -2, -3, and -5 have been elucidated, there is currently no report on the full-length structure of a fish IGFBP-4 nor its biological action. In this study, we cloned and characterized the IGFBP-4 gene from fugu. Sequence comparison, phylogenetic, and synteny analyses indicate that its chromosomal location, gene, and protein structure are similar to its mammalian orthologs. Fugu IGFBP-4 mRNA was easily detectable in all adult tissues examined with the exception of spleen. Older animals tended to have higher levels of IGFBP-4 mRNA in the muscle and eyes compared with younger animals. Starvation resulted in significant increases in IGFBP-4 mRNA abundance in the muscle, liver, gallbladder, and brain. Overexpression of fugu and human IGFBP-4 in zebrafish embryos caused a significant decrease in body size and somite number, suggesting that fugu IGFBP-4 inhibits growth and development, possibly by binding to IGFs and inhibiting their binding to the IGF receptors. These results provide new information about the structural and functional conservation, expression patterns, and physiological regulation of the IGFBP-4 gene in a teleost fish.
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Affiliation(s)
- Mingyu Li
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
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105
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Yamanoue Y, Miya M, Matsuura K, Miyazawa S, Tsukamoto N, Doi H, Takahashi H, Mabuchi K, Nishida M, Sakai H. Explosive speciation of Takifugu: another use of fugu as a model system for evolutionary biology. Mol Biol Evol 2008; 26:623-9. [PMID: 19074759 DOI: 10.1093/molbev/msn283] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although the fugu Takifugu rubripes has attracted attention as a model organism for genomic studies because of its compact genome, it is not generally appreciated that there are approximately 25 closely related species with limited distributions in the waters of East Asia. We performed molecular phylogenetic analyses and constructed a time tree using whole mitochondrial genome sequences from 15 Takifugu species together with 10 outgroups to examine patterns of diversification. The resultant time tree showed that the modern Takifugu species underwent explosive speciation during the Pliocene 1.8-5.3 Ma, which is comparable with that of the Malawi cichlids and tropheine cichlids in Lake Tanganyika. Considering their limited distributions and remarkable variations in coloration, morphology, and behavior, the results of the present study strongly suggest that Takifugu species are strong candidates as a model system for evolutionary studies of speciation mechanisms in marine environments where few such organisms are available.
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Affiliation(s)
- Yusuke Yamanoue
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.
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106
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Dios S, Novoa B, Buonocore F, Scapigliati G, Figueras A. Genomic Resources for Immunology and Disease of Salmonid and Non-Salmonid Fish. ACTA ACUST UNITED AC 2008. [DOI: 10.1080/10641260802325484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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107
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Dynamics and differential proliferation of transposable elements during the evolution of the B and A genomes of wheat. Genetics 2008; 180:1071-86. [PMID: 18780739 DOI: 10.1534/genetics.108.092304] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces.
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108
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Yamanoue Y, Miya M, Matsuura K, Katoh M, Sakai H, Nishida M. A new perspective on phylogeny and evolution of tetraodontiform fishes (Pisces: Acanthopterygii) based on whole mitochondrial genome sequences: basal ecological diversification? BMC Evol Biol 2008; 8:212. [PMID: 18638411 PMCID: PMC2500030 DOI: 10.1186/1471-2148-8-212] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2008] [Accepted: 07/19/2008] [Indexed: 11/24/2022] Open
Abstract
Background The order Tetraodontiformes consists of approximately 429 species of fishes in nine families. Members of the order exhibit striking morphological diversity and radiated into various habitats such as freshwater, brackish and coastal waters, open seas, and deep waters along continental shelves and slopes. Despite extensive studies based on both morphology and molecules, there has been no clear resolution except for monophyly of each family and sister-group relationships of Diodontidae + Tetraodontidae and Balistidae + Monacanthidae. To address phylogenetic questions of tetraodontiform fishes, we used whole mitochondrial genome (mitogenome) sequences from 27 selected species (data for 11 species were newly determined during this study) that fully represent all families and subfamilies of Tetraodontiformes (except for Hollardinae of the Triacanthodidae). Partitioned maximum likelihood (ML) and Bayesian analyses were performed on two data sets comprising concatenated nucleotide sequences from 13 protein-coding genes (all positions included; third codon positions converted into purine [R] and pyrimidine [Y]), 22 transfer RNA and two ribosomal RNA genes (total positions = 15,084). Results The resultant tree topologies from the two data sets were congruent, with many internal branches showing high support values. The mitogenomic data strongly supported monophyly of all families and subfamilies (except the Tetraodontinae) and sister-group relationships of Balistidae + Monacanthidae and Tetraodontidae + Diodontidae, confirming the results of previous studies. However, we also found two unexpected basal splits into Tetraodontoidei (Triacanthidae + Balistidae + Monacanthidae + Tetraodontidae + Diodontidae + Molidae) and Triacanthodoidei (Ostraciidae + Triodontidae + Triacanthodidae). Conclusion This basal split into the two clades has never been reported and challenges previously proposed hypotheses based on both morphology and nuclear gene sequences. It is likely that the basal split had involved ecological diversification, because most members of Tetraodontoidei exclusively occur in shallow waters (freshwater, brackish and coastal waters, and open seas), while those of Triacanthodoidei occur mainly in relatively deep waters along continental shelves and slopes except for more derived ostraciids. This suggests that the basal split between the two clades led to subsequent radiation into the two different habitats.
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Affiliation(s)
- Yusuke Yamanoue
- Ocean Research Institute, University of Tokyo, 1-15-1 Minamidai, Nakano-ku, Tokyo 164-8639, Japan.
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109
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Elgar G, Vavouri T. Tuning in to the signals: noncoding sequence conservation in vertebrate genomes. Trends Genet 2008; 24:344-52. [PMID: 18514361 DOI: 10.1016/j.tig.2008.04.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Revised: 04/14/2008] [Accepted: 04/14/2008] [Indexed: 01/25/2023]
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110
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Singer T, Keir K, Hinton M, Scott G, McKinley R, Schulte P. Structure and regulation of the cystic fibrosis transmembrane conductance regulator (CFTR) gene in killifish: A comparative genomics approach. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2008; 3:172-85. [DOI: 10.1016/j.cbd.2008.02.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 02/04/2008] [Accepted: 02/07/2008] [Indexed: 01/11/2023]
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111
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Cobb J, Büsst C, Petrou S, Harrap S, Ellis J. Searching for functional genetic variants in non-coding DNA. Clin Exp Pharmacol Physiol 2008; 35:372-5. [PMID: 18307723 DOI: 10.1111/j.1440-1681.2008.04880.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
1. The search for DNA sequence variants for complex human polygenic conditions has been a strong focus of recent genetic research. While gene loci have been identified, few variants in the coding sequences of these genes have been found, suggesting that non-coding sequence variation may underlie many complex conditions. 2. Non-coding DNA harbours regulatory elements capable of making changes to gene expression. However, regulatory DNA sequences are currently difficult to recognize and their function is poorly understood, complicating the task of assigning potential functional significance to non-coding variation. 3. Comparative genomics, the study of evolutionary DNA conservation, has enabled the emergent field of non-coding DNA identification in human disease analysis. 4. This brief review will focus on the potential of a relatively high throughput technique based on comparative genomics, that may aid in the identification of functionally important non-coding sequence variation in complex diseases.
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Affiliation(s)
- Joanna Cobb
- Department of Physiology, The University of Melbourne, Victoria, Australia
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112
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Rashid H, Kitano H, Lee KH, Nii S, Shigematsu T, Kadomura K, Yamaguchi A, Matsuyama M. Fugu (Takifugu rubripes) sexual differentiation: CYP19 regulation and aromatase inhibitor induced testicular development. Sex Dev 2008; 1:311-22. [PMID: 18391543 DOI: 10.1159/000108935] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Accepted: 09/13/2007] [Indexed: 11/19/2022] Open
Abstract
In order to assess the involvement of aromatase CYP19 isoforms and endogenous sex steroids in gonadal sex differentiation and development of the Japanese fugu (Takifugu rubripes), an aromatase inhibitor (AI, fadrozole) was administered to developing fishes from the 'first feeding' till the 100th day after hatching. It was observed that ovarian cavity formation was inhibited by fadrozole at doses of 500 and 1000 microg/g diet, which was followed by testicular differentiation in all treated fugu. In the non-treated fugu, CYP19A was predominantly expressed in the ovary and CYP19B in the brain (in both sexes), although both were expressed interchangeably at low levels. An exceptionally high expression of CYP19B was also evident in testis throughout the study period. Both forms of CYP19 mRNA showed low levels of expression in brain and gonad with no significant differences between the two AI treatments. AI treatment inhibited CYP19A mRNA in trunk during the crucial period of ovarian cavity formation and CYP19B in gonad and brain by the end of gonadal sex differentiation. An elevation of testosterone and 11-ketotestosterone was observed which can be associated with the down-regulation of the circulating 17beta-estradiol production during the AI treatment period. After stopping AI treatment, both circulating estrogen and androgen were normalized. The current results suggest that suppression of CYP19A before and during morphological sex differentiation inhibits ovarian cavity formation in fugu. Furthermore, non-detectable limits of 17beta-estradiol and high testosterone levels by the end of the gonadal differentiation period can be ascribed to inhibition of CYP19B, suggesting that conversion of 17beta-estradiol from testosterone is plausibly regulated by CYP19B, and that this factor (CYP19B) may play an important role in AI-induced testicular development after gonadal sex differentiation through regulation of the testosterone-17beta-estradiol balance in fugu.
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Affiliation(s)
- H Rashid
- Laboratory of Marine Biology, Faculty of Agriculture, Kyushu University, Hakozaki, Higashi-Ku, Fukuoka, Japan
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113
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Fish genomics: A mini-review on some structural and evolutionary issues. Mar Genomics 2008; 1:3-7. [DOI: 10.1016/j.margen.2008.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2008] [Accepted: 04/13/2008] [Indexed: 11/17/2022]
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114
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Jost MC, Hillis DM, Lu Y, Kyle JW, Fozzard HA, Zakon HH. Toxin-resistant sodium channels: parallel adaptive evolution across a complete gene family. Mol Biol Evol 2008; 25:1016-24. [PMID: 18258611 DOI: 10.1093/molbev/msn025] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Approximately 75% of vertebrate proteins belong to protein families encoded by multiple evolutionarily related genes, a pattern that emerged as a result of gene and genome duplications over the course of vertebrate evolution. In families of genes with similar or related functions, adaptation to a strong selective agent should involve multiple adaptive changes across the entire gene family. However, we know of no evolutionary studies that have explicitly addressed this point. Here, we show how 4 taxonomically diverse species of pufferfishes (Tetraodontidae) each evolved resistance to the guanidinium toxins tetrodotoxin (TTX) and saxitoxin (STX) via parallel amino acid replacements across all 8 sodium channels present in teleost fish genomes. This resulted in diverse suites of coexisting sodium channel types that all confer varying degrees of toxin resistance, yet show remarkable convergence among genes and phylogenetically diverse species. Using site-directed mutagenesis and expression of a vertebrate sodium channel, we also demonstrate that resistance to TTX/STX is enhanced up to 15-fold by single, frequently observed replacements at 2 sites that have not previously been implicated in toxin binding but show similar or identical replacements in pufferfishes and in distantly related vertebrate and nonvertebrate animals. This study presents an example of natural selection acting upon a complete gene family, repeatedly arriving at a diverse but limited number of adaptive changes within the same genome. To be maximally informative, we suggest that future studies of molecular adaptation should consider all functionally similar paralogs of the affected gene family.
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Affiliation(s)
- Manda Clair Jost
- Sections of Integrative Biology and Neurobiology and Center for Computational Biology, School of Biological Sciences, University of Texas at Austin, USA.
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115
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Moreno TA, Jappelli R, Izpisúa Belmonte JC, Kintner C. Retinoic acid regulation of the Mesp-Ripply feedback loop during vertebrate segmental patterning. Dev Biol 2008; 315:317-30. [PMID: 18261720 DOI: 10.1016/j.ydbio.2007.12.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 12/13/2007] [Accepted: 12/14/2007] [Indexed: 12/16/2022]
Abstract
The Mesp bHLH genes play a conserved role during segmental patterning of the mesoderm in the vertebrate embryo by specifying segmental boundaries and anteroposterior (A-P) segmental polarity. Here we use a xenotransgenic approach to compare the transcriptional enhancers that drive expression of the Mesp genes within segments of the presomitic mesoderm (PSM) of different vertebrate species. We find that the genomic sequences upstream of the mespb gene in the pufferfish Takifugu rubripes (Tr-mespb) are able to drive segmental expression in transgenic Xenopus embryos while those from the Xenopus laevis mespb (Xl-mespb) gene drive segmental expression in transgenic zebrafish. In both cases, the anterior segmental boundary of transgene expression closely matches the expression of the endogenous Mesp genes, indicating that many inputs into segmental gene expression are highly conserved. By contrast, we find that direct retinoic acid (RA) regulation of endogenous Mesp gene expression is variable among vertebrate species. Both Tr-mespb and Xl-mespb are directly upregulated by RA, through a complex, distal element. By contrast, RA represses the zebrafish Mesp genes. We show that this repression is mediated, in part, by RA-mediated activation of the Ripply genes, which together with Mesp genes form an RA-responsive negative feedback loop. These observations suggest that variations in a direct response to RA input may allow for changes in A-P patterning of the segments in different vertebrate species.
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Affiliation(s)
- Tanya A Moreno
- The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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116
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Moreno C, Lazar J, Jacob HJ, Kwitek AE. Comparative genomics for detecting human disease genes. ADVANCES IN GENETICS 2008; 60:655-97. [PMID: 18358336 DOI: 10.1016/s0065-2660(07)00423-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Originally, comparative genomics was geared toward defining the synteny of genes between species. As the human genome project accelerated, there was an increase in the number of tools and means to make comparisons culminating in having the genomic sequence for a large number of organisms spanning the evolutionary tree. With this level of resolution and a long history of comparative biology and comparative genetics, it is now possible to use comparative genomics to build or select better animal models and to facilitate gene discovery. Comparative genomics takes advantage of the functional genetic information from other organisms, (vertebrates and invertebrates), to apply it to the study of human physiology and disease. It allows for the identification of genes and regulatory regions, and for acquiring knowledge about gene function. In this chapter, the current state of comparative genomics and the available tools are discussed in the context of developing animal model systems that reflect the clinical picture.
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Affiliation(s)
- Carol Moreno
- Human and Molecular Genetics Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA
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117
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Woolfe A, Elgar G. Organization of conserved elements near key developmental regulators in vertebrate genomes. ADVANCES IN GENETICS 2008; 61:307-38. [PMID: 18282512 DOI: 10.1016/s0065-2660(07)00012-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Sequence conservation has traditionally been used as a means to target functional regions of complex genomes. In addition to its use in identifying coding regions of genes, the recent availability of whole genome data for a number of vertebrates has permitted high-resolution analyses of the noncoding "dark matter" of the genome. This has resulted in the identification of a large number of highly conserved sequence elements that appear to be preserved in all bony vertebrates. Further positional analysis of these conserved noncoding elements (CNEs) in the genome demonstrates that they cluster around genes involved in developmental regulation. This chapter describes the identification and characterization of these elements, with particular reference to their composition and organization.
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Affiliation(s)
- Adam Woolfe
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
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118
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Zhang Y, He S. Investigations into the perplexing interrelationship of the Genus Takifugu Abe, 1949 (Tetraodontiformes, Tetraodontidae). ACTA ACUST UNITED AC 2008. [DOI: 10.1007/s11434-008-0066-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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119
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Suetake H, Araki K, Akatsu K, Somamoto T, Dijkstra JM, Yoshiura Y, Kikuchi K, Suzuki Y. Genomic organization and expression of CD8alpha and CD8beta genes in fugu Takifugu rubripes. FISH & SHELLFISH IMMUNOLOGY 2007; 23:1107-18. [PMID: 17629710 DOI: 10.1016/j.fsi.2007.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2007] [Revised: 05/19/2007] [Accepted: 05/21/2007] [Indexed: 05/16/2023]
Abstract
We have cloned cDNAs encoding the alpha and beta chains of CD8 from the tiger pufferfish (fugu), Takifugu rubripes. The cDNA sequences encode a putative leader peptide, extracellular immunoglobulin variable region-like domain, stalk region, transmembrane region, and cytoplasmic tail. A protein tyrosine kinase p56lck binding motif was not found in the putative fugu CD8alpha cytoplasmic tail. O-linked glycosylation sites were found in the stalk of both CD8 chains, suggesting possible stalk formation. Phylogenetic analysis showed that fugu CD8alpha and CD8beta chains cluster with other vertebrate CD8alpha and CD8beta chains, respectively. The fugu CD8 genes comprise six exons separated by five introns. The genes are tandemly aligned 3.6 kb apart and are in the same transcription orientation. Quantitative RT-PCR analysis demonstrated that fugu CD8 is expressed predominantly in lymphoid tissues. In situ hybridization showed that fugu CD8 genes are expressed in thymocytes and lymphocytes within lymphoid organs. Molecular characterization of CD8 in fish provides the basis for development of specific antibodies to identify T-cell subsets, as well as potentially important insights into the evolution of CD8 and the adaptive immunity.
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Affiliation(s)
- Hiroaki Suetake
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Hamamatsu, Shizuoka 431-0214, Japan.
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120
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Ikeda D, Ono Y, Snell P, Edwards YJK, Elgar G, Watabe S. Divergent evolution of the myosin heavy chain gene family in fish and tetrapods: evidence from comparative genomic analysis. Physiol Genomics 2007; 32:1-15. [PMID: 17940200 DOI: 10.1152/physiolgenomics.00278.2006] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Myosin heavy chain genes (MYHs) are the most important functional domains of myosins, which are highly conserved throughout evolution. The human genome contains 15 MYHs, whereas the corresponding number in teleost appears to be much higher. Although teleosts comprise more than one-half of all vertebrate species, our knowledge of MYHs in teleosts is rather limited. A comprehensive analysis of the torafugu (Takifugu rubripes) genome database enabled us to detect at least 28 MYHs, almost twice as many as in humans. RT-PCR revealed that at least 16 torafugu MYH representatives (5 fast skeletal, 3 cardiac, 2 slow skeletal, 1 superfast, 2 smooth, and 3 nonmuscle types) are actually transcribed. Among these, MYH(M743-2) and MYH(M5) of fast and slow skeletal types, respectively, are expressed during development of torafugu embryos. Syntenic analysis reveals that torafugu fast skeletal MYHs are distributed across five genomic regions, three of which form clusters. Interestingly, while human fast skeletal MYHs form one cluster, its syntenic region in torafugu is duplicated, although each locus contains just a single MYH in torafugu. The results of the syntenic analysis were further confirmed by corresponding analysis of MYHs based on databases from Tetraodon, zebrafish, and medaka genomes. Phylogenetic analysis suggests that fast skeletal MYHs evolved independently in teleosts and tetrapods after fast skeletal MYHs had diverged from four ancestral MYHs.
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Affiliation(s)
- Daisuke Ikeda
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
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Liu R, Vitte C, Ma J, Mahama AA, Dhliwayo T, Lee M, Bennetzen JL. A GeneTrek analysis of the maize genome. Proc Natl Acad Sci U S A 2007; 104:11844-9. [PMID: 17615239 PMCID: PMC1913904 DOI: 10.1073/pnas.0704258104] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2007] [Indexed: 11/18/2022] Open
Abstract
Analysis of the sequences of 74 randomly selected BACs demonstrated that the maize nuclear genome contains approximately 37,000 candidate genes with homologues in other plant species. An additional approximately 5,500 predicted genes are severely truncated and probably pseudogenes. The distribution of genes is uneven, with approximately 30% of BACs containing no genes. BAC gene density varies from 0 to 7.9 per 100 kb, whereas most gene islands contain only one gene. The average number of genes per gene island is 1.7. Only 72% of these genes show collinearity with the rice genome. Particular LTR retrotransposon families (e.g., Gyma) are enriched on gene-free BACs, most of which do not come from pericentromeres or other large heterochromatic regions. Gene-containing BACs are relatively enriched in different families of LTR retrotransposons (e.g., Ji). Two major bursts of LTR retrotransposon activity in the last 2 million years are responsible for the large size of the maize genome, but only the more recent of these is well represented in gene-containing BACs, suggesting that LTR retrotransposons are more efficiently removed in these domains. The results demonstrate that sample sequencing and careful annotation of a few randomly selected BACs can provide a robust description of a complex plant genome.
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Affiliation(s)
- Renyi Liu
- *Department of Genetics, University of Georgia, Athens, GA 30602; and
| | - Clémentine Vitte
- *Department of Genetics, University of Georgia, Athens, GA 30602; and
| | - Jianxin Ma
- *Department of Genetics, University of Georgia, Athens, GA 30602; and
| | | | - Thanda Dhliwayo
- Department of Agronomy, Iowa State University, Ames, IA 50011
| | - Michael Lee
- Department of Agronomy, Iowa State University, Ames, IA 50011
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Kimura-Yoshida C, Tian E, Nakano H, Amazaki S, Shimokawa K, Rossant J, Aizawa S, Matsuo I. Crucial roles of Foxa2 in mouse anterior-posterior axis polarization via regulation of anterior visceral endoderm-specific genes. Proc Natl Acad Sci U S A 2007; 104:5919-24. [PMID: 17389379 PMCID: PMC1851592 DOI: 10.1073/pnas.0607779104] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anterior visceral endoderm (AVE) plays essential roles with respect to anterior-posterior axis development in the early mouse embryo. To assess the genetic cascade involved in AVE formation, the cis-regulatory elements directing expression of vertebrate Otx2 genes in the AVE were analyzed via generation of transgenic mice. Otx2 expression in AVE is regulated directly by the forkhead transcription factor, Foxa2. Moreover, Foxa2 is essential for expression of the Wnt antagonists, Dkk1 and Cerl, in visceral endoderm during the pre- to early streak stages; however, Foxa2 appears to be dispensable for subsequent Dkk1 expression associated with forebrain induction. Thus, we propose that Foxa2 is crucial in early anterior-posterior axis polarization in terms of regulation of expression of AVE-specific genes. These findings provide profound insights into conserved roles of Foxa2 transcription factors in anterior specification throughout the evolution of the chordate body plan.
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Affiliation(s)
- Chiharu Kimura-Yoshida
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
| | - E. Tian
- Department of Morphogenesis, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 860-0811, Japan
| | - Hiroshi Nakano
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
| | - Saori Amazaki
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Kayo Shimokawa
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
| | - Janet Rossant
- Program in Developmental Biology, Hospital for Sick Children, 555 University Avenue, Toronto, ON, Canada M5G 1X8; and
| | - Shinichi Aizawa
- Vertebrate Body Plan Group, RIKEN CDB, Kobe, Hyogo 650-0047, Japan
| | - Isao Matsuo
- *Department of Molecular Embryology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka Prefectural Hospital Organization, Murodo-cho, Izumi, Osaka 594-1101, Japan
- Head Organizer Project, Vertebrate Body Plan Group, RIKEN Center for Developmental Biology (CDB), Kobe, Hyogo 650-0047, Japan
- To whom correspondence should be addressed. E-mail:
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Ferreira IA, Martins C. Physical chromosome mapping of repetitive DNA sequences in Nile tilapia Oreochromis niloticus: evidences for a differential distribution of repetitive elements in the sex chromosomes. Micron 2007; 39:411-8. [PMID: 17395473 DOI: 10.1016/j.micron.2007.02.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2007] [Revised: 02/23/2007] [Accepted: 02/24/2007] [Indexed: 10/23/2022]
Abstract
Repetitive DNAs have been extensively applied as physical chromosome markers on comparative studies, identification of chromosome rearrangements and sex chromosomes, chromosome evolution analysis, and applied genetics. Here we report the characterization of repetitive DNA sequences from the Nile tilapia (Oreochromis niloticus) genome by construction and screening of plasmid library enriched with repetitive DNAs, analysis of a BAC-based physical map, and hybridization to chromosomes. The physical mapping of BACs enriched with repetitive sequences and C(o)t-1 DNA (DNA enriched for highly and moderately repetitive DNA sequences) to chromosomes using FISH showed a predominant distribution of repetitive elements in the centromeric and telomeric regions and along the entire length of the largest chromosome pair (X and Y sex chromosomes) of the species. The distribution of repetitive DNAs differed significantly between the p arm of X and Y chromosomes. These findings suggest that repetitive DNAs have had an important role in the differentiation of sex chromosomes.
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Affiliation(s)
- Irani A Ferreira
- Departamento de Morfologia, Instituto de Biociências, UNESP-Universidade Estadual Paulista, 18618-000 Botucatu, SP, Brazil
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124
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Affiliation(s)
- Michael C. Schmale
- Division of Marine Biology and Fisheries, Rosenstiel School of Marine and Atmospheric Science, University of Miami, 4600 Rickenbacker Cswy. Miami, FL 33149, USA, phone: 305-421-4140, fax: 305-421-4600,
| | - Rodney S. Nairn
- University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Richard N. Winn
- Aquatic Biotechnology and Environmental Lab (ABEL), 2580 Devil’s Ford Road, Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602, USA, Phone: 706.369.5858, Fax: 706.353.2620,
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125
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Zou J, Beermann F, Wang J, Kawakami K, Wei X. The Fugu tyrp1 promoter directs specific GFP expression in zebrafish: tools to study the RPE and the neural crest-derived melanophores. ACTA ACUST UNITED AC 2007; 19:615-27. [PMID: 17083488 PMCID: PMC2920493 DOI: 10.1111/j.1600-0749.2006.00349.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In vertebrates, pigment cells account for a small percentage of the total cell population and they intermingle with other cell types. This makes it difficult to isolate them for analyzes of their functions in the context of development. To alleviate such difficulty, we generated two stable transgenic zebrafish lines (pt101 and pt102) that express green fluorescent protein (GFP) in melanophores under the control of the 1 kb Fugu tyrp1 promoter. In pt101, GFP is expressed in both retinal pigment epithelium (RPE) cells and the neural crest-derived melanophores (NCDM), whereas in pt102, GFP is predominately expressed in the NCDM. Our results indicate that the Fugu tyrp1 promoter can direct transgene expression in a cell-type-specific manner in zebrafish. In addition, our findings provide evidence supporting differential regulations of melanin-synthesizing genes in RPE cells and the NCDM in zebrafish. Utilizing the varying GFP expression levels in these fish, we have isolated melanophores via flow cytometry and revealed the capability of sorting the NCDM from RPE cells as well. Thus, these transgenic lines are useful tools to study melanophores in zebrafish.
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Affiliation(s)
- Jian Zou
- Department of Ophthalmology, University of Pittsburgh School of Medicine, 203 Lothrop Street, Pittsburgh, PA 15213, USA
| | - Friedrich Beermann
- ISREC (Swiss Institute for Experimental Cancer Research), National Center of Competence in Research (NCCR) Molecular Oncology, Chemin des Boveresses, 1066 Epalinges, Switzerland
| | - Jianxin Wang
- Znomics, Inc. 2611 S.W. 3rd Ave. Suite 200, Portland, OR 97201, USA
| | - Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Xiangyun Wei
- Department of Ophthalmology, University of Pittsburgh School of Medicine, 203 Lothrop Street, Pittsburgh, PA 15213, USA
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, 203 Lothrop Street, Pittsburgh, PA 15213, USA
- Corresponding author: Tel: 412-647-3537 Fax: 412-647-5880
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Abstract
Tetrodotoxin (TTX) is one of the most potent and oldest known neurotoxins. The poisoning cases due to ingestion of TTX-containing marine animals, especially for puffer, have frequently occurred in Asia since a long time ago. This chapter describes various topics on TTX poisoning including the tendency of poisoning incidents, typical case report, treatment and prevention, biology distribution, original source, infestation mechanism, detection methods, characteristics of chemistry and pharmacology, and therapeutic application. Furthermore, the protocols for how to make puffer safe to eat and how to prevent puffer products made from toxic puffers have been suggested. Finally, the biological significance and neurophysiological role of TTX have been elucidated and TTX may act as an important drug like anesthetic in future.
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Affiliation(s)
- Deng-Fwu Hwang
- Department of Food Science, National Taiwan Ocean University Taiwan, Taiwan, Republic of China
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127
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Roh TY, Wei G, Farrell CM, Zhao K. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res 2006; 17:74-81. [PMID: 17135569 PMCID: PMC1716270 DOI: 10.1101/gr.5767907] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Comparative genomic studies have been useful in identifying transcriptional regulatory elements in higher eukaryotic genomes, but many important regulatory elements cannot be detected by such analyses due to evolutionary variations and alignment tool limitations. Therefore, in this study we exploit the highly conserved nature of epigenetic modifications to identify potential transcriptional enhancers. By using a high-resolution genome-wide mapping technique, which combines the chromatin immunoprecipitation and serial analysis of gene expression assays, we have recently determined the distribution of lysine 9/14-diacetylated histone H3 in human T cells. We showed the existence of 46,813 regions with clusters of histone acetylation, termed histone acetylation islands, some of which correspond to known transcriptional regulatory elements. In the present study, we find that 4679 sequences conserved between human and pufferfish coincide with histone acetylation islands, and random sampling shows that 33% (13/39) of these can function as transcriptional enhancers in human Jurkat T cells. In addition, by comparing the human histone acetylation island sequences with mouse genome sequences, we find that despite the conservation of many of these regions between these species, 21,855 of these sequences are not conserved. Furthermore, we demonstrate that about 50% (26/51) of these nonconserved sequences have enhancer activity in Jurkat cells, and that many of the orthologous mouse sequences also have enhancer activity in addition to conserved epigenetic modification patterns in mouse T-cell chromatin. Therefore, by combining epigenetic modification and sequence data, we have established a novel genome-wide method for identifying regulatory elements not discernable by comparative genomics alone.
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Affiliation(s)
- Tae-young Roh
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Gang Wei
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Catherine M. Farrell
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Keji Zhao
- Laboratory of Molecular Immunology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
- Corresponding authorE-mail ; fax (301) 480-0961
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128
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Martins C, Ferreira IA, Oliveira C, Foresti F, Galetti PM. A tandemly repetitive centromeric DNA sequence of the fish Hoplias malabaricus (Characiformes: Erythrinidae) is derived from 5S rDNA. Genetica 2006; 127:133-41. [PMID: 16850219 DOI: 10.1007/s10709-005-2674-y] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2005] [Accepted: 08/31/2005] [Indexed: 10/24/2022]
Abstract
A substantial fraction of the eukaryotic genome consists of repetitive DNA sequences that include satellites, minisatellites, microsatellites, and transposable elements. Although extensively studied for the past three decades, the molecular forces that generate, propagate and maintain repetitive DNAs in the genomes are still discussed. To further understand the dynamics and the mechanisms of evolution of repetitive DNAs in vertebrate genome, we searched for repetitive sequences in the genome of the fish species Hoplias malabaricus. A satellite sequence, named 5SHindIII-DNA, which has a conspicuous similarity with 5S rRNA genes and spacers was identified. FISH experiments showed that the 5S rRNA bona fide gene repeats were clustered in the interstitial position of two chromosome pairs of H. malabaricus, while the satellite 5SHindIII-DNA sequences were clustered in the centromeric position in nine chromosome pairs of the species. The presence of the 5SHindIII-DNA sequences in the centromeres of several chromosomes indicates that this satellite family probably escaped from the selective pressure that maintains the structure and organization of the 5S rDNA repeats and become disperse into the genome. Although it is not feasible to explain how this sequence has been maintained in the centromeric regions, it is possible to hypothesize that it may be involved in some structural or functional role of the centromere organization.
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Affiliation(s)
- Cesar Martins
- Departamento de Morfologia, UNESP-Universidade Estadual Paulista, Instituto de Biociências, CEP 18618-000, Botucatu, SP, Brazil.
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129
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Jang S, Zhou F, Xia L, Zhao W, Cheng H, Zhou R. Construction of a BAC library and identification of Dmrt1 gene of the rice field eel, Monopterus albus. Biochem Biophys Res Commun 2006; 348:775-80. [PMID: 16893514 DOI: 10.1016/j.bbrc.2006.07.145] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 07/25/2006] [Indexed: 11/24/2022]
Abstract
A bacterial artificial chromosome (BAC) library was constructed using nuclear DNA from the rice field eel (Monopterus albus). The BAC library consists of a total of 33,000 clones with an average insert size of 115 kb. Based on the rice field eel haploid genome size of 600 Mb, the BAC library is estimated to contain approximately 6.3 genome equivalents and represents 99.8% of the genome of the rice field eel. This is first BAC library constructed from this species. To estimate the possibility of isolating a specific clone, high-density colony hybridization-based library screening was performed using Dmrt1 cDNA of the rice field eel as a probe. Both library screening and PCR identification results revealed three positive BAC clones which were overlapped, and formed a contig covering the Dmrt1 gene of 195 kb. By sequence comparisons with the Dmrt1 cDNA and sequencing of first four intron-exon junctions, Dmrt1 gene of the rice field eel was predicted to contain four introns and five exons. The sizes of first and second intron are 1.5 and 2.6 kb, respectively, and the sizes of last two introns were predicted to be about 20 kb. The Dmrt1 gene structure was conserved in evolution. These results also indicate that the BAC library is a useful resource for BAC contig construction and molecular isolation of functional genes.
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Affiliation(s)
- Songhun Jang
- Department of Genetics and Center for Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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130
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Prabhakar S, Poulin F, Shoukry M, Afzal V, Rubin EM, Couronne O, Pennacchio LA. Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res 2006; 16:855-63. [PMID: 16769978 PMCID: PMC1484452 DOI: 10.1101/gr.4717506] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Cross-species DNA sequence comparison is the primary method used to identify functional noncoding elements in human and other large genomes. However, little is known about the relative merits of evolutionarily close and distant sequence comparisons. To address this problem, we identified evolutionarily conserved noncoding regions in primate, mammalian, and more distant comparisons using a uniform approach (Gumby) that facilitates unbiased assessment of the impact of evolutionary distance on predictive power. We benchmarked computational predictions against previously identified cis-regulatory elements at diverse genomic loci and also tested numerous extremely conserved human-rodent sequences for transcriptional enhancer activity using an in vivo enhancer assay in transgenic mice. Human regulatory elements were identified with acceptable sensitivity (53%-80%) and true-positive rate (27%-67%) by comparison with one to five other eutherian mammals or six other simian primates. More distant comparisons (marsupial, avian, amphibian, and fish) failed to identify many of the empirically defined functional noncoding elements. Our results highlight the practical utility of close sequence comparisons, and the loss of sensitivity entailed by more distant comparisons. We derived an intuitive relationship between ancient and recent noncoding sequence conservation from whole-genome comparative analysis that explains most of the observations from empirical benchmarking. Lastly, we determined that, in addition to strength of conservation, genomic location and/or density of surrounding conserved elements must also be considered in selecting candidate enhancers for in vivo testing at embryonic time points.
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Affiliation(s)
- Shyam Prabhakar
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
- Corresponding authors.E-mail ; fax (510) 486-4229. E-mail ; fax (510) 486-4229
| | - Francis Poulin
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Malak Shoukry
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Veena Afzal
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Edward M. Rubin
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Olivier Couronne
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Len A. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
- Corresponding authors.E-mail ; fax (510) 486-4229. E-mail ; fax (510) 486-4229
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131
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Braasch I, Salzburger W, Meyer A. Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration. Mol Biol Evol 2006; 23:1192-202. [PMID: 16547150 DOI: 10.1093/molbev/msk003] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The occurrence of a fish-specific genome duplication (FSGD) in the lineage leading to teleost fishes is widely accepted, but the consequences of this event remain elusive. Teleosts, and the cichlid fishes from the species flocks in the East African Great Lakes in particular, evolved a unique complexity and diversity of body coloration and color patterning. Several genes involved in pigment cell development have been retained in duplicate copies in the teleost genome after the FSGD. Here we investigate the evolutionary fate of one of these genes, the type III receptor tyrosine kinase (RTK) colony-stimulating factor 1 receptor (csf1r). We isolated and shotgun sequenced two paralogous csf1r genes from a bacterial artificial chromosome library of the cichlid fish Astatotilapia burtoni that are both linked to paralogs of the pdgfr beta gene, another type III RTK. Two pdgfr beta-csf1r paralogons were also identified in the genomes of pufferfishes and medaka, and our phylogenetic analyses suggest that the pdgfr beta-csf1r locus was duplicated during the course of the FSGD. Comparisons of teleosts and tetrapods suggest asymmetrical divergence at different levels of genomic organization between the teleost-specific pdgfr beta-csf1r paralogons, which seem to have evolved as coevolutionary units. The high-evolutionary rate in the teleost B-paralogon, consisting of csf1rb and pdgfr betab, further suggests neofunctionalization by functional divergence of the extracellular, ligand-binding region of these cell-surface receptors. Finally, we hypothesize that genome duplications and the associated expansion of the RTK family might be causally linked to the evolution of coloration in vertebrates and teleost fishes in particular.
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Affiliation(s)
- Ingo Braasch
- Lehrstuhl für Zoologie und Evolutionsbiologie, Department of Biology, University of Konstanz, Konstanz, Germany
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132
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Novel mannose-specific lectins found in torafugu, Takifugu rubripes: A review. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2006; 1:122-7. [DOI: 10.1016/j.cbd.2005.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2005] [Revised: 09/28/2005] [Accepted: 09/29/2005] [Indexed: 11/23/2022]
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133
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Uji S, Suzuki T, Kurokawa T. Molecular cloning and expression of retinoic-acid synthesizing enzyme raldh2 from Takifugu rubripes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2006; 1:133-8. [DOI: 10.1016/j.cbd.2005.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2005] [Revised: 07/27/2005] [Accepted: 08/05/2005] [Indexed: 11/27/2022]
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134
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Abstract
The last common ancestor between fish and mammals dates back to the very origin of the vertebrate lineage and today, half of modern vertebrates are fish. It is thus not surprising that several fish species have played important roles in recent years to advance our understanding of vertebrate genome evolution, to inform us on the structure of human genes, and, somewhat more unexpectedly, to provide leads to understanding the function of genes involved in human diseases. Genome sequence comparisons between such distantly related organisms are highly informative due to the accumulation of neutral mutations in nonfunctional regions. Yet humans and fishes share many developmental pathways, organ systems, and physiological mechanisms, making conclusions relevant to human biology. The respective advantages of zebrafish, medaka, Tetraodon, or Takifugu have been well exploited so far with bioinformatics analyses and molecular biology techniques. However the full potential of fish genomics is about to be unleashed with the integration of more traditional disciplines such as biochemistry and physiology, with the study of additional species such as carp, trout, or tilapia and a broadening of its applications to environmental genomics or aquaculture.
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Affiliation(s)
- Hugues Roest Crollius
- Dyogen Lab, Centre National de la Recherche Scientifique UMR8541, Ecole Normale Supérieure, 75005 Paris, France.
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135
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Watabe S, Ikeda D. Diversity of the pufferfish Takifugu rubripes fast skeletal myosin heavy chain genes. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2006; 1:28-34. [PMID: 20483232 DOI: 10.1016/j.cbd.2005.12.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2005] [Revised: 10/23/2005] [Accepted: 12/06/2005] [Indexed: 10/25/2022]
Abstract
Myosin is a highly conserved, ubiquitous actin-based molecular motor that is distributed as diverse as from prokaryotes to mammalian tissues. Among various types in the myosin family proteins, class II, also called sarcomeric, myosin is a classical, conventional molecule that has been extensively studies on its functional and structural properties. It consists of two heavy chains (MYH) of about 200 kDa and four light chains of about 20 kDa. The exon-intron organization was determined for the major subunit of MYH, which contains ATP-hydrolysis and actin-binding sites, from torafugu (tiger pufferfish) Takifugu rubripes fast skeletal muscles. Comprehensive investigation for fast skeletal MYHs based on the fugu (torafugu) genome database and subsequent construction of their physical map revealed that torafugu contains at least 8 putative skeletal MYHs. Furthermore, genomic structural analysis revealed that skeletal MYHs are not clustered in a single locus, but rather spread to at least four loci, with two of them locating at the mammalian syntenic regions. Such arrangement of torafugu MYHs are in a marked contrast to mammalian fast skeletal MYHs that are clustered in a single locus. These data suggest that an ancient segmental duplication or whole-genome duplication occurred in fish lineage as in many other reported torafugu genes.
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Affiliation(s)
- Shugo Watabe
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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136
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Van Hellemont R, Monsieurs P, Thijs G, De Moor B, Van de Peer Y, Marchal K. A novel approach to identifying regulatory motifs in distantly related genomes. Genome Biol 2005; 6:R113. [PMID: 16420672 PMCID: PMC1414112 DOI: 10.1186/gb-2005-6-13-r113] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2005] [Revised: 08/22/2005] [Accepted: 12/01/2005] [Indexed: 11/25/2022] Open
Abstract
A two-step procedure for identifying regulatory motifs in distantly related organisms is described that combines the advantages of sequence alignment and motif detection approaches. Although proven successful in the identification of regulatory motifs, phylogenetic footprinting methods still show some shortcomings. To assess these difficulties, most apparent when applying phylogenetic footprinting to distantly related organisms, we developed a two-step procedure that combines the advantages of sequence alignment and motif detection approaches. The results on well-studied benchmark datasets indicate that the presented method outperforms other methods when the sequences become either too long or too heterogeneous in size.
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Affiliation(s)
- Ruth Van Hellemont
- ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium
| | - Pieter Monsieurs
- ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium
| | - Gert Thijs
- ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium
| | - Bart De Moor
- ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium
| | - Yves Van de Peer
- Plant Systems Biology, Bioinformatics and Evolutionary Genomics, VIB/Ghent University, Technologiepark 927, 9052 Gent, Belgium
| | - Kathleen Marchal
- ESAT-SCD, KU Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven-Heverlee, Belgium
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137
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Characterisation of conserved non-coding sequences in vertebrate genomes using bioinformatics, statistics and functional studies. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2005; 1:46-58. [PMID: 20483234 DOI: 10.1016/j.cbd.2005.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 03/16/2005] [Accepted: 03/20/2005] [Indexed: 10/25/2022]
Abstract
We recently identified approximately 1400 conserved non-coding elements (CNEs) shared by the genomes of fugu (Takifugu rubripes) and human that appear to be associated with developmental regulation in vertebrates [Woolfe, A., Goodson, M., Goode, D.K., Snell, P., McEwen, G.K., Vavouri, T., Smith, S.F., North, P., Callaway, H., Kelly, K., Walter, K., Abnizova, I., Gilks, W., Edwards, Y.J.K., Cooke, J.E., Elgar, G., 2005. Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol. 3 (1), e7]. This study encompassed a multi-disciplinary approach using bioinformatics, statistical methods and functional assays to identify and characterise the CNEs. Using an in vivo enhancer assay, over 90% of tested CNEs up-regulate tissue-specific GFP expression. Here we review our group's research in the field of characterising non-coding sequences conserved in vertebrates. We take this opportunity to discuss our research in progress and present some results of new and additional analyses. These include a phylogenomics analysis of CNEs, sequence conservation patterns in vertebrate CNEs and the distribution of human SNPs in the CNEs. We highlight the usefulness of the CNE dataset to help correlate genetic variation in health and disease. We also discuss the functional analysis using the enhancer assay and the enrichment of predicted transcription factor binding sites for two CNEs. Public access to the CNEs plus annotation is now possible and is described. The content of this review was presented by Dr. Y.J.K. Edwards at the TODAI International Symposium on Functional Genomics of the Pufferfish, Tokyo, Japan, 3-6 November 2004.
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138
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Walter K, Abnizova I, Elgar G, Gilks WR. Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences. Trends Genet 2005; 21:436-40. [PMID: 15979195 DOI: 10.1016/j.tig.2005.06.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2005] [Revised: 04/11/2005] [Accepted: 06/03/2005] [Indexed: 11/18/2022]
Abstract
In a recent study, 1373 highly conserved non-coding elements (CNEs) were detected by aligning the human and Takifugu rubripes (Fugu) genomes. The remarkable degree of sequence conservation in CNEs compared with their surroundings suggested comparing the base composition within CNEs with their 5' and 3' flanking regions. The analysis reveals a novel, sharp and distinct signal of nucleotide frequency bias precisely at the border between CNEs and flanking regions.
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Affiliation(s)
- Klaudia Walter
- MRC Rosalind Franklin Centre for Genomics Research, Hinxton, Cambridge CB10 1SB, UK
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139
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Itoi S, Misaki R, Hirayama M, Nakaniwa M, Liang CS, Kondo H, Watabe S. Identification of three isoforms for mitochondrial adenine nucleotide translocator in the pufferfish Takifugu rubripes. Mitochondrion 2005; 5:162-72. [PMID: 16050982 DOI: 10.1016/j.mito.2005.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2004] [Revised: 12/20/2004] [Accepted: 01/26/2005] [Indexed: 11/21/2022]
Abstract
Three adenine nucleotide translocator (ANT) genes were identified through in silico data mining of the Fugu genome database along with isolation of their corresponding cDNAs in vivo from the pufferfish (Takifugu rubripes). As a result of phylogenetic analysis, the ANT gene on scaffold_254 corresponded to mammalian ANT1, whereas both of those on scaffold_6 and scaffold_598 to mammalian ANT3. The ANT gene encoded by scaffold_6 was expressed ubiquitously in various tissues, whereas the ANT genes encoded by scaffold_254 and scaffold_598 were predominantly expressed in skeletal muscle and heart, respectively.
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MESH Headings
- Amino Acid Sequence
- Animals
- Base Sequence
- Cloning, Molecular
- Computational Biology
- Conserved Sequence
- DNA, Complementary
- Genome
- Isoenzymes/chemistry
- Isoenzymes/genetics
- Isoenzymes/isolation & purification
- Mitochondria, Heart/enzymology
- Mitochondria, Muscle/enzymology
- Mitochondrial ADP, ATP Translocases/chemistry
- Mitochondrial ADP, ATP Translocases/genetics
- Mitochondrial ADP, ATP Translocases/isolation & purification
- Molecular Sequence Data
- Nucleic Acid Amplification Techniques
- Phylogeny
- Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Takifugu/genetics
- Tissue Distribution
- Transcription, Genetic
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Affiliation(s)
- Shiro Itoi
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
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140
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Metpally RPR, Sowdhamini R. Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis. BMC Evol Biol 2005; 5:41. [PMID: 16022726 PMCID: PMC1187884 DOI: 10.1186/1471-2148-5-41] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2005] [Accepted: 07/15/2005] [Indexed: 11/23/2022] Open
Abstract
Background The G-protein-coupled receptors (GPCRs) constitute one of the largest and most ancient superfamilies of membrane proteins. They play a central role in physiological processes affecting almost all aspects of the life cycle of an organism. Availability of the complete sets of putative members of a family from diverse species provides the basis for cross genome comparative studies. Results We have defined the repertoire of GPCR superfamily of Tetraodon complement with the availability of complete sequence of the freshwater puffer fish Tetraodon nigroviridis. Almost all 466 Tetraodon GPCRs (Tnig-GPCRs) identified had a clear human homologue. 189 putative human and Tetraodon GPCR orthologous pairs could be identified. Tetraodon GPCRs are classified into five GRAFS families, by phylogenetic analysis, concurrent with human GPCR classification. Conclusion Direct comparison of GPCRs in Tetraodon and human genomes displays a high level of orthology and supports large-scale gene duplications in Tetraodon. Examples of lineage specific gene expansions were also observed in opsin and odorant receptors. The human and Tetraodon GPCR sequences are analogous in terms of GPCR subfamilies but display disproportionate numbers of receptors at the subfamily level. The teleost genome with its expanded set of GPCRs provides additional and interesting comparators to study both evolution and function of these receptors.
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Affiliation(s)
- Raghu Prasad Rao Metpally
- National centre for biological sciences, Tata institute of fundamental research, UAS-GKVK campus, Bellary road, Bangalore 560065, India
| | - Ramanathan Sowdhamini
- National centre for biological sciences, Tata institute of fundamental research, UAS-GKVK campus, Bellary road, Bangalore 560065, India
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141
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de la Calle-Mustienes E, Feijóo CG, Manzanares M, Tena JJ, Rodríguez-Seguel E, Letizia A, Allende ML, Gómez-Skarmeta JL. A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res 2005; 15:1061-72. [PMID: 16024824 PMCID: PMC1182218 DOI: 10.1101/gr.4004805] [Citation(s) in RCA: 163] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recent studies of the genome architecture of vertebrates have uncovered two unforeseen aspects of its organization. First, large regions of the genome, called gene deserts, are devoid of protein-coding sequences and have no obvious biological role. Second, comparative genomics has highlighted the existence of an array of highly conserved non-coding regions (HCNRs) in all vertebrates. Most surprisingly, these structural features are strongly associated with genes that have essential functions during development. Among these, the vertebrate Iroquois (Irx) genes stand out on both fronts. Mammalian Irx genes are organized in two clusters (IrxA and IrxB) that span >1 Mb each with no other genes interspersed. Additionally, a large number of HCNRs exist within Irx clusters. We have systematically examined the enhancer activity of HCNRs from the IrxB cluster using transgenic Xenopus and zebrafish embryos. Most of these HCNRs are active in subdomains of endogenous Irx expression, and some are candidates to contain shared enhancers of neighboring genes, which could explain the evolutionary conservation of Irx clusters. Furthermore, HCNRs present in tetrapod IrxB but not in fish may be responsible for novel Irx expression domains that appeared after their divergence. Finally, we have performed a more detailed analysis on two IrxB ultraconserved non-coding regions (UCRs) duplicated in IrxA clusters in similar relative positions. These four regions share a core region highly conserved among all of them and drive expression in similar domains. However, inter-species conserved sequences surrounding the core, specific for each of these UCRs, are able to modulate their expression.
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Affiliation(s)
- Elisa de la Calle-Mustienes
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, 41013 Sevilla, Spain
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142
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Nakano T, Windrem M, Zappavigna V, Goldman SA. Identification of a conserved 125 base-pair Hb9 enhancer that specifies gene expression to spinal motor neurons. Dev Biol 2005; 283:474-85. [PMID: 15913596 DOI: 10.1016/j.ydbio.2005.04.017] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 04/08/2005] [Accepted: 04/12/2005] [Indexed: 11/26/2022]
Abstract
The homeobox gene Hb9 is expressed selectively by motor neurons (MNs) in the developing CNS. Previous studies have identified a 9-kb 5' fragment of the mouse Hb9 gene that is sufficient to direct gene expression to spinal MNs in vivo. Here, we sought to identify more discrete MN-specifying elements, using homology searches between genomic sequences of evolutionarily distant species. Based on homology screening of the mouse and human Hb9 promoters, we identified a 3.6-kb Hb9 enhancer that proved sufficient to drive MN-specific lacZ expression. We then compared mouse, human, and pufferfish (Fugu rubripes) genomic sequences, and identified a conserved 438-bp sequence, consisting of noncontiguous 313-bp and 125-bp fragments, residing within the 3.6-kb Hb9 enhancer. The zebrafish (Danio rerio) Hb9 genomic region was then found to have two identical copies of the 125-bp sequence, but no counterpart for the 313-bp sequence. Transgenic analysis showed that the 125-bp alone was both necessary and sufficient to direct spinal MN-specific lacZ expression, whereas the 313-bp sequence had no such enhancer activity. Moreover, the 125-bp Hb9 enhancer was found to harbor two Hox/Pbx consensus-binding sequences, mutations of which completely disrupted thoracolumbar Hb9 expression. These data suggest that Hox/Pbx plays a critical role in the segmental specification of spinal MNs. Together, these results indicate that the molecular pathways regulating Hb9 expression are evolutionarily conserved, and that MN-specific gene expression may be directed and achieved using a small 125-bp 5' enhancer.
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Affiliation(s)
- Takahiro Nakano
- Department of Neurology and Neuroscience, Cornell University Medical Center, New York, NY 10021, USA
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143
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Kai W, Kikuchi K, Fujita M, Suetake H, Fujiwara A, Yoshiura Y, Ototake M, Venkatesh B, Miyaki K, Suzuki Y. A genetic linkage map for the tiger pufferfish, Takifugu rubripes. Genetics 2005; 171:227-38. [PMID: 15972462 PMCID: PMC1456513 DOI: 10.1534/genetics.105.042051] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The compact genome of the tiger pufferfish, Takifugu rubripes (fugu), has been sequenced to the "draft" level and annotated to identify all the genes. However, the assembly of the draft genome sequence is highly fragmented due to the lack of a genetic or a physical map. To determine the long-range linkage relationship of the sequences, we have constructed the first genetic linkage map for fugu. The maps for the male and female spanning 697.1 and 1213.5 cM, respectively, were arranged into 22 linkage groups by markers heterozygous in both parents. The resulting map consists of 200 microsatellite loci physically linked to genome sequences spanning approximately 39 Mb in total. Comparisons of the genome maps of fugu, other teleosts, and mammals suggest that syntenic relationship is more conserved in the teleost lineage than in the mammalian lineage. Map comparisons also show a pufferfish lineage-specific rearrangement of the genome resulting in colocalization of two Hox gene clusters in one linkage group. This map provides a foundation for development of a complete physical map, a basis for comparison of long-range linkage of genes with other vertebrates, and a resource for mapping loci responsible for phenotypic differences among Takifugu species.
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Affiliation(s)
- Wataru Kai
- Fisheries Laboratory, The University of Tokyo, Maisaka, Shizuoka, Japan
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144
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Abstract
Teleost fish, which roughly make up half of the extant vertebrate species, exhibit an amazing level of biodiversity affecting their morphology, ecology and behaviour as well as many other aspects of their biology. This huge variability makes fish extremely attractive for the study of many biological questions, particularly of those related to evolution. New insights gained from different teleost species and sequencing projects have recently revealed several peculiar features of fish genomes that might have played a role in fish evolution and speciation. There is now substantial evidence that a round of tetraploidization/rediploidization has taken place during the early evolution of the ray-finned fish lineage, and that hundreds of duplicate pairs generated by this event have been maintained over hundreds of millions of years of evolution. Differential loss or subfunction partitioning of such gene duplicates might have been involved in the generation of fish variability. In contrast to mammalian genomes, teleost genomes also contain multiple families of active transposable elements, which might have played a role in speciation by affecting hybrid sterility and viability. Finally, the amazing diversity of sex determination systems and the plasticity of sex chromosomes observed in teleost might have been involved in both pre- and postmating reproductive isolation. Comparison of data generated by current and future genome projects as well as complementary studies in other species will allow one to approach the molecular and evolutionary mechanisms underlying genome diversity in fish, and will certainly significantly contribute to our understanding of gene evolution and function in humans and other vertebrates.
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Affiliation(s)
- J-N Volff
- BioFuture Research Group, Physiologische Chemie I, Biozentrum, University of Würzburg, am Hubland, D-97074 Würzburg, Germany.
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145
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Poulin F, Nobrega MA, Plajzer-Frick I, Holt A, Afzal V, Rubin EM, Pennacchio LA. In vivo characterization of a vertebrate ultraconserved enhancer. Genomics 2005; 85:774-81. [PMID: 15885503 DOI: 10.1016/j.ygeno.2005.03.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2005] [Revised: 03/04/2005] [Accepted: 03/07/2005] [Indexed: 02/03/2023]
Abstract
Genomic sequence comparisons among human, mouse, and pufferfish (Takifugu rubripes (Fugu)) have revealed a set of extremely conserved noncoding sequences. While this high degree of sequence conservation suggests severe evolutionary constraint and predicts a lack of tolerance to change to retain in vivo functionality, such elements have been minimally explored experimentally. In this study, we describe the in-depth characterization of an ancient conserved enhancer, Dc2, located near the dachshund gene, which displays a human-Fugu identity of 84% over 424 basepairs (bp). In addition to this large overall conservation, we find that Dc2 is characterized by the presence of a large block of sequence (144 bp) that is completely identical among human, mouse, chicken, zebrafish, and Fugu. Through the testing of reporter vector constructs in transgenic mice, we observed that the 424-bp Dc2-conserved element is necessary and sufficient for brain tissue enhancer activity. In vivo analyses also revealed that the 144-bp 100% conserved sequence is necessary, but not sufficient, to replicate Dc2 enhancer function. However, the introduction of two separate 16-bp insertions into the highly conserved enhancer core did not cause any detectable modification of its in vivo activity. Our observations indicate that the 144-bp 100% conserved element is tolerant of change at least at the resolution of this transgenic mouse assay and suggest that purifying selection on the Dc2 sequence might not be as strong as we predicted or that some unknown property also constrains this highly conserved enhancer sequence.
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Affiliation(s)
- Francis Poulin
- Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
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146
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Marshall CR, Fox JA, Butland SL, Ouellette BFF, Brinkman FSL, Tibbits GF. Phylogeny of Na+/Ca2+exchanger (NCX) genes from genomic data identifies new gene duplications and a new family member in fish species. Physiol Genomics 2005; 21:161-73. [PMID: 15741504 DOI: 10.1152/physiolgenomics.00286.2004] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The Na+/Ca2+exchanger (NCX) is a member of the cation/Ca2+antiporter (CaCA) family and plays a key role in maintaining cellular Ca2+homeostasis in a variety of cell types. NCX is present in a diverse group of organisms and exhibits high overall identity across species. To date, three separate genes, i.e., NCX1, NCX2, and NCX3, have been identified in mammals. However, phylogenetic analysis of the exchanger has been hindered by the lack of nonmammalian NCX sequences. In this study, we expand and diversify the list of NCX sequences by identifying NCX homologs from whole-genome sequences accessible through the Ensembl Genome Browser. We identified and annotated 13 new NCX sequences, including 4 from zebrafish, 4 from Japanese pufferfish, 2 from chicken, and 1 each from honeybee, mosquito, and chimpanzee. Examination of NCX gene structure, together with construction of phylogenetic trees, provided novel insights into the molecular evolution of NCX and allowed us to more accurately annotate NCX gene names. For the first time, we report the existence of NCX2 and NCX3 in organisms other than mammals, yielding the hypothesis that two serial NCX gene duplications occurred around the time vertebrates and invertebrates diverged. In addition, we have found a putative new NCX protein, named NCX4, that is related to NCX1 but has been observed only in fish species genomes. These findings present a stronger foundation for our understanding of the molecular evolution of the NCX gene family and provide a framework for further NCX phylogenetic and molecular studies.
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Affiliation(s)
- Christian R Marshall
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
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147
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Hikima JI, Lennard ML, Wilson MR, Miller NW, Clem LW, Warr GW. Evolution of vertebrate E protein transcription factors: comparative analysis of the E protein gene family in Takifugu rubripes and humans. Physiol Genomics 2005; 21:144-51. [PMID: 15713784 DOI: 10.1152/physiolgenomics.00312.2004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
E proteins are essential for B lymphocyte development and function, including immunoglobulin (Ig) gene rearrangement and expression. Previous studies of B cells in the channel catfish ( Ictalurus punctatus) identified E protein homologs that are capable of binding the μE5 motif and driving a strong transcriptional response. There are three E protein genes in mammals, HEB (TCF12), E2A (TCF3), and E2-2 (TCF4). The major expressed E proteins found in catfish B cells are homologs of HEB and of E2A. Here we sought to define the complete family of E protein genes in a teleost fish, Takifugu rubripes, taking advantage of the completed genome sequence. The catfish CFEB (HEB homolog) sequence identified homologous E-protein-encoding sequences in five scaffolds in the Takifugu genome database. Detailed comparative analysis with the human genome revealed the presence of five E protein homologs in Takifugu. Single genes orthologous to HEB and to E2-2 were identified. In contrast, two members of the E2A gene family were identified in Takifugu; one of these shows the alternative processing of transcripts that identifies it as the ortholog of the E12/E47-encoding mammalian E2A gene, whereas the second Takifugu E2A gene has no predicted alternative splice products. A novel fifth E protein gene (EX) was identified in Takifugu. Phylogenetic analysis revealed four E protein branches among vertebrates: EX, E2A, HEB, and E2-2.
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Affiliation(s)
- Jun-ichi Hikima
- Marine Biomedicine and Environmental Sciences Center, Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina, USA
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148
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Akifyev AP, Grishanin AK. Some conclusions on the role of redundant DNA and the mechanisms of eukaryotic genome evolution inferred from studies of chromatin diminution in Cyclopoida. RUSS J GENET+ 2005. [DOI: 10.1007/s11177-005-0100-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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149
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Araki K, Suetake H, Kikuchi K, Suzuki Y. Characterization and expression analysis of CD3? and CD3?/? in fugu, Takifugu rubripes. Immunogenetics 2005; 57:158-63. [PMID: 15756549 DOI: 10.1007/s00251-005-0772-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2004] [Revised: 12/12/2004] [Indexed: 10/25/2022]
Abstract
CD3 is an essential component of the CD3-TCR complex. In this report, we describe the cloning, characterization, and expression analysis of the CD3varepsilon and CD3gamma/delta chain genes from fugu, Takifugu rubripes. Two distinct CD3varepsilon homologue cDNAs, designated as CD3varepsilon-1 and CD3varepsilon-2, and a CD3gamma/delta homologue cDNA were isolated from the fugu thymus. The deduced amino acid sequences of these cDNAs exhibit conserved essential CD3 chain motifs and overall structures. RT-PCR analysis demonstrated that the CD3varepsilon and CD3gamma/delta genes were expressed in lymphoid organs (e.g. thymus, head kidney, trunk kidney and spleen), mucosal tissues (gill, skin, and intestine), and peripheral blood leucocytes (PBL). The CD3 and TCRalpha genes were expressed only in the surface IgM- population, which were separated from PBL using an anti-fugu IgM monoclonal antibody. In addition, in situ hybridization confirmed that CD3-expressing cells were distributed randomly in the head kidney, trunk kidney, and spleen, but in the thymus were restricted to the lymphoid outer zone and epithelioid inner zone only. Collectively, these results suggest that CD3 molecules are useful markers for the identification of T cells in teleost fish. The present study thus provides a critical step in identifying T cells in this model organism.
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Affiliation(s)
- Kyosuke Araki
- Fisheries Laboratory, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 2971-4 Maisaka, Shizuoka, 431-0211, Japan
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150
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Venkatesh B, Yap WH. Comparative genomics using fugu: a tool for the identification of conserved vertebrate cis-regulatory elements. Bioessays 2005; 27:100-7. [PMID: 15612032 DOI: 10.1002/bies.20134] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
With the imminent completion of the whole genome sequence of humans, increasing attention is being focused on the annotation of cis-regulatory elements in the human genome. Comparative genomics approaches based on evolutionary conservation have proved useful in the detection of conserved cis-regulatory elements. The pufferfish, Fugu rubripes, is an attractive vertebrate model for comparative genomics, by virtue of its compact genome and maximal phylogenetic distance from mammals. Fugu has lost a large proportion of nonessential DNA, and retained single orthologs for many duplicate genes that arose in the fish lineage. Non-coding sequences conserved between fugu and mammals have been shown to be functional cis-regulatory elements. Thus, fugu is a model fish genome of choice for discovering evolutionarily conserved regulatory elements in the human genome. Such evolutionarily conserved elements are likely to be shared by all vertebrates, and related to regulatory interactions fundamental to all vertebrates. 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.
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Affiliation(s)
- Byrappa Venkatesh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.
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