The Experts below are selected from a list of 2865 Experts worldwide ranked by ideXlab platform
Sydney Brenner - One of the best experts on this subject based on the ideXlab platform.
-
Figure S1. Expression Patterns of the Fish Skeletal Muscle Sodium
2014Co-Authors: Nidhi D, Sydney Brenner, Shean Long See, Tuck Wah SoongAbstract:The Fugu genome sequenc
-
integration of the genetic map and genome assembly of Fugu facilitates insights into distinct features of genome evolution in teleosts and mammals
Genome Biology and Evolution, 2011Co-Authors: Wataru Kai, Alice Tay, Hiroaki Suetake, Kiyoshi Kikuchi, Sho Hosoya, Sumanty Tohari, Ah Keng Chew, Atushi Fujiwara, Kiyoshi Naruse, Sydney BrennerAbstract:The compact genome of Fugu (TakiFugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. However, the fragmented nature of the Fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. To extend the contiguity of the assembly to the chromosomal level, we have generated a comprehensive genetic map of Fugu and anchored the scaffolds of the assembly to the 22 chromosomes of Fugu. The map consists of 1,220 microsatellite markers that provide anchor points to 697 scaffolds covering 86% of the genome assembly (http://www.Fugu-sg.org/). The integrated genome map revealed a higher recombination rate in Fugu compared with other vertebrates and a wide variation in the recombination rate between sexes and across chromosomes of Fugu. We used the extended assembly to explore recent rearrangement events in the lineages of Fugu, Tetraodon, and medaka and compared them with rearrangements in three mammalian (human, mouse, and opossum) lineages. Between the two pufferfishes, Fugu has experienced fewer chromosomal rearrangements than Tetraodon. The gene order is more highly conserved in the three teleosts than in mammals largely due to a lower rate of interchromosomal rearrangements in the teleosts. These results provide new insights into the distinct patterns of genome evolution between teleosts and mammals. The consolidated genome map and the genetic map of Fugu are valuable resources for comparative genomics of vertebrates and for elucidating the genetic basis of the phenotypic diversity of ~25 species of TakiFugu that evolved within the last 5 My.
-
Sequence and organization of coelacanth neurohypophysial hormone genes: Evolutionary history of the vertebrate neurohypophysial hormone gene locus-2
2011Co-Authors: Paichung Gwee, Chris T Amemiya, Sydney BrennerAbstract:Numbers of sequences used in the alignment: NP_000481.2 (human VP), AAA48556.1 (VT), BAA24026.1 (lungfish VT), O42499 (Fugu VT), BAA98140.1 (flounder VT), BAD27476.1 (VT) and BAA06669.1 (lamprey VT), NP_000906.1 (human OT), P08162 (MT), BAA24027.1 (lungfish [Phe]MT), O42493 (Fugu IT), BAA98141.1 (flounder IT), BAD27478.1 (phasitocin) and BAD27477.1 (asvatocin). Sequences for and coelacanth were generated in this study.Copyright information:Taken from "Sequence and organization of coelacanth neurohypophysial hormone genes: Evolutionary history of the vertebrate neurohypophysial hormone gene locus"http://www.biomedcentral.com/1471-2148/8/93BMC Evolutionary Biology 2008;8():93-93.Published online 26 Mar 2008PMCID:PMC2315648.
-
elephant shark callorhinchus milii provides insights into the evolution of hox gene clusters in gnathostomes
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Vydianathan Ravi, Alice Tay, Sydney Brenner, Kevin Lam, Boonhui Tay, Byrappa VenkateshAbstract:We have sequenced and analyzed Hox gene clusters from elephant shark, a holocephalian cartilaginous fish. Elephant shark possesses 4 Hox clusters with 45 Hox genes that include orthologs for a higher number of ancient gnathostome Hox genes than the 4 clusters in tetrapods and the supernumerary clusters in teleost fishes. Phylogenetic analysis of elephant shark Hox genes from 7 paralogous groups that contain all of the 4 members indicated an ((AB)(CD)) topology for the order of Hox cluster duplication, providing support for the 2R hypothesis (i.e., 2 rounds of whole-genome duplication during the early evolution of vertebrates). Comparisons of noncoding sequences of the elephant shark and human Hox clusters have identified a large number of conserved noncoding elements (CNEs), which represent putative cis-regulatory elements that may be involved in the regulation of Hox genes. Interestingly, in Fugu more than 50% of these ancient CNEs have diverged beyond recognition in the duplicated (HoxA, HoxB, and HoxD) as well as the singleton (HoxC) Hox clusters. Furthermore, the b-paralogs of the duplicated Fugu Hox clusters are virtually devoid of unique ancient CNEs. In contrast to Fugu Hox clusters, elephant shark and human Hox clusters have lost fewer ancient CNEs. If these ancient CNEs are indeed enhancers directing tissue-specific expression of Hox genes, divergence of their sequences in vertebrate lineages might have led to altered expression patterns and presumably the functions of their associated Hox genes.
-
highly conserved syntenic blocks at the vertebrate hox loci and conserved regulatory elements within and outside hox gene clusters
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Alison P Lee, Alice Tay, Sydney Brenner, Esther G L Koh, Byrappa VenkateshAbstract:Hox genes in vertebrates are clustered, and the organization of the clusters has been highly conserved during evolution. The conservation of Hox clusters has been attributed to enhancers located within and outside the Hox clusters that are essential for the coordinated "temporal" and "spatial" expression patterns of Hox genes in developing embryos. To identify evolutionarily conserved regulatory elements within and outside the Hox clusters, we obtained contiguous sequences for the conserved syntenic blocks from the seven Hox loci in Fugu and carried out a systematic search for conserved noncoding sequences (CNS) in the human, mouse, and Fugu Hox loci. Our analysis has uncovered unusually large conserved syntenic blocks at the HoxA and HoxD loci. The conserved syntenic blocks at the human and mouse HoxA and HoxD loci span 5.4 Mb and 4 Mb and contain 21 and 19 genes, respectively. The corresponding regions in Fugu are 16- and 12-fold smaller. A large number of CNS was identified within the Hox clusters and outside the Hox clusters spread over large regions. The CNS include previously characterized enhancers and overlap with the 5' global control regions of HoxA and HoxD clusters. Most of the CNS are likely to be control regions involved in the regulation of Hox and other genes in these loci. We propose that the regulatory elements spread across large regions on either side of Hox clusters are a major evolutionary constraint that has maintained the exceptionally long syntenic blocks at the HoxA and HoxD loci.
Byrappa Venkatesh - One of the best experts on this subject based on the ideXlab platform.
-
Phylogenetic tree (Bayesian inference) of chordate Runx sequences.
2014Co-Authors: Giselle Sek Suan Nah, Boonhui Tay, Zhi Wei Lim, Motomi Osato, Byrappa VenkateshAbstract:Values adjacent to the nodes represent branch support (Bayesian posterior probability). Lancelet (Branchiostoma floridae) Runt (BfRunt) was used as the outgroup. Hs, human; Dr, Danio rerio; Fr, Fugu (TakiFugu) rubripes; Cm, Callorhinchus milii; Sc, Scyliorhinus canicula; Ci, Ciona intestinalis.
-
elephant shark callorhinchus milii provides insights into the evolution of hox gene clusters in gnathostomes
Proceedings of the National Academy of Sciences of the United States of America, 2009Co-Authors: Vydianathan Ravi, Alice Tay, Sydney Brenner, Kevin Lam, Boonhui Tay, Byrappa VenkateshAbstract:We have sequenced and analyzed Hox gene clusters from elephant shark, a holocephalian cartilaginous fish. Elephant shark possesses 4 Hox clusters with 45 Hox genes that include orthologs for a higher number of ancient gnathostome Hox genes than the 4 clusters in tetrapods and the supernumerary clusters in teleost fishes. Phylogenetic analysis of elephant shark Hox genes from 7 paralogous groups that contain all of the 4 members indicated an ((AB)(CD)) topology for the order of Hox cluster duplication, providing support for the 2R hypothesis (i.e., 2 rounds of whole-genome duplication during the early evolution of vertebrates). Comparisons of noncoding sequences of the elephant shark and human Hox clusters have identified a large number of conserved noncoding elements (CNEs), which represent putative cis-regulatory elements that may be involved in the regulation of Hox genes. Interestingly, in Fugu more than 50% of these ancient CNEs have diverged beyond recognition in the duplicated (HoxA, HoxB, and HoxD) as well as the singleton (HoxC) Hox clusters. Furthermore, the b-paralogs of the duplicated Fugu Hox clusters are virtually devoid of unique ancient CNEs. In contrast to Fugu Hox clusters, elephant shark and human Hox clusters have lost fewer ancient CNEs. If these ancient CNEs are indeed enhancers directing tissue-specific expression of Hox genes, divergence of their sequences in vertebrate lineages might have led to altered expression patterns and presumably the functions of their associated Hox genes.
-
highly conserved syntenic blocks at the vertebrate hox loci and conserved regulatory elements within and outside hox gene clusters
Proceedings of the National Academy of Sciences of the United States of America, 2006Co-Authors: Alison P Lee, Alice Tay, Sydney Brenner, Esther G L Koh, Byrappa VenkateshAbstract:Hox genes in vertebrates are clustered, and the organization of the clusters has been highly conserved during evolution. The conservation of Hox clusters has been attributed to enhancers located within and outside the Hox clusters that are essential for the coordinated "temporal" and "spatial" expression patterns of Hox genes in developing embryos. To identify evolutionarily conserved regulatory elements within and outside the Hox clusters, we obtained contiguous sequences for the conserved syntenic blocks from the seven Hox loci in Fugu and carried out a systematic search for conserved noncoding sequences (CNS) in the human, mouse, and Fugu Hox loci. Our analysis has uncovered unusually large conserved syntenic blocks at the HoxA and HoxD loci. The conserved syntenic blocks at the human and mouse HoxA and HoxD loci span 5.4 Mb and 4 Mb and contain 21 and 19 genes, respectively. The corresponding regions in Fugu are 16- and 12-fold smaller. A large number of CNS was identified within the Hox clusters and outside the Hox clusters spread over large regions. The CNS include previously characterized enhancers and overlap with the 5' global control regions of HoxA and HoxD clusters. Most of the CNS are likely to be control regions involved in the regulation of Hox and other genes in these loci. We propose that the regulatory elements spread across large regions on either side of Hox clusters are a major evolutionary constraint that has maintained the exceptionally long syntenic blocks at the HoxA and HoxD loci.
-
variation in sequence and organization of splicing regulatory elements in vertebrate genes
Proceedings of the National Academy of Sciences of the United States of America, 2004Co-Authors: Shawn Hoon, Byrappa Venkatesh, Christopher B BurgeAbstract:Although core mechanisms and machinery of premRNA splicing are conserved from yeast to human, the details of intron recognition often differ, even between closely related organisms. For example, genes from the pufferfish Fugu rubripes generally contain one or more introns that are not properly spliced in mouse cells. Exploiting available genome sequence data, a battery of sequence analysis techniques was used to reach several conclusions about the organization and evolution of splicing regulatory elements in vertebrate genes. The classical splice site and putative branch site signals are completely conserved across the vertebrates studied (human, mouse, pufferfish, and zebrafish), and exonic splicing enhancers also appear broadly conserved in vertebrates. However, another class of splicing regulatory elements, the intronic splicing enhancers, appears to differ substantially between mammals and fish, with G triples (GGG) very abundant in mammalian introns but comparatively rare in fish. Conversely, short repeats of AC and GT are predicted to function as intronic splicing enhancers in fish but are not enriched in mammalian introns. Consistent with this pattern, exonic splicing enhancer-binding SR proteins are highly conserved across all vertebrates, whereas heterogeneous nuclear ribonucleoproteins, which bind many intronic sequences, vary in domain structure and even presence/absence between mammals and fish. Exploiting differences in intronic sequence composition, a statistical model was developed to predict the splicing phenotype of Fugu introns in mammalian systems and was used to engineer the spliceability of a Fugu intron in human cells by insertion of specific sequences, thereby rescuing splicing in human cells.
-
origin and diversity of the sox transcription factor gene family genome wide analysis in Fugu rubripes
Gene, 2004Co-Authors: Peter Koopman, Sydney Brenner, Goslik Schepers, Byrappa VenkateshAbstract:The SOX family of transcription factors are found throughout the animal kingdom and are important in a variety of developmental contexts. Genome analysis has identified 20 Sox genes in human and mouse, which can be subdivided into 8 groups, based on sequence comparison and intron-exon structure. Most of the SOX groups identified in mammals are represented by a single SOX sequence in invertebrate model organisms, suggesting a duplication and divergence mechanism has operated during vertebrate evolution. We have now analysed the Sox gene complement in the pufferfish, Fugu rubripes, in order to shed further light on the diversity and origins of the Sox gene family. Major differences were found between the Sox family in Fugu and those in humans and mice. In particular, Fugu does not have orthologues of Sry, Sox15 and Sox30, which appear to be specific to mammals, while Sox19, found in Fugu and zebrafish but absent in mammals, seems to be specific to fishes. Six mammalian Sox genes are represented by two copies each in Fugu, indicating a large-scale gene duplication in the fish lineage. These findings point to recent Sox gene loss, duplication and divergence occurring during the evolution of tetrapod and teleost lineages, and provide further evidence for large-scale segmental or a whole-genome duplication occurring early in the radiation of teleosts.
Hiroaki Suetake - One of the best experts on this subject based on the ideXlab platform.
-
mucosal igm antibody with d mannose affinity in Fugu takiFugu rubripes is utilized by a monogenean parasite heterobothrium okamotoi for host recognition
Journal of Immunology, 2017Co-Authors: Kento Igarashi, Hiroaki Suetake, Kiyoshi Kikuchi, Yuzuru Suzuki, Sho Hosoya, Ryohei Matsunaga, Sachi Hirakawa, Osamu Nakamura, Toshiaki Miyadai, Satoshi TasumiAbstract:How parasites recognize their definitive hosts is a mystery; however, parasitism is reportedly initiated by recognition of certain molecules on host surfaces. Fish ectoparasites make initial contact with their hosts at body surfaces, such as skin and gills, which are covered with mucosa that are similar to those of mammalian guts. Fish are among the most primitive vertebrates with immune systems that are equivalent to those in mammals, and they produce and secrete IgM into mucus. In this study, we showed that the monogenean parasite Heterobothrium okamotoi utilizes IgM to recognize its host, Fugu TakiFugu rubripes . Oncomiracidia are infective larvae of H. okamotoi that shed their cilia and metamorphose into juveniles when exposed to purified d-mannose–binding fractions from Fugu mucus. Using liquid chromatography–tandem mass spectrometry analysis, proteins contained in the fraction were identified as d-mannose–specific IgM with two d-mannose–binding lectins. However, although deciliation was significantly induced by IgM and was inhibited by d-mannose or a specific Ab against Fugu IgM, other lectins had no effect, and IgM without d-mannose affinity induced deciliation to a limited degree. Subsequent immunofluorescent staining experiments showed that Fugu d-mannose–specific IgM binds ciliated epidermal cells of oncomiracidium. These observations suggest that deciliation is triggered by binding of Fugu IgM to cell surface Ags via Ag binding sites. Moreover, concentrations of d-mannose–binding IgM in gill mucus were sufficient to induce deciliation in vitro, indicating that H. okamotoi parasites initially use host Abs to colonize host gills.
-
a trans species missense snp in amhr2 is associated with sex determination in the tiger pufferfish takiFugu rubripes Fugu
PLOS Genetics, 2012Co-Authors: Takashi Kamiya, Satoshi Tasumi, Hiroaki Suetake, Masashi Fujita, Naoki Mizuno, Wataru Kai, Ayumi Oka, Takayoshi Matsunaga, Shigenori Suzuki, Sho HosoyaAbstract:Heterogametic sex chromosomes have evolved independently in various lineages of vertebrates. Such sex chromosome pairs often contain nonrecombining regions, with one of the chromosomes harboring a master sex-determining (SD) gene. It is hypothesized that these sex chromosomes evolved from a pair of autosomes that diverged after acquiring the SD gene. By linkage and association mapping of the SD locus in Fugu (TakiFugu rubripes), we show that a SNP (C/G) in the anti-Mullerian hormone receptor type II (Amhr2) gene is the only polymorphism associated with phenotypic sex. This SNP changes an amino acid (His/Asp384) in the kinase domain. While females are homozygous (His/His384), males are heterozygous. Sex in Fugu is most likely determined by a combination of the two alleles of Amhr2. Consistent with this model, the medaka hotei mutant carrying a substitution in the kinase domain of Amhr2 causes a female phenotype. The association of the Amhr2 SNP with phenotypic sex is conserved in two other species of TakiFugu but not in Tetraodon. The Fugu SD locus shows no sign of recombination suppression between X and Y chromosomes. Thus, Fugu sex chromosomes represent an unusual example of proto–sex chromosomes. Such undifferentiated X-Y chromosomes may be more common in vertebrates than previously thought.
-
A trans-species missense SNP in Amhr2 is associated with sex determination in the tiger pufferfish, TakiFugu rubripes (Fugu). PLoS Genet 8: e1002798. doi:10.1371/ journal.pgen.1002798
2012Co-Authors: Takashi Kamiya, Satoshi Tasumi, Hiroaki Suetake, Masashi Fujita, Naoki Mizuno, Wataru Kai, Ayumi Oka, Takayoshi Matsunaga, Shigenori Suzuki, Sho HosoyaAbstract:Heterogametic sex chromosomes have evolved independently in various lineages of vertebrates. Such sex chromosome pairs often contain nonrecombining regions, with one of the chromosomes harboring a master sex-determining (SD) gene. It is hypothesized that these sex chromosomes evolved from a pair of autosomes that diverged after acquiring the SD gene. By linkage and association mapping of the SD locus in Fugu (TakiFugu rubripes), we show that a SNP (C/G) in the anti-Müllerian hormone receptor type II (Amhr2) gene is the only polymorphism associated with phenotypic sex. This SNP changes an amino acid (His/Asp384) in the kinase domain. While females are homozygous (His/His384), males are heterozygous. Sex in Fugu is most likely determined by a combination of the two alleles of Amhr2. Consistent with this model, the medaka hotei mutant carrying a substitution in the kinase domain of Amhr2 causes a female phenotype. The association of the Amhr2 SNP with phenotypic sex is conserved in two other species of TakiFugu but not in Tetraodon. The Fugu SD locus shows no sign of recombination suppression between X and Y chromosomes. Thus, Fugu sex chromosomes represent an unusual example of proto–sex chromosomes. Such undifferentiated X-Y chromosomes may be more common i
-
integration of the genetic map and genome assembly of Fugu facilitates insights into distinct features of genome evolution in teleosts and mammals
Genome Biology and Evolution, 2011Co-Authors: Wataru Kai, Alice Tay, Hiroaki Suetake, Kiyoshi Kikuchi, Sho Hosoya, Sumanty Tohari, Ah Keng Chew, Atushi Fujiwara, Kiyoshi Naruse, Sydney BrennerAbstract:The compact genome of Fugu (TakiFugu rubripes) has been used widely as a reference genome for understanding the evolution of vertebrate genomes. However, the fragmented nature of the Fugu genome assembly has restricted its use for comparisons of genome architecture in vertebrates. To extend the contiguity of the assembly to the chromosomal level, we have generated a comprehensive genetic map of Fugu and anchored the scaffolds of the assembly to the 22 chromosomes of Fugu. The map consists of 1,220 microsatellite markers that provide anchor points to 697 scaffolds covering 86% of the genome assembly (http://www.Fugu-sg.org/). The integrated genome map revealed a higher recombination rate in Fugu compared with other vertebrates and a wide variation in the recombination rate between sexes and across chromosomes of Fugu. We used the extended assembly to explore recent rearrangement events in the lineages of Fugu, Tetraodon, and medaka and compared them with rearrangements in three mammalian (human, mouse, and opossum) lineages. Between the two pufferfishes, Fugu has experienced fewer chromosomal rearrangements than Tetraodon. The gene order is more highly conserved in the three teleosts than in mammals largely due to a lower rate of interchromosomal rearrangements in the teleosts. These results provide new insights into the distinct patterns of genome evolution between teleosts and mammals. The consolidated genome map and the genetic map of Fugu are valuable resources for comparative genomics of vertebrates and for elucidating the genetic basis of the phenotypic diversity of ~25 species of TakiFugu that evolved within the last 5 My.
-
characterization of cd8 leukocytes in Fugu takiFugu rubripes with antiserum against Fugu cd8α
Developmental and Comparative Immunology, 2008Co-Authors: Kyosuke Araki, Hiroaki Suetake, Kiyoshi Kikuchi, Kanako Akatsu, Yuzuru SuzukiAbstract:We have investigated the characteristics of CD8+ leukocytes by using an anti-CD8alpha antiserum raised in mouse by DNA-immunization. The magnetically sorted CD8alpha+ peripheral blood leukocyte (PBL) population comprised lymphocytes/thrombocytes and monocytes, whereas CD8alpha- PBLs consisted of lymphocytes/thrombocytes, monocytes, and neutrophils. Expression analysis demonstrated that both groups of cells expressed the CD3epsilon and TCRalpha genes. The CD8alpha and CD8beta genes were detected only in CD8alpha+ cells, whereas expression of CD4 and immunoglobulin light chain (IgL) was observed only in CD8alpha- cells. These results suggest that Fugu CD8alpha+ leukocytes contain CD8+ T cells, but not CD4+ T cells or B cells. Furthermore, mitogenesis of the CD8+ lymphocyte/thrombocyte population was induced by phytohemaglutinin stimulation, suggesting that fish CD8+ lymphocytes/thrombocytes (probably CD8+ T cells) have characteristics similar to mammalian CD8+ T cells. Neutrophils and monocytes/macrophages infiltrating a subcutaneous inflammatory site expressed only CD8alpha, but not CD8beta, CD4, TCRalpha, or IgL. This result suggests that similar to mammalian dendritic cells, Fugu monocytes/macrophages express CD8alpha.
Greg Elgar - One of the best experts on this subject based on the ideXlab platform.
-
Special Issue papers
2015Co-Authors: Greg Elgar, Rosalind Franklin Centre For, On Fugu GenomicsAbstract:now a career track scientist with the MRC. Greg is a member of the BBSRC’s Animal Sciences Board. His research interests cover the whole range of vertebrate comparative genomics, but two key areas are the use of comparative genomics to annotate the human genome and the analysis of non-coding regulatory DNA. He is one of the key members of the Fugu Sequencing Consortium, which has recently completed the draft sequence of the Fugu genome, the first vertebrate, after human, to reach this stage of completion. To date he has published over 60 papers on the Fugu genome
-
Figure 1
2013Co-Authors: Amir Ali Abbasi, Greg Elgar, Zissis Paparidis, Sajid Malik, Debbie K Goode, Heather Callaway, Karlheinz GrzeschikAbstract:Comparative Sequence Analysis of the GLI3 Locus Detects Conserved Non-coding Sequence Elements. (A) Sequence alignments of the genomic interval containing the human GLI3 locus and flanking human genes INHBA and PSMA2 with orthologous counterparts from representative members of rodent, bird, amphibian, and fish lineages. These are shown as SLAGAN derived VISTA representations. Conserved coding sequences are depicted in blue and conserved non-coding sequences are in pink. Criteria of alignment were 60 bp window and 50% conservation cutoff. Conservation between human and Fugu (scaffold_210 ENSEMBL genome browser) is restricted to the GLI3 gene. Red bars above the conservation plot depict the approximate length of intergenic regions flanking human GLI3. The blue arrow shows the length of the GLI3 gene and the direction of transcription. A graphic representation showing exons and introns of GLI3 is shown below the homology plot. Green vertical lines indicate the positions of alterations affecting the genomic structure of the locus which result in loss of GLI3 function: a translocation event associated with Greig cephalopolysyndactyly syndrome (GCPS) [36], and two insertions (ins) in mouse mutants anterior digit pattern deformity (add) [7], [37] and polydactyly Nagoya (Pdn) [38]. (B) Magnified view of the human/Fugu conservation plot and the genomic structure of human GLI3. The red vertical bars below the plot show the position of human/Fugu highly conserved non-coding sequence elements (CNEs) that were functionally tested as putative enhancers.
-
human gli3 intragenic conserved non coding sequences are tissue specific enhancers
PLOS ONE, 2007Co-Authors: Amir Ali Abbasi, Greg Elgar, Zissis Paparidis, Sajid Malik, Debbie K Goode, Heather Callaway, Karlheinz GrzeschikAbstract:The zinc-finger transcription factor GLI3 is a key regulator of development, acting as a primary transducer of Sonic hedgehog (SHH) signaling in a combinatorial context dependent fashion controlling multiple patterning steps in different tissues/organs. A tight temporal and spatial control of gene expression is indispensable, however, cis-acting sequence elements regulating GLI3 expression have not yet been reported. We show that 11 ancient genomic DNA signatures, conserved from the pufferfish TakiFugu (Fugu) rubripes to man, are distributed throughout the introns of human GLI3. They map within larger conserved non-coding elements (CNEs) that are found in the tetrapod lineage. Full length CNEs transiently transfected into human cell cultures acted as cell type specific enhancers of gene transcription. The regulatory potential of these elements is conserved and was exploited to direct tissue specific expression of a reporter gene in zebrafish embryos. Assays of deletion constructs revealed that the human-Fugu conserved sequences within the GLI3 intronic CNEs were essential but not sufficient for full-scale transcriptional activation. The enhancer activity of the CNEs is determined by a combinatorial effect of a core sequence conserved between human and teleosts (Fugu) and flanking tetrapod-specific sequences, suggesting that successive clustering of sequences with regulatory potential around an ancient, highly conserved nucleus might be a possible mechanism for the evolution of cis-acting regulatory elements.
-
faithful expression of a tagged Fugu wt1 protein from a genomic transgene in zebrafish
Nucleic Acids Research, 2003Co-Authors: Colin G Miles, Greg Elgar, Lesley Rankin, Shirley I Smith, Martina Niksic, Nicholas D. HastieAbstract:The teleost ®sh are widely used as model organisms in vertebrate biology. The compact genome of the puffer®sh, Fugu rubripes, has proven a valuable tool in comparative genome analyses, aiding the annotation of mammalian genomes and the identi®cation of conserved regulatory elements, whilst the zebra®sh is particularly suited to genetic and developmental studies. We demonstrate that a puffer®sh WT1 transgene can be expressed and spliced appropriately in transgenic zebra®sh, contrasting with the situation in transgenic mice. By creating both transgenic mice and transgenic zebra®sh with the same construct, we show that Fugu RNA is processed correctly in zebra®sh but not in mice. Furthermore, we show for the ®rst time that a Fugu genomic construct can produce protein in transgenic zebra®sh: a full-length Fugu WT1 transgene with a C-terminal b-galactosidase fusion is spliced and translated correctly in zebra®sh, mimicking the expression of the endogenous WT1 gene. These data demonstrate that the zebra®sh:Fugu system is a powerful and convenient tool for dissecting both vertebrate gene regulation and gene function in vivo.
-
faithful expression of a tagged Fugu wt1 protein from a genomic transgene in zebrafish efficient splicing of pufferfish genes in zebrafish but not mice
Nucleic Acids Research, 2003Co-Authors: Colin G Miles, Greg Elgar, Lesley Rankin, Shirley I Smith, Martina Niksic, Nicholas D. HastieAbstract:The teleost fish are widely used as model organisms in vertebrate biology. The compact genome of the pufferfish, Fugu rubripes, has proven a valuable tool in comparative genome analyses, aiding the annotation of mammalian genomes and the identification of conserved regulatory elements, whilst the zebrafish is particularly suited to genetic and developmental studies. We demonstrate that a pufferfish WT1 transgene can be expressed and spliced appropriately in transgenic zebrafish, contrasting with the situation in transgenic mice. By creating both transgenic mice and transgenic zebrafish with the same construct, we show that Fugu RNA is processed correctly in zebrafish but not in mice. Furthermore, we show for the first time that a Fugu genomic construct can produce protein in transgenic zebrafish: a full-length Fugu WT1 transgene with a C-terminal β-galactosidase fusion is spliced and translated correctly in zebrafish, mimicking the expression of the endogenous WT1 gene. These data demonstrate that the zebrafish:Fugu system is a powerful and convenient tool for dissecting both vertebrate gene regulation and gene function in vivo.
Sho Hosoya - One of the best experts on this subject based on the ideXlab platform.
-
Association test for phenotypic sex and marker genotypes, and QTL (quantitative trait loci) analysis in T. niphobles Family 1.
2018Co-Authors: Risa Ieda, Satoshi Tasumi, Aoi Nozawa, Sho Hosoya, Takashi Kamiya, Shota Tajima, Kazufumi Atsumi, Yuma Aoki, Takashi Koyama, Osamu NakamuraAbstract:(A) Plot of–log10 (P value) versus chromosome position for the association test. The chromosomal position of the markers was first inferred from the draft genome sequence of Fugu, and later confirmed partially by linkage analysis shown in Fig 4B and S1B Fig. Closed and open circles indicate data from paternally and maternally inherited markers, respectively. Bonferroni correction gave a significance threshold of–log10 (P) = 2.5 (blue vertical dotted line). The segmented bar next to the–log10 (P) plot illustrates the sequence map of Fugu chromosome 19, in which each segment schematic represents a scaffold in the Fugu5/fr3 assembly [35,36]. (B) Chromosome-wide mapping of sex-determining QTL. Log of odds (LOD) scores are plotted in the linkage map of T. niphobles LG19. The blue dotted line indicates chromosome-wide significant (0.1%) levels of LOD scores, calculated from 10,000 permutations. The red line in the graph indicates the 95% Bayesian confidence interval (CI). Genetic markers are ordered and placed based on both the linkage analysis of T. niphobles (in the graph) and their comparative location in the Fugu genome (on the segmented bar). There was no discrepancy in the order at this resolution of linkage analysis. The Amhr2 locus (in red letters) did not co-segregate with 95% CI (red line).
-
Derivative melting curves of PCR products by HRM analysis of SNP7271 at the Amhr2 locus from Fugu and T. niphobles.
2018Co-Authors: Risa Ieda, Satoshi Tasumi, Aoi Nozawa, Sho Hosoya, Takashi Kamiya, Shota Tajima, Kazufumi Atsumi, Yuma Aoki, Takashi Koyama, Osamu NakamuraAbstract:The red curve denotes a profile obtained from a male Fugu heterozygous (XY) at the SNP site in exon 9 at the Amhr2 locus (SNP7271). The 81 gray curves denote profiles obtained from 40 female and 40 male wild T. niphobles, and one female homozygous (XX) Fugu. The same pattern (gray curves) was obtained from another 120 samples of T. niphobles (60 female and 60 male; data not shown), indicating that T. niphobles is homozygous at the SNP7271 position in the Amhr2 gene regardless of the sex.
-
Fugu scaffolds corresponding to the sex-determining QTL in T. niphobles.
2018Co-Authors: Risa Ieda, Satoshi Tasumi, Aoi Nozawa, Sho Hosoya, Takashi Kamiya, Shota Tajima, Kazufumi Atsumi, Yuma Aoki, Takashi Koyama, Osamu NakamuraAbstract:Fugu scaffolds corresponding to the sex-determining QTL in T. niphobles.
-
mucosal igm antibody with d mannose affinity in Fugu takiFugu rubripes is utilized by a monogenean parasite heterobothrium okamotoi for host recognition
Journal of Immunology, 2017Co-Authors: Kento Igarashi, Hiroaki Suetake, Kiyoshi Kikuchi, Yuzuru Suzuki, Sho Hosoya, Ryohei Matsunaga, Sachi Hirakawa, Osamu Nakamura, Toshiaki Miyadai, Satoshi TasumiAbstract:How parasites recognize their definitive hosts is a mystery; however, parasitism is reportedly initiated by recognition of certain molecules on host surfaces. Fish ectoparasites make initial contact with their hosts at body surfaces, such as skin and gills, which are covered with mucosa that are similar to those of mammalian guts. Fish are among the most primitive vertebrates with immune systems that are equivalent to those in mammals, and they produce and secrete IgM into mucus. In this study, we showed that the monogenean parasite Heterobothrium okamotoi utilizes IgM to recognize its host, Fugu TakiFugu rubripes . Oncomiracidia are infective larvae of H. okamotoi that shed their cilia and metamorphose into juveniles when exposed to purified d-mannose–binding fractions from Fugu mucus. Using liquid chromatography–tandem mass spectrometry analysis, proteins contained in the fraction were identified as d-mannose–specific IgM with two d-mannose–binding lectins. However, although deciliation was significantly induced by IgM and was inhibited by d-mannose or a specific Ab against Fugu IgM, other lectins had no effect, and IgM without d-mannose affinity induced deciliation to a limited degree. Subsequent immunofluorescent staining experiments showed that Fugu d-mannose–specific IgM binds ciliated epidermal cells of oncomiracidium. These observations suggest that deciliation is triggered by binding of Fugu IgM to cell surface Ags via Ag binding sites. Moreover, concentrations of d-mannose–binding IgM in gill mucus were sufficient to induce deciliation in vitro, indicating that H. okamotoi parasites initially use host Abs to colonize host gills.
-
a trans species missense snp in amhr2 is associated with sex determination in the tiger pufferfish takiFugu rubripes Fugu
PLOS Genetics, 2012Co-Authors: Takashi Kamiya, Satoshi Tasumi, Hiroaki Suetake, Masashi Fujita, Naoki Mizuno, Wataru Kai, Ayumi Oka, Takayoshi Matsunaga, Shigenori Suzuki, Sho HosoyaAbstract:Heterogametic sex chromosomes have evolved independently in various lineages of vertebrates. Such sex chromosome pairs often contain nonrecombining regions, with one of the chromosomes harboring a master sex-determining (SD) gene. It is hypothesized that these sex chromosomes evolved from a pair of autosomes that diverged after acquiring the SD gene. By linkage and association mapping of the SD locus in Fugu (TakiFugu rubripes), we show that a SNP (C/G) in the anti-Mullerian hormone receptor type II (Amhr2) gene is the only polymorphism associated with phenotypic sex. This SNP changes an amino acid (His/Asp384) in the kinase domain. While females are homozygous (His/His384), males are heterozygous. Sex in Fugu is most likely determined by a combination of the two alleles of Amhr2. Consistent with this model, the medaka hotei mutant carrying a substitution in the kinase domain of Amhr2 causes a female phenotype. The association of the Amhr2 SNP with phenotypic sex is conserved in two other species of TakiFugu but not in Tetraodon. The Fugu SD locus shows no sign of recombination suppression between X and Y chromosomes. Thus, Fugu sex chromosomes represent an unusual example of proto–sex chromosomes. Such undifferentiated X-Y chromosomes may be more common in vertebrates than previously thought.
