1
|
Ali S, Abrar M, Hussain I, Batool F, Raza RZ, Khatoon H, Zoia M, Visel A, Shubin NH, Osterwalder M, Abbasi AA. Identification of ancestral gnathostome Gli3 enhancers with activity in mammals. Dev Growth Differ 2024; 66:75-88. [PMID: 37925606 PMCID: PMC10841732 DOI: 10.1111/dgd.12901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/01/2023] [Accepted: 10/23/2023] [Indexed: 11/06/2023]
Abstract
Abnormal expression of the transcriptional regulator and hedgehog (Hh) signaling pathway effector Gli3 is known to trigger congenital disease, most frequently affecting the central nervous system (CNS) and the limbs. Accurate delineation of the genomic cis-regulatory landscape controlling Gli3 transcription during embryonic development is critical for the interpretation of noncoding variants associated with congenital defects. Here, we employed a comparative genomic analysis on fish species with a slow rate of molecular evolution to identify seven previously unknown conserved noncoding elements (CNEs) in Gli3 intronic intervals (CNE15-21). Transgenic assays in zebrafish revealed that most of these elements drive activities in Gli3 expressing tissues, predominantly the fins, CNS, and the heart. Intersection of these CNEs with human disease associated SNPs identified CNE15 as a putative mammalian craniofacial enhancer, with conserved activity in vertebrates and potentially affected by mutation associated with human craniofacial morphology. Finally, comparative functional dissection of an appendage-specific CNE conserved in slowly evolving fish (elephant shark), but not in teleost (CNE14/hs1586) indicates co-option of limb specificity from other tissues prior to the divergence of amniotes and lobe-finned fish. These results uncover a novel subset of intronic Gli3 enhancers that arose in the common ancestor of gnathostomes and whose sequence components were likely gradually modified in other species during the process of evolutionary diversification.
Collapse
Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| | - Fatima Batool
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| | - Rabail Zehra Raza
- Department of Biological Sciences, Faculty of Multidisciplinary Studies, National University of Medical Sciences Rawalpindi, Pakistan
| | - Hizran Khatoon
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| | - Matteo Zoia
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
| | - Axel Visel
- Environmental Genomics and System Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
- U.S. Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, USA
- School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Neil H. Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, IL 60637, USA
| | - Marco Osterwalder
- Department for Biomedical Research (DBMR), University of Bern, Bern, Switzerland
- Department of Cardiology, Bern University Hospital, Bern, Switzerland
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i-Azam University, 45320, Islamabad Pakistan
| |
Collapse
|
2
|
Ali S, Arif I, Iqbal A, Hussain I, Abrar M, Khan MR, Shubin N, Abbasi AA. Comparative genomic analysis of human GLI2 locus using slowly evolving fish revealed the ancestral gnathostome set of early developmental enhancers. Dev Dyn 2021; 250:669-683. [PMID: 33381902 PMCID: PMC9292287 DOI: 10.1002/dvdy.291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/03/2022] Open
Abstract
Background The zinc finger‐containing transcription factor Gli2, is a key mediator of Hedgehog (Hh) signaling and participates in embryonic patterning of various organs including the central nervous system (CNS) and limbs. Abnormal expression of Gli2 can impede the transcription of Hh target genes through disruption of proper balance between Gli2 and Gli3 functions. Therefore, delineation of enhancers that are required for complementary roles of Glis would allow the interrogation of those pathogenic variants that cause gene dysregulation, and a corresponding abnormal phenotype. Previously, we reported tissue‐specific enhancers for Gli family including Gli2 through direct tetrapod‐teleost comparisons. Results Here, we employed the sequence alignments of slowly evolving spotted gar and elephant shark and have identified six novel conserved noncoding elements in human GLI2 containing locus. Zebrafish‐based transgenic assays revealed that combined action of these autonomous CNEs reflects many aspects of Gli2 specific endogenous transcriptional activity, including CNS and pectoral fins. Conclusion Taken together with our previous findings, this study suggests that Hh‐signaling controlled deployment of Gli2 activity in embryonic patterning arose in the common ancestor of gnathostomes. These GLI2 specific cis‐regulatory modules will help to identify DNA variants that probably reside outside of coding intervals and are associated with congenital anomalies. We performed a phylogenetic footprint analyses of human GLI2 containing locus by incorporating relatively slowly evolving gar and elephant shark genomes and have identified multiple novel conserved non‐coding elements (CNEs) that were not predicted by direct human‐teleostcomparisons. Comparative analyses suggest that majority of the GLI2 associated CNEs identified in the present data and reported previously arose in the common ancestor of gnathostomes but lost in teleosts, presumably because of fast teleost sequence evolution. Functional testing of GLI2 associated CNEs by employing zebrafish based transgenic reporter assays revealed their tissue specific cis‐regulatory potential that corresponds with the results based on whole‐mount in situ hybridization analysis of gli2 mRNA in zebrafish. The delineated set of GLI2 associated enhancers can be further interrogated to determine their role in canonical Hh signaling, gene dysregulation, and a corresponding congenital anomaly.
Collapse
Affiliation(s)
- Shahid Ali
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irum Arif
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Ayesha Iqbal
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Irfan Hussain
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Abrar
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| | - Muhammad Ramzan Khan
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Center, Islamabad, Pakistan
| | - Neil Shubin
- Department of Organismal Biology and Anatomy, The University of Chicago, Chicago, Illinois, USA
| | - Amir Ali Abbasi
- National Center for Bioinformatics, Program of Comparative and Evolutionary Genomics, Faculty of Biological Sciences, Quaid-i- Azam University, Islamabad, Pakistan
| |
Collapse
|
3
|
Light- and circadian-controlled genes respond to a broad light spectrum in Puffer Fish-derived Fugu eye cells. Sci Rep 2017; 7:46150. [PMID: 28418034 PMCID: PMC5394683 DOI: 10.1038/srep46150] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/10/2017] [Indexed: 11/08/2022] Open
Abstract
Some cell lines retain intrinsic phototransduction pathways to control the expression of light-regulated genes such as the circadian clock gene. Here we investigated the photosensitivity of a Fugu eye, a cell line established from the eye of Takifugu rubripes, to examine whether such a photosensitive nature is present. Microarray analysis identified 15 genes that showed blue light-dependent change at the transcript level. We investigated temporal profiles of the light-induced genes, as well as Cry and Per, under light-dark, constant light (LL), and constant dark (DD) conditions by quantitative RT-PCR. Transcript levels of Per1a and Per3 genes showed circadian rhythmic changes under both LL and DD conditions, while those of Cry genes were controlled by light. All genes examined, including DNA-damage response genes and photolyase genes, were upregulated not only by blue light but also green and red light, implying the contribution of multiple photopigments. The present study is the first to identify a photosensitive clock cell line originating from a marine fish. These findings may help to characterize the molecular mechanisms underlying photic synchronization of the physiological states of fishes to not only daily light-dark cycles but also to various marine environmental cycles such as the lunar or semi-lunar cycle.
Collapse
|
4
|
Upadhyay U, Srivastava S, Khatri I, Nanda JS, Subramanian S, Arora A, Singh J. Ablation of RNA interference and retrotransposons accompany acquisition and evolution of transposases to heterochromatin protein CENPB. Mol Biol Cell 2017; 28:1132-1146. [PMID: 28228545 PMCID: PMC5391189 DOI: 10.1091/mbc.e16-07-0485] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 01/19/2017] [Accepted: 02/14/2017] [Indexed: 02/02/2023] Open
Abstract
Fission yeast have adapted to retrotransposon invasion by RNAi-mediated silencing, which has coevolved into a mechanism involving CENPB-mediated heterochromatinization together with ablation of RNAi components via accumulation of recombinogenic repeats in recently diverged species of Schizosaccharomyces. Similar trends are seen in the metazoans. Inactivation of retrotransposons is accompanied by the emergence of centromere-binding protein-B (CENPB) in Schizosaccharomyces, as well as in metazoans. The RNA interference (RNAi)-induced transcriptional silencing (RITS) complex, comprising chromodomain protein-1 (Chp1), Tas3 (protein with unknown function), and Argonaute (Ago1), plays an important role in RNAi-mediated heterochromatinization. We find that whereas the Ago1 subunit of the RITS complex is highly conserved, Tas3 is lost and Chp1 is truncated in Schizosaccharomyces cryophilus and Schizosaccharomyces octosporus. We show that truncated Chp1 loses the property of heterochromatin localization and silencing when transformed in Schizosaccharomyces pombe. Furthermore, multiple copies of CENPB, related to Tc1/mariner and Tc5 transposons, occur in all Schizosaccharomyces species, as well as in humans, but with loss of transposase function (except Schizosaccharomyces japonicus). We propose that acquisition of Tc1/mariner and Tc5 elements by horizontal transfer in S. pombe (and humans) is accompanied by alteration of their function from a transposase/endonuclease to a heterochromatin protein, designed to suppress transposon expression and recombination. The resulting redundancy of RITS may have eased the selection pressure, resulting in progressive loss or truncation of tas3 and chp1 genes in S. octosporus and S. cryophilus and triggered similar evolutionary dynamics in the metazoan orthologues.
Collapse
Affiliation(s)
- Udita Upadhyay
- Department of Anesthesiology, Miller School of Medicine, University of Miami, Miami, FL 33136
| | - Suchita Srivastava
- Yeast Epigenetic Regulation Laboratory, Council of Scientific and Industrial Research, Chandigarh 160036, India
| | - Indu Khatri
- Department of Medicine and Biology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215
| | - Jagpreet Singh Nanda
- Department of Pharmacology, Case Western Reserve University, Cleveland, OH 44106
| | - Srikrishna Subramanian
- Protein Evolution Laboratory, Council of Scientific and Industrial Research, Chandigarh 160036, India
| | - Amit Arora
- Microbial Type Culture Collection, Institute of Microbial Technology, Council of Scientific and Industrial Research, Chandigarh 160036, India
| | - Jagmohan Singh
- Yeast Epigenetic Regulation Laboratory, Council of Scientific and Industrial Research, Chandigarh 160036, India
| |
Collapse
|
5
|
Zhang Z, Nie C, Jia Y, Jiang R, Xia H, Lv X, Chen Y, Li J, Li X, Ning Z, Xu G, Chen J, Yang N, Qu L. Parallel Evolution of Polydactyly Traits in Chinese and European Chickens. PLoS One 2016; 11:e0149010. [PMID: 26859147 PMCID: PMC4747547 DOI: 10.1371/journal.pone.0149010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 01/26/2016] [Indexed: 12/26/2022] Open
Abstract
Polydactyly is one of the most common hereditary congenital limb malformations in chickens and other vertebrates. The zone of polarizing activity regulatory sequence (ZRS) is critical for the development of polydactyly. The causative mutation of polydactyly in the Silkie chicken has been mapped to the ZRS; however, the causative mutations of other chicken breeds are yet to be established. To understand whether the same mutation decides the polydactyly phenotype in other chicken breeds, we detected the single-nucleotide polymorphism in 26 different chicken breeds, specifically, 24 Chinese indigenous breeds and 2 European breeds. The mutation was found to have fully penetrated chickens with polydactyly in China, indicating that it is causative for polydactyly in Chinese indigenous chickens. In comparison, the mutation showed no association with polydactyly in Houdan chickens, which originate from France, Europe. Based on the different morphology of polydactyly in Chinese and European breeds, we assumed that the trait might be attributable to different genetic foundations. Therefore, we subsequently performed genome-wide association analysis (GWAS) to locate the region associated with polydactyly. As a result, a ~0.39 Mb genomic region on GGA2p was identified. The region contains six candidate genes, with the causative mutation found in Chinese indigenous breeds also being located in this region. Our results demonstrate that polydactyly in chickens from China and Europe is caused by two independent mutation events that are closely located in the chicken genome.
Collapse
Affiliation(s)
- Zebin Zhang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Changsheng Nie
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yaxiong Jia
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Runshen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, 230036, China
| | - Haijian Xia
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xueze Lv
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Junying Li
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xianyao Li
- College of Animal Science, Shandong Agricultural University, Taian, 271018, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Guiyun Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jilan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ning Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- * E-mail:
| |
Collapse
|
6
|
Bhatia S, Kleinjan DA. Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet 2014; 133:815-45. [DOI: 10.1007/s00439-014-1424-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 01/18/2014] [Indexed: 01/05/2023]
|
7
|
Ravi V, Bhatia S, Gautier P, Loosli F, Tay BH, Tay A, Murdoch E, Coutinho P, van Heyningen V, Brenner S, Venkatesh B, Kleinjan DA. Sequencing of Pax6 loci from the elephant shark reveals a family of Pax6 genes in vertebrate genomes, forged by ancient duplications and divergences. PLoS Genet 2013; 9:e1003177. [PMID: 23359656 PMCID: PMC3554528 DOI: 10.1371/journal.pgen.1003177] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 10/31/2012] [Indexed: 11/18/2022] Open
Abstract
Pax6 is a developmental control gene essential for eye development throughout the animal kingdom. In addition, Pax6 plays key roles in other parts of the CNS, olfactory system, and pancreas. In mammals a single Pax6 gene encoding multiple isoforms delivers these pleiotropic functions. Here we provide evidence that the genomes of many other vertebrate species contain multiple Pax6 loci. We sequenced Pax6-containing BACs from the cartilaginous elephant shark (Callorhinchus milii) and found two distinct Pax6 loci. Pax6.1 is highly similar to mammalian Pax6, while Pax6.2 encodes a paired-less Pax6. Using synteny relationships, we identify homologs of this novel paired-less Pax6.2 gene in lizard and in frog, as well as in zebrafish and in other teleosts. In zebrafish two full-length Pax6 duplicates were known previously, originating from the fish-specific genome duplication (FSGD) and expressed in divergent patterns due to paralog-specific loss of cis-elements. We show that teleosts other than zebrafish also maintain duplicate full-length Pax6 loci, but differences in gene and regulatory domain structure suggest that these Pax6 paralogs originate from a more ancient duplication event and are hence renamed as Pax6.3. Sequence comparisons between mammalian and elephant shark Pax6.1 loci highlight the presence of short- and long-range conserved noncoding elements (CNEs). Functional analysis demonstrates the ancient role of long-range enhancers for Pax6 transcription. We show that the paired-less Pax6.2 ortholog in zebrafish is expressed specifically in the developing retina. Transgenic analysis of elephant shark and zebrafish Pax6.2 CNEs with homology to the mouse NRE/Pα internal promoter revealed highly specific retinal expression. Finally, morpholino depletion of zebrafish Pax6.2 resulted in a "small eye" phenotype, supporting a role in retinal development. In summary, our study reveals that the pleiotropic functions of Pax6 in vertebrates are served by a divergent family of Pax6 genes, forged by ancient duplication events and by independent, lineage-specific gene losses.
Collapse
Affiliation(s)
- Vydianathan Ravi
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Shipra Bhatia
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Philippe Gautier
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Felix Loosli
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
| | - Boon-Hui Tay
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Alice Tay
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Emma Murdoch
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Pedro Coutinho
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Veronica van Heyningen
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Sydney Brenner
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Biopolis, Singapore, Singapore
| | - Byrappa Venkatesh
- Institute of Molecular and Cell Biology, Agency for Science Technology and Research (A*STAR), Biopolis, Singapore, Singapore
- * E-mail: (DA Kleinjan); (B Venkatesh)
| | - Dirk A. Kleinjan
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (DA Kleinjan); (B Venkatesh)
| |
Collapse
|
8
|
Repertoire of Protein Kinases Encoded in the Genome of Takifugu rubripes. Comp Funct Genomics 2012; 2012:258284. [PMID: 22666085 PMCID: PMC3359783 DOI: 10.1155/2012/258284] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Revised: 02/14/2012] [Accepted: 02/28/2012] [Indexed: 12/02/2022] Open
Abstract
Takifugu rubripes is teleost fish widely used in comparative genomics to understand the human system better due to its similarities both in number of genes and structure of genes. In this work we survey the fugu genome, and, using sensitive computational approaches, we identify the repertoire of putative protein kinases and classify them into groups and subfamilies. The fugu genome encodes 519 protein kinase-like sequences and this number of putative protein kinases is comparable closely to that of human. However, in spite of its similarities to human kinases at the group level, there are differences at the subfamily level as noted in the case of KIS and DYRK subfamilies which contribute to differences which are specific to the adaptation of the organism. Also, certain unique domain combination of galectin domain and YkA domain suggests alternate mechanisms for immune response and binding to lipoproteins. Lastly, an overall similarity with the MAPK pathway of humans suggests its importance to understand signaling mechanisms in humans. Overall the fugu serves as a good model organism to understand roles of human kinases as far as kinases such as LRRK and IRAK and their associated pathways are concerned.
Collapse
|
9
|
Fraser GJ, Britz R, Hall A, Johanson Z, Smith MM. Replacing the first-generation dentition in pufferfish with a unique beak. Proc Natl Acad Sci U S A 2012; 109:8179-84. [PMID: 22566613 PMCID: PMC3361446 DOI: 10.1073/pnas.1119635109] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Teleost fishes comprise approximately half of all living vertebrates. The extreme range of diversity in teleosts is remarkable, especially, extensive morphological variation in their jaws and dentition. Some of the most unusual dentitions are found among members of the highly derived teleost order Tetraodontiformes, which includes triggerfishes, boxfishes, ocean sunfishes, and pufferfishes. Adult pufferfishes (Tetraodontidae) exhibit a distinctive parrot-like beaked jaw, forming a cutting edge, unlike in any other group of teleosts. Here we show that despite novelty in the structure and development of this "beak," it is initiated by formation of separate first-generation teeth that line the embryonic pufferfish jaw, with timing of development and gene expression patterns conserved from the last common ancestor of osteichthyans. Most of these first-generation larval teeth are lost in development. Continuous tooth replacement proceeds in only four parasymphyseal teeth, as sequentially stacked, multigenerational, jaw-length dentine bands, before development of the functional beak. These data suggest that dental novelties, such as the pufferfish beak, can develop later in ontogeny through modified continuous tooth addition and replacement. We conclude that even highly derived morphological structures like the pufferfish beak form via a conserved developmental bauplan capable of modification during ontogeny by subtle respecification of the developmental module.
Collapse
Affiliation(s)
- Gareth J Fraser
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom.
| | | | | | | | | |
Collapse
|
10
|
Levering J, Musters MWJM, Bekker M, Bellomo D, Fiedler T, de Vos WM, Hugenholtz J, Kreikemeyer B, Kummer U, Teusink B. Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach. FEBS J 2012; 279:1274-90. [DOI: 10.1111/j.1742-4658.2012.08523.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
11
|
Kuhl H, Beck A, Wozniak G, Canario AVM, Volckaert FAM, Reinhardt R. The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing. BMC Genomics 2010; 11:68. [PMID: 20105308 PMCID: PMC2837037 DOI: 10.1186/1471-2164-11-68] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2009] [Accepted: 01/27/2010] [Indexed: 11/20/2022] Open
Abstract
Background Food supply from the ocean is constrained by the shortage of domesticated and selected fish. Development of genomic models of economically important fishes should assist with the removal of this bottleneck. European sea bass Dicentrarchus labrax L. (Moronidae, Perciformes, Teleostei) is one of the most important fishes in European marine aquaculture; growing genomic resources put it on its way to serve as an economic model. Results End sequencing of a sea bass genomic BAC-library enabled the comparative mapping of the sea bass genome using the three-spined stickleback Gasterosteus aculeatus genome as a reference. BAC-end sequences (102,690) were aligned to the stickleback genome. The number of mappable BACs was improved using a two-fold coverage WGS dataset of sea bass resulting in a comparative BAC-map covering 87% of stickleback chromosomes with 588 BAC-contigs. The minimum size of 83 contigs covering 50% of the reference was 1.2 Mbp; the largest BAC-contig comprised 8.86 Mbp. More than 22,000 BAC-clones aligned with both ends to the reference genome. Intra-chromosomal rearrangements between sea bass and stickleback were identified. Size distributions of mapped BACs were used to calculate that the genome of sea bass may be only 1.3 fold larger than the 460 Mbp stickleback genome. Conclusions The BAC map is used for sequencing single BACs or BAC-pools covering defined genomic entities by second generation sequencing technologies. Together with the WGS dataset it initiates a sea bass genome sequencing project. This will allow the quantification of polymorphisms through resequencing, which is important for selecting highly performing domesticated fish.
Collapse
Affiliation(s)
- Heiner Kuhl
- Max Planck Institute for Molecular Genetics, D-14195 Berlin, Germany.
| | | | | | | | | | | |
Collapse
|
12
|
Coccia M, Brooks SP, Webb TR, Christodoulou K, Wozniak IO, Murday V, Balicki M, Yee HA, Wangensteen T, Riise R, Saggar AK, Park SM, Kanuga N, Francis PJ, Maher ER, Moore AT, Russell-Eggitt IM, Hardcastle AJ. X-linked cataract and Nance-Horan syndrome are allelic disorders. Hum Mol Genet 2009; 18:2643-55. [PMID: 19414485 PMCID: PMC2701339 DOI: 10.1093/hmg/ddp206] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Nance-Horan syndrome (NHS) is an X-linked developmental disorder characterized by congenital cataract, dental anomalies, facial dysmorphism and, in some cases, mental retardation. Protein truncation mutations in a novel gene (NHS) have been identified in patients with this syndrome. We previously mapped X-linked congenital cataract (CXN) in one family to an interval on chromosome Xp22.13 which encompasses the NHS locus; however, no mutations were identified in the NHS gene. In this study, we show that NHS and X-linked cataract are allelic diseases. Two CXN families, which were negative for mutations in the NHS gene, were further analysed using array comparative genomic hybridization. CXN was found to be caused by novel copy number variations: a complex duplication-triplication re-arrangement and an intragenic deletion, predicted to result in altered transcriptional regulation of the NHS gene. Furthermore, we also describe the clinical and molecular analysis of seven families diagnosed with NHS, identifying four novel protein truncation mutations and a novel large deletion encompassing the majority of the NHS gene, all leading to no functional protein. We therefore show that different mechanisms, aberrant transcription of the NHS gene or no functional NHS protein, lead to different diseases. Our data highlight the importance of copy number variation and non-recurrent re-arrangements leading to different severity of disease and describe the potential mechanisms involved.
Collapse
|
13
|
Yang H, Tiersch TR. Current status of sperm cryopreservation in biomedical research fish models: zebrafish, medaka, and Xiphophorus. Comp Biochem Physiol C Toxicol Pharmacol 2009; 149:224-32. [PMID: 18691673 PMCID: PMC2676784 DOI: 10.1016/j.cbpc.2008.07.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Revised: 07/10/2008] [Accepted: 07/11/2008] [Indexed: 12/11/2022]
Abstract
Aquarium fishes are becoming increasingly important because of their value in biomedical research and the ornamental fish trade, and because many have become threatened or endangered in the wild. This review summarizes the current status of sperm cryopreservation in three fishes widely used in biomedical research: zebrafish, medaka, and live-bearing fishes of the genus Xiphophorus, and will focus on the needs and opportunities for future research and application of cryopreservation in aquarium fish. First, we summarize the basic biological characteristics regarding natural habitat, testis structure, spermatogenesis, sperm morphology, and sperm physiology. Second, we compare protocol development of sperm cryopreservation. Third, we emphasize the importance of artificial fertilization in sperm cryopreservation to evaluate the viability of thawed sperm. We conclude with a look to future research directions for sperm cryopreservation and the application of this technique in aquarium species.
Collapse
Affiliation(s)
- Huiping Yang
- Aquaculture Research Station, Louisiana Agricultural Experiment Station, Louisiana State University Agricultural Center, 2410 Ben Hur Road, Baton Rouge, Louisiana 70820, USA
- Ocean College, Hainan University, 58 Renmin Road, Haikou, 570228, the Peoples Republic of China
| | - Terrence R. Tiersch
- Aquaculture Research Station, Louisiana Agricultural Experiment Station, Louisiana State University Agricultural Center, 2410 Ben Hur Road, Baton Rouge, Louisiana 70820, USA
| |
Collapse
|
14
|
|
15
|
Shen XY, Cui JZ, Gong QL, Liu YJ, Nagahama Y. Transcript expression profiles of Takifugu rubripes spermatozoa and eggs by expressed sequence tag analysis. FISH PHYSIOLOGY AND BIOCHEMISTRY 2008; 34:235-243. [PMID: 18665461 DOI: 10.1007/s10695-007-9182-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2007] [Accepted: 08/13/2007] [Indexed: 05/26/2023]
Abstract
Two cDNA libraries from Takifugu rubripes spermatozoa and eggs were constructed and a total of 620 expressed sequence tag (EST) clones were generated from the two libraries: 300 clones are from the spermatozoa library and 320 clones are from the eggs library. The most abundant cDNA clones in the two libraries were identified. A total of 207 'contigs' (or single) EST clones were found to share significant sequence identity with known sequences in the GenBank database, representing at least 51 different genes. In order to understand the two types of germ cells further, the expression profiles of the identified clones in these cDNA libraries were analyzed. Furthermore, the presence of specific messenger RNAs in the spermatozoa and eggs has been demonstrated with BLAST analysis; the spermatozoa and egg library can supply unique and novel cDNA sequences in the Takifugu rubripes EST project. Another aim of this study is to identify cDNA clones that can be used as molecular markers for the analysis of the spermatogenesis and oogenesis in Takifugu rubripes. Six potential clones (S1-3 from spermatozoa and E1-3 from eggs) were selected to analyze their expression patterns by reverse transcription (RT)-PCR analyses. Half of these showed a specific expression in the expected tissue. Two of the clones were found by RT-PCR and in situ hybridization to be expressed specifically in the testis or ovary, and they maybe suitable molecular markers for the analysis of spermatogenesis and oogenesis.
Collapse
Affiliation(s)
- Xue-Yan Shen
- Division of Life Science and Technology, Ocean University of China, Qingdao, 266003, PR China
| | | | | | | | | |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- Adam Woolfe
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, United Kingdom
| | | |
Collapse
|
17
|
Liang CS, Kobiyama A, Shimizu A, Sasaki T, Asakawa S, Shimizu N, Watabe S. Fast skeletal muscle myosin heavy chain gene cluster of medaka Oryzias latipes enrolled in temperature adaptation. Physiol Genomics 2007; 29:201-14. [PMID: 17227888 DOI: 10.1152/physiolgenomics.00078.2006] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To disclose mechanisms involved in temperature acclimation of fish muscle, we subjected eurythermal fish of medaka Oryzias latipes to cloning of myosin heavy chain genes (MYHs). We cloned cDNAs encoding fast skeletal muscle myosin heavy chain (MYH) isoforms from cDNA libraries of medaka acclimated to 10 and 30 degrees C and observed that different MYH cDNA clones are expressed in the two temperature-acclimated fish. Subsequently, we isolated several overlapping MYH contigs by shotgun cloning strategy from a medaka genomic library. Contig assembly of the complete medaka MYH (mMYH) locus of 219 kbp revealed a cluster of tandemly arrayed 11 mMYHs, in which eight genes are actually transcribed, with the remaining three being pseudogenes. Expression analysis of the transcribed genes revealed that two genes were each highly expressed in medaka acclimated to 10 and 30 degrees C, whereas comparatively lower expression levels of the three genes were exclusively observed in medaka acclimated to 30 degrees C. cDNAs of the remaining genes were too underrepresented in the libraries to determine the expression levels, and the transcripts could only be obtained by reverse transcription-polymerase chain reaction. Deduced amino acid sequences in the loop 1 and loop 2 regions of mMYHs were highly variable, suggesting that these isoforms were functionally different. The present findings consolidate our knowledge on teleost MYH multigene family and would provide further insight into the mechanisms by which expressions of individual MYH molecules are fine-tuned with environmental temperature fluctuations with further functional analysis of the genes concerned.
Collapse
Affiliation(s)
- Chun-Shi Liang
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | | | | | | | | | | | | |
Collapse
|
18
|
Abstract
With the availability of genomic sequence from numerous vertebrates, a paradigm shift has occurred in the identification of distant-acting gene regulatory elements. In contrast to traditional gene-centric studies in which investigators randomly scanned genomic fragments that flank genes of interest in functional assays, the modern approach begins electronically with publicly available comparative sequence datasets that provide investigators with prioritized lists of putative functional sequences based on their evolutionary conservation. However, although a large number of tools and resources are now available, application of comparative genomic approaches remains far from trivial. In particular, it requires users to dynamically consider the species and methods for comparison depending on the specific biological question under investigation. While there is currently no single general rule to this end, it is clear that when applied appropriately, comparative genomic approaches exponentially increase our power in generating biological hypotheses for subsequent experimental testing. It is anticipated that cardiac-related genes and the identification of their distant-acting transcriptional enhancers are particularly poised to benefit from these modern capabilities.
Collapse
Affiliation(s)
- Axel Visel
- Genomics Division, MS 84-171, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | | | | |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
- Deng-Fwu Hwang
- Department of Food Science, National Taiwan Ocean University Taiwan, Taiwan, Republic of China
| | | |
Collapse
|
20
|
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.
Collapse
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
| | | |
Collapse
|
21
|
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.
Collapse
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
| |
Collapse
|
22
|
Muramatsu-Uno M, Kikuchi K, Suetake H, Ikeda D, Watabe S. The complete genomic sequence of the carp fast skeletal myosin heavy chain gene. Gene 2005; 349:143-51. [PMID: 15777658 DOI: 10.1016/j.gene.2004.11.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Revised: 11/16/2004] [Accepted: 11/26/2004] [Indexed: 11/21/2022]
Abstract
We have determined the complete DNA nucleotide sequence of the carp Cyprinus carpio fast skeletal myosin heavy chain (MYH) gene. Introns and exons were predicted by comparison with the corresponding carp MYH cDNAs previously reported. The gene encoded the entire mRNA transcript and contained 5958 nucleotides (nt) including 77 nt 5'-untranslated region, 5796 nt coding region for 1931 amino acids, and 85 nt 3'-untranslated region. The coding region was split by 38 introns and the complete gene contained 11,385 nt. This integration of the carp fast skeletal MYH gene was comparable to those of the rat and chicken embryonic MYH genes, which have 41 and 40 exons, respectively. However, the entire gene size of carp MYH was about half those of rat and chicken due to much smaller size of carp introns. We have also demonstrated that this carp MYH gene belonged to so-called intermediate type in a multigene family of carp fast skeletal muscle MYH in comparison of its nucleotide and deduced amino acid sequences to those of carp MYH cDNAs reported previously.
Collapse
Affiliation(s)
- Maiko Muramatsu-Uno
- Laboratory of Aquatic Molecular Biology and Biotechnology, Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | | | | | | | | |
Collapse
|
23
|
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.
Collapse
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
| | | | | | | | | | | |
Collapse
|
24
|
Muller C, Denis M, Gentzbittel L, Faraut T. The Iccare web server: an attempt to merge sequence and mapping information for plant and animal species. Nucleic Acids Res 2004; 32:W429-34. [PMID: 15215424 PMCID: PMC441598 DOI: 10.1093/nar/gkh460] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Iccare web server, http://genopole.toulouse.inra.fr/bioinfo/Iccare, provides a simple yet efficient tool for crude EST (expressed sequence tag) annotation specifically dedicated to comparative mapping approaches. Iccare uses all the EST and mRNA sequences from public databases for an organism of interest (query species) and compares them to all the transcripts of one reference organism (Homo sapiens or Arabidopsis thaliana). The results are displayed according to the location of the genes on the chromosomes of the reference organism. Gene structure information and sequence similarities are combined in a graphical representation in order to pinpoint the nature of the transcript query sequence. The user can subsequently design primers or probes for the purpose of physical or genetic mapping. In addition to the query organisms already available in Iccare, users can perform a tailor-made search with their own sequences against the animal or plant reference organism genes.
Collapse
Affiliation(s)
- Cédric Muller
- INP-ENSAT, Laboratoire de biotechnologies et d'amélioration des plantes, Castanet Tolosan 31326, France
| | | | | | | |
Collapse
|
25
|
Miyake T, Amemiya CT. BAC libraries and comparative genomics of aquatic chordate species. Comp Biochem Physiol C Toxicol Pharmacol 2004; 138:233-44. [PMID: 15533781 DOI: 10.1016/j.cca.2004.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/25/2004] [Revised: 07/09/2004] [Accepted: 07/14/2004] [Indexed: 11/26/2022]
Abstract
The bacterial artificial chromosome (BAC) system is useful for creating a representation of the genomes of target species. The system is advantageous in that it can accommodate exogenous inserts that are very large (>100 kilobases, kb), thereby allowing entire eukaryotic genes (including flanking regulatory regions) to be encompassed in a single clone. The interest in BACs has recently been spawned by vast improvements in high throughput genomic sequencing such that comparisons of orthologous regions from different genomes (comparative genomics) are being routinely investigated, and comprise a significant component, of all major sequencing centers. In this review, we discuss the general principles of BAC cloning, the resources that are currently available, and some of the applications of the technology. It is not intended to be an exhaustive treatise; rather our goal is to provide a primer of the BAC technology in order to make readers aware of these resources and how they may utilize them in their own research programs.
Collapse
Affiliation(s)
- Tsutomu Miyake
- Molecular Genetics Department, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101, USA.
| | | |
Collapse
|
26
|
Hordvik I, Torvund J, Moore L, Endresen C. Structure and organization of the T cell receptor alpha chain genes in Atlantic salmon. Mol Immunol 2004; 41:553-9. [PMID: 15183934 DOI: 10.1016/j.molimm.2004.03.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2003] [Indexed: 10/26/2022]
Abstract
A cDNA fragment of the T cell receptor (TCR) alpha chain mRNA in Atlantic salmon (Salmo salar) was amplified by PCR and used as a probe to isolate a full-length clone from a leukocyte cDNA library. Additionally, a genomic lambda clone comprising the TCR alpha chain constant region (Calpha) gene and flanking regions was isolated and partially sequenced. The Calpha gene consists of three exons corresponding to the immunoglobulin (Ig) domain, the hinge region and the transmembrane peptide/cytoplasmatic tail, and two exons corresponding to the untranslated tail of the mRNA. Remnants of a transposase gene and a partial duplication of the Calpha gene were found nearby the intact gene. One J segment was found 1.5kb upstream of the Calpha gene. Twenty-six other J elements were identified among cDNA fragments covering the V/J/Calpha junction. Representatives of five Valpha gene families were identified by PCR amplification of genomic DNA fragments. PCR amplification of Calpha fragments from another individual revealed a slightly different Calpha gene which most likely represents an allelic variant.
Collapse
Affiliation(s)
- Ivar Hordvik
- Department of Biology, University of Bergen, High Technology Centre in Bergen, 5020 Bergen, Norway.
| | | | | | | |
Collapse
|
27
|
Abstract
Interpreting the functional content of a given genomic sequence is one of the central challenges of biology today. Perhaps the most promising approach to this problem is based on the comparative method of classic biology in the modern guise of sequence comparison. For instance, protein-coding regions tend to be conserved between species. Hence, a simple method for distinguishing a functional exon from the chance absence of stop codons is to investigate its homologue from closely related species. Predicting regulatory elements is even more difficult than exon prediction, but again, comparisons pinpointing conserved sequence motifs upstream of translation start sites are helping to unravel gene regulatory networks. In addition to interspecific studies, intraspecific sequence comparison yields insights into the evolutionary forces that have acted on a species in the past. Of particular interest here is the identification of selection events such as selective sweeps. Both intra- and interspecific sequence comparisons are based on a variety of computational methods, including alignment, phylogenetic reconstruction, and coalescent theory. This article surveys the biology and the central computational ideas applied in recent comparative genomics projects. We argue that the most fruitful method of understanding the functional content of genomes is to study them in the context of related genomic sequences. In particular, such a study may reveal selection, a fundamental pointer to biological relevance.
Collapse
Affiliation(s)
- Bernhard Haubold
- Fachbereich Biotechnologie & Bioinformatik, Fachhochschule Weihenstephan, 85350 Freising, Germany.
| | | |
Collapse
|
28
|
Chen TY, Shiau CY, Wei CI, Hwang DF. Preliminary study on puffer fish proteome-species identification of puffer fish by two-dimensional electrophoresis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2004; 52:2236-2241. [PMID: 15080627 DOI: 10.1021/jf035033n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The aims of this work were to determine the differential characterization of the urea soluble protein components of puffer fish species and to establish a preliminary proteomic database using an immobilized pH gradient two-dimensional electrophoresis (2DE) technique. The puffer fish muscle proteins resolved into 171-260 spots in the 2DE gels, with a pI range of 3-10 and molecular mass range of 7.4-205.0 kDa, following Comassie blue staining. Puffer fish muscle proteins fell in the region with pI values of 3.5-7.0, and molecular masses of 7.4-45.0 kDa were well-resolved and were good for species comparison. The more acidic proteins of lower molecular masses showed species specific characteristics. Therefore, the species of puffer fish can be differentiated from the comparison of the characteristic 2DE protein patterns.
Collapse
Affiliation(s)
- Tai-Yuan Chen
- Department of Food Science, National Taiwan Ocean University, Keelung 202, Taiwan, Republic of China
| | | | | | | |
Collapse
|
29
|
Sibthorpe D, Baker AM, Gilmartin BJ, Blackwell JM, White JK. Comparative analysis of two slc11 (Nramp) loci in Takifugu rubripes. DNA Cell Biol 2004; 23:45-58. [PMID: 14965472 DOI: 10.1089/104454904322745925] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
To study the evolution of the solute carrier family 11 (slc11; formerly Nramp) protein, we isolated and characterized two paralogs from the pufferfish Takifugu rubripes (Fugu). These teleost genes, designated Fugu slc11a-a and Fugu slc11a-b, comprise open reading frames of 1743 nucleotides (581 amino acids) and 1662 nt (554 aa), respectively. The proteins are 81% similar, and both exhibit signature features of the slc11 family of proteins including 12 transmembrane domains, a conserved transport motif and a glycosylated loop. Both Fugu paralogs are more Slc11a2-like based on sequence homology and phylogenetic studies. Analysis of gene environment placed both in the proximity of multiple loci syntenic to human chromosome 12q13, that is, within a SLC11A2 gene environment. However, Fugu slc11a-a also gave one match with chromosome 2q35, where human SLC11A1 resides. Functional diversification was suggested by differences in tissue distribution and subcellular localization. Fugu slc11a-a exhibits a restricted expression profile and a complex subcellular localization, including LAMP1 positive late endosomes/lysosomes in transiently transfected mouse macrophages. Fugu slc11a-b is expressed ubiquitously and localizes solely to late endosomes/lysosomes. This comparative analysis extends our understanding of the evolution and function of this important family of divalent cation transporters. [Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. AJ496547/8/9 and AJ496550.]
Collapse
Affiliation(s)
- Dean Sibthorpe
- Division of Environmental and Evolutionary Biology, The Gatty Marine Laboratory, University of St. Andrews, Fife KY16 8LB, UK
| | | | | | | | | |
Collapse
|
30
|
Kleinjan DA, Seawright A, Childs AJ, van Heyningen V. Conserved elements in Pax6 intron 7 involved in (auto)regulation and alternative transcription. Dev Biol 2004; 265:462-77. [PMID: 14732405 DOI: 10.1016/j.ydbio.2003.09.011] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Pax6 is a transcription factor with an essential role in eye, central nervous system, and pancreas development. Its expression pattern is restricted to these specific domains within the developing embryo. Here four conserved elements are identified in Pax6 intron 7, showing a high level of sequence conservation between human, mouse, pufferfish, and zebrafish. Three of these are shown to act as cis-regulatory elements, directing expression of a reporter gene to distinct subsets of the Pax6 expression domain. CE1 regulates gene expression in late eye development, CE2 drives expression in the diencephalon and in the developing heart tube where Pax6 is not normally expressed, while CE3 directs expression in rhombencephalon. CE2 is shown to be autoregulated in the diencephalon, responding to absence of Pax6. We identify a highly conserved Pax6 recognition site and demonstrate its ability to bind Pax6 specifically. CE1 is embedded in a CpG island, and we identify a novel Pax6 transcript which initiates from this region. Functional analysis of evolutionary conserved sequences pinpoints novel cis-acting elements that govern the regulation of the complex spatio-temporal and quantitative expression of Pax6.
Collapse
Affiliation(s)
- Dirk A Kleinjan
- MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK.
| | | | | | | |
Collapse
|
31
|
Chang MH, Chou CM, Hsieh YC, Lu IC, Devi MKN, Chang JP, Kuo TF, Huang CJ. Identification of 5'-upstream region of pufferfish ribosomal protein L29 gene as a strong constitutive promoter to drive GFP expression in zebrafish. Biochem Biophys Res Commun 2004; 314:249-58. [PMID: 14715273 DOI: 10.1016/j.bbrc.2003.12.080] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The genomic structure of Tetraodon fluviatilis L29 gene was determined and its promoter activity was analyzed in COS-1 cells and zebrafish embryos. The TfL29 gene comprises four exons and three introns, spanning approximately 1.7kb. The 5(')-upstream 2.2-kb of the first exon contains 10 E-boxes and many putative binding motifs for transcription factors GATA-1, AML-1a, c-Myb, Oct-1, CdxA, and NRF-2. Promoter activity assay showed that the distal 2.2-kb fragment not only had high luciferase activity in COS-1 cells, but also strong and ubiquitous GFP expression in a variety of tissues in zebrafish embryos. On the other hand, there are no TATA or CAAT boxes within a 300-bp region upstream from the transcription initiation site. Although this region has high luciferase activity in COS-1 cells, it is not sufficient to drive GFP expression in zebrafish embryos. In this proximal 300-bp region, there are two E-boxes, two CdxA sites, and one NRF-2 site that is immediately downstream of the transcription start site.
Collapse
Affiliation(s)
- Ming-Huang Chang
- Graduate Institute of Veterinary Medicine, National Taiwan University, Taipei, Taiwan, TOC
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Enerly E, Ahmadi H, Shalchian-Tabrizi K, Lambertsson A. Identification and comparative analysis of the RpL14 gene from Takifugu rubripes. Hereditas 2004; 139:143-50. [PMID: 15061815 DOI: 10.1111/j.1601-5223.2003.01762.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The ribosomal protein RpL14 gene has been characterized in several species, including, human, rat and fruit fly. Haploinsufficiency for the gene causes the Minute phenotype in Drosophila, and it has been proposed as a regulator in the tumorigenic pathway in human. Several features concerning the gene structure have been studied, and some of these differ between human/rat and Drosophila. To address functional and evolutionary questions about these differences we have isolated and sequenced a cDNA and a genomic clone covering the RpL14 gene from the pufferfish Takifugu rubripes (Fugu). The Fugu RpL14 gene is approximately 2 Kb, with 5 introns, and encodes a protein of 137 amino acids. The protein contains a KOW-motif and a nuclear localization signal, which are conserved among a wide range of RPL14 proteins. On the other hand, a variable amino acid (alanine) repeat observed in human is missing in Takifugu rubripes, and the protein is shorter than its mammalian counterparts. Compared with human, the RpL14 gene in Fugu contains introns localized at identical positions in the gene, and most of them are shorter. A comparison of the RpL14 gene structure from a broad range of organisms indicates that both loss and gain of introns have occurred during the evolution of the gene.
Collapse
Affiliation(s)
- Espen Enerly
- Institute of Biology, Division of Cell and Molecular Biology, University of Oslo, Blindern, Oslo, Norway
| | | | | | | |
Collapse
|
33
|
Abstract
Various experimental and computational approaches have been used to identify genomic locations of transcription-factor binding sites; methods involving computational comparisons of related genomes have been particularly successful. Identifying genomic locations of transcription-factor binding sites, particularly in higher eukaryotic genomes, has been an enormous challenge. Various experimental and computational approaches have been used to detect these sites; methods involving computational comparisons of related genomes have been particularly successful.
Collapse
Affiliation(s)
- Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, New Research Building, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| |
Collapse
|
34
|
Santagati F, Abe K, Schmidt V, Schmitt-John T, Suzuki M, Yamamura KI, Imai K. Identification of Cis-regulatory Elements in the Mouse Pax9/Nkx2-9 Genomic Region: Implication for Evolutionary Conserved Synteny. Genetics 2003; 165:235-42. [PMID: 14504231 PMCID: PMC1462746 DOI: 10.1093/genetics/165.1.235] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
We previously reported close physical linkage between Pax9 and Nkx2-9 in the human, mouse, and pufferfish (Fugu rubripes) genomes. In this study, we analyzed cis-regulatory elements of the two genes by comparative sequencing in the three species and by transgenesis in the mouse. We identified two regions including conserved noncoding sequences that possessed specific enhancer activities for expression of Pax9 in the medial nasal process and of Nkx2-9 in the ventral neural tube. Remarkably, the latter contained the consensus Gli-binding motif. Interestingly, the identified Pax9 cis-regulatory sequences were located in an intron of the neighboring gene Slc25a21. Close examination of an extended genomic interval around Pax9 revealed the presence of strong synteny conservation in the human, mouse, and Fugu genomes. We propose such an intersecting organization of cis-regulatory sequences in multigenic regions as a possible mechanism that maintains evolutionary conserved synteny.
Collapse
Affiliation(s)
- Fabio Santagati
- GSF-National Research Center for Environment and Health, Institute of Developmental Genetics, D-85764 Neuherberg, Germany
| | | | | | | | | | | | | |
Collapse
|
35
|
Montpetit A, Wilson MD, Chevrette M, Koop BF, Sinnett D. Analysis of the conservation of synteny between Fugu and human chromosome 12. BMC Genomics 2003; 4:30. [PMID: 12877756 PMCID: PMC179898 DOI: 10.1186/1471-2164-4-30] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 07/23/2003] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The pufferfish Fugu rubripes (Fugu) with its compact genome is increasingly recognized as an important vertebrate model for comparative genomic studies. In particular, large regions of conserved synteny between human and Fugu genomes indicate its utility to identify disease-causing genes. The human chromosome 12p12 is frequently deleted in various hematological malignancies and solid tumors, but the actual tumor suppressor gene remains unidentified. RESULTS We investigated approximately 200 kb of the genomic region surrounding the ETV6 locus in Fugu (fETV6) in order to find conserved functional features, such as genes or regulatory regions, that could give insight into the nature of the genes targeted by deletions in human cancer cells. Seven genes were identified near the fETV6 locus. We found that the synteny with human chromosome 12 was conserved, but extensive genomic rearrangements occurred between the Fugu and human ETV6 loci. CONCLUSION This comparative analysis led to the identification of previously uncharacterized genes in the human genome and some potentially important regulatory sequences as well. This is a good indication that the analysis of the compact Fugu genome will be valuable to identify functional features that have been conserved throughout the evolution of vertebrates.
Collapse
Affiliation(s)
- Alexandre Montpetit
- Division of Hematology-Oncology, Charles-Bruneau Cancer Center, Research Center, Sainte-Justine Hospital, 3175 Côte Ste-Catherine, Montreal, QC, H3T 1C5, Canada
- Department of Biochemistry, University of Montreal, Montreal, QC, Canada
| | - Michael D Wilson
- Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Mario Chevrette
- The Research Institute of the McGill University Health Centre and Department of Surgery, McGill University, Montreal, QC, H3G 1A4, Canada
| | - Ben F Koop
- Centre for Biomedical Research, University of Victoria, Victoria, BC, V8W 2Y2, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, Charles-Bruneau Cancer Center, Research Center, Sainte-Justine Hospital, 3175 Côte Ste-Catherine, Montreal, QC, H3T 1C5, Canada
- Department of Biochemistry, University of Montreal, Montreal, QC, Canada
- Department of Pediatrics, University of Montreal, Montreal, QC, Canada
| |
Collapse
|
36
|
Pennacchio LA. Insights from human/mouse genome comparisons. Mamm Genome 2003; 14:429-36. [PMID: 12925891 DOI: 10.1007/s00335-002-4001-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2003] [Accepted: 02/20/2003] [Indexed: 10/27/2022]
Abstract
Large-scale public genomic sequencing efforts have provided a wealth of vertebrate sequence data poised to provide insights into mammalian biology. These include deep genomic sequence coverage of human, mouse, rat, zebrafish, and two pufferfish ( Fugu rubripes and Tetraodon nigroviridis) (Aparicio et al. 2002; Lander et al. 2001; Venter et al. 2001; Waterston et al. 2002). In addition, a high-priority has been placed on determining the genomic sequence of chimpanzee, dog, cow, frog, and chicken (Boguski 2002). While only recently available, whole genome sequence data have provided the unique opportunity to globally compare complete genome contents. Furthermore, the shared evolutionary ancestry of vertebrate species has allowed the development of comparative genomic approaches to identify ancient conserved sequences with functionality. Accordingly, this review focuses on the initial comparison of available mammalian genomes and describes various insights derived from such analysis.
Collapse
Affiliation(s)
- Len A Pennacchio
- Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California, USA.
| |
Collapse
|
37
|
Miles CG, Rankin L, Smith SI, Niksic M, Elgar G, Hastie ND. 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 Res 2003; 31:2795-802. [PMID: 12771206 PMCID: PMC156718 DOI: 10.1093/nar/gkg383] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2003] [Revised: 04/03/2003] [Accepted: 04/03/2003] [Indexed: 11/12/2022] Open
Abstract
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 beta-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.
Collapse
Affiliation(s)
- Colin G Miles
- Medical Research Council Human Genetics Unit, Western General Hospital, Creve Road, Edinburgh EH4 2XU, UK
| | | | | | | | | | | |
Collapse
|
38
|
Ikeda D, Toramoto T, Ochiai Y, Suetake H, Suzuki Y, Minoshima S, Shimizu N, Watabe S. Identification of novel tropomyosin 1 genes of pufferfish (Fugu rubripes) on genomic sequences and tissue distribution of their transcripts. Mol Biol Rep 2003; 30:83-90. [PMID: 12841578 DOI: 10.1023/a:1023995208279] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Fugu genome database enabled us to identify two novel tropomyosin 1 (TPM1) genes through in silico data mining and isolation of their corresponding cDNAs in vivo. The duplicate TPM1 genes in Japanese pufferfish Fugu rubripes suggest that additional an ancient segmental duplication or whole genome duplication occurred in fish lineage, which, like many other reported Fugu genes, showed reduction in genomic size in comparison with their human homologue. Computer analysis predicted that the coiled-coil probabilities, that were thought to be the most major function of TPM, were the same between the two TPM1 isoforms. We confirmed that the tissue expression profiles of the two TPM1 genes differed from each other, which implied that changes in expression pattern could fix duplicated TPM1 genes although the two TPM1 isoforms appear to have similar function.
Collapse
Affiliation(s)
- Daisuke Ikeda
- Laboratory of Aquatic Molecular Biology and Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo, Tokyo 113-8657, Japan
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Manning CM, Mathews WR, Fico LP, Thackeray JR. Phospholipase C-gamma contains introns shared by src homology 2 domains in many unrelated proteins. Genetics 2003; 164:433-42. [PMID: 12807765 PMCID: PMC1462583 DOI: 10.1093/genetics/164.2.433] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Many proteins with novel functions were created by exon shuffling around the time of the metazoan radiation. Phospholipase C-gamma (PLC-gamma) is typical of proteins that appeared at this time, containing several different modules that probably originated elsewhere. To gain insight into both PLC-gamma evolution and structure-function relationships within the Drosophila PLC-gamma encoded by small wing (sl), we cloned and sequenced the PLC-gamma homologs from Drosophila pseudoobscura and D. virilis and compared their gene structure and predicted amino acid sequences with PLC-gamma homologs in other animals. PLC-gamma has been well conserved throughout, although structural differences suggest that the role of tyrosine phosphorylation in enzyme activation differs between vertebrates and invertebrates. Comparison of intron positions demonstrates that extensive intron loss has occurred during invertebrate evolution and also reveals the presence of conserved introns in both the N- and C-terminal PLC-gamma SH2 domains that are present in SH2 domains in many other genes. These and other conserved SH2 introns suggest that the SH2 domains in PLC-gamma are derived from an ancestral domain that was shuffled not only into PLC-gamma, but also into many other unrelated genes during animal evolution.
Collapse
Affiliation(s)
- Charlene M Manning
- Biology Department, Clark University, Worcester, Massachusetts 01610, USA
| | | | | | | |
Collapse
|
40
|
Pozzoli U, Elgar G, Cagliani R, Riva L, Comi GP, Bresolin N, Bardoni A, Sironi M. Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature. Genome Res 2003; 13:764-72. [PMID: 12727896 PMCID: PMC430921 DOI: 10.1101/gr.776503] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The human DMD gene is the largest known to date, spanning > 2000 kb on the X chromosome. The gene size is mainly accounted for by huge intronic regions. We sequenced 190 kb of Fugu rubripes (pufferfish) genomic DNA corresponding to the complete dystrophin gene (FrDMD) and provide the first report of gene structure and sequence comparison among dystrophin genomic sequences from different vertebrate organisms. Almost all intron positions and phases are conserved between FrDMD and its mammalian counterparts, and the predicted protein product of the Fugu gene displays 55% identity and 71% similarity to human dystrophin. In analogy to the human gene, FrDMD presents several-fold longer than average intronic regions. Analysis of intron sequences of the human and murine genes revealed that they are extremely conserved in size and that a similar fraction of total intron length is represented by repetitive elements; moreover, our data indicate that intron expansion through repeat accumulation in the two orthologs is the result of independent insertional events. The hypothesis that intron length might be functionally relevant to the DMD gene regulation is proposed and substantiated by the finding that dystrophin intron gigantism is common to the three vertebrate genes.
Collapse
Affiliation(s)
- Uberto Pozzoli
- IRCCS E. Medea, Associazione La Nostra Famiglia, 23842 Bosisio Parini (LC), Italy.
| | | | | | | | | | | | | | | |
Collapse
|
41
|
Gillemans N, McMorrow T, Tewari R, Wai AWK, Burgtorf C, Drabek D, Ventress N, Langeveld A, Higgs D, Tan-Un K, Grosveld F, Philipsen S. Functional and comparative analysis of globin loci in pufferfish and humans. Blood 2003; 101:2842-9. [PMID: 12517812 DOI: 10.1182/blood-2002-09-2850] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To further our understanding of the regulation of vertebrate globin loci, we have isolated cosmids containing alpha- and beta-globin genes from the pufferfish Fugu rubripes. By DNA fluorescence in situ hybridization (FISH) analysis, we show that Fugu contains 2 distinct hemoglobin loci situated on separate chromosomes. One locus contains only alpha-globin genes (alpha-locus), whereas the other also contains a beta-globin gene (alpha beta-locus). This is the first poikilothermic species analyzed in which the physical linkage of the alpha- and beta-globin genes has been uncoupled, supporting a model in which the separation of the alpha- and beta-globin loci has occurred through duplication of a locus containing both types of genes. Surveys for transcription factor binding sites and DNaseI hypersensitive site mapping of the Fugu alpha beta-locus suggest that a strong distal locus control region regulating the activity of the globin genes, as found in mammalian beta-globin clusters, may not be present in the Fugu alpha beta-locus. Searching the human and mouse genome databases with the genes surrounding the pufferfish hemoglobin loci reveals that homologues of some of these genes are proximal to cytoglobin, a recently described novel member of the globin family. This provides evidence that duplication of the globin loci has occurred several times during evolution, resulting in the 5 human globin loci known to date, each encoding proteins with specific functions in specific cell types.
Collapse
Affiliation(s)
- Nynke Gillemans
- MGC Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Blader P, Plessy C, Strähle U. Multiple regulatory elements with spatially and temporally distinct activities control neurogenin1 expression in primary neurons of the zebrafish embryo. Mech Dev 2003; 120:211-8. [PMID: 12559493 DOI: 10.1016/s0925-4773(02)00413-6] [Citation(s) in RCA: 144] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The basic Helix-Loop-Helix gene neurogenin1 (ngn1) is expressed in a complex pattern in the neural plate of zebrafish embryos, demarcating the sites of primary neurogenesis. We have dissected the ngn1 locus to identify cis-regulatory regions that control this expression. We have isolated two upstream elements that drive expression in precursors of Rohon-Beard sensory neurons and hindbrain interneurons and in clusters of neuronal precursors in the anterior neural plate, respectively. A third regulatory region mediates later expression. Thus, regulatory sequences with temporally and spatially distinct activities control ngn1 expression in primary neurons of the zebrafish embryo. These regions are highly similar to 5' sequences in the mouse and human ngn1 gene, suggesting that amniote embryos, despite lacking primary neurons, utilize related mechanism to control ngn1 expression.
Collapse
Affiliation(s)
- Patrick Blader
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 1 rue Laurent Fries, BP 10142, 67404 Illkirch Cedex, C.U. de Strasbourg, France
| | | | | |
Collapse
|
43
|
Mandrioli M, Manicardi GC. Cytogenetic and molecular analysis of the pufferfish Tetraodon fluviatilis (Osteichthyes). Genetica 2002; 111:433-8. [PMID: 11841187 DOI: 10.1023/a:1013787230829] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In view of their compact genome, pufferfish (Tetraodontiformes) have been proposed as model animal for the study of the vertebrate genome. Despite such interest, cytogenetic information about puffers is still scanty. To fill this gap, a cytogenetic analysis of T. fluviatilis has been performed using both classical and molecular techniques. C-banding, followed by DAPI staining, evidenced that in T. fluviatilis, like all other puffer species so far examined, heterochromatin is essentially AT-rich and it is located at centromeres, whereas staining with CMA3, silver staining and FISH with a 28S ribosomal RNA gene DNA probe showed 2-4 nucleolar organizing regions (NORs) located in heterochromatic regions in the considered puffer species. FISH with the 5S probe put in evidence both in T. fluviatilis and in T. nigroviridis only a 5S cluster per haploid genome that is physically unlinked with the major ribosomal RNA genes including the 28S rRNA genes. Hybridization with the (TTAGGG)n probe showed in all the puffers brightly fluorescent signals uniform both in size and intensity at the end of all the chromosomes. Finally, mariner-like elements (MLEs) have been identified in T. fluviatilis and they have located into the NOR-associated heterochromatin.
Collapse
Affiliation(s)
- M Mandrioli
- Dipartimento di Biologia Animale, Università degli Studi di Modena e Reggio Emilia, Modena, Italy.
| | | |
Collapse
|
44
|
Abrahams BS, Mak GM, Berry ML, Palmquist DL, Saionz JR, Tay A, Tan YH, Brenner S, Simpson EM, Venkatesh B. Novel vertebrate genes and putative regulatory elements identified at kidney disease and NR2E1/fierce loci. Genomics 2002; 80:45-53. [PMID: 12079282 DOI: 10.1006/geno.2002.6795] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Fierce (frc) mice are deleted for nuclear receptor 2e1 (Nr2e1), and exhibit cerebral hypoplasia, blindness, and extreme aggression. To characterize the Nr2e1 locus, which may also contain the mouse kidney disease (kd) allele, we compared sequence from human, mouse, and the puffer fish Fugu rubripes. We identified a novel gene, c222389, containing conserved elements in noncoding regions. We also discovered a novel vertebrate gene conserved across its length in prokaryotes and invertebrates. Based on a dramatic upregulation in lactating breast, we named this gene lactation elevated-1 (LACE1). Two separate 100-bp elements within the first NR2E1 intron were virtually identical between the three species, despite an estimated 450 million years of divergent evolution. These elements represent strong candidates for functional NR2E1 regulatory elements in vertebrates. A high degree of conservation across NR2E1 combined with a lack of interspersed repeats suggests that an array of regulatory elements embedded within the gene is required for proper gene expression.
Collapse
Affiliation(s)
- Brett S Abrahams
- Centre for Molecular Medicine & Therapeutics, British Columbia Research Institute for Children's and Women's Health, and Department of Medical Genetics, University of British Columbia, 980 West 28(th) Avenue, Vancouver, British Columbia, V5Z 4H4, Canada
| | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Müller F, Blader P, Strähle U. Search for enhancers: teleost models in comparative genomic and transgenic analysis of cis regulatory elements. Bioessays 2002; 24:564-72. [PMID: 12111739 DOI: 10.1002/bies.10096] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Homology searches between DNA sequences of evolutionary distant species (phylogenetic footprinting) offer a fast detection method for regulatory sequences. Because of the small size of their genomes, tetraodontid species such as the Japanese pufferfish and green spotted pufferfish have become attractive models for comparative genomics. A disadvantage of the tetraodontid species is, however, that they cannot be bred and manipulated routinely under laboratory conditions, so these species are less attractive for developmental and genetic analysis. In contrast, an increasing arsenal of transgene techniques with the developmental model species zebrafish and medaka are being used for functional analysis of cis regulatory sequences. The main disadvantage is the much larger genome. While comparison between many loci proved the suitability of phylogenetic footprinting using fish and mammalian sequences, fast rate of change in enhancer structure and gene duplication within teleosts may obscure detection of homologies. Here we discuss the contribution and potentials provided by different teleost models for the detection and functional analysis of conserved cis-regulatory elements.
Collapse
Affiliation(s)
- Ferenc Müller
- Institute of Toxicology and Genetics, Research Center Karlsruhe, Germany.
| | | | | |
Collapse
|
46
|
Altschmied J, Delfgaauw J, Wilde B, Duschl J, Bouneau L, Volff JN, Schartl M. Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish. Genetics 2002; 161:259-67. [PMID: 12019239 PMCID: PMC1462118 DOI: 10.1093/genetics/161.1.259] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The microphthalmia-associated transcription factor (MITF) exists in at least four isoforms. These are generated in higher vertebrates using alternative 5' exons and promoters from a single gene. Two separate genes (mitf-m and mitf-b), however, are present in different teleost fish species including the poeciliid Xiphophorus, the pufferfishes Fugu rubripes and Tetraodon nigroviridis, and the zebrafish Danio rerio. Fish proteins MITF-m and MITF-b correspond at both the structural and the expression levels to one particular bird/mammalian MITF isoform. In the teleost lineage subfunctionalization of mitf genes after duplication at least 100 million years ago is associated with the degeneration of alternative exons and, probably, regulatory elements and promoters. For example, a remnant of the first exon specific for MITF-m is detected within the pufferfish gene encoding MITF-b. Retracing the evolutionary history of mitf genes in vertebrates uncovered the differential recruitment of new introns specific for either the teleost or the bird/mammalian lineage.
Collapse
Affiliation(s)
- Joachim Altschmied
- Department of Physiological Chemistry I, Biocenter (Theodor-Boveri Institute), University of Würzburg, D-97074 Würzburg, Germany
| | | | | | | | | | | | | |
Collapse
|
47
|
Hsieh Y, Shiu Y, Cheng C, Chen S, Hwang D. Identification of Toxin and Fish Species in Cooked Fish Liver Implicated in Food Poisoning. J Food Sci 2002. [DOI: 10.1111/j.1365-2621.2002.tb09433.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Beck S, Trowsdale J. The human major histocompatability complex: lessons from the DNA sequence. Annu Rev Genomics Hum Genet 2002; 1:117-37. [PMID: 11701627 DOI: 10.1146/annurev.genom.1.1.117] [Citation(s) in RCA: 137] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The entire 3.6-MbpDNA sequence of a human major histocompatibility complex derived from a composite of DNA clones from different haplotypes, was completed in 1999, primarily through the work of four main groups. At that time, it was the longest contiguous human DNA sequence to have been determined. The sequence is of extremely high quality and accuracy. In this review, we discuss how the DNA sequence has facilitated our understanding of the biology and genetics of the major histocompatibility complex. We suggest some ways in which the sequence may be exploited in the future to explore the relationship between the extraordinary polymorphism of the region and its association with both autoimmune and infectious diseases.
Collapse
Affiliation(s)
- S Beck
- The Sanger Centre, Wellcome Trust Genome Campus, University of Cambridge, Cambridge CB10 1SA United Kindgom.
| | | |
Collapse
|
49
|
Bagheri-Fam S, Ferraz C, Demaille J, Scherer G, Pfeifer D. Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions. Genomics 2001; 78:73-82. [PMID: 11707075 DOI: 10.1006/geno.2001.6648] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Campomelic dysplasia (CD), a human skeletal malformation syndrome with XY sex reversal, is caused by heterozygous mutations in and around the gene SOX9. SOX9 has an extended 5' control region, as indicated by CD translocation breakpoints scattered over 1 Mb proximal to SOX9 and by expression data from mice transgenic for human SOX9-spanning yeast artificial chromosomes. To identify long-range regulatory elements within the SOX9 5' control region, we compared approximately 3.7 Mb and 195 kb of sequence around human and Fugu rubripes SOX9, respectively. We identified only seven and five protein-coding genes in the human and F. rubripes sequences, respectively. Four of the F. rubripes genes have been mapped in humans; all reside on chromosome 17 but show extensive intrachromosomal gene shuffling compared with the gene order in F. rubripes. In both species, very large intergenic distances separate SOX9 from its directly flanking genes: 2 Mb and 500 kb on either side of SOX9 in humans, and 68 and 97 kb on either side of SOX9 in F. rubripes. Comparative sequence analysis of the intergenic regions revealed five conserved elements, E1-E5, up to 290 kb 5' to human SOX9 and up to 18 kb 5' to F. rubripes SOX9, and three such elements, E6-E8, 3' to SOX9. Where available, mouse sequences confirm conservation of the elements. From the yeast artificial chromosome transgenic data, elements E3-E5 are candidate enhancers for SOX9 expression in limb and vertebral column, and 8 of 10 CD translocation breakpoints separate these elements from SOX9.
Collapse
Affiliation(s)
- S Bagheri-Fam
- Institute of Human Genetics and Anthropology, University of Freiburg, Breisacherstr. 33, Freiburg, D-79106, Germany
| | | | | | | | | |
Collapse
|
50
|
Morizot DC, Nairn RS, Walter RB, Kazianis S. The Linkage Map of Xiphophorus Fishes. ILAR J 2001; 39:237-248. [PMID: 11528083 DOI: 10.1093/ilar.39.2-3.237] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Donald C. Morizot
- University of Texas, M.D. Anderson Cancer Center, Science Park, Research Division, Smithville, Texas, USA
| | | | | | | |
Collapse
|