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Turner D, Adriaenssens EM, Lehman SM, Moraru C, Kropinski AM. Bacteriophage Taxonomy: A Continually Evolving Discipline. Methods Mol Biol 2024; 2734:27-45. [PMID: 38066361 DOI: 10.1007/978-1-0716-3523-0_3] [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] [Indexed: 12/18/2023]
Abstract
While taxonomy is an often underappreciated branch of science, it serves very important roles. Bacteriophage taxonomy has evolved from a discipline based mainly on morphology, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the sequence-based approach that is taken today. The Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a holistic approach to classifying prokaryote viruses by measuring overall DNA and protein similarity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with the National Center for Biotechnology Information (NCBI) and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.
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Affiliation(s)
- Dann Turner
- School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol, UK
| | | | - Susan M Lehman
- Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Cristina Moraru
- Department of The Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Andrew M Kropinski
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, Canada
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2
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An evolutionarily ancient mechanism for regulation of hemoglobin expression in vertebrate red cells. Blood 2020; 136:269-278. [PMID: 32396940 DOI: 10.1182/blood.2020004826] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 04/23/2020] [Indexed: 11/20/2022] Open
Abstract
The oxygen transport function of hemoglobin (HB) is thought to have arisen ∼500 million years ago, roughly coinciding with the divergence between jawless (Agnatha) and jawed (Gnathostomata) vertebrates. Intriguingly, extant HBs of jawless and jawed vertebrates were shown to have evolved twice, and independently, from different ancestral globin proteins. This raises the question of whether erythroid-specific expression of HB also evolved twice independently. In all jawed vertebrates studied to date, one of the HB gene clusters is linked to the widely expressed NPRL3 gene. Here we show that the nprl3-linked hb locus of a jawless vertebrate, the river lamprey (Lampetra fluviatilis), shares a range of structural and functional properties with the equivalent jawed vertebrate HB locus. Functional analysis demonstrates that an erythroid-specific enhancer is located in intron 7 of lamprey nprl3, which corresponds to the NPRL3 intron 7 MCS-R1 enhancer of jawed vertebrates. Collectively, our findings signify the presence of an nprl3-linked multiglobin gene locus, which contains a remote enhancer that drives globin expression in erythroid cells, before the divergence of jawless and jawed vertebrates. Different globin genes from this ancestral cluster evolved in the current NPRL3-linked HB genes in jawless and jawed vertebrates. This provides an explanation of the enigma of how, in different species, globin genes linked to the same adjacent gene could undergo convergent evolution.
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3
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Hänske J, Hammacher T, Grenkowitz F, Mansfeld M, Dau TH, Maksimov P, Friedrich C, Zimmermann W, Kammerer R. Natural selection supports escape from concerted evolution of a recently duplicated CEACAM1 paralog in the ruminant CEA gene family. Sci Rep 2020; 10:3404. [PMID: 32099040 PMCID: PMC7042247 DOI: 10.1038/s41598-020-60425-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/31/2020] [Indexed: 11/24/2022] Open
Abstract
Concerted evolution is often observed in multigene families such as the CEA gene family. As a result, sequence similarity of paralogous genes is significantly higher than expected from their evolutionary distance. Gene conversion, a “copy paste” DNA repair mechanism that transfers sequences from one gene to another and homologous recombination are drivers of concerted evolution. Nevertheless, some gene family members escape concerted evolution and acquire sufficient sequence differences that orthologous genes can be assigned in descendant species. Reasons why some gene family members can escape while others are captured by concerted evolution are poorly understood. By analyzing the entire CEA gene family in cattle (Bos taurus) we identified a member (CEACAM32) that was created by gene duplication and cooption of a unique transmembrane domain exon in the most recent ancestor of ruminants. CEACAM32 shows a unique, testis-specific expression pattern. Phylogenetic analysis indicated that CEACAM32 is not involved in concerted evolution of CEACAM1 paralogs in ruminants. However, analysis of gene conversion events revealed that CEACAM32 is subject to gene conversion but remarkably, these events are found in the leader exon and intron sequences but not in exons coding for the Ig-like domains. These findings suggest that natural selection hinders gene conversion affecting protein sequences of the mature protein and thereby support escape of CEACAM32 from concerted evolution.
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Affiliation(s)
- Jana Hänske
- Institute of Immunology, Friedrich-Loeffler-Institute, Greifswald - Insel Riems, Germany.,Landesuntersuchungsanstalt für das Gesundheits- und Veterinärwesen Sachsen, Dresden, Germany
| | - Tim Hammacher
- Institute of Immunology, Friedrich-Loeffler-Institute, Greifswald - Insel Riems, Germany
| | - Franziska Grenkowitz
- Institute of Immunology, Friedrich-Loeffler-Institute, Greifswald - Insel Riems, Germany
| | - Martin Mansfeld
- Institute of Immunology, Friedrich-Loeffler-Institute, Greifswald - Insel Riems, Germany
| | - Tung Huy Dau
- Institute of Immunology, Friedrich-Loeffler-Institute, Greifswald - Insel Riems, Germany
| | - Pavlo Maksimov
- Institute of Epidemiology, Friedrich-Loeffler-Institute, Greifswald - InselRiems, Germany
| | - Christin Friedrich
- Institute of Immunology, Friedrich-Loeffler-Institute, Greifswald - Insel Riems, Germany.,Institute of Systems Immunology, University of Würzburg, Würzburg, Germany
| | - Wolfgang Zimmermann
- Tumor Immunology Laboratory, LIFE Center, Department of Urology, Ludwig-Maximilians-University, Munich, Germany
| | - Robert Kammerer
- Institute of Immunology, Friedrich-Loeffler-Institute, Greifswald - Insel Riems, Germany.
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Tanave A, Imai Y, Koide T. Nested retrotransposition in the East Asian mouse genome causes the classical nonagouti mutation. Commun Biol 2019; 2:283. [PMID: 31396563 PMCID: PMC6677723 DOI: 10.1038/s42003-019-0539-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 07/10/2019] [Indexed: 01/31/2023] Open
Abstract
Black coat color (nonagouti) is a widespread classical mutation in laboratory mouse strains. The intronic insertion of endogenous retrovirus VL30 in the nonagouti (a) allele of agouti gene was previously reported as the cause of the nonagouti phenotype. Here, we report agouti mouse strains from East Asia that carry the VL30 insertion, indicating that VL30 alone does not cause the nonagouti phenotype. We find that a rare type of endogenous retrovirus, β4, was integrated into the VL30 region at the a allele through nested retrotransposition, causing abnormal splicing. Targeted complete deletion of the β4 element restores agouti gene expression and agouti coat color, whereas deletion of β4 except for a single long terminal repeat results in black-and-tan coat color. Phylogenetic analyses show that the a allele and the β4 retrovirus originated from an East Asian mouse lineage most likely related to Japanese fancy mice. These findings reveal the causal mechanism and historic origin of the classical nonagouti mutation.
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Affiliation(s)
- Akira Tanave
- Mouse Genomics Resource Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
- Present Address: Laboratory for Mouse Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 1–3 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Yuji Imai
- Mouse Genomics Resource Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
| | - Tsuyoshi Koide
- Mouse Genomics Resource Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540 Japan
- Department of Genetics, SOKENDAI (The Graduate University for Advanced Studies), 1111 Yata, Mishima, Shizuoka 411-8540 Japan
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5
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Abstract
While taxonomy is an often-unappreciated branch of science it serves very important roles. Bacteriophage taxonomy has evolved from a mainly morphology-based discipline, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the holistic approach that is taken today. The Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a comprehensive approach to classifying prokaryote viruses measuring overall DNA and protein identity and phylogeny before making decisions about the taxonomic position of a new virus. The huge number of complete genomes being deposited with NCBI and other public databases has resulted in a reassessment of the taxonomy of many viruses, and the future will see the introduction of new viral families and higher orders.
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Affiliation(s)
- Igor Tolstoy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
| | - Andrew M Kropinski
- Department of Food Science, University of Guelph, Guelph, ON, Canada, N1G 2W1.
- Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON, Canada, N1G 2W1.
- Department of Pathobiology, University of Guelph, 6 Mayfield Ave, Guelph, ON, Canada, N1G 2W1.
| | - J Rodney Brister
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA
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6
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dos Santos FC, Peixoto MGCD, Fonseca PADS, Pires MDFÁ, Ventura RV, Rosse IDC, Bruneli FAT, Machado MA, Carvalho MRS. Identification of Candidate Genes for Reactivity in Guzerat (Bos indicus) Cattle: A Genome-Wide Association Study. PLoS One 2017; 12:e0169163. [PMID: 28125592 PMCID: PMC5268462 DOI: 10.1371/journal.pone.0169163] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 12/13/2016] [Indexed: 01/24/2023] Open
Abstract
Temperament is fundamental to animal production due to its direct influence on the animal-herdsman relationship. When compared to calm animals, the aggressive, anxious or fearful ones exhibit less weight gain, lower reproductive efficiency, decreased milk production and higher herd maintenance costs, all of which contribute to reduced profits. However, temperament is a trait that is complex and difficult to assess. Recently, a new quantitative system, REATEST®, for assessing reactivity, a phenotype of temperament, was developed. Herein, we describe the results of a Genome-wide association study for reactivity, assessed using REATEST® with a sample of 754 females from five dual-purpose (milk and meat production) Guzerat (Bos indicus) herds. Genotyping was performed using a 50k SNP chip and a two-step mixed model approach (Grammar-Gamma) with a one-by-one marker regression was used to identify QTLs. QTLs for reactivity were identified on chromosomes BTA1, BTA5, BTA14, and BTA25. Five intronic and two intergenic markers were significantly associated with reactivity. POU1F1, DRD3, VWA3A, ZBTB20, EPHA6, SNRPF and NTN4 were identified as candidate genes. Previous QTL reports for temperament traits, covering areas surrounding the SNPs/genes identified here, further corroborate these associations. The seven genes identified in the present study explain 20.5% of reactivity variance and give a better understanding of temperament biology.
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Affiliation(s)
| | | | | | | | - Ricardo Vieira Ventura
- Center for Genetic Improvement of Livestock, University of Guelph, Guelph, Canada
- Beef Improvement Opportunities, Guelph, Canada
| | - Izinara da Cruz. Rosse
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Mahadevan P. An Analysis of Adenovirus Genomes Using Whole Genome Software Tools. Bioinformation 2016; 12:301-310. [PMID: 28293072 PMCID: PMC5320926 DOI: 10.6026/97320630012301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 11/23/2022] Open
Abstract
The evolution of sequencing technology has lead to an enormous increase in the number of genomes that have been sequenced. This is especially true in the field of virus genomics. In order to extract meaningful biological information from these genomes, whole genome data mining software tools must be utilized. Hundreds of tools have been developed to analyze biological sequence data. However, only some of these tools are user-friendly to biologists. Several of these tools that have been successfully used to analyze adenovirus genomes are described here. These include Artemis, EMBOSS, pDRAW, zPicture, CoreGenes, GeneOrder, and PipMaker. These tools provide functionalities such as visualization, restriction enzyme analysis, alignment, and proteome comparisons that are extremely useful in the bioinformatics analysis of adenovirus genomes.
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Affiliation(s)
- Padmanabhan Mahadevan
- Department of Biology, University of Tampa, 401 W. Kennedy Blvd. Box 3F, Tampa, FL 33606
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Hodonsky CJ, Kleinbrink EL, Charney KN, Prasad M, Bessling SL, Jones EA, Srinivasan R, Svaren J, McCallion AS, Antonellis A. SOX10 regulates expression of the SH3-domain kinase binding protein 1 (Sh3kbp1) locus in Schwann cells via an alternative promoter. Mol Cell Neurosci 2011; 49:85-96. [PMID: 22037207 DOI: 10.1016/j.mcn.2011.10.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 10/07/2011] [Accepted: 10/11/2011] [Indexed: 12/31/2022] Open
Abstract
The transcription factor SOX10 has essential roles in neural crest-derived cell populations, including myelinating Schwann cells-specialized glial cells responsible for ensheathing axons in the peripheral nervous system. Importantly, SOX10 directly regulates the expression of genes essential for proper myelin function. To date, only a handful of SOX10 target loci have been characterized in Schwann cells. Addressing this lack of knowledge will provide a better understanding of Schwann cell biology and candidate loci for relevant diseases such as demyelinating peripheral neuropathies. We have identified a highly-conserved SOX10 binding site within an alternative promoter at the SH3-domain kinase binding protein 1 (Sh3kbp1) locus. The genomic segment identified at Sh3kbp1 binds to SOX10 and displays strong promoter activity in Schwann cells in vitro and in vivo. Mutation of the SOX10 binding site ablates promoter activity, and ectopic expression of SOX10 in SOX10-negative cells promotes the expression of endogenous Sh3kbp1. Combined, these data reveal Sh3kbp1 as a novel target of SOX10 and raise important questions regarding the function of SH3KBP1 isoforms in Schwann cells.
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Affiliation(s)
- Chani J Hodonsky
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
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9
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Abstract
The original report of sex in fungi dates 2 centuries ago to the species Syzygites megalocarpus (Mucoromycotina). The organism was subsequently used in 1904 to represent self-fertile homothallic species when the concepts of heterothallism and homothallism were developed for the fungal kingdom. In this study, two putative sex/MAT loci were identified in individual strains of S. megalocarpus, accounting for its homothallic behavior. The strains encode both of the high-mobility-group domain-containing proteins, SexM and SexP, flanked by RNA helicase and glutathione oxidoreductase genes that are found adjacent to the mating-type loci in other Mucoromycotina species. The presence of pseudogenes and the arrangement of genes suggest that the origin of homothallism in this species is from a heterothallic relative, obtained via a chromosomal rearrangement to switch two alleles into two separated loci within a single genetic background. Similar events have given rise to homothallic species from heterothallic species in ascomycete fungi, demonstrating that conserved forces shape the evolution of sex determination and speciation in highly diverged fungi.
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Antonellis A, Dennis MY, Burzynski G, Huynh J, Maduro V, Hodonsky CJ, Khajavi M, Szigeti K, Mukkamala S, Bessling SL, Pavan WJ, McCallion AS, Lupski JR, Green ED. A rare myelin protein zero (MPZ) variant alters enhancer activity in vitro and in vivo. PLoS One 2010; 5:e14346. [PMID: 21179557 PMCID: PMC3002941 DOI: 10.1371/journal.pone.0014346] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2010] [Accepted: 11/26/2010] [Indexed: 01/16/2023] Open
Abstract
Background Myelin protein zero (MPZ) is a critical structural component of myelin in the peripheral nervous system. The MPZ gene is regulated, in part, by the transcription factors SOX10 and EGR2. Mutations in MPZ, SOX10, and EGR2 have been implicated in demyelinating peripheral neuropathies, suggesting that components of this transcriptional network are candidates for harboring disease-causing mutations (or otherwise functional variants) that affect MPZ expression. Methodology We utilized a combination of multi-species sequence comparisons, transcription factor-binding site predictions, targeted human DNA re-sequencing, and in vitro and in vivo enhancer assays to study human non-coding MPZ variants. Principal Findings Our efforts revealed a variant within the first intron of MPZ that resides within a previously described SOX10 binding site is associated with decreased enhancer activity, and alters binding of nuclear proteins. Additionally, the genomic segment harboring this variant directs tissue-relevant reporter gene expression in zebrafish. Conclusions This is the first reported MPZ variant within a cis-acting transcriptional regulatory element. While we were unable to implicate this variant in disease onset, our data suggests that similar non-coding sequences should be screened for mutations in patients with neurological disease. Furthermore, our multi-faceted approach for examining the functional significance of non-coding variants can be readily generalized to study other loci important for myelin structure and function.
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Affiliation(s)
- Anthony Antonellis
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Neurology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Megan Y. Dennis
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Grzegorz Burzynski
- McKusick–Nathans Institute of Genetic Medicine and Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jimmy Huynh
- McKusick–Nathans Institute of Genetic Medicine and Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Valerie Maduro
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chani J. Hodonsky
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Mehrdad Khajavi
- Department of Molecular and Human Genetics, Houston, Texas, United States of America
| | - Kinga Szigeti
- Department of Molecular and Human Genetics, Houston, Texas, United States of America
- Department of Neurology, Houston, Texas, United States of America
| | - Sandeep Mukkamala
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Seneca L. Bessling
- McKusick–Nathans Institute of Genetic Medicine and Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - NISC Comparative Sequencing Program
- NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - William J. Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Andrew S. McCallion
- McKusick–Nathans Institute of Genetic Medicine and Department of Molecular and Comparative Pathobiology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - James R. Lupski
- Department of Molecular and Human Genetics, Houston, Texas, United States of America
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Texas Children's Hospital, Houston, Texas, United States of America
| | - Eric D. Green
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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11
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Kim DW, Choi SH, Kim RN, Kim SH, Paik SG, Nam SH, Kim DW, Kim A, Kang A, Park HS. Comparative genomic analysis of the false killer whale (Pseudorca crassidens) LMBR1 locus. Genome 2010; 53:658-66. [PMID: 20924415 DOI: 10.1139/g10-043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The sequencing and comparative genomic analysis of LMBR1 loci in mammals or other species, including human, would be very important in understanding evolutionary genetic changes underlying the evolution of limb development. In this regard, comparative genomic annotation of the false killer whale LMBR1 locus could shed new light on the evolution of limb development. We sequenced two false killer whale BAC clones, corresponding to 156 kb and 144 kb, respectively, harboring the tightly linked RNF32, LMBR1, and NOM1 genes. Our annotation of the false killer whale LMBR1 gene showed that it consists of 17 exons (1473 bp), in contrast to 18 exons (1596 bp) in human, and it displays 93.1% and 95.6% nucleotide and amino acid sequence similarity, respectively, compared with the human gene. In particular, we discovered that exon 10, deleted in the false killer whale LMBR1 gene, is present only in primates, and this fact strongly implies that exon 10 might be crucial in determining primate-specific limb development. ZRS and TFBS sequences have been well conserved across 11 species, suggesting that these regions could be involved in an important function of limb development and limb patterning. The neighboring gene RNF32 showed several lineage-conserved exons, such as exons 2 through 9 conserved in eutherian mammals, exons 3 through 9 conserved in mammals, and exons 5 through 9 conserved in vertebrates. The other neighboring gene, NOM1, had undergone a substitution (ATG→GTA) at the start codon, giving rise to a 36 bp shorter N-terminal sequence compared with the human sequence. Our comparative analysis of the false killer whale LMBR1 genomic locus provides important clues regarding the genetic regions that may play crucial roles in limb development and patterning.
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Affiliation(s)
- Dae-Won Kim
- Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea
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12
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Reed NP, Mortlock DP. Identification of a distant cis-regulatory element controlling pharyngeal arch-specific expression of zebrafish gdf6a/radar. Dev Dyn 2010; 239:1047-60. [PMID: 20201106 DOI: 10.1002/dvdy.22251] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Skeletal formation is an essential and intricately regulated part of vertebrate development. Humans and mice deficient in growth and differentiation factor 6 (Gdf6) have numerous skeletal abnormalities, including joint fusions and cartilage reductions. The expression of Gdf6 is dynamic and in part regulated by distant evolutionarily conserved cis-regulatory elements. radar/gdf6a is a zebrafish ortholog of Gdf6 and has an essential role in embryonic patterning. Here, we show that radar is transcribed in the cells surrounding and between the developing cartilages of the ventral pharyngeal arches, similar to mouse Gdf6. A 312 bp evolutionarily conserved region (ECR5), 122 kilobases downstream, drives expression in a pharyngeal arch-specific manner similar to endogenous radar/gdf6a. Deletion analysis identified a 78 bp region within ECR5 that is essential for transgene activity. This work illustrates that radar is regulated in the pharyngeal arches by a distant conserved element and suggests radar has similar functions in skeletal development in fish and mammals.
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Affiliation(s)
- Nykolaus P Reed
- Department of Microbial Pathogenesis and Immune Response, School of Graduate Studies and Research, Meharry Medical College, Nashville, Tennessee, USA
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13
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Chalphin AV, Saha MS. The specification of glycinergic neurons and the role of glycinergic transmission in development. Front Mol Neurosci 2010; 3:11. [PMID: 20461146 PMCID: PMC2866564 DOI: 10.3389/fnmol.2010.00011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Accepted: 03/23/2010] [Indexed: 12/16/2022] Open
Abstract
Glycine's role as an inhibitory neurotransmitter in the adult vertebrate nervous system has been well characterized in a number of different model organisms. However, a full understanding of glycinergic transmission requires a knowledge of how glycinergic synapses emerge and the role of glycinergic signaling during development. Recent literature has provided a detailed picture of the developmental expression of many of the molecular components that comprise the glycinergic phenotype, namely the glycine transporters and the glycine receptor subunits; the transcriptional networks leading to the expression of this important neurotransmitter phenotype are also being elucidated. An equally important focus of research has revealed the critical role of glycinergic signaling in sculpting many different aspects of neural development. This review examines the current literature detailing the expression patterns of the components of the glycinergic phenotype in various vertebrate model organisms over the course of development and the molecular mechanisms governing the expression of the glycinergic phenotype. The review then surveys the recent work on the role of glycinergic signaling in the developing nervous system and concludes with an overview of areas for further research.
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14
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Brower CS, Veiga L, Jones RH, Varshavsky A. Mouse Dfa is a repressor of TATA-box promoters and interacts with the Abt1 activator of basal transcription. J Biol Chem 2010; 285:17218-34. [PMID: 20356838 DOI: 10.1074/jbc.m110.118638] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Our study of the mouse Ate1 arginyltransferase, a component of the N-end rule pathway, has shown that Ate1 pre-mRNA is produced from a bidirectional promoter that also expresses, in the opposite direction, a previously uncharacterized gene (Hu, R. G., Brower, C. S., Wang, H., Davydov, I. V., Sheng, J., Zhou, J., Kwon, Y. T., and Varshavsky, A. (2006) J. Biol. Chem. 281, 32559-32573). In this work, we began analyzing this gene, termed Dfa (divergent from Ate1). Mouse Dfa was found to be transcribed from both the bidirectional P(Ate1/Dfa) promoter and other nearby promoters. The resulting transcripts are alternatively spliced, yielding a complex set of Dfa mRNAs that are present largely, although not exclusively, in the testis. A specific Dfa mRNA encodes, via its 3'-terminal exon, a 217-residue protein termed Dfa(A). Other Dfa mRNAs also contain this exon. Dfa(A) is sequelogous (similar in sequence) to a region of the human/mouse HTEX4 protein, whose physiological function is unknown. We produced an affinity-purified antibody to recombinant mouse Dfa(A) that detected a 35-kDa protein in the mouse testis and in several cell lines. Experiments in which RNA interference was used to down-regulate Dfa indicated that the 35-kDa protein was indeed Dfa(A). Furthermore, Dfa(A) was present in the interchromatin granule clusters and was also found to bind to the Ggnbp1 gametogenetin-binding protein-1 and to the Abt1 activator of basal transcription that interacts with the TATA-binding protein. Given these results, RNA interference was used to probe the influence of Dfa levels in luciferase reporter assays. We found that Dfa(A) acts as a repressor of TATA-box transcriptional promoters.
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Affiliation(s)
- Christopher S Brower
- Division of Biology, California Institute of Technology, Pasadena, California 91125, USA
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Frazer KA, Elnitski L, Church DM, Dubchak I, Hardison RC. Cross-species sequence comparisons: a review of methods and available resources. Genome Res 2003; 13:1-12. [PMID: 12529301 PMCID: PMC430969 DOI: 10.1101/gr.222003] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
With the availability of whole-genome sequences for an increasing number of species, we are now faced with the challenge of decoding the information contained within these DNA sequences. Comparative analysis of DNA sequences from multiple species at varying evolutionary distances is a powerful approach for identifying coding and functional noncoding sequences, as well as sequences that are unique for a given organism. In this review, we outline the strategy for choosing DNA sequences from different species for comparative analyses and describe the methods used and the resources publicly available for these studies.
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Affiliation(s)
- Kelly A Frazer
- Perlegen Sciences, Mountain View, California 94043, USA.
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