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Pathak RU, Phanindhar K, Mishra RK. Transposable elements as scaffold/matrix attachment regions: shaping organization and functions in genomes. Front Mol Biosci 2024; 10:1326933. [PMID: 38455359 PMCID: PMC10918478 DOI: 10.3389/fmolb.2023.1326933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/27/2023] [Indexed: 03/09/2024] Open
Abstract
The hierarchical structure of eukaryotic genomes has regulatory layers, one of them being epigenetic "indexing" of the genome that leads to cell-type-specific patterns of gene expression. By establishing loops and defining chromatin domains, cells can achieve coordinated control over multi-locus segments of the genome. This is thought to be achieved using scaffold/matrix attachment regions (S/MARs) that establish structural and functional loops and topologically associating domains (TADs) that define a self-interacting region of the genome. Large-scale genome-wide mapping of S/MARs has begun to uncover these aspects of genome organization. A recent genome-wide study showed the association of transposable elements (TEs) with a significant fraction of S/MARs, suggesting that the multitude of TE-derived repeats constitute a class of anchorage sites of chromatin loops to nuclear architecture. In this study, we provide an insight that TE-driven dispersal of S/MARs has the potential to restructure the chromosomes by creating novel loops and domains. The combination of TEs and S/MARs, as elements that can hop through the genome along with regulatory capabilities, may provide an active mechanism of genome evolution leading to the emergence of novel features in biological systems. The significance is that a genome-wide study mapping developmental S/MARs reveals an intriguing link between these elements and TEs. This article highlights the potential of the TE-S/MAR combination to drive evolution by restructuring and shaping the genome.
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Affiliation(s)
| | | | - Rakesh K. Mishra
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- Tata Institute for Genetics and Society, Bengaluru, India
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Rutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, Theissinger K, Lecompte O. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes (Basel) 2023; 14:1627. [PMID: 37628678 PMCID: PMC10454600 DOI: 10.3390/genes14081627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Repetitive elements are a major component of DNA sequences due to their ability to propagate through the genome. Characterization of Metazoan repetitive profiles is improving; however, current pipelines fail to identify a significant proportion of divergent repeats in non-model organisms. The Decapoda order, for which repeat content analyses are largely lacking, is characterized by extremely variable genome sizes that suggest an important presence of repetitive elements. Here, we developed a new standardized pipeline to annotate repetitive elements in non-model organisms, which we applied to twenty Decapoda and six other Crustacea genomes. Using this new tool, we identified 10% more repetitive elements than standard pipelines. Repetitive elements were more abundant in Decapoda species than in other Crustacea, with a very large number of highly repeated satellite DNA families. Moreover, we demonstrated a high correlation between assembly size and transposable elements and different repeat dynamics between Dendrobranchiata and Reptantia. The patterns of repetitive elements largely reflect the phylogenetic relationships of Decapoda and the distinct evolutionary trajectories within Crustacea. In summary, our results highlight the impact of repetitive elements on genome evolution in Decapoda and the value of our novel annotation pipeline, which will provide a baseline for future comparative analyses.
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Affiliation(s)
- Christelle Rutz
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Lena Bonassin
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Arnaud Kress
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Caterina Francesconi
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Ljudevit Luka Boštjančić
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
- Department of Molecular Ecology, Institute for Environmental Sciences, Rhineland-Palatinate Technical University Kaiserslautern Landau, Fortstr. 7, 76829 Landau, Germany
| | - Dorine Merlat
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
| | - Kathrin Theissinger
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberg Biodiversity and Climate Research Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany; (C.F.); (K.T.)
| | - Odile Lecompte
- Department of Computer Science, ICube, UMR 7357, University of Strasbourg, CNRS, Rue Eugène Boeckel 1, 67000 Strasbourg, France; (C.R.); (L.B.); (A.K.); (L.L.B.); (D.M.)
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Paquette A, Baloni P, Holloman AB, Nigam S, Bammler T, Mao Q, Price ND. Temporal transcriptomic analysis of metabolic genes in maternal organs and placenta during murine pregnancy. Biol Reprod 2018; 99:1255-1265. [PMID: 29939228 PMCID: PMC6692859 DOI: 10.1093/biolre/ioy148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/22/2018] [Accepted: 06/22/2018] [Indexed: 01/11/2023] Open
Abstract
Maternal pregnancy adaptation is crucial for fetal development and long-term health. Complex interactions occur between maternal digestive and excretory systems as they interface with the developing fetus through the placenta, and transcriptomic regulation in these organs throughout pregnancy is poorly understood. Our objective is to characterize transcriptomic changes across gestation in maternal organs and placenta. Gene expression was quantified in the kidney, liver, and small intestine harvested from nonpregnant and pregnant FVB mice at four time points and placenta at three time points (N = 5/time point) using Affymetrix Mouse Gene 1.0 ST arrays. In maternal organs, we identified 476 genes in the liver, 207 genes in the kidney, and 27 genes in the small intestine that were differentially expressed across gestation (False Discovery Rate [FDR] adjusted q < 0.05). The placenta had a total of 1576 differentially expressed genes between the placenta at either/gd15 or gd19 compared to gd10. We identified a number of pathways enriched for genes differentially expressed across gestation, including 5 pathways in the placenta, 9 pathways in the kidney, and 28 pathways in the liver, including the citrate cycle, retinol metabolism, bile acid synthesis, and steroid bile synthesis, which play functional roles in fetal development and pregnancy maintenance. Characterization of normal longitudinal changes that occur in pregnancy provides context to understand how perturbations in these biochemical pathways and perturbations in nutrient signaling may impact pregnancy.
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Affiliation(s)
| | | | | | - Sanjay Nigam
- Departments of Pediatrics and Medicine, University of California San Diego, San Diego, California, USA
| | - Theo Bammler
- Department of Environmental and Occupational Health Science, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Qingcheng Mao
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, Washington, USA
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Wang L, Liu H, Jiao Y, Wang E, Clark SH, Postlethwaite AE, Gu W, Chen H. Differences between Mice and Humans in Regulation and the Molecular Network of Collagen, Type III, Alpha-1 at the Gene Expression Level: Obstacles that Translational Research Must Overcome. Int J Mol Sci 2015; 16:15031-56. [PMID: 26151842 PMCID: PMC4519886 DOI: 10.3390/ijms160715031] [Citation(s) in RCA: 16] [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: 03/24/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 11/17/2022] Open
Abstract
Collagen, type III, alpha-1 (COL3A1) is essential for normal collagen I fibrillogenesis in many organs. There are differences in phenotypes of mutations in the COL3A1 gene in humans and mutations in mice. In order to investigate whether the regulation and gene network of COL3A1 is the same in healthy populations of mice and humans, we compared the quantitative trait loci (QTL) that regulate the expression level of COL3A1 and the gene network of COL3A1 pathways between humans and mice using whole genome expression profiles. Our results showed that, for the regulation of expression of Col3a1 in mice, an eQTL on chromosome (Chr) 12 regulates the expression of Col3a1. However, expression of genes in the syntenic region on human Chr 7 has no association with the expression level of COL3A1. For the gene network comparison, we identified 44 top genes whose expression levels are strongly associated with that of Col3a1 in mice. We next identified 41 genes strongly associated with the expression level of COL3A1 in humans. There are a few but significant differences in the COL3A1 gene network between humans and mice. Several genes showed opposite association with expression of COL3A1. These genes are known to play important roles in development and function of the extracellular matrix of the lung. Difference in the molecular pathway of key genes in the COL3A1 gene network in humans and mice suggest caution should be used in extrapolating results from models of human lung diseases in mice to clinical lung diseases in humans. These differences may influence the efficacy of drugs in humans whose development employed mouse models.
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Affiliation(s)
- Lishi Wang
- Department of Orthopedic Surgery and BME-Campbell Clinic, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
- Department of Basic Research, Inner Mongolia Medical College, Inner Mongolia 010110, China.
| | - Hongchao Liu
- Integrative Research Center, the first Hospital of Qiqihaer City, Qiqihaer 161005, China.
| | - Yan Jiao
- Department of Orthopedic Surgery and BME-Campbell Clinic, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
- Department of Medicine, Mudanjiang Medical College, Mudanjiang 157001, China.
| | - Erjian Wang
- Integrative Research Center, the first Hospital of Qiqihaer City, Qiqihaer 161005, China.
| | - Stephen H Clark
- Department of Genetics and Developmental Biology, University of Connecticut Health Center, Farmington, CT 06030, USA.
| | - Arnold E Postlethwaite
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
- Research Service, Veterans Affairs Medical Center, Memphis, TN 38104, USA.
| | - Weikuan Gu
- Department of Orthopedic Surgery and BME-Campbell Clinic, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
- Research Service, Veterans Affairs Medical Center, Memphis, TN 38104, USA.
| | - Hong Chen
- Integrative Research Center, the first Hospital of Qiqihaer City, Qiqihaer 161005, China.
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Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ. A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. BMC SYSTEMS BIOLOGY 2010; 4:140. [PMID: 20959003 PMCID: PMC2978158 DOI: 10.1186/1752-0509-4-140] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Accepted: 10/19/2010] [Indexed: 12/16/2022]
Abstract
BACKGROUND Well-curated and validated network reconstructions are extremely valuable tools in systems biology. Detailed metabolic reconstructions of mammals have recently emerged, including human reconstructions. They raise the question if the various successful applications of microbial reconstructions can be replicated in complex organisms. RESULTS We mapped the published, detailed reconstruction of human metabolism (Recon 1) to other mammals. By searching for genes homologous to Recon 1 genes within mammalian genomes, we were able to create draft metabolic reconstructions of five mammals, including the mouse. Each draft reconstruction was created in compartmentalized and non-compartmentalized version via two different approaches. Using gap-filling algorithms, we were able to produce all cellular components with three out of four versions of the mouse metabolic reconstruction. We finalized a functional model by iterative testing until it passed a predefined set of 260 validation tests. The reconstruction is the largest, most comprehensive mouse reconstruction to-date, accounting for 1,415 genes coding for 2,212 gene-associated reactions and 1,514 non-gene-associated reactions.We tested the mouse model for phenotype prediction capabilities. The majority of predicted essential genes were also essential in vivo. However, our non-tissue specific model was unable to predict gene essentiality for many of the metabolic genes shown to be essential in vivo. Our knockout simulation of the lipoprotein lipase gene correlated well with experimental results, suggesting that softer phenotypes can also be simulated. CONCLUSIONS We have created a high-quality mouse genome-scale metabolic reconstruction, iMM1415 (Mus Musculus, 1415 genes). We demonstrate that the mouse model can be used to perform phenotype simulations, similar to models of microbe metabolism. Since the mouse is an important experimental organism, this model should become an essential tool for studying metabolic phenotypes in mice, including outcomes from drug screening.
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Affiliation(s)
- Martin I Sigurdsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Reykjavik, Iceland
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Edelstein LC, Collins T. The SCAN domain family of zinc finger transcription factors. Gene 2005; 359:1-17. [PMID: 16139965 DOI: 10.1016/j.gene.2005.06.022] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2005] [Revised: 05/26/2005] [Accepted: 06/03/2005] [Indexed: 12/29/2022]
Abstract
Zinc finger transcription factor genes represent a significant portion of the genes in the vertebrate genome. Some Cys2His2 type zinc fingers are associated with conserved protein domains that help to define these regulators. A novel domain of this type, the SCAN domain, is a highly conserved 84-residue motif that is found near the N-terminus of a subfamily of C2H2 zinc finger proteins. The SCAN domain, which is also known as the leucine rich region, functions as a protein interaction domain, mediating self-association or selective association with other proteins. Here we define the mouse SCAN domain and annotate the mouse SCAN family members. In addition to a single SCAN domain, some of the members of the mouse SCAN family members have a conserved N-terminal motif, a KRAB domain, SANT domains and a variable number of C2H2 type zinc fingers (3-14). The genes encoding mouse SCAN domains are clustered, often in tandem arrays, and are capable of generating isoforms that may affect the function of family members. Although the function of most of the family members is not known, an overview of selected members of this group of transcription factors suggests that some of the mouse SCAN domain family members play roles in cell survival and differentiation.
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Affiliation(s)
- Leonard C Edelstein
- Department of Pathology, Children's Hospital Boston and Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, USA
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von Sternberg R, Shapiro JA. How repeated retroelements format genome function. Cytogenet Genome Res 2005; 110:108-16. [PMID: 16093662 DOI: 10.1159/000084942] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2004] [Accepted: 08/03/2004] [Indexed: 11/19/2022] Open
Abstract
Genomes operate as sophisticated information storage systems. Generic repeated signals in the DNA format expression of coding sequence files and organize additional functions essential for genome replication and accurate transmission to progeny cells. Retroelements comprise a major fraction of many genomes and contain a surprising diversity of functional signals. In this article, we summarize some features of the taxonomic distribution of retroelements, especially mammalian SINEs, tabulate functional roles documented for different classes of retroelements, and discuss their potential roles as genome organizers. In particular, the fact that certain retroelements serve as boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the reversed transcribed component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the "functionalist" perspective on repetitive DNA leads to new ways of thinking about the systemic organization of cellular genomes and provides several novel possibilities involving retroelements in evolutionarily significant genome reorganization.
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Affiliation(s)
- R von Sternberg
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
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Abstract
There are clear theoretical reasons and many well-documented examples which show that repetitive, DNA is essential for genome function. Generic repeated signals in the DNA are necessary to format expression of unique coding sequence files and to organise additional functions essential for genome replication and accurate transmission to progeny cells. Repetitive DNA sequence elements are also fundamental to the cooperative molecular interactions forming nucleoprotein complexes. Here, we review the surprising abundance of repetitive DNA in many genomes, describe its structural diversity, and discuss dozens of cases where the functional importance of repetitive elements has been studied in molecular detail. In particular, the fact that repeat elements serve either as initiators or boundaries for heterochromatin domains and provide a significant fraction of scaffolding/matrix attachment regions (S/MARs) suggests that the repetitive component of the genome plays a major architectonic role in higher order physical structuring. Employing an information science model, the 'functionalist' perspective on repetitive DNA leads to new ways of thinking about the systemic organisation of cellular genomes and provides several novel possibilities involving repeat elements in evolutionarily significant genome reorganisation. These ideas may facilitate the interpretation of comparisons between sequenced genomes, where the repetitive DNA component is often greater than the coding sequence component.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago, 920 E. 58th Street, Chicago, IL 60637, USA.
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Kelly MA, Beuckmann CT, Williams SC, Sinton CM, Motoike T, Richardson JA, Hammer RE, Garry MG, Yanagisawa M. Neuropeptide B-deficient mice demonstrate hyperalgesia in response to inflammatory pain. Proc Natl Acad Sci U S A 2005; 102:9942-7. [PMID: 15983370 PMCID: PMC1174999 DOI: 10.1073/pnas.0503795102] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Neuropeptide B (NPB) and neuropeptide W (NPW) have been recently identified as ligands for the G protein-coupled receptor (GPR) 7 and GPR8. The precise in vivo role of this neuropeptide-receptor pathway has not been fully demonstrated. In this paper, we report that NPB-deficient mice manifest a mild adult-onset obesity, similar to that reported in GPR7-null mice. NPB-deficient mice also exhibit hyperalgesia in response to inflammatory pain. Hyperalgesia was not observed in response to chemical pain, thermal pain, or electrical stimulation. NPB-deficient mice demonstrated intact behavioral responses to pain, and learning from the negative reinforcement of electrical stimulation was unaltered. Baseline anxiety was also unchanged as measured in both the elevated plus maze and time spent immobile in a novel environment. These data support the idea that NPB is a factor in the modulation of responses to inflammatory pain and body weight homeostasis.
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Affiliation(s)
- Michele A Kelly
- Howard Hughes Medical Institute and Departments of Molecular Genetics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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Diament AL, Farahani P, Chiu S, Fisler J, Warden CH. A novel mouse Chromosome 2 congenic strain with obesity phenotypes. Mamm Genome 2005; 15:452-9. [PMID: 15181537 DOI: 10.1007/s00335-004-2352-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2003] [Accepted: 01/21/2004] [Indexed: 11/29/2022]
Abstract
Linkage studies have identified many chromosomal regions containing obesity genes in mice. However, only a few of these quantitative trait loci (QTLs) have been used to guide the production of congenic mouse strains that retain obesity phenotypes. We seek to identify chromosomal regions containing obesity genes in the BSB model of spontaneous obesity because the BSB model is a multigenic obesity model. Previous studies identified QTLs on Chromosomes (Chrs) 2, 6, 7,12, and 15. BSB mice are made by backcross of lean C57BL/6J x Mus spretus. F(1)s were backcrossed to C57BL/6J mice to produce BSB progeny. We have constructed a new BSB cross and produced congenic mice with obesity phenotypes by marker-directed selection called B6.S- D2Mit194- D2Mit311. We found a highly significant QTL for percentage body lipid on Chr 2 just proximal to the Agouti locus. Chr 2 congenics were constructed to determine whether the main effects would be detectable. We observed highly significant linkage of the Chr 2 congenic containing Agouti and containing markers distal to D2Mit311 and proximal to D2Mit194. Thus, this congenic contains approximately 14.6 cM or 30 Mb (about 1.1% of the spretus mouse genome) and several hundred genes. The obesity phenotype of the QTL is retained in the congenic. The congenic can now be used to model the genetic and physiological basis for a relatively simple, perhaps monogenic, obesity.
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Affiliation(s)
- Adam L Diament
- Rowe Program in Genetics and Department of Pediatrics, University of California-Davis, 4435 Tupper Hall, Davis, CA 95616, USA
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Hu ZL, Glenn K, Ramos AM, Otieno CJ, Reecy JM, Rothschild MF. Expeditor: a pipeline for designing primers using human gene structure and livestock animal EST information. ACTA ACUST UNITED AC 2004; 96:80-2. [PMID: 15598711 DOI: 10.1093/jhered/esi015] [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: 11/14/2022]
Abstract
We have developed software, called Expeditor, that can be used to combine known gene structure information from human and coding sequence information from farm animal species for a streamlined primer design in target farm animal species. This software has many utilities, which include PCR-based SNP discovery for identification of genes/markers associated with economically important traits in farm animals, comparative mapping analysis, and evolution studies. The use of this software helps minimize tedious manual operations and reduces the chance of errors by more conventional approaches.
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Affiliation(s)
- Z-L Hu
- Department of Animal Science, 2255 Kildee Hall, Center for Integrated Animal Genomics, Iowa State University, Ames, IA 50011, USA.
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Elphinstone MS, Gordon RD, So A, Jeske YWA, Stratakis CA, Stowasser M. Genomic structure of the human gene for protein kinase A regulatory subunit R1-beta (PRKAR1B) on 7p22: no evidence for mutations in familial hyperaldosteronism type II in a large affected kindred. Clin Endocrinol (Oxf) 2004; 61:716-23. [PMID: 15579186 DOI: 10.1111/j.1365-2265.2004.02155.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE Familial hyperaldosteronism type II (FH-II) is characterized by inheritance of primary aldosteronism (PAL) but, unlike FH-I, is not glucocorticoid remediable and not associated with the hybrid CYP11B1/CYP11B2 gene mutation. Analysis of two pedigrees previously demonstrated linkage of FH-II with a locus at chromosome 7p22. We sought to determine whether mutations in the exons or intron/exon boundaries in PRKAR1B (encoding protein kinase A regulatory subunit R1-beta), which resides within the linked locus, are associated with FH-II. METHODS Primers enabling sequencing of all exons and intron/exon boundaries were designed by BLAT search using known mRNA sequence, and comparison with an orthologous mouse gene. Sequences from four affected and two unaffected subjects from an Australian family with FH-II demonstrating linkage at 7p22 were compared with published sequences. RESULTS A probable two-nucleotide GenBank sequence error, resulting in an amino acid change, was detected. Two of seven single nucleotide polymorphisms (SNPs) identified were in exons and five in introns. Neither exon-localized SNP resulted in an amino acid change. All intron-localized SNPs were at least 16 nucleotides from the closest intron/exon boundary and therefore unlikely to interfere with gene splicing. Importantly, none of the identified SNPs was exclusively associated with affectation status. CONCLUSIONS Mutations in the exons or intron/exon boundaries of PRKAR1B do not appear to be responsible for FH-II in this family, but a mutation in the promoter or remaining intronic or 5' or 3' untranslated regions could be. Alternatively, a mutation within another gene residing at the 7p22 locus may be responsible.
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Affiliation(s)
- Martin S Elphinstone
- Hypertension Units, University of Queensland Department of Medicine, Princess Alexandra and Greenslopes Hospitals, Brisbane 4102, Australia
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