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Lu Y, Boswell M, Boswell W, Kneitz S, Hausmann M, Klotz B, Regneri J, Savage M, Amores A, Postlethwait J, Warren W, Schartl M, Walter R. Molecular genetic analysis of the melanoma regulatory locus in Xiphophorus interspecies hybrids. Mol Carcinog 2017; 56:1935-1944. [PMID: 28345808 DOI: 10.1002/mc.22651] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Revised: 03/07/2017] [Accepted: 03/23/2017] [Indexed: 01/10/2023]
Abstract
Development of spontaneous melanoma in Xiphophorus interspecies backcross hybrid progeny, (X. hellerii × [X. maculatus Jp 163 A × X. hellerii]) is due to Mendelian segregation of a oncogene (xmrk) and a molecularly uncharacterized locus, called R(Diff), on LG5. R(Diff) is thought to suppresses the activity of xmrk in healthy X. maculatus Jp 163 A parental species that rarely develop melanoma. To better understand the molecular genetics of R(Diff), we utilized RNA-Seq to study allele-specific gene expression of spontaneous melanoma tumors and corresponding normal skin samples derived from 15 first generation backcross (BC1 ) hybrids and 13 fifth generation (BC5 ) hybrids. Allele-specific expression was determined for all genes and assigned to parental allele inheritance for each backcross hybrid individual. Results showed that genes residing in a 5.81 Mbp region on LG5 were exclusively expressed from the X. hellerii alleles in tumor-bearing BC1 hybrids. This observation indicates this region is consistently homozygous for X. hellerii alleles in tumor bearing animals, and therefore defines this region to be the R(Diff) locus. The R(Diff) locus harbors 164 gene models and includes the previously characterized R(Diff) candidate, cdkn2x. Twenty-one genes in the R(Diff) region show differential expression in the tumor samples compared to normal skin tissue. These results further characterize the R(Diff) locus and suggest tumor suppression may require a multigenic region rather than a single gene variant. Differences in gene expression between tumor and normal skin tissue in this region may indicate interactions among several genes are required for backcross hybrid melanoma development.
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Affiliation(s)
- Yuan Lu
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Mikki Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - William Boswell
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Susanne Kneitz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Michael Hausmann
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Barbara Klotz
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Janine Regneri
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany
| | - Markita Savage
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, Oregon
| | | | - Wesley Warren
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Manfred Schartl
- Physiological Chemistry, Biozentrum, University of Würzburg, Würzburg, Germany.,Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, Würzburg, Germany.,Texas A&M Institute for Advanced Studies and Department of Biology, Texas A&M University, College Station, Texas
| | - Ronald Walter
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, Texas
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Michalak K, Maciak S, Kim YB, Santopietro G, Oh JH, Kang L, Garner HR, Michalak P. Nucleolar dominance and maternal control of 45S rDNA expression. Proc Biol Sci 2015; 282:20152201. [PMID: 26645200 PMCID: PMC4685780 DOI: 10.1098/rspb.2015.2201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 11/10/2015] [Indexed: 12/17/2022] Open
Abstract
Using a system of interspecies hybrids, trihybrids, and recombinants with varying proportions of genomes from three distinct Xenopus species, we provide evidence for de novo epigenetic silencing of paternal 45 S ribosomal ribonucleic acid (rRNA) genes and their species-dependent expression dominance that escapes transcriptional inactivation after homologous recombination. The same pattern of imprinting is maintained in the offspring from mothers being genetic males (ZZ) sex-reversed to females, indicating that maternal control of ribosomal deoxyribonucleic acid (rDNA) expression is not sex-chromosome linked. Nucleolar dominance (nucleolus underdevelopment) in Xenopus hybrids appears to be associated with a major non-Mendelian reduction in the number of 45 S rDNA gene copies rather than a specific pattern of their expression. The loss of rRNA gene copies in F1 hybrids was non-random with respect to the parental species, with the transcriptionally dominant variant preferentially removed from hybrid zygotes. This dramatic disruption in the structure and function of 45 S rDNA impacts transcriptome patterns of small nucleolar RNAs and messenger RNAs, with genes from the ribosome and oxidative stress pathways being among the most affected. Unorthodoxies of rDNA inheritance and expression may be interpreted as hallmarks of genetic conflicts between parental genomes, as well as defensive epigenetic mechanisms employed to restore genome integrity.
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Affiliation(s)
- Katarzyna Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Sebastian Maciak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA Institute of Biology, University of Bialystok, PL-15-245, Poland
| | - Young Bun Kim
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | | | - Jung Hun Oh
- Department of Medical Physics, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Lin Kang
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
| | - Harold R Garner
- The Edward Via College of Osteopathic Medicine, Blacksburg, VA 24060, USA
| | - Pawel Michalak
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA 24061, USA
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Zuchowska M, Jaenicke E, König H, Claus H. Allelic variants of hexose transporter Hxt3p and hexokinases Hxk1p/Hxk2p in strains of Saccharomyces cerevisiae and interspecies hybrids. Yeast 2015. [PMID: 26202678 DOI: 10.1002/yea.3087] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The transport of sugars across the plasma membrane is a critical step in the utilization of glucose and fructose by Saccharomyces cerevisiae during must fermentations. Variations in the molecular structure of hexose transporters and kinases may affect the ability of wine yeast strains to finish sugar fermentation, even under stressful wine conditions. In this context, we sequenced and compared genes encoding the hexose transporter Hxt3p and the kinases Hxk1p/Hxk2p of Saccharomyces strains and interspecies hybrids with different industrial usages and regional backgrounds. The Hxt3p primary structure varied in a small set of amino acids, which characterized robust yeast strains used for the production of sparkling wine or to restart stuck fermentations. In addition, interspecies hybrid strains, previously isolated at the end of spontaneous fermentations, revealed a common amino acid signature. The location and potential influence of the amino acids exchanges is discussed by means of a first modelled Hxt3p structure. In comparison, hexokinase genes were more conserved in different Saccharomyces strains and hybrids. Thus, molecular variants of the hexose carrier Hxt3p, but not of kinases, correlate with different fermentation performances of yeast.
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Affiliation(s)
- Magdalena Zuchowska
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Germany
| | - Elmar Jaenicke
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Germany.,Institute for Molecular Biophysics, Johannes Gutenberg University Mainz, Germany
| | - Helmut König
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Germany
| | - Harald Claus
- Institute of Microbiology and Wine Research, Johannes Gutenberg University Mainz, Germany
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Shen Y, Catchen J, Garcia T, Amores A, Beldroth I, Wagner JR, Zhang Z, Postlethwait J, Warren W, Schartl M, Walter RB. Identification of transcriptome SNPs between Xiphophorus lines and species for assessing allele specific gene expression within F₁ interspecies hybrids. Comp Biochem Physiol C Toxicol Pharmacol 2012; 155:102-8. [PMID: 21466860 PMCID: PMC3178741 DOI: 10.1016/j.cbpc.2011.03.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Revised: 03/28/2011] [Accepted: 03/28/2011] [Indexed: 12/25/2022]
Abstract
Variations in gene expression are essential for the evolution of novel phenotypes and for speciation. Studying allelic specific gene expression (ASGE) within interspecies hybrids provides a unique opportunity to reveal underlying mechanisms of genetic variation. Using Xiphophorus interspecies hybrid fishes and high-throughput next generation sequencing technology, we were able to assess variations between two closely related vertebrate species, Xiphophorus maculatus and Xiphophorus couchianus, and their F(1) interspecies hybrids. We constructed transcriptome-wide SNP polymorphism sets between two highly inbred X. maculatus lines (JP 163 A and B), and between X. maculatus and a second species, X. couchianus. The X. maculatus JP 163 A and B parental lines have been separated in the laboratory for ≈70 years and we were able to identify SNPs at a resolution of 1 SNP per 49 kb of transcriptome. In contrast, SNP polymorphisms between X. couchianus and X. maculatus species, which diverged ≈5-10 million years ago, were identified about every 700 bp. Using 6524 transcripts with identified SNPs between the two parental species (X. maculatus and X. couchianus), we mapped RNA-seq reads to determine ASGE within F(1) interspecies hybrids. We developed an in silico X. couchianus transcriptome by replacing 90,788 SNP bases for X. maculatus transcriptome with the consensus X. couchianus SNP bases and provide evidence that this procedure overcomes read mapping biases. Employment of the in silico reference transcriptome and tolerating 5 mismatches during read mapping allow direct assessment of ASGE in the F(1) interspecies hybrids. Overall, these results show that Xiphophorus is a tractable vertebrate experimental model to investigate how genetic variations that occur during speciation may affect gene interactions and the regulation of gene expression.
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Affiliation(s)
- Yingjia Shen
- Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Julian Catchen
- Institute of Neuroscience, University of Oregon, 1425 E. 13th Avenue, Eugene, OR 97403 USA
| | - Tzintzuni Garcia
- Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Angel Amores
- Institute of Neuroscience, University of Oregon, 1425 E. 13th Avenue, Eugene, OR 97403 USA
| | - Ion Beldroth
- Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Jonathon R Wagner
- Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - Ziping Zhang
- Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
| | - John Postlethwait
- Institute of Neuroscience, University of Oregon, 1425 E. 13th Avenue, Eugene, OR 97403 USA
| | - Wes Warren
- Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Blvd., St Louis, MO 63108, USA
| | - Manfred Schartl
- Physiological Chemistry I, University of Würzburg, Biozentrum, Am Hubland, 97074 Würzburg, Germany
| | - Ronald B. Walter
- Department of Chemistry and Biochemistry, 419 Centennial Hall, Texas State University, 601 University Drive, San Marcos, TX 78666, USA
- Corresponding author. , PHONE: (512) 245-0357, FAX: (512) 245-2374, Address: Department of Chemistry & Biochemistry, 419 CEN, Texas State University, 601 University Drive, San Marcos, TX, 78666
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