Two SINE families associated with equine microsatellite loci.
Abstract: BLAST searches of 61 equine microsatellite sequences revealed two related families of retroposons. The first family included seven markers, all of which showed significant homology to the Equine Repetitive Element-1 (ERE-1) Short Interspersed Nucleotide Element (SINE) sequence. Length of homology ranged from 76 to 171 bases with identities to the ERE-1 consensus sequence ranging from 71% to 83%. The second family referred to as Equine Repetitive Element-2 (ERE-2) has a consensus sequence that showed homology to ERE-1 over approximately 60 bases. These 60 bases comprised subunit I. Sequence comparisons for the two retroposons led to the identification of a subunit II, subunit III, as well as the tRNAser subunit. The subunit structure of ERE-1 was tRNAser-I-II. By contrast, the subunit structure of ERE-2 was I-III-III. The nine markers related to ERE-2 showed homology lengths ranging from 84 to 163 bases with identities ranging from 75% to 99%. In addition to being present in microsatellites, ERE-2 appeared in three separate equine genes. It occurred in an intron of DNA-PK, in an untranslated region as well as in the promoter of PGHS, and in the coding region of PAM. The amino acids corresponding to the ERE-2 sequence in PAM were not present in the human or mouse PAM homologs. These amino acids associated with the ERE-2 sequence were present on the cytosolic side of the transmembrane domain of the PAM enzyme. Microsatellite markers in the ERE-1 and ERE-2 families were found throughout the genus equus and also for rhinoceros, indicating that the appearance of both retroposons predates the divergence of equids from the other perissodactyls. The markers did not amplify in human or bovine DNA. This indicated that ERE-1 and ERE-2 are, at least, perissodactyl specific.
Publication Date: 1999-01-29 PubMed ID: 9922394DOI: 10.1007/s003359900959Google Scholar: Lookup
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- Journal Article
- Research Support
- Non-U.S. Gov't
Summary
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This research article describes the identification of two families of retroposons, termed ERE-1 and ERE-2, linked to microsatellite markers in equine species. The retroposons’ presence predates the divergence of equines from perissodactyls but is not found in human or bovine DNA.
Detection of Retroposon Families
- Researchers used BLAST searches in 61 equine microsatellite sequences, identifying two retroposon families – ERE-1 and ERE-2.
- ERE-1 was significantly similar to seven equine markers, with 76 to 171 bases showing homology and identities ranging from 71% to 83% to the ERE-1 consensus sequence.
- ERE-2 showed homology over 60 bases with ERE-1, which was called subunit I.
Comparison and Identification
- Upon comparing the sequences of ERE-1 and ERE-2 retroposons, researchers identified three subunits – subunit I, subunit II, and subunit III, along with a tRNAser subunit.
- The subunit structure of ERE-1 was designated tRNAser-I-II, while ERE-2 presented the structure I-III-III.
- Nine markers linked to ERE-2 showed homology lengths ranging between 84 to 163 bases with identities being 75% to 99%.
Presence in Genes and Proteins
- Beyond microsatellites, ERE-2 was also present in three distinct equine genes: DNA-PK, PGHS, and PAM.
- In PAM, the ERE-2 sequence translated into specific amino acids that were only present in the equine enzyme and not in its human or mouse counterparts. These amino acids were found on the cytosolic side of the transmembrane domain of the PAM enzyme.
Distribution and Specificity
- The microsatellite markers in ERE-1 and ERE-2 families were observed throughout the genus equus and also in rhinoceros, implying that the retroposons appeared before these species diverged from other perissodactyls.
- No amplification in human or bovine DNA indicated that the ERE-1 and ERE-2 sequences are perissodactyl-specific.
Cite This Article
APA
Gallagher PC, Lear TL, Coogle LD, Bailey E.
(1999).
Two SINE families associated with equine microsatellite loci.
Mamm Genome, 10(2), 140-144.
https://doi.org/10.1007/s003359900959 Publication
Researcher Affiliations
- M.H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky 40546-0099, USA.
MeSH Terms
- Amidine-Lyases / genetics
- Animals
- Base Sequence
- Chromosome Mapping / veterinary
- Cyclooxygenase 2
- DNA / genetics
- DNA-Activated Protein Kinase
- DNA-Binding Proteins
- Genes / genetics
- Horses / genetics
- Interspersed Repetitive Sequences
- Isoenzymes / genetics
- Microsatellite Repeats
- Molecular Sequence Data
- Polymerase Chain Reaction
- Prostaglandin-Endoperoxide Synthases / genetics
- Protein Serine-Threonine Kinases / genetics
- Sequence Alignment
- Sequence Homology, Nucleic Acid
- Species Specificity
Citations
This article has been cited 6 times.- Santagostino M, Khoriauli L, Gamba R, Bonuglia M, Klipstein O, Piras FM, Vella F, Russo A, Badiale C, Mazzagatti A, Raimondi E, Nergadze SG, Giulotto E. Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression. BMC Genet 2015 Oct 26;16:126.
- Hamilton NA, Tammen I, Raadsma HW. Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16. PLoS One 2013;8(2):e55434.
- Bhargava A, Fuentes FF. Mutational dynamics of microsatellites. Mol Biotechnol 2010 Mar;44(3):250-66.
- López-Giráldez F, Andrés O, Domingo-Roura X, Bosch M. Analyses of carnivore microsatellites and their intimate association with tRNA-derived SINEs. BMC Genomics 2006 Oct 23;7:269.
- Burke D, Raychaudhuri J, Chuong E, Taylor W, Layer R. TEPEAK: A novel method for identifying and characterizing polymorphic transposable elements in non-model species populations. PLoS Comput Biol 2026 Jan;22(1):e1013122.
- Ustyantsev IG, Kosushkin SA, Borodulina OR, Vassetzky NS, Kramerov DA. Ere, a Family of Short Interspersed Elements in the Genomes of Odd-Toed Ungulates (Perissodactyla). Animals (Basel) 2024 Jul 5;14(13).
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