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Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets.
Mol Biol Evol. 2004 Feb; 21(2):207-17.MB

Abstract

Although most LINEs (long interspersed nuclear elements), which are autonomous non-long-terminal-repeat retrotransposons, are inserted throughout the host genome, three groups of LINEs, the early-branched group, the Tx group, and the R1 clade, are inserted into specific sites within the target sequence. We previously characterized the sequence specificity of the R1 clade elements. In this study, we screened the other two groups of sequence-specific LINEs from public DNA databases, reconstructed elements from fragmented sequences, identified their target sequences, and analyzed them phylogenetically. We characterized 13 elements in the early-branched group and 13 in the Tx group. In the early-branched group, we identified R2 elements from sea squirts and zebrafish in this study, although R2 has not been characterized outside the arthropod group to date. This is the first evidence of cross-phylum distribution of sequence-specific LINEs. The Dong element also occurs across phyla, among arthropods and mollusks. In the Tx group, we characterized five novel sequence-specific families: Kibi for TC repeats, Koshi for TTC repeats, Keno for the U2 snRNA gene, Dewa for the tRNA tandem arrays, and Mutsu for the 5S rRNA gene. Keno and Mutsu insert into the highly conserved region within small RNA genes and destroy the targets. Several copies of Dewa insert different positions of tRNA tandem array, which indicates a certain "site specifier" other than sequence-specific endonuclease. In all three groups, LINEs specific for the rRNA genes or microsatellites can occur as multiple families in one organism. This indicates that the copy number of a target sequence is the primary factor to restrict the variety of sequence specificity of LINEs.

Authors+Show Affiliations

Department of Integrated Biosciences, Graduate School of Frontier Sciences, University of Tokyo.No affiliation info available

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

12949131

Citation

Kojima, Kenji K., and Haruhiko Fujiwara. "Cross-genome Screening of Novel Sequence-specific non-LTR Retrotransposons: Various Multicopy RNA Genes and Microsatellites Are Selected as Targets." Molecular Biology and Evolution, vol. 21, no. 2, 2004, pp. 207-17.
Kojima KK, Fujiwara H. Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets. Mol Biol Evol. 2004;21(2):207-17.
Kojima, K. K., & Fujiwara, H. (2004). Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets. Molecular Biology and Evolution, 21(2), 207-17.
Kojima KK, Fujiwara H. Cross-genome Screening of Novel Sequence-specific non-LTR Retrotransposons: Various Multicopy RNA Genes and Microsatellites Are Selected as Targets. Mol Biol Evol. 2004;21(2):207-17. PubMed PMID: 12949131.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Cross-genome screening of novel sequence-specific non-LTR retrotransposons: various multicopy RNA genes and microsatellites are selected as targets. AU - Kojima,Kenji K, AU - Fujiwara,Haruhiko, Y1 - 2003/08/29/ PY - 2003/9/2/pubmed PY - 2004/11/13/medline PY - 2003/9/2/entrez SP - 207 EP - 17 JF - Molecular biology and evolution JO - Mol. Biol. Evol. VL - 21 IS - 2 N2 - Although most LINEs (long interspersed nuclear elements), which are autonomous non-long-terminal-repeat retrotransposons, are inserted throughout the host genome, three groups of LINEs, the early-branched group, the Tx group, and the R1 clade, are inserted into specific sites within the target sequence. We previously characterized the sequence specificity of the R1 clade elements. In this study, we screened the other two groups of sequence-specific LINEs from public DNA databases, reconstructed elements from fragmented sequences, identified their target sequences, and analyzed them phylogenetically. We characterized 13 elements in the early-branched group and 13 in the Tx group. In the early-branched group, we identified R2 elements from sea squirts and zebrafish in this study, although R2 has not been characterized outside the arthropod group to date. This is the first evidence of cross-phylum distribution of sequence-specific LINEs. The Dong element also occurs across phyla, among arthropods and mollusks. In the Tx group, we characterized five novel sequence-specific families: Kibi for TC repeats, Koshi for TTC repeats, Keno for the U2 snRNA gene, Dewa for the tRNA tandem arrays, and Mutsu for the 5S rRNA gene. Keno and Mutsu insert into the highly conserved region within small RNA genes and destroy the targets. Several copies of Dewa insert different positions of tRNA tandem array, which indicates a certain "site specifier" other than sequence-specific endonuclease. In all three groups, LINEs specific for the rRNA genes or microsatellites can occur as multiple families in one organism. This indicates that the copy number of a target sequence is the primary factor to restrict the variety of sequence specificity of LINEs. SN - 0737-4038 UR - https://www.unboundmedicine.com/medline/citation/12949131/Cross_genome_screening_of_novel_sequence_specific_non_LTR_retrotransposons:_various_multicopy_RNA_genes_and_microsatellites_are_selected_as_targets_ L2 - https://academic.oup.com/mbe/article-lookup/doi/10.1093/molbev/msg235 DB - PRIME DP - Unbound Medicine ER -