title: BARE-1 insertion site preferences and evolutionary conservation of RNA and cDNA processing sites.
abstract: The BARE-1 copia-like retrotransposon constitutes nearly 7% of the barley (Hordeum vulgare L.) genome as a family of more than 2 x 10(4) mostly full-length copies dispersed on all chromosomes. BARE-1 elements are transcribed in barley tissues from promoters within the LTR (long terminal repeat). The predicted, translated polyprotein contains conserved domains for GAG, aspartic proteinase, integrase, reverse-transcriptase, and RNase H. Here, we have used inverse PCR with LTR-based primers to establish the consensus sequences for the terminal region of the LTR, the external dinucleotides of the cDNA integration intermediate, and the minus- and plus-strand priming sites. These key functional entities are well-conserved in the BARE-1 family, including wheat Wis2, but differ from those of other plant retrotransposons. The target site duplication was established as 5 bp. Of the 13 integration sites identified here, 8 were other BARE-1 elements and 1 another retrotransposon; 59% of the total 17 identified BARE-1 insertion sites are retrotransposons. This nested insertion pattern may represent a basic feature of plant retrotransposons.
authors.affiliation: Institute of Biotechnology, University of Helsinki, Finland.
authors.forename: A
authors.initials: A
authors.lastname: Suoniemi
authors.forename: D
authors.initials: D
authors.lastname: Schmidt
authors.forename: A H
authors.initials: AH
authors.lastname: Schulman
mesh_terms: D001483:Base Sequence; D003001:Cloning, Molecular; D016384:Consensus Sequence; D017124:Conserved Sequence; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D019143:Evolution, Molecular; D015698:Genomic Library; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D018749:RNA, Plant / Q000235:genetics*; D012091:Repetitive Sequences, Nucleic Acid; D018626:Retroelements / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017931:DNA Primers; D018076:DNA, Complementary; D018744:DNA, Plant; D018749:RNA, Plant; D018626:Retroelements