title: PCR and magnetic bead-mediated target capture for the isolation of short interspersed nucleotide elements in fishes.
abstract: Short interspersed nucleotide elements (SINEs), a type of retrotransposon, are widely distributed in various genomes with multiple copies arranged in different orientations, and cause changes to genes and genomes during evolutionary history. This can provide the basis for determining genome diversity, genetic variation and molecular phylogeny, etc. SINE DNA is transcribed into RNA by polymerase III from an internal promoter, which is composed of two conserved boxes, box A and box B. Here we present an approach to isolate novel SINEs based on these promoter elements. Box A of a SINE is obtained via PCR with only one primer identical to box B (B-PCR). Box B and its downstream sequence are acquired by PCR with one primer corresponding to box A (A-PCR). The SINE clone produced by A-PCR is selected as a template to label a probe with biotin. The full-length SINEs are isolated from the genomic pool through complex capture using the biotinylated probe bound to magnetic particles. Using this approach, a novel SINE family, Cn-SINE, from the genomes of Coilia nasus, was isolated. The members are 180-360 bp long. Sequence homology suggests that Cn-SINEs evolved from a leucine tRNA gene. This is the first report of a tRNA(Leu)-related SINE obtained without the use of a genomic library or inverse PCR. These results provide new insights into the origin of SINEs.
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
authors.forename: Dong
authors.initials: D
authors.lastname: Liu
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
authors.forename: Guoli
authors.initials: G
authors.lastname: Zhu
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
authors.forename: Wenqiao
authors.initials: W
authors.lastname: Tang
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
authors.forename: Jinquan
authors.initials: J
authors.lastname: Yang
authors.affiliation: College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
authors.forename: Hongyi
authors.initials: H
authors.lastname: Guo
mesh_terms: D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular / Q000379:methods*; D004247:DNA / Q000302:isolation & purification; D005399:Fishes / Q000235:genetics*; D060328:Magnetic Phenomena; D008863:Microspheres; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000295:instrumentation / Q000379:methods; D012343:RNA, Transfer / Q000235:genetics; D012689:Sequence Homology, Nucleic Acid; D020086:Short Interspersed Nucleotide Elements
chemical_list: D004247:DNA; D012343:RNA, Transfer