Wide distribution of short interspersed elements among eukaryotic genomes

Abstract

Most short interspersed elements (SINEs) in eukaryotic genomes originate from tRNA and have internal promoters for RNA polymerase III. The promoter contains two boxes (A and B) spaced by V V33 bp. We used oligonucleotide primers specific to these boxes to detect SINEs in the genomic DNA by polymerase chain reaction (PCR). Appropriate DNA fragments were revealed by PCR in 30 out of 35 eukaryotic species suggesting the wide distribution of SINEs. The PCR products were used for hybridization screening of genomic libraries which resulted in identification of four novel SINE families. The application of this approach is illustrated by discovery of a SINE family in the genome of the bat Myotis daubentoni. Members of this SINE family termed VES have an additional B-like box, a putative polyadenylation signal and RNA polymerase III terminator.z 1999 Federation of European Biochemical Societies.

Transcripts synthesized by RNA polymerase III can be polyadenylated in an AAUAAA-dependent manner

“…Nucleotide sequence of this SINE demonstrates no similarity with that of B2 except for the presence of a pol III promoter (A and B boxes), a hexamer AATAAA, and a pol III terminator, TTTT (Borodulina and Kramerov 1999). A VES element (copy Mda01) with AATAAA (construct Ves-pA 1 ) or AACAAA (construct Ves-pA o ) in its Arich tail was obtained (Fig.…”

“…Mouse B2 SINE from clone Mm14 (Krayev et al 1982) and bat VES SINE from clone Mda01 (Acc. No Y19051) (Borodulina and Kramerov 1999) were used for preparation of the constructs. To remove the flanking sequences and to introduce nucleotides substitutions, PCRs with specific primers and Mm14 and Mda01 plasmid DNA were carried out.…”

CAN—a pan-carnivore SINE family

“…The walrus, kangaroo, and elephant shrew tissues were provided by S. Popov (Moscow Zoo); the civet and tree shrew tissues were provided by O. Likhnova (Institute of Ecology and Evolution, Moscow), and the armadillo tissue was provided by R. DeBry (University of Cincinnati). For other DNA sources and isolation technique, see Borodulina and Kramerov (1999).…”

“…It is also specific for several other mammalian SINEs including rabbit C repeat (Cheng et al 1984), rodent DIP (Serdobova and Kramerov 1998), bat VES (Borodulina and Kramerov 1999), and insectivore TAL, ERI-1, Fig. 2.…”

Inverse PCR-Based Method for Isolating Novel SINEs from Genome

“…In 1999, Borodulina and Kramerov [31] utilized the promoter sequences of RNA pol III as primers, and amplified the tRNA-derived region of SINEs. The tRNA-derived region was labeled and used to screen the genomic library.…”