Retrotransposons and their recognition of pol II promoters: a comprehensive survey of the transposable elements from the complete genome sequence of Schizosaccharomyces pombe. Genome Res

Section on Eukaryotic Transposable Elements, Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA.
Genome Research (Impact Factor: 13.85). 10/2003; 13(9):1984-97. DOI: 10.1101/gr.1191603
Source: PubMed

ABSTRACT The complete DNA sequence of the genome of Schizosaccharomyces pombe provides the opportunity to investigate the entire complement of transposable elements (TEs), their association with specific sequences, their chromosomal distribution, and their evolution. Using homology-based sequence identification, we found that the sequenced strain of S. pombe contained only one family of full-length transposons. This family, Tf2, consisted of 13 full-length copies of a long terminal repeat (LTR) retrotransposon. We found that LTR-LTR recombination of previously existing transposons had resulted in extensive populations of solo LTRs. These included 35 solo LTRs of Tf2, as well as 139 solo LTRs from other Tf families. Phylogenetic analysis of solo Tf LTRs reveals that Tf1 and Tf2 were the most recently active elements within the genome. The solo LTRs also served as footprints for previous insertion events by the Tf retrotransposons. Analysis of 186 genomic insertion events revealed a close association with RNA polymerase II promoters. These insertions clustered in the promoter-proximal regions of genes, upstream of protein coding regions by 100 to 400 nucleotides. The association of Tf insertions with pol II promoters was very similar to the preference previously observed for Tf1 integration. We found that the recently active Tf elements were absent from centromeres and pericentromeric regions of the genome containing tandem tRNA gene clusters. In addition, our analysis revealed that chromosome III has twice the density of insertion events compared to the other two chromosomes. Finally we describe a novel repetitive sequence, wtf, which was also preferentially located on chromosome III, and was often located near solo LTRs of Tf elements.

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Available from: Nathan J Bowen, Aug 21, 2015
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    • "The fission yeast genome has been colonized by Tf1 and Tf2 retrotransposons, referred to as Tf elements in this article. The sequenced genome contains 13 full-length Tf2s and more than 200 solo-LTRs distributed throughout the fission yeast genome (Bowen et al., 2003). Therefore, associations among dispersed Tf elements should have a great impact on global genome organization. "
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    Molecular cell 10/2012; 48(4). DOI:10.1016/j.molcel.2012.09.011 · 14.46 Impact Factor
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    • "Bowen et al. (2003) suggested that 80% of the enrichment of LTRs on chromosome III may be due to their preferential insertion into intergenic sequences flanking S. pombe–specific wtf (with Tf ) sequences that belong to a high-copy family of 1-kb-long sequences strongly enriched on chromosome III. It was proposed that this biased distribution of wtf sequences in the original 972 strain may be the result of acquisition of chromosome III from an isolated population of S. pombe that had wtfs distributed on all three chromosomes (Bowen et al. 2003). If chromosome III of strain 972 has indeed originated from another S. pombe population, this may explain the absence of detectable NUMT on chromosome III as, based on a previous comparison of three S. pombe mitochondrial genomes (Bullerwell et al. 2003), the mtDNA sequences of these two populations may be very different. "
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    ABSTRACT: Chromosomal double-strand breaks (DSBs) threaten genome integrity and repair of these lesions is often mutagenic. How and where DSBs are formed is a major question conveniently addressed in simple model organisms like yeast. NUMTs, nuclear DNA sequences of mitochondrial origin, are present in most eukaryotic genomes and probably result from the capture of mitochondrial DNA (mtDNA) fragments into chromosomal breaks. NUMT formation is ongoing and was reported to cause de novo human genetic diseases. Study of NUMTs is likely to contribute to the understanding of naturally occurring chromosomal breaks. We show that Schizosaccharomyces pombe NUMTs are exclusively located in noncoding regions with no preference for gene promoters and, when located into promoters, do not affect gene transcription level. Strikingly, most noncoding regions comprising NUMTs are also associated with a DNA replication origin (ORI). Chromatin immunoprecipitation experiments revealed that chromosomal NUMTs are probably not acting as ORI on their own but that mtDNA insertions occurred directly next to ORIs, suggesting that these loci may be prone to DSB formation. Accordingly, induction of excessive DNA replication origin firing, a phenomenon often associated with human tumor formation, resulted in frequent nucleotide deletion events within ORI3001 subtelomeric chromosomal locus, illustrating a novel aspect of DNA replication-driven genomic instability. How mtDNA is fragmented is another important issue that we addressed by sequencing experimentally induced NUMTs. This highlighted regions of S. pombe mtDNA prone to breaking. Together with an analysis of human NUMTs, we propose that these fragile sites in mtDNA may correspond to replication pause sites.
    Genome Research 09/2010; 20(9):1250-61. DOI:10.1101/gr.104513.109 · 13.85 Impact Factor
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    • "As developed for sequencing insertion sites of human immunodeficiency virus 1, (HIV-1) and murine leukemia virus (MLV), we applied ligationmediated PCR to generate libraries of Tf1-neo associated with the downstream flanking DNA (Schroder et al. 2002; Wu et al. 2003). Unlike the cases of HIV-1 and MLV, there are hundreds of preexisting transposon LTRs in S. pombe with sequences identical to that of Tf1-neo (Bowen et al. 2003). To distinguish new integration sites from the preexisting elements, a unique tag of substituted nucleotides was introduced in the U5 sequence of Tf1-neo at a position previously shown to be unimportant for transposition (Lin and Levin 1998). "
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