Cent advances in novel sequencing and hybridization technologies [16,17] have permitted an
Cent advances in novel sequencing and hybridization technologies [16,17] have permitted an unforeseen depth in detection of transcriptional activity. Recently, Faulkner and colleagues reported that 6-30 of capselected mammalian transcripts were initiated in repetitive elements [4]. We set out to test if transcriptome data could provide information on the transcriptional activity of presumably functional (i.e. retrotranspositioncompetent) retrotransposons, and turned our attention to the single-celled fission yeast Schizosaccharomyces pombe. The genome of S. pombe is highly compact and well annotated [18], and harbours only a few families of Long Terminal Repeat (LTR) retrotransposons [19,20]. LTR retrotransposons are transposable elements that typically contain gag and pol genes required for transposition, are related to retroviruses, and have their name from the two repeated LTR sequences flanking them. Two LTR sequences may recombine resulting in a solitary LTR sequence. All full-length LTR PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26240184 retrotransposons in the S. pombe reference genome (strain 972) belong to the Tf2 family, while all members of the other dominant LTR family, Tf1, PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/27107493 are found as solitary LTR sequences [18,21]. S. pombe LTR elements are predominantly inserted upstream of protein-coding genes [22,23], where transcription activators are responsible for targeting the site of insertion [24]. Intriguingly, the Tf1 elements were shown to harbour promoter regions restoring the regulatory functions that are disrupted by LTR integration [24]. We have analysed the data from two recent studies: First, a high throughput sequencing of complementary DNAs generating short reads (30-51 nucleotides) from S. pombe growth phase and five time points during meiosis from the B ler lab [25]. This study is henceforth referred to as RNA-Seq. Second, a study from the Cairns lab [26] using a novel approach (called HybMap) in which RNA from growth phase was directly hybridized to a whole-genome microarray with 60 base pair DNA probes, followed by antibody procedures ensuring perfect matches as well as subsequent quantification by light emission [16]. The direct hybridization approach hence allows the assignment of transcriptional activity to a specific strand. We refer to this study simply as HybMap. The available data samples are summarized in Additional file 1; Table S1. From purchase Pan-RAS-IN-1 RNA-Seq sequence reads and signal intensities of HybMap array probes we recorded the transcriptional activity from LTR sequences, analysed the extent and orientation of LTR transcription, and how the expression profiles of LTR sequences correlate with nearby genes.Results and discussion We retrieved 239 LTR sequences with lengths from 75 to 412 base pairs (bp) (median/average size: 346/321 bp) from the S. pombe genome annotation. Of these, 25 LTR sequences were residing in full-length LTR retrotransposons. This uneven number results from a single chimerical LTR retrotransposon with an [LTR-internal sequence-LTR-internal sequence-LTR] organization that potentially is a result of an ectopic recombination event. Two full-length LTR retrotransposons (SPBC1E8.04 and SPCC1494.11c) are frame shifted and annotated as pseudogenes http://www.genedb.org/. Genomic coordinates of the LTR sequences are provided in Additional file 1; Table S2. From a biological point of view, we are interested in distinguishing between transcriptional activity stemming from full-length LTR retrotransposons and from solitary LTRs. Analysis of transcript.