B - D ) Expression fold-change between prostate cancer tumor tissue and normal tissue computed by the GLM on the 14 patients. Group 1 showed a marked overexpression of the primate-specific L1s, while group 2 showed a lower level of overexpression and in some cases underrepresentation.

To assure our observations were not restricted to in silico data we compared the performance of the fractional counting and unique counting methods on real ChIP-seq data. With the exception of Pol I, which specializes in ribosomal RNA (rRNA) transcription, both Pol II and III are known to transcribe repetitive elements [ 5, 23]. After working in the publishing field for many years she is now retired, pursuing her first love: writing stories. A) Clustering of log2 expression fold-changes in the subset of primate specific L1s that showed significant differential expression reveals two major classes of patients (Group 1 and Group 2). A single HERV-Fc1 internal element on chromosome 7 displayed RNA expression from the minus strand in K562 cells but not in any other ENCODE cell line for which PolyA + RNA-seq is available (Figure 4C).Hence, to address the question of how repetitive elements are transcribed we utilized ChIP-seq data for Pol II, Pol III, and TFIIIB (a Pol III-associated transcription factor complex). Furthermore, requiring unambiguous assignment of reads to individual subfamilies will introduce a bias towards less conserved repeats, which will be assigned relatively higher counts. Some Pol II transcribed snRNA psuedogenes may also be transcribed, and have been found to be associated with L1-encoded proteins [ 25]. One interesting feature we identified was significant co-occupancy of Pol II and Pol III at some repetitive elements.

To investigate the transcription and regulation of repetitive elements in a variety of cell types, we collected data from multiple cell lines. First, we can compute the total number of reads mapping to each repetitive element subfamily (Additional file 1: Figure S1A), which we refer to as total counts. However, in this dataset the transformed and normal cells were derived from a variety of tissues and hence direct comparison of retrotransposon transcription was not possible. In addition, we provide 10ml and 20ml nic salts from Element's collection, catering to those who prefer a more potent nicotine hit with a smoother throat sensation. To do so we compared the SVA, L1, and Alu enriched samples to their input samples via a Generalized Linear Model (GLM) fit to a negative binomial distribution (see Methods).As expected, the tRNA transcripts were localized to the cytosol and not polyadenylated (Additional file 1: Figure S12).