title: TE-array--a high throughput tool to study transposon transcription.
abstract: BACKGROUND
  Although transposable element (TE) derived DNA accounts for more than half of mammalian genomes and initiates a significant proportion of RNA transcripts, high throughput methods are rarely leveraged specifically to detect expression from interspersed repeats.
  
  
  RESULTS
  To characterize the contribution of transposons to mammalian transcriptomes, we developed a custom microarray platform with probes covering known human and mouse transposons in both sense and antisense orientations. We termed this platform the "TE-array" and profiled TE repeat expression in a panel of normal mouse tissues. Validation with nanoString® and RNAseq technologies demonstrated that TE-array is an effective method. Our data show that TE transcription occurs preferentially from the sense strand and is regulated in highly tissue-specific patterns.
  
  
  CONCLUSIONS
  Our results are consistent with the hypothesis that transposon RNAs frequently originate within genomic TE units and do not primarily accumulate as a consequence of random 'read-through' from gene promoters. Moreover, we find TE expression is highly dependent on the tissue context. This suggests that TE expression may be related to tissue-specific chromatin states or cellular phenotypes. We anticipate that TE-array will provide a scalable method to characterize transposable element RNAs.
authors: Veena P
authors: VP
authors: Gnanakkan
authors: Andrew E
authors: AE
authors: Jaffe
authors: Lixin
authors: L
authors: Dai
authors: Jie
authors: J
authors: Fu
authors: Sarah J
authors: SJ
authors: Wheelan
authors: Hyam I
authors: HI
authors: Levitsky
authors: The Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building (MRB) Room 469, Baltimore, MD 21205, USA. jboeke@jhmi.edu.
authors: Jef D
authors: JD
authors: Boeke
authors: Kathleen H
authors: KH
authors: Burns
mesh_terms: D000818:Animals; D002460:Cell Line; D004251:DNA Transposable Elements; D005260:Female; D015870:Gene Expression; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D006801:Humans; D008297:Male; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D009928:Organ Specificity / Q000235:genetics; D015203:Reproducibility of Results; D014158:Transcription, Genetic; D014162:Transfection
chemical_list: D004251:DNA Transposable Elements