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CGR

Seminar

Transposed element RNAs detected by massively parallel sequencing

Faulkner, G (University of Edinburgh)
Thursday 15 July 2010, 11:00-11:30

Seminar Room 1, Newton Institute

Abstract

Transposed elements (TEs) typically comprise 30-50% of the mammalian genome and, until recently, their repetitive composition has restricted our ability to study individual TEs. Here I will present our early statistical modelling that indicated high throughput sequencing could be successfully applied to detect transcription from specific TEs, as well as a computational solution to the related “multi-map tag” phenomenon. These works formed the basis for a subsequent landmark publication proving that TEs were heavily transcribed in mammals. The associated transcripts, dubbed “teRNAs”, supplied up to 30% of the capped RNA molecules in cancer, germ and somatic cells. An analysis of 250 000 TE promoter regions revealed that these frequently functioned as alternative promoters for nearby genes and/or expressed ncRNAs. Overall, we discovered that the abundance of teRNAs far exceeded prior estimates, with a common theme of strong tissue specificity and association with nearby protein-coding genes, demonstrating that TEs were an essential part of the mammalian transcriptome and regulome.

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