Short Sequence Tags Reveal Global Transcription of Repetitive Elements in the Mammalian Genome

Geoffrey Faulkner
Morning Session 1 September (11th MGED Meeting, 1-4 September, 2008)

Transcriptional Elements (TEs) include: LINEs, SINEs, LTRs, and DNA transposons. TEs were first characterized in maized, and thought they were regulators of nearby genes via an unknown mechanisms. The discoveries of regulatory ncRNAs and active promoters of TEs has helped. It's difficult to detect genome-wide TE transcription. They use CAGE, mentioned in the first talk of the day. CAGE detects transcription start sites (TSSs), and reliably detects TE promoters.80% of CAGE tags mapping to a repetitive element are unique on the genome. TE promoters are sharp, in that there is a single dominant transcription start site. TE promoters were more than twice as likely to be tissue-specific than other promoters (40% rather than 17%). TE promoters were enriched for protein-encoding genes. TEs are known to provide alternative promoters to nearby genes. More than 700 of the ones he studied were confirmed as such alternative promoters (Worked with FANTOM3 and FANTOM4 mouse libraries for CAGE stuff). Also, ncRNAs can be derived from TEs and could produce "anti-silencing" or "transcriptional interfence", but are more likely to provide the former rather than the latter. TEs provide 1000s of functional elements to the genome, even though they're not usually very well conserve. They contain an interesting subclass of promoters, and are enriched near protein-coding genes, and they provide alternative promoter to nearby genes.

These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. :)