TT-seq maps the human transient transcriptome
2016 | journal article; research paper. A publication with affiliation to the University of Göttingen.
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- Authors
- Schwalb, B.; Michel, M.; Zacher, B.; Fruehauf, K.; Demel, C.; Tresch, A.; Gagneur, J.; Cramer, P.
- Abstract
- Pervasive transcription of the genome produces both stable and transient RNAs. We developed transient transcriptome sequencing (TT-seq), a protocol that uniformly maps the entire range of RNA-producing units and estimates rates of RNA synthesis and degradation. Application of TT-seq to human K562 cells recovers stable messenger RNAs and long intergenic noncoding RNAs and additionally maps transient enhancer, antisense, and promoter-associated RNAs. TT-seq analysis shows that enhancer RNAs are short-lived and lack U1 motifs and secondary structure. TT-seq also maps transient RNA downstream of polyadenylation sites and uncovers sites of transcription termination; we found, on average, four transcription termination sites, distributed in a window with a median width of similar to 3300 base pairs. Termination sites coincide with a DNA motif associated with pausing of RNA polymerase before its release from the genome.
- Issue Date
- 2016
- Journal
- Science
- ISSN
- 0036-8075
- eISSN
- 1095-9203
- Language
- English