title: TT-seq maps the human transient transcriptome.
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 ~3300 base pairs. Termination sites coincide with a DNA motif associated with pausing of RNA polymerase before its release from the genome.
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Schwalb
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany.
authors.forename: Margaux
authors.initials: M
authors.lastname: Michel
authors.affiliation: Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
authors.forename: Benedikt
authors.initials: B
authors.lastname: Zacher
authors.affiliation: Department of Biosciences and Nutrition, Center for Innovative Medicine, and Science for Life Laboratory, Karolinska Institutet, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden.
authors.forename: Katja
authors.initials: K
authors.lastname: Frühauf
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany.
authors.forename: Carina
authors.initials: C
authors.lastname: Demel
authors.affiliation: Department of Biology, University of Cologne, Zülpicher Straße 47, 50647 Cologne, Germany. Max Planck Institute for Plant Breeding Research, Carl-von-Linné Weg 10, 50829 Cologne, Germany.
authors.forename: Achim
authors.initials: A
authors.lastname: Tresch
authors.affiliation: Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany. gagneur@in.tum.de patrick.cramer@mpibpc.mpg.de.
authors.forename: Julien
authors.initials: J
authors.lastname: Gagneur
authors.affiliation: Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen, Germany. Department of Biosciences and Nutrition, Center for Innovative Medicine, and Science for Life Laboratory, Karolinska Institutet, Novum, Hälsovägen 7, 141 83 Huddinge, Sweden. gagneur@in.tum.de patrick.cramer@mpibpc.mpg.de.
authors.forename: Patrick
authors.initials: P
authors.lastname: Cramer
mesh_terms: D020029:Base Pairing; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D020869:Gene Expression Profiling; D006801:Humans; D026723:Polyadenylation; D011401:Promoter Regions, Genetic; D062085:RNA, Long Noncoding / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D013728:Terminator Regions, Genetic; D061806:Transcription Termination, Genetic; D059467:Transcriptome
chemical_list: D062085:RNA, Long Noncoding; D012333:RNA, Messenger; D012321:DNA-Directed RNA Polymerases