TT-seq maps the human transient transcriptome

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…

• CD
  California Department of Fish and Game

  Award: SFB 680
• DF
  Deutsche Forschungsgemeinschaft
• VF
  Volkswagen Foundation
• BF
  Bundesministerium für Bildung und Forschung

  Award: FKZ 01ZX1405A
• KI
  Karolinska Institutet
• SF
  Science for Life Laboratory
• HE
  H2020 European Research Council