Journal
SCIENCE
Volume 352, Issue 6290, Pages 1225-1228Publisher
AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/science.aad9841
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Funding
- Center for Innovative Medicine (CIMED) at Karolinska Institutet
- Science for Life Laboratory (SciLifeLab) in Stockholm
- Deutsche Forschungsgemeinschaft (DFG) fellowship at the Graduate School of Quantitative Biosciences Munich
- German Federal Ministry of Education and Research (BMBF)
- DFG [SFB 680]
- Bavarian Research Center for Molecular Biosystems
- Bundesministerium fur Bildung und Forschung, Juniorverbund in der Systemmedizin mitOmics [FKZ 01ZX1405A]
- Advanced Grant TRANSIT of the European Research Council
- DFG
- Volkswagen Foundation
- CIMED
- SciLifeLab
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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.
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