Schwalb, Bjorn ORCID: 0000-0003-2987-2622, Michel, Margaux, Zacher, Benedikt, Fruehauf, Katja, Demel, Carina, Tresch, Achim, Gagneur, Julien ORCID: 0000-0002-8924-8365 and Cramer, Patrick (2016). TT-seq maps the human transient transcriptome. Science, 352 (6290). S. 1225 - 1229. WASHINGTON: AMER ASSOC ADVANCEMENT SCIENCE. ISSN 1095-9203

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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.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Schwalb, BjornUNSPECIFIEDorcid.org/0000-0003-2987-2622UNSPECIFIED
Michel, MargauxUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Zacher, BenediktUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Fruehauf, KatjaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Demel, CarinaUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Tresch, AchimUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
Gagneur, JulienUNSPECIFIEDorcid.org/0000-0002-8924-8365UNSPECIFIED
Cramer, PatrickUNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-272500
DOI: 10.1126/science.aad9841
Journal or Publication Title: Science
Volume: 352
Number: 6290
Page Range: S. 1225 - 1229
Date: 2016
Publisher: AMER ASSOC ADVANCEMENT SCIENCE
Place of Publication: WASHINGTON
ISSN: 1095-9203
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
RNA-POLYMERASE-II; U1 SNRNP; HUMAN GENOME; INITIATION; TERMINATION; PROMOTERS; ENHANCERS; POLYADENYLATION; EXPRESSION; RESOLUTIONMultiple languages
Multidisciplinary SciencesMultiple languages
Refereed: Yes
URI: http://kups.ub.uni-koeln.de/id/eprint/27250

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