Universität zu Köln

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:	Creators Email ORCID ORCID Put Code Schwalb, Bjorn UNSPECIFIED orcid.org/0000-0003-2987-2622 UNSPECIFIED Michel, Margaux UNSPECIFIED UNSPECIFIED UNSPECIFIED Zacher, Benedikt UNSPECIFIED UNSPECIFIED UNSPECIFIED Fruehauf, Katja UNSPECIFIED UNSPECIFIED UNSPECIFIED Demel, Carina UNSPECIFIED UNSPECIFIED UNSPECIFIED Tresch, Achim UNSPECIFIED UNSPECIFIED UNSPECIFIED Gagneur, Julien UNSPECIFIED orcid.org/0000-0002-8924-8365 UNSPECIFIED Cramer, Patrick UNSPECIFIED UNSPECIFIED UNSPECIFIED
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:	Keywords Language RNA-POLYMERASE-II; U1 SNRNP; HUMAN GENOME; INITIATION; TERMINATION; PROMOTERS; ENHANCERS; POLYADENYLATION; EXPRESSION; RESOLUTION Multiple languages Multidisciplinary Sciences Multiple languages
Refereed:	Yes
URI:	http://kups.ub.uni-koeln.de/id/eprint/27250