@article{e696c0116c614884b6671140e19497d4,
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 windowwith amedianwidth of 3300 base pairs.Termination sites coincidewith a DNA motif associated with pausing of RNA polymerase before its release from the genome.",
author = "Bj{\"o}rn Schwalb and Margaux Michel and Benedikt Zacher and Hauf, {Katja Fr{\"u}} and Carina Demel and Achim Tresch and Julien Gagneur and Patrick Cramer",
note = "Funding Information: The sequencing data and the annotation file have been deposited in the Gene Expression Omnibus database under accession code GSE75792. We thank H. Blum, S. Krebs, and A. Graf (Laboratory for Functional Genome Analysis, Gene Center, Ludwig-Maximilians-Universit{\"a}t M{\"u}nchen) for help with sequencing and J. A. Feuillet, J. Soeding, A. Sawicka, and C. Bernecky for help and discussions. K.F. was supported by the Center for Innovative Medicine (CIMED) at Karolinska Institutet and by the Science for Life Laboratory (SciLifeLab) in Stockholm. C.D. was supported by a Deutsche Forschungsgemeinschaft (DFG) fellowship at the Graduate School of Quantitative Biosciences Munich. A.T. was supported by a German Federal Ministry of Education and Research (BMBF) e:Bio grant and by DFG grant SFB 680. J.G. was supported by the Bavarian Research Center for Molecular Biosystems and the Bundesministerium f{\"u}r Bildung und Forschung, Juniorverbund in der Systemmedizin {"}mitOmics{"} (grant FKZ 01ZX1405A). P.C. was funded by the Advanced Grant TRANSIT of the European Research Council, the DFG, the Volkswagen Foundation, CIMED, and SciLife Lab",
year = "2016",
month = jun,
day = "3",
doi = "10.1126/science.aad9841",
language = "English",
volume = "352",
pages = "1225--1228",
journal = "Science",
issn = "0036-8075",
publisher = "American Association for the Advancement of Science",
number = "6290",
}