TT-seq maps the human transient transcriptome

Schwalb B, Michel M, Zacher B, Fruehauf K, Demel C, Tresch A, Gagneur J, Cramer P (2016)

Publication Type: Journal article

Publication year: 2016

Journal

Science American Association for the Advancement of Science

Book Volume: 352

Pages Range: 1225-1228

Journal Issue: 6290

DOI: 10.1126/science.aad9841

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.

Involved external institutions

Max-Planck-Institut für biophysikalische Chemie (Karl-Friedrich-Bonhoeffer-Institut) / Max Planck Institute for Biophysical Chemistry DE Germany (DE) Ludwig-Maximilians-Universität (LMU) DE Germany (DE) Karolinska Institute SE Sweden (SE) Universität zu Köln DE Germany (DE)

How to cite

APA:

Schwalb, B., Michel, M., Zacher, B., Fruehauf, K., Demel, C., Tresch, A.,... Cramer, P. (2016). TT-seq maps the human transient transcriptome. Science, 352(6290), 1225-1228. https://doi.org/10.1126/science.aad9841

MLA:

Schwalb, Bjorn, et al. "TT-seq maps the human transient transcriptome." Science 352.6290 (2016): 1225-1228.

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