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Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution
Open accessAbstract
Major features of transcription by human RNA polymerase II (Pol II) remain poorly defined due to a lack of quantitative approaches for visualizing Pol II progress at nucleotide resolution. We developed a simple and powerful approach for performing native elongating transcript sequencing (NET-seq) in human cells that globally maps strand-specific Pol II density at nucleotide resolution. NET-seq exposes a mode of antisense transcription that originates downstream and converges on transcription from the canonical promoter. Convergent transcription is associated with a distinctive chromatin configuration and is characteristic of lower-expressed genes. Integration of NET-seq with genomic footprinting data reveals stereotypic Pol II pausing coincident with transcription factor occupancy. Finally, exons retained in mature transcripts display Pol II pausing signatures that differ markedly from skipped exons, indicating an intrinsic capacity for Pol II to recognize exons with different processing fates. Together, human NET-seq exposes the topography and regulatory complexity of human gene expression.
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“In mammals and many other metazoans, promoter‐proximal pausing occurs 25–50 base pairs downstream from the TSS and is a major rate‐limiting step of the transcription cycle (Jonkers et al, 2014; Mayer et al, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Mayer et al, 2015
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“These methods also confirmed the existence of a pause at the 3′ splice site in budding yeast (Harlen et al, 2016) and Drosophila (Kwak et al, 2013), at the 3′ and 5′ splice sites in human cells (Mayer et al, 2015; Nojima et al, 2015) and at the 5′ splice site in plants (Kindgren et al, 2020).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Mayer et al, 2015
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“Moreover, higher RNA Pol II accumulation has been reported at spliced exons, as compared to skipped exons (Kwak et al, 2013; Mayer et al, 2015; Nojima et al, 2015).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Mayer et al, 2015
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Metadata
- Authors
- Mayer, A., di Iulio, J., Maleri, S., Eser, U., Vierstra, J., Reynolds, A., Sandstrom, R., Stamatoyannopoulos, J. A., & Churchman, L. S.
- Affiliations
- Harvard University (US)
- University of Washington (US)
- Corresponding author
- Churchman, L. Stirling
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2015-04
- Volume
- 161
- Issue
- 3
- Pages
- 541-554
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC4528962
- OpenAlex
- W2037429489
- Cited by
- 367
- References
- 86
- Citations by year
- 2026: 15 · 2025: 19 · 2024: 24 · 2023: 30 · 2022: 37 · 2021: 40 · 2020: 36 · 2019: 39 · 2018: 32 · 2017: 39 · 2016: 38 · 2015: 16
- FWCI
- 18.10
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Human Genome Research Institute (U54HG007010, R01HG007173)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- RNA polymerase II, transcription elongation, antisense transcription, convergent transcription, transcription factor occupancy, genomic footprinting, exon skipping
- MeSH terms
- Enhancer Elements, Genetic, Exons, HeLa Cells, Humans, Promoter Regions, Genetic, RNA Polymerase II, Transcription Factors, Transcription, Genetic, RNA, Antisense, Alternative Splicing, Sequence Analysis, RNA, Transcription Elongation, Genetic
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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