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Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
Open accessAbstract
RNA polymerases are highly regulated molecular machines. We present a method (global run-on sequencing, GRO-seq) that maps the position, amount, and orientation of transcriptionally engaged RNA polymerases genome-wide. In this method, nuclear run-on RNA molecules are subjected to large-scale parallel sequencing and mapped to the genome. We show that peaks of promoter-proximal polymerase reside on ∼30% of human genes, transcription extends beyond pre-messenger RNA 3′ cleavage, and antisense transcription is prevalent. Additionally, most promoters have an engaged polymerase upstream and in an orientation opposite to the annotated gene. This divergent polymerase is associated with active genes but does not elongate effectively beyond the promoter. These results imply that the interplay between polymerases and regulators over broad promoter regions dictates the orientation and efficiency of productive transcription.
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Wang, M., Wei, P.-C., Lim, C. K., Gallina, I. S., Marshall, S., Marchetto, M. C., Alt, F. W., & Gage, F. H. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2019.12.013 · Cited by 105
The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages
Daniel, B., Nagy, G., Hah, N., Horvath, A., Czimmerer, Z., Poliska, S., Gyuris, T., Keirsse, J., Gysemans, C., Van Ginderachter, J. A., et al. (2014) · Genes & Development · doi:10.1101/gad.242685.114 · Cited by 97
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Baranasic, D., Hörtenhuber, M., Balwierz, P. J., Zehnder, T., Mukarram, A. K., Nepal, C., Várnai, C., Hadzhiev, Y., Jimenez-Gonzalez, A., Li, N., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01089-w · Cited by 101
Intragenic Enhancers Attenuate Host Gene Expression
Cinghu, S., Yang, P., Kosak, J. P., Conway, A. E., Kumar, D., Oldfield, A. J., Adelman, K., & Jothi, R. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.010 · Cited by 100
A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting
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“Live imaging and genome-wide studies have shown that RNAP pausing before initiation is common in eukaryotes [102–105] and that its half-life of up to 20 min can be consistent with transcriptional bursting [106–113].”
BackgroundSchweikhard, V., Meng, C., Murakami, K., Kaplan, C. D., Kornberg, R. D., & Block, S. M. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405181111 · Cited by 92
Post-transcriptional gene silencing mediated by microRNAs is controlled by nucleoplasmic Sfpq
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Metadata
- Authors
- Core, L. J., Waterfall, J. J., & Lis, J. T.
- Venue
- Science
- Published
- 2008-12-19
- Volume
- 322
- Issue
- 5909
- Pages
- 1845-1848
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2007844697
- Cited by
- 2,022
- References
- 3
- FWCI
- 37.97
- Type
- journal article
- Language
- en
- Open access
- green
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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Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
