The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
Defining the Status of RNA Polymerase at Promoters
Open accessAbstract
Recent genome-wide studies in metazoans have shown that RNA polymerase II (Pol II) accumulates to high densities on many promoters at a rate-limited step in transcription. However, the status of this Pol II remains an area of debate. Here, we compare quantitative outputs of a global run-on sequencing assay and chromatin immunoprecipitation sequencing assays and demonstrate that the majority of the Pol II on Drosophila promoters is transcriptionally engaged; very little exists in a preinitiation or arrested complex. These promoter-proximal polymerases are inhibited from further elongation by detergent-sensitive factors, and knockdown of negative elongation factor, NELF, reduces their levels. These results not only solidify the notion that pausing occurs at most promoters, but demonstrate that it is the major rate-limiting step in early transcription at these promoters. Finally, the divergent elongation complexes seen at mammalian promoters are far less prevalent in Drosophila, and this specificity in orientation correlates with directional core promoter elements, which are abundant in Drosophila.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 1×
“Enhancers themselves can be found within or outside of genes and are enriched in monomethylation of histone 3 at lysine 4 (H3K4me1) but have lower levels of trimethylation at the same site (H3K4me3) (Heintzman et al., 2007).”
Widespread transcription at neuronal activity-regulated enhancers
Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450
Nechaev, S., Fargo, D. C., dos Santos, G., Liu, L., Gao, Y., & Adelman, K. (2010) · Science · doi:10.1126/science.1181421 · Cited by 424
Self-citation
Cited by
Transcriptional enhancers: from properties to genome-wide predictions
Shlyueva, D., Stampfel, G., & Stark, A. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3682 · Cited by 1,356
Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq
Arnold, C. D., Gerlach, D., Stelzer, C., Boryń, Ł. M., Rath, M., & Stark, A. (2013) · Science · doi:10.1126/science.1232542 · Cited by 1,125
Getting up to speed with transcription elongation by RNA polymerase II
Jonkers, I., & Lis, J. T. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3953 · Cited by 876
Self-citationPrecise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
Kwak, H., Fuda, N. J., Core, L. J., & Lis, J. T. (2013) · Science · doi:10.1126/science.1229386 · Cited by 849
Self-citationEvolutionarily Conserved Principles Predict 3D Chromatin Organization
Rowley, M. J., Nichols, M. H., Lyu, X., Ando-Kuri, M., Rivera, I. S. M., Hermetz, K., Wang, P., Ruan, Y., & Corces, V. G. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.07.022 · Cited by 555
Mahat, D. B., Kwak, H., Booth, G. T., Jonkers, I. H., Danko, C. G., Patel, R. K., Waters, C. T., Munson, K., Core, L. J., & Lis, J. T. (2016) · Nature Protocols · doi:10.1038/nprot.2016.086 · Cited by 508
Self-citationBorn to run: control of transcription elongation by RNA polymerase II
Chen, F. X., Smith, E. R., & Shilatifard, A. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0010-5 · Cited by 447
Widespread transcriptional pausing and elongation control at enhancers
Henriques, T., Scruggs, B. S., Inouye, M. O., Muse, G. W., Williams, L. H., Burkholder, A. B., Lavender, C. A., Fargo, D. C., & Adelman, K. (2018) · Genes & Development · doi:10.1101/gad.309351.117 · Cited by 350
Self-citationTranscription termination and the control of the transcriptome: why, where and how to stop
Porrua, O., & Libri, D. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3943 · Cited by 324
Mikhaylichenko, O., Bondarenko, V., Harnett, D., Schor, I. E., Males, M., Viales, R. R., & Furlong, E. E. M. (2018) · Genes & Development · doi:10.1101/gad.308619.117 · Cited by 293
PAF1, a Molecular Regulator of Promoter-Proximal Pausing by RNA Polymerase II
Chen, F. X., Woodfin, A. R., Gardini, A., Rickels, R. A., Marshall, S. A., Smith, E. R., Shiekhattar, R., & Shilatifard, A. (2015) · Cell · doi:10.1016/j.cell.2015.07.042 · Cited by 253
Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters
Krebs, A. R., Imanci, D., Hoerner, L., Gaidatzis, D., Burger, L., & Schübeler, D. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.06.027 · Cited by 249
Henriques, T., Gilchrist, D. A., Nechaev, S., Bern, M., Muse, G. W., Burkholder, A., Fargo, D. C., & Adelman, K. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.10.001 · Cited by 240
Self-citationNuclear stability and transcriptional directionality separate functionally distinct RNA species
Andersson, R., Refsing Andersen, P., Valen, E., Core, L. J., Bornholdt, J., Boyd, M., Heick Jensen, T., & Sandelin, A. (2014) · Nature Communications · doi:10.1038/ncomms6336 · Cited by 171
Self-citationMYC Recruits SPT5 to RNA Polymerase II to Promote Processive Transcription Elongation
Baluapuri, A., Hofstetter, J., Dudvarski Stankovic, N., Endres, T., Bhandare, P., Vos, S. M., Adhikari, B., Schwarz, J. D., Narain, A., Vogt, M., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.031 · Cited by 138
Single-cell nascent RNA sequencing unveils coordinated global transcription
Mahat, D. B., Tippens, N. D., Martin-Rufino, J. D., Waterton, S. K., Fu, J., Blatt, S. E., & Sharp, P. A. (2024) · Nature · doi:10.1038/s41586-024-07517-7 · Cited by 131
Andersson, R. (2015) · BioEssays · doi:10.1002/bies.201400162 · Cited by 127
Pause & go: from the discovery of RNA polymerase pausing to its functional implications
Mayer, A., Landry, H. M., & Churchman, L. S. (2017) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2017.03.002 · Cited by 125
Fitz, J., Neumann, T., & Pavri, R. (2018) · The EMBO Journal · doi:10.15252/embj.201797965 · Cited by 74
Biophysically Motivated Regulatory Network Inference: Progress and Prospects
Äijö, T., & Bonneau, R. (2016) · Human Heredity · doi:10.1159/000446614 · Cited by 30
(2025) · doi:10.1016/j.molcel.2025.04.012 · Cited by 21
Metadata
- Authors
- Core, L. J., Waterfall, J. J., Gilchrist, D. A., Fargo, D. C., Kwak, H., Adelman, K., & Lis, J. T.
- Venue
- Cell Reports
- Publisher
- Elsevier BV
- Published
- 2012-10
- Volume
- 2
- Issue
- 4
- Pages
- 1025-1035
- ISSN
- 2211-1247 (ISSN-L)
- OpenAlex
- W2039269859
- Cited by
- 257
- References
- 3
- FWCI
- 8.48
- Type
- journal article
- Language
- en
- Open access
- gold
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 ›
Are you an author, or do you see a problem with this page? Request a review
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.
