The DOI matches its Crossref record; 67 of the 67 references it cites were found in a registry or an index.
Genome-wide dynamics of Pol II elongation and its interplay with promoter proximal pausing, chromatin, and exons
Open accessAbstract
Production of mRNA depends critically on the rate of RNA polymerase II (Pol II) elongation. To dissect Pol II dynamics in mouse ES cells, we inhibited Pol II transcription at either initiation or promoter-proximal pause escape with Triptolide or Flavopiridol, and tracked Pol II kinetically using GRO-seq. Both inhibitors block transcription of more than 95% of genes, showing that pause escape, like initiation, is a ubiquitous and crucial step within the transcription cycle. Moreover, paused Pol II is relatively stable, as evidenced from half-life measurements at ∼3200 genes. Finally, tracking the progression of Pol II after drug treatment establishes Pol II elongation rates at over 1000 genes. Notably, Pol II accelerates dramatically while transcribing through genes, but slows at exons. Furthermore, intergenic variance in elongation rates is substantial, and is influenced by a positive effect of H3K79me2 and negative effects of exon density and CG content within genes.
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.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Inhibition of P‐TEFb and thus repression of the release of RNA Pol II from promoter‐proximal pausing has been shown to block transcription of almost all genes (Henriques et al, 2013; Jonkers et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“RNA Pol II speed was furthermore also shown to be highly variable within individual genes, as RNA Pol II accelerates while traveling throughout the gene body, starting at 0.5 kb/min in the first 10–15 kb and accelerating up to 2–4 kb/min downstream (Danko et al, 2013; Fuchs et al, 2014b; Jonkers et al, 2014; Saponaro et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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 Jonkers et al, 2014
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“All these techniques showed in various human cell lines that the average RNA Pol II speed ranges between 1.25 kb/min and 3.5 kb/min (Danko et al, 2013; Fuchs et al, 2014b; Jonkers et al, 2014; Saponaro et al, 2014; Veloso et al, 2014; Liang et al, 2018; Baluapuri et al, 2019; Gregersen et al, 2020).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Although no general correlation has been found between nucleosome occupancy and RNA Pol II speed (Jonkers et al, 2014), nucleosomes bound within exons could nonetheless slow down RNA Pol II transcription.”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
Experimental — accuracy not yet measured
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Moreover, the GC content within gene bodies has been shown to correlate negatively with RNA Pol II speed (Jonkers et al, 2014; Veloso et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
Experimental — accuracy not yet measuredThe source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Genome‐wide studies have shown that H3K79me2, H2B mono‐ubiquitylation, and H4K20me1 positively correlate with RNA Pol II speed in the gene body (Fuchs et al, 2014a; Jonkers et al, 2014; Veloso et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Indeed, fast transcription correlates with distal localization of H3K36me3 (Jonkers et al, 2014).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The cited source says what the claim attributes to it.
In the citing paper
“Indeed, genes with the highest measured RNA Pol II velocity have been shown to generate more mRNAs (Danko et al, 2013; Jonkers et al, 2014; Cohen et al, 2018).”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The cited source says what the claim attributes to it.
In the citing paper
“Indeed, a positive correlation has been identified between intron 1 size and RNA Pol II speed (Jonkers et al, 2014)”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
The cited source says what the claim attributes to it.
In the citing paper
“Conversely, exon density correlates negatively with RNA Pol II velocity (Jonkers et al, 2014; Veloso et al, 2014)”
From RNA polymerase II speed: a key player in controlling and adapting transcriptome composition (2021) · cites this paper as Jonkers et al, 2014
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
1 retracted
Genomic organization of human transcription initiation complexes
Venters, B. J., & Pugh, B. F. (2013) · Nature · doi:10.1038/nature12535 · Cited by 79
RetractedLandscape of transcription in human cells
Djebali, S., Davis, C. A., Merkel, A., Dobin, A., Lassmann, T., Mortazavi, A., Tanzer, A., Lagarde, J., Lin, W., Schlesinger, F., et al. (2012) · Nature · doi:10.1038/nature11233 · Cited by 5,187
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986
Self-citationDNA-binding factors shape the mouse methylome at distal regulatory regions
Stadler, M. B., Murr, R., Burger, L., Ivanek, R., Lienert, F., Schöler, A., Nimwegen, E. V., Wirbelauer, C., Oakeley, E. J., Gaidatzis, D., et al. (2011) · Nature · doi:10.1038/nature10716 · Cited by 1,383
c-Myc Regulates Transcriptional Pause Release
Rahl, P. B., Lin, C. Y., Seila, A. C., Flynn, R. A., McCuine, S., Burge, C. B., Sharp, P. A., & Young, R. A. (2010) · Cell · doi:10.1016/j.cell.2010.03.030 · Cited by 1,279
Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans
Adelman, K., & Lis, J. T. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3293 · Cited by 1,221
Self-citationControlling the elongation phase of transcription with P-TEFb
Peterlin, B. M., & Price, D. H. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.06.014 · Cited by 1,144
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
Shukla, S., Kavak, E., Gregory, M., Imashimizu, M., Shutinoski, B., Kashlev, M., Oberdoerffer, P., Sandberg, R., & Oberdoerffer, S. (2011) · Nature · doi:10.1038/nature10442 · Cited by 973
Precise 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-citationYamaguchi, Y., Takagi, T., Wada, T., Yano, K., Furuya, A., Sugimoto, S., Hasegawa, J., & Handa, H. (1999) · Cell · doi:10.1016/s0092-8674(00)80713-8 · Cited by 841
Flagged first, then by citations
Cited by
Sorted by citations
Items 401–500 of 585
Regulation of Pol II Pausing Is Involved in Daily Gene Transcription in the Mouse Liver
Zhu, J., Li, C., Gong, C., & Li, X. (2018) · Journal of Biological Rhythms · doi:10.1177/0748730418779526 · Cited by 8
Donnio, L., Lagarou, A., Sueur, G., Mari, P., & Giglia‐Mari, G. (2019) · Molecular and Cellular Biology · doi:10.1128/mcb.00225-18 · Cited by 8
Ali, M. Z., & Choubey, S. (2019) · Physical Biology · doi:10.1088/1478-3975/ab45bf · Cited by 8
Li, J., Mao, H., Pan, Y., Li, H., & Lei, L. (2020) · Inflammation · doi:10.1007/s10753-020-01274-1 · Cited by 8
RNA Polymerase II, the BAF remodeler and transcription factors synergize to evict nucleosomesPreprint
Brahma, S., & Henikoff, S. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.22.525083 · Cited by 8
Kinetic control of mammalian transcription elongation
Wang, Y., Chen, X., Kümmecke, M., Watters, J. W., Cohen, J. E., Xu, Y., & Liu, S. (2025) · Nature Structural & Molecular Biology · doi:10.1038/s41594-025-01707-1 · Cited by 7
Regulatory Mechanisms for Transcriptional Bursting Revealed by an Event-Based Model
Wu, R., Zhou, B., Wang, W., & Liu, F. (2023) · Research · doi:10.34133/research.0253 · Cited by 8
G-quadruplex forming motifs in the promoter region of the B-MYB proto-oncogene.
Miranda, A., Cucchiarini, A., Esnault, C., Andrau, J., Oliveira, P. A., Mergny, J., & Cruz, C. (2024) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2024.132244 · Cited by 7
Mouse promoters are characterised by low occupancy and high turnover of RNA polymerase II
Chatsirisupachai, K., Moene, C. J. I., Kleinendorst, R., Kreibich, E., Molina, N., & Krebs, A. R. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00094-5 · Cited by 7
Statistical inference of the rate of RNA polymerase II elongation by total RNA sequencing
Kawamura, Y., Koyama, S., & Yoshida, R. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty886 · Cited by 7
Ballard, A., Bieniek, S., & Carlini, D. B. (2019) · Gene · doi:10.1016/j.gene.2019.01.031 · Cited by 8
Aging-associated changes in transcriptional elongation influence metazoan longevityPreprint
Debès, C., Papadakis, A., Grönke, S., Karalay, Ö., Tain, L. S., Mizi, A., Nakamura, S., Hahn, O., Weigelt, C. M., Josipović, N., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/719864 · Cited by 7
Interdependence between histone marks and steps in Pol II transcriptionPreprint
Wang, Z., Chivu, A. G., Choate, L. A., Rice, E. J., Miller, D. C., Chu, T., Chou, S., Kingsley, N. B., Petersen, J. L., Finno, C. J., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.08.032730 · Cited by 7
Self-citationTime-resolved analysis of transcription kinetics in single live mammalian cells
Choi, H., Lee, B. H., & Park, H. Y. (2022) · Frontiers in Physics · doi:10.3389/fphy.2022.977125 · Cited by 6
Krasikova, A., Kulikova, T., Schelkunov, M. I., Makarova, N., Fedotova, A., Plotnikov, V., Berngardt, V., Maslova, A., & Fedorov, A. V. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae941 · Cited by 6
Transcript accumulation rates in the early Caenorhabditis elegans embryo
Sivaramakrishnan, P., Watkins, C., & Murray, J. I. (2023) · Science Advances · doi:10.1126/sciadv.adi1270 · Cited by 6
A rapid, sensitive, scalable method for Precision Run-On sequencing (qPRO-seq) v1Preprint
Judd, J., Wojenski, L., Wainman, L. M., Tippens, N. D., Rice, E. J., Dziubek, A., Villafano, G. J., Wissink, E. M., Versluis, P. P., Bagepalli, L., et al. (2019) · doi:10.17504/protocols.io.57dg9i6 · Cited by 9
Self-citationMuskovic, W., Slavich, E., Maslen, B., Kaczorowski, D. C., Cursons, J., Crampin, E. J., & Kavallaris, M. (2022) · Genome Research · doi:10.1101/gr.276818.122 · Cited by 6
Zhang, H.-L., Sun, Y., Saha, S. T., Saha, L. K., Pongor, L. S., Dhall, A., & Pommier, Y. G. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.17.599352 · Cited by 6
Liu, R. (2023) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2023.05.114 · Cited by 5
Control of cell state transitions by post-transcriptional regulation
Mulas, C. (2024) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2023.0050 · Cited by 6
Shenasa, H., Fong, N., Erickson, B., Iosub, I. A., Ule, J., & Bentley, D. L. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2504034122 · Cited by 4
Szaker, H. M., Verma, R., Szádeczky-Kardoss, I., Gál, N., Abbas, S. H., Darkó, É., Pettkó‐Szandtner, A., Silhavy, D., & Csorba, T. (2025) · The Plant Cell · doi:10.1093/plcell/koaf256 · Cited by 5
Mutant FOXO1 controls an oncogenic network via enhancer accessibility
Layden, H. M., Ellis, J. D., Bomber, M. L., Bartlett, L. N., Hiebert, S. W., & Stengel, K. R. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100537 · Cited by 5
Enhancer RNA transcription pinpoints functional genetic variants linked to asthma
Sasse, S. K., Dahlin, A., Sanford, L., Gruca, M. A., Gupta, A. A., Gally, F., Wu, A. C., Iribarren, C., Dowell, R. D., Weiss, S. T., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-57693-x · Cited by 5
Arib, G., Cléard, F., Maeda, R. K., & Karch, F. (2015) · Mechanisms of Development · doi:10.1016/j.mod.2015.08.004 · Cited by 5
Mutzel, V., Okamoto, I., Dunkel, I., Saitou, M., Giorgetti, L., Heard, É., & Schulz, E. G. (2017) · Max Planck Digital Library · Cited by 5
Insights into active intragenic enhancers
Yang, Y., Dai, Z., & Dai, X. (2019) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2019.05.160 · Cited by 4
Timing RNA polymerase pausing with TV-PRO-seq
Zhang, J., Cavallaro, M., & Hebenstreit, D. (2021) · Cell Reports Methods · doi:10.1016/j.crmeth.2021.100083 · Cited by 6
Stability analysis of an autocatalytic protein model
Lee, J. (2016) · AIP Advances · doi:10.1063/1.4950702 · Cited by 5
Spatial organization of transcript elongation and splicing kineticsPreprint
Casill, A. D., Haimowitz, A., Kosmyna, B., Query, C. C., Ye, K. Q., & Gamble, M. J. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.01.28.428713 · Cited by 5
NELF coordinates Pol II transcription termination and DNA replication initiationPreprint
Nakayama, C., Daigaku, Y., Aoi, Y., Fang, Q., Kimurâ, H., Shilatifard, A., Tellier, M., & Nojima, T. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.31.578294 · Cited by 5
Genome-wide dynamic nascent transcript profiles reveal that most paused RNA polymerases terminate
Mukherjee, R., & Guertin, M. J. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag128 · Cited by 4
Rtf1-dependent transcriptional pausing regulates cardiogenesis
Langenbacher, A. D., Lu, F., Tsang, L., Huang, Z. Y. S., Keer, B., Tian, Z., Eide, A., Pellegrini, M. A., Nakano, H., Nakano, A., et al. (2026) · eLife · doi:10.7554/elife.94524.3 · Cited by 4
A Histone Code Functionally Linked to Replicative Senescence
Suter, T., Friedman, M. J., Tazearslan, C., Gamliel, A., Merkurjev, D., Ohgi, K. A., Zhou, Z., Rosenfeld, M. G., & Suh, Y. (2026) · Aging Cell · doi:10.1111/acel.70343 · Cited by 3
The Promoter-Proximal Pause: A Decision Point Governing RNA Polymerase II Fate
Hyder, U., & Bentley, D. L. (2026) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-051424-053703 · Cited by 5
Kinetic pathway of HIV-1 TAR cotranscriptional folding
Jin, L., Zhang, S., Song, Z., Heng, X., & Chen, S. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae362 · Cited by 4
Bhandare, P., Narain, A., Hofstetter, J., Rummel, T., Wenzel, J., Schülein‐Völk, C., Lamer, S., Eilers, U., Schlösser, A., Eilers, M., et al. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1219 · Cited by 4
Application of nucleoside or nucleotide analogues in RNA dynamics and RNA ‐binding protein analysis
Zheng, M., Lin, Y., Wang, W., Zhao, Y. F., & Bao, X. (2022) · Wiley Interdisciplinary Reviews - RNA · doi:10.1002/wrna.1722 · Cited by 4
DSIF modulates RNA polymerase II occupancy according to template G + C content
Deng, N., Zhang, Y., Ma, Z., Lin, R., Cheng, T., Tang, H., Snyder, M. P., & Cohen, S. N. (2022) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqac054 · Cited by 4
Influence of cell volume on the gene transcription rate
Pérez-Ortín, J. E., García-Marcelo, M. J., Delgado-Román, I., Muñoz-Centeno, M. C., & Chávez, S. (2024) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2024.195008 · Cited by 3
RNA polymerase II clusters form in line with liquid phase wetting of chromatinPreprint
Pancholi, A., Klingberg, T., Zhang, W., Prizak, R., Mamontova, I., Noa, A., Kobitski, A. Y., Nienhaus, G. U., Zaburdaev, V., & Hilbert, L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.03.429626 · Cited by 4
RPRD Proteins Control Transcription in Human CellsPreprint
Winczura, K., Ceylan, H., Śledziowska, M., Jones, M., Fagarasan, H., Wang, J., Saponaro, M., Arnold, R. R., Hebenstreit, D., & Grzechnik, P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.06.20.449126 · Cited by 4
Single-cell nascent RNA sequencing using click-chemistry unveils coordinated transcriptionPreprint
Mahat, D. B., Tippens, N. D., Martin-Rufino, J. D., Waterton, S. K., Fu, J., Blatt, S. E., & Sharp, P. A. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.15.558015 · Cited by 4
ATRX Promotes Transcription Initiation of HSV-1 Immediate Early Genes During Early Lytic Infection
Dunn, L. E. M., Clark, M. M., & Baines, J. D. (2025) · Viruses · doi:10.3390/v17091169 · Cited by 3
Ma, L., Huang, Y., Han, M., Wang, B., Guo, X., Wang, Z., Zhang, F., Xie, Y., Ren, J., Wang, J., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65935-1 · Cited by 4
Subramani, P. G., Seija, N., Ridani, J., Boulais, J., Donnelly, P. A., Provencher, M., Bagci, H., Poitras, C., Côté, J., Robert, F., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-68332-4 · Cited by 3
NELF prevents transcriptional readthrough into DNA replication zones in cancer cells
Nakayama, C., Fang, Q., Daigaku, Y., Aoi, Y., Ito, S., Takahashi, M., Shimatani, R., Minamisawa, T., Ozturk, Y., Kimura, H., et al. (2026) · EMBO Reports · doi:10.1038/s44319-026-00700-z · Cited by 3
Transcriptional interference revisited
Fischer, M., & Hoffmann, S. (2026) · Nature Genetics · doi:10.1038/s41588-026-02536-8 · Cited by 3
Internal and external normalization of nascent RNA sequencing run-on experiments
Maas, Z. L., & Dowell, R. D. (2024) · BMC Bioinformatics · doi:10.1186/s12859-023-05607-3 · Cited by 3
The NONO protein regulates nonclassical DNA structure: Effects on circadian genes and DNA damage
Moriggi, E., Pisteljic, M., Rosi‐Andersen, A., Opitz, L., Azzi, A., & Brown, S. A. (2025) · iScience · doi:10.1016/j.isci.2025.112408 · Cited by 3
DSS1 is required for proper Integrator–PP2A function
Xu, C., Zhou, Q.-X., Zheng, H., Song, A., Zhao, W.-Y., Xu, T., Xiong, Y., Zhang, Y., Huang, Z., Xu, Y., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-61257-4 · Cited by 3
Targeting the Transcriptome Through Globally Acting Components
Parrello, D., Vlasenok, M., Kranz, L. A., & Nechaev, S. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.749850 · Cited by 3
Akcan, T. S., Вилов, С. А., & Heinig, M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkac1272 · Cited by 4
The regulation of transcription elongation in embryonic stem cells
Wang, X., Fan, Y., & Wu, Q. (2023) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2023.1145611 · Cited by 4
Regulation of Pol II Pausing during Daily Gene Transcription in Mouse Liver
Xu, W. Q., & Li, X. (2023) · Biology · doi:10.3390/biology12081107 · Cited by 3
Liu, L., Zhao, Y., Hassett, R., Toneyan, S., Koo, P. K., & Siepel, A. C. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf092 · Cited by 3
Zhou, J., Gao, G., Hou, P., Li, C., & Guo, D. (2017) · Journal of Cellular Biochemistry · doi:10.1002/jcb.26058 · Cited by 3
Zurita, M., & Murillo-Maldonado, J. M. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21020630 · Cited by 3
Profiling histone modifications in the normal mouse kidney and after unilateral ureteric obstruction
Hewitson, T. D., Holt, S. G., Samuel, C. S., Wigg, B., & Smith, E. R. (2019) · American Journal of Physiology-Renal Physiology · doi:10.1152/ajprenal.00262.2019 · Cited by 3
Fast and furious: insights of back splicing regulation during nascent RNA synthesis
Xue, W., Ma, X.-K., & Yang, L. C. (2021) · Science China Life Sciences · doi:10.1007/s11427-020-1881-1 · Cited by 5
Bayesian inference of polymerase dynamics over the exclusion process
Cavallaro, M., Wang, Y., Hebenstreit, D., & Dutta, R. (2023) · Royal Society Open Science · doi:10.1098/rsos.221469 · Cited by 2
Integrating regulatory information via combinatorial control of the transcription cyclePreprint
Scholes, C., DePace, A. H., & Sánchez, Á. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/039339 · Cited by 3
Genome-wide analysis of transcriptional bursting-induced noise in mammalian cellsPreprint
Ochiai, H., Hayashi, T., Umeda, M., Yoshimura, M., Harada, A., Shimizu, Y., Nakano, K., Saitoh, N., Kimurâ, H., Liu, Z. J., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/736207 · Cited by 3
Zapater, A. G., Mackowiak, S. D., Guo, Y., Jordán‐Pla, A., Friedländer, M. R., Visa, N., & Farrants, A. Ö. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/858852 · Cited by 3
Zeng, Y., Zeng, H., Fair, B. J., Krishnamohan, A., Hou, Y., Hall, J. M., Ruthenburg, A. J., Li, Y., & Staley, J. P. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.10.18.464728 · Cited by 3
Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalizationPreprint
Salari, H., Fourel, G., & Jost, D. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.18.549489 · Cited by 3
Revisiting models of enhancer–promoter communication in gene regulationPreprint
Barshad, G., & Danko, C. G. (2025) · Genome Research · doi:10.1101/gr.278389.123 · Cited by 4
A Drosophila screen identifies a role for histone methylation in ER stress preconditioning
Owings, K. G., & Chow, C. Y. (2023) · G3 Genes Genomes Genetics · doi:10.1093/g3journal/jkad265 · Cited by 2
Chromatin Regulatory Targets for Anticancer Therapeutics
Barta, P. A., Carter, T. R., & Erb, M. A. (2025) · Chemical Reviews · doi:10.1021/acs.chemrev.5c00231 · Cited by 2
Sequence-specific RNA recognition drives Restrictor-mediated termination of extragenic transcription
Polizzese, D., Mandana, G. M., Russo, M., Polletti, S., Prosperini, E., Ciossani, G., Monzani, S., Scietti, L., Rodighiero, S., Gualdrini, F., et al. (2026) · Molecular Cell · doi:10.1016/j.molcel.2026.02.006 · Cited by 2
Cao, D., Chen, Z., Gao, Y., Roesler, C., Gooneratne, I., Mera, C., Zhuang, L., Slack, J., Nudell-Cook, E., Vy, J., et al. (2026) · Nature Communications · doi:10.1038/s41467-026-72519-0 · Cited by 2
Regulation of RNA transcript elongation in metazoans and its relevance to disease
Mimoso, C. A., Fianu, I., & Adelman, K. (2026) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-026-01003-w · Cited by 2
Analytic delay distributions for a family of gene transcription models
Hosseini, S. H., & Roussel, M. R. (2024) · Mathematical Biosciences & Engineering · doi:10.3934/mbe.2024273 · Cited by 2
de Sande, A. H., Turunen, T., Bouvy‐Liivrand, M., Örd, T., Palani, S., Lahnalampi, M., Tundidor-Centeno, C., Liljenbäck, H., Virta, J., Niskanen, H., et al. (2025) · Genome Medicine · doi:10.1186/s13073-025-01530-9 · Cited by 3
Antisense transcription can induce expression memory via stable promoter repression
Mutzel, V., Schwämmle, T., Oeverdieck, S., Librenjak, L., Boesen, B. B., Bothe, M., Gjaltema, R. A. F., Dunkel, I., Noviello, G., & Schulz, E. G. (2025) · Genome biology · doi:10.1186/s13059-025-03875-1 · Cited by 1
Epigenetics: Chromatin Organization and Function
Delcuve, G. P., Khan, D. H., Liyanage, V. R. B., Jahan, S., Rastegar, M., Kirshenbaum, L. A., & Davie, J. (2016) · Cardiac and vascular biology · doi:10.1007/978-3-319-41457-7_1 · Cited by 3
Hitting the brakes on transcription to extend lifespan
Burkewitz, K. (2023) · Trends in Genetics · doi:10.1016/j.tig.2023.07.007 · Cited by 2
Lessons from (pre-)mRNA Imaging
Adivarahan, S., & Zenklusen, D. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-31434-7_9 · Cited by 2
Fuchs, G., Rosenthal, E., Bublik, D. R., Kaplan, T., & Oren, M. (2015) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/035386 · Cited by 2
Morf, J., Wingett, S., Farabella, I., Cairns, J., Furlan-Magaril, M., Liu, X., Craig, F. F., Andrews, S., Martı́-Renom, M. A., & Fraser, P. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/196147 · Cited by 2
Alexander, K. A., & García‐García, M. J. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/536102 · Cited by 2
Enhancers predominantly regulate gene expression in vivo via transcription initiationPreprint
Larke, M., Nojima, T., Telenius, J. M., Sharpe, J. A., Sloane-Stanley, J. A., Butler, S., Beagrie, R. A., Downes, D. J., Schweßinger, R., Oudelaar, A. M., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/844191 · Cited by 2
DNA-sequence and epigenomic determinants of local rates of transcription elongationPreprint
Liu, L., Zhao, Y., & Siepel, A. C. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.12.21.572932 · Cited by 2
NELF coordinates Pol II transcription termination and DNA replication initiationPreprint
Nojima, T., Nakayama, C., Daigaku, Y., Aoi, Y., Fang, Q., Kimurâ, H., Shilatifard, A., & Tellier, M. (2024) · Research Square · doi:10.21203/rs.3.rs-3991504/v1 · Cited by 2
An intrinsic chromatin timer sets the tempo for developmentPreprint
Catalano, C., Levine, M., & Tullius, T. W. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.28.685222 · Cited by 2
Stalling of elongating Pol II triggers Ser7 phosphorylation in trans to drive transcription recoveryPreprint
Shlamovitz, I., Bao, Y., Toteva, T., Crisp, A., Ye, S., Wingett, S., Cacioppo, R., Edmondson, A., Castiblanco, D., Boemo, M. A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.04.692291 · Cited by 2
ELOF1 is a core component of the promoter-proximal paused RNA polymerase II complexPreprint
Nunez, R. J. V., Bressin, A., Shao, Z., Mayer, A., & Vos, S. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.05.26.728003 · Cited by 2
Dasmeh, P. (2017) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2017.11.004 · Cited by 1
Enhancer-promoter communication in Drosophila developmental gene transcription
Hunt, G., & Mannervik, M. (2024) · The International Journal of Developmental Biology · doi:10.1387/ijdb.230218gh · Cited by 1
Domain acquisition enabled functional expansion of the TFIIS transcription factor family
Matveyeva, K., de Diego, A. S., García-López, M. Á., Gutiérrez, J., Fischer, T., & van Wely, K. H. M. (2025) · Cell & Bioscience · doi:10.1186/s13578-025-01423-9 · Cited by 1
Himanen, S. V., Rabenius, A., Aktay, S., Tekoniemi, J., & Vihervaara, A. (2025) · Cell Reports · doi:10.1016/j.celrep.2025.116698 · Cited by 1
Morse, R. H. (2024) · Elsevier eBooks · doi:10.1016/b978-0-12-814809-9.00002-0 · Cited by 1
Ghasemi, S. M., Pankaj Singh, K., Hannah Johnson, L., Koksoy, A. A., Michael Mancini, A., Stossi, F., & Azencott, R. (2024) · Journal of Bioinformatics and Systems Biology · doi:10.26502/jbsb.5107084 · Cited by 1
Sansó, M., Pinto, D., Svensson, J. P., Pagé, V., Parua, P. K., Bitton, D. A., Mbogning, J., Garcia, P., Hidalgo, E., Robert, F., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/240135 · Cited by 1
ten-Caten, F. (2019) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.95.2019.tde-17042019-143232 · Cited by 1
Segelle, A., Núñez‐Álvarez, Y., Oldfield, A., Webb, K. M., Voigt, P., & Luco, R. F. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.04.442453 · Cited by 1
Newly synthesized RNA Sequencing Characterizes Transcription Dynamics in Three Pluripotent StatesPreprint
Shao, R., Kumar, B., Lidschreiber, K., Lidschreiber, M., Cramer, P., & Elsässer, S. (2021) · bioRxiv · doi:10.1101/2021.06.11.448016
Muskovic, W., Slavich, E., Maslen, B., Kaczorowski, D. C., Cursons, J., Crampin, E. J., & Kavallaris, M. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.08.25.457323 · Cited by 1
Zhang, J., Cavallaro, M., & Hebenstreit, D. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/461442 · Cited by 1
Metadata
- Authors
- Jonkers, I., Kwak, H., & Lis, J. T.
- Affiliations
- Cornell University (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Jonkers, Iris
- Lis, John T
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2014-04-29
- Volume
- 3
- Pages
- e02407-e02407
- ISSN
- 2050-084X (ISSN-L)
- PMC
- PMC4001325
- OpenAlex
- W2038894647
- Cited by
- 581
- References
- 67
- Citations by year
- 2026: 26 · 2025: 40 · 2024: 52 · 2023: 48 · 2022: 46 · 2021: 74 · 2020: 40 · 2019: 57 · 2018: 53 · 2017: 53 · 2016: 49 · 2015: 35 · 2014: 8
- FWCI
- 19.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- eLife (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by)
- Funders
- National Institutes of Health (GM25232)
- Helen Hay Whitney Foundation
- Howard Hughes Medical Institute
- 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 › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- RNA polymerase II elongation, promoter-proximal pausing, transcription kinetics, mouse embryonic stem cells, triptolide, flavopiridol, GRO-seq, H3K79me2, chromatin
- MeSH terms
- Animals, Cells, Cultured, Chromatin, Diterpenes, Epoxy Compounds, Exons, Flavonoids, Humans, Phenanthrenes, Piperidines, Promoter Regions, Genetic, RNA Polymerase II, RNA, Messenger, Transcription, Genetic, Genetic Variation, Gene Library, Sequence Alignment, Sequence Analysis, DNA, Chromatin Immunoprecipitation, Mice, Embryonic Stem Cells, Genetic Association Studies
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
