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Global Regulation of Promoter Melting in Naive Lymphocytes
Open accessAbstract
Lymphocyte activation is initiated by a global increase in messenger RNA synthesis. However, the mechanisms driving transcriptome amplification during the immune response are unknown. By monitoring single-stranded DNA genome wide, we show that the genome of naive cells is poised for rapid activation. In G0, ∼90% of promoters from genes to be expressed in cycling lymphocytes are polymerase loaded but unmelted and support only basal transcription. Furthermore, the transition from abortive to productive elongation is kinetically limiting, causing polymerases to accumulate nearer to transcription start sites. Resting lymphocytes also limit the expression of the transcription factor IIH complex, including XPB and XPD helicases involved in promoter melting and open complex extension. To date, two rate-limiting steps have been shown to control global gene expression in eukaryotes: preinitiation complex assembly and polymerase pausing. Our studies identify promoter melting as a third key regulatory step and propose that this mechanism ensures a prompt lymphocyte response to invading pathogens.
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“Including exogenous reference transcripts (‘spike-ins’) is useful both for quality control [1, 197] and for library-size normalization [198].”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [198]
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Cites
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Langmead, B., Trapnell, C., Pop, M., & Salzberg, S. L. (2009) · Genome Biology · doi:10.1186/gb-2009-10-3-r25 · Cited by 21,849
Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., van Baren, M. J., Salzberg, S. L., Wold, B. J., & Pachter, L. (2010) · Nature Biotechnology · doi:10.1038/nbt.1621 · Cited by 15,556
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,682
A bivalent chromatin structure marks key developmental genes in embryonic stem cells
Bernstein, B. E., Mikkelsen, T. S., Xie, X., Kamal, M., Huebert, D. J., Cuff, J., Fry, B., Meissner, A., Wernig, M., Plath, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.041 · Cited by 5,361
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 5×
“(H) Alignment of PolII (black line, left y axis) and ssDNA (red line, right y axis) at p300+H3K4me1highH2AZlow enhancers.”
BackgroundInfluentialWidespread 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
Combinatorial patterns of histone acetylations and methylations in the human genome
Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Peng, W., Zhang, M. Q., et al. (2008) · Nature Genetics · doi:10.1038/ng.154 · Cited by 2,331
Control of Developmental Regulators by Polycomb in Human Embryonic Stem Cells
Lee, T. I., Jenner, R. G., Boyer, L. A., Guenther, M. G., Levine, S. S., Kumar, R., Chevalier, B. S., Johnstone, S. E., Cole, M. F., Isono, K., et al. (2006) · Cell · doi:10.1016/j.cell.2006.02.043 · Cited by 2,296
A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells
Guenther, M. G., Levine, S. S., Boyer, L. A., Jaenisch, R., & Young, R. A. (2007) · Cell · doi:10.1016/j.cell.2007.05.042 · Cited by 2,002
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
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Aiden, E. L., & Casellas, R. C. (2015) · Cell · doi:10.1016/j.cell.2015.07.034 · Cited by 15
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Salloum, D., Singh, K., Davidson, N. R., Cao, L., Kuo, D. C., Sanghvi, V. R., Jiang, M., Tello‐Lafoz, M., Viale, A. J., Rätsch, G., et al. (2022) · The Journal of Immunology · doi:10.4049/jimmunol.2100537 · Cited by 15
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Self-citationGala, H., Saha, D., Venugopal, N., Aloysius, A., Purohit, G., & Dhawan, J. (2022) · Journal of Cell Science · doi:10.1242/jcs.259789 · Cited by 17
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Fonseca, G. J., Cohen, M. J., & Mymryk, J. S. (2014) · Journal of Virology · doi:10.1128/jvi.03518-13 · Cited by 13
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Michel, M., & Cramer, P. (2013) · Cell · doi:10.1016/j.cell.2013.04.050 · Cited by 12
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Pannunzio, N. R., & Lieber, M. R. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.03.034 · Cited by 12
Costea, J., Schoeberl, U. E., Malzl, D., von der Linde, M., Fitz, J., Gupta, A., Makharova, M., Goloborodko, A. A., & Pavri, R. (2022) · Molecular Cell · doi:10.1016/j.molcel.2023.01.014 · Cited by 12
Benham, C. J. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1092 · Cited by 12
FUBP/KH domain proteins in transcription: Back to the future
Quinn, L. M. (2017) · Transcription · doi:10.1080/21541264.2017.1293595 · Cited by 13
Martella, C., Tollenaere, A. I., Waast, L., Lacombe, B., Groussaud, D., Margottin-Goguet, F., Ramirez, B. C., & Pique, C. (2020) · Journal of Virology · doi:10.1128/jvi.02171-19 · Cited by 12
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Zaytseva, O., & Quinn, L. M. (2018) · BioEssays · doi:10.1002/bies.201700235 · Cited by 11
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Pérez-Salvia, M., Simó‐Riudalbas, L., Ausió, J., & Esteller, M. (2015) · Epigenetics · doi:10.1080/15592294.2015.1039222 · Cited by 10
Stretton, C., Lipina, C., Hyde, R., Cwiklinski, E., Hoffmann, T. M., Taylor, P. M., & Hundal, H. S. (2019) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2019.03.002 · Cited by 10
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Kuzin, V., Wiegard, A., Cameron, D. P., & Baranello, L. (2022) · STAR Protocols · doi:10.1016/j.xpro.2022.101581 · Cited by 9
Mapping DNA Breaks by Next-Generation Sequencing
Baranello, L., Kouzine, F., Wójtowicz, D., Cui, K., Zhao, K., Przytycka, T. M., Capranico, G., & Levens, D. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7306-4_13 · Cited by 8
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Torchia, N., Brescia, C., Chiarella, E., Audia, S., Trapasso, F., & Amato, R. (2024) · Immuno · doi:10.3390/immuno4040032 · Cited by 8
Srivastava, S., Gala, H., Mishra, R. K., & Dhawan, J. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-7371-2_16 · Cited by 6
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Unraveling Non-B DNA Structures in the Era of Telomere-to-Telomere Genomes
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Martella, C., Waast, L., & Pique, C. (2022) · médecine/sciences · doi:10.1051/medsci/2022039 · Cited by 3
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Scarpa, M., Kapoor, S., Tvedte, E. S., Doshi, K. A., Zou, Y. S., Singh, P., Lee, J. K., Chatterjee, A., Ali, M. K. M., Bromley, R. E., et al. (2021) · Oncotarget · doi:10.18632/oncotarget.28042 · Cited by 3
Gala, H., Saha, D., Venugopal, N., Aloysius, A., & Dhawan, J. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/250910 · Cited by 3
Baranello, L., Levens, D., & Kouzine, F. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803480-4.00003-x · Cited by 2
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Lian, Q., Ma, J., Hua, K., Rong, Z., Cai, J., Jiang, X., Zhou, J., Xu, J., Zhang, Z., Fan, L., et al. (2022) · Research Square · doi:10.21203/rs.3.rs-2211167/v1 · Cited by 2
Sakhuja, K., Hartono, S. R., Sanz, L. A., Ijiri, E., Darling, C. L., Dye, L., Iben, J., Chon, H., Cerritelli, S. M., Crouch, R. J., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.30.651504 · Cited by 2
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Chan, W. F., Johanson, T. M., & Allan, R. S. (2020) · Biochemical Society Transactions · doi:10.1042/bst20191104 · Cited by 1
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Dutton, C. E. (1881) · Science · doi:10.1126/science.os-2.66.453 · Cited by 1
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Herbert, A. G., Pavlov, F., Konovalov, D., & Poptsova, M. S. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.06.495008 · Cited by 1
KDM4-dependent DNA breaks at active promoters facilitate +1 nucleosome evictionPreprint
Imre, L., Nánási, P. P., Szatmári, I., Kókai, E., Austin, C. A., Dombrádi, V., & Szabó, G. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.14.548993 · Cited by 1
Sieg, J. P., Zeng, H., Pálová, H., Smeds, L., Mohanty, S. K., Lahnsteiner, A., Chiaromonte, F., & Makova, K. D. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.11.03.686349 · Cited by 2
Faculty Opinions recommendation of Dynamic turnover of paused Pol II complexes at human promoters.
Tora, L., & El-Saafin, F. (2018) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.733879465.793553445
Faculty Opinions recommendation of Genome organization drives chromosome fragility.
El‐Khamisy, S. F. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.727835478.793556820
Faculty Opinions recommendation of Genome organization drives chromosome fragility.
Kaufmann, S. H. (2019) · Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature · doi:10.3410/f.727835478.793565203
Costea, J., Schoeberl, U. E., Malzl, D., von der Linde, M., Fitz, J., Makharova, M., Goloborodko, A. A., & Pavri, R. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4102622
Xu, J., Sun, X., Chen, Z., & Liu, Y. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4164236
Radial genome organization and cellular heterogeneity in quiescence
Laenen, G. (2024) · theses.fr (ABES) · doi:10.70675/769979d2z0966z4966za649z22d7ed97a7c4
Deriglazov, D. A., Petrova, N. V., Luzhin, A. V., Pavlenko, N. G., Tatarskiy, V. V., Kazakov, E. P., Kireev, I. I., Kurkin, A. V., Novoselov, A. M., Efremov, Y. M., et al. (2026) · Nucleus · doi:10.1080/19491034.2026.2672818
Werner, F., Cackett, G., Dulson, C., Sýkora, M., Pilotto, S., Roberts, A. P., & Gouge, J. (2026) · Research Square · doi:10.21203/rs.3.rs-10472653/v1
CpG islands act as topological sinks for transcription-induced DNA supercoilingPreprint
Naughton, C., Bonato, A., Chiang, M., Corless, S., Stocks, J., Grimes, G. R., Halliday, D., Bentivoglio, A., Brackley, C., Marenduzzo, D., et al. (2026) · bioRxiv · doi:10.64898/2026.08.24.746546
Host Factor Experiment (FLX0001-siSETX)
J. Craig Venter Institute, & University of Chicago (2015) · Influenza Research Database · doi:10.35094/qfnt-yj65
Host Factor Experiment (FLX0001-siXRN2)
J. Craig Venter Institute, & University of Chicago (2015) · Influenza Research Database · doi:10.35094/3bgk-x643
Wang, Q., Zhai, Z., Lian, Q., Song, D., & Li, J. J. (2026) · Cell Systems · doi:10.1016/j.cels.2026.101762 · Cited by 4
Metadata
- Authors
- Kouzine, F., Wojtowicz, D., Yamane, A., Resch, W., Kieffer-Kwon, K.-R., Bandle, R., Nelson, S., Nakahashi, H., Awasthi, P., Feigenbaum, L., Menoni, H., Hoeijmakers, J., Vermeulen, W., Ge, H., Przytycka, T. M., Levens, D., & Casellas, R.
- Affiliations
- National Institutes of Health (US)
- Erasmus MC (NL)
- Corresponding author
- Levens, David
- Casellas, Rafael
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2013-05
- Volume
- 153
- Issue
- 5
- Pages
- 988-999
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3684982
- OpenAlex
- W1991098988
- Cited by
- 154
- References
- 83
- Citations by year
- 2026: 5 · 2025: 4 · 2024: 6 · 2023: 9 · 2022: 16 · 2021: 6 · 2020: 11 · 2019: 12 · 2018: 13 · 2017: 11 · 2016: 16 · 2015: 13 · 2014: 19 · 2013: 12
- FWCI
- 9.20
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- EUR Research Repository (Erasmus University Rotterdam) (submittedVersion)
- Funders
- Cancer Research Institute
- National Institutes of Health
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (ZIAAR041149)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- promoter melting, naive lymphocytes, lymphocyte activation, transcriptional activation, RNA polymerase II, abortive transcription, TFIIH, XPB helicase, XPD helicase, single-stranded DNA, preinitiation complex, polymerase pausing
- MeSH terms
- Animals, B-Lymphocytes, DNA, Single-Stranded, Enhancer Elements, Genetic, Gene Expression Regulation, Humans, Lymphocyte Activation, Lymphocytes, Promoter Regions, Genetic, Transcription, Genetic, Cell Line, Tumor, Mice, Transcription Factor TFIIH, Genome-Wide Association Study
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