The DOI matches its Crossref record; 83 of the 83 references it cites were found in a registry or an index.
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.
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?
In the citing paper
“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]
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
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
Clonal selection and learning in the antibody system
Rajewsky, K. (1996) · Nature · doi:10.1038/381751a0 · Cited by 1,701
Transcriptional Amplification in Tumor Cells with Elevated c-Myc
Lin, C. Y., Lovén, J., Rahl, P. B., Paranal, R. M., Burge, C. B., Bradner, J. E., Lee, T. I., & Young, R. A. (2012) · Cell · doi:10.1016/j.cell.2012.08.026 · Cited by 1,543
Dynamic Regulation of Nucleosome Positioning in the Human Genome
Schones, D. E., Cui, K., Cuddapah, S., Roh, T., Barski, A., Wang, Z., Wei, G., & Zhao, K. (2008) · Cell · doi:10.1016/j.cell.2008.02.022 · Cited by 1,473
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
Transcriptional activation by recruitment
Ptashne, M., & Gann, A. (1997) · Nature · doi:10.1038/386569a0 · Cited by 1,158
c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells
Nie, Z., Hu, G., Wei, G., Cui, K., Yamane, A., Resch, W., Wang, R., Green, D. R., Tessarollo, L., Casellas, R. C., et al. (2012) · Cell · doi:10.1016/j.cell.2012.08.033 · Cited by 1,106
Self-citationA clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Zang, C., Schones, D. E., Zeng, C., Cui, K., Zhao, K., & Peng, W. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp340 · Cited by 1,072
A high-resolution map of active promoters in the human genome
Kim, T. H., Barrera, L. O., Zheng, M., Qu, C., Singer, M. A., Richmond, T., Wu, Y., Green, R. D., & Ren, B. (2005) · Nature · doi:10.1038/nature03877 · Cited by 954
Regulation of plasma-cell development
Shelef, M. A., & Calame, K. L. (2005) · Nature reviews. Immunology · doi:10.1038/nri1572 · Cited by 917
TRANSCRIPTION OF EUKARYOTIC PROTEIN-CODING GENES
Lee, T. I., & Young, R. A. (2000) · Annual Review of Genetics · doi:10.1146/annurev.genet.34.1.77 · Cited by 889
Bentley, D. L., & Groudine, M. T. (1986) · Nature · doi:10.1038/321702a0 · Cited by 781
RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo
Zeitlinger, J., Stark, A., Kellis, M., Hong, J., Nechaev, S., Adelman, K., Levine, M., & Young, R. A. (2007) · Nature Genetics · doi:10.1038/ng.2007.26 · Cited by 766
RNA polymerase is poised for activation across the genome
Muse, G. W., Gilchrist, D. A., Nechaev, S., Shah, R., Parker, J. S., Grissom, S. F., Zeitlinger, J., & Adelman, K. (2007) · Nature Genetics · doi:10.1038/ng.2007.21 · Cited by 762
Hubbard, T., Aken, B. L., Ayling, S., Ballester, B., Beal, K. M., Bragin, E., Brent, S., Chen, Y., Clapham, P., Clarke, L., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn828 · Cited by 682
Revisiting Global Gene Expression Analysis
Lovén, J., Orlando, D. A., Sigova, A. A., Lin, C. Y., Rahl, P. B., Burge, C. B., Levens, D. L., Lee, T. I., & Young, R. A. (2012) · Cell · doi:10.1016/j.cell.2012.10.012 · Cited by 616
Self-citationDefining mechanisms that regulate RNA polymerase II transcription in vivo
Fuda, N. J., Ardehali, M. B., & Lis, J. T. (2009) · Nature · doi:10.1038/nature08449 · Cited by 576
Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis.
Keller, W. D. (1975) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.72.12.4876 · Cited by 541
Identification of Early Replicating Fragile Sites that Contribute to Genome Instability
Barlow, J. H., Faryabi, R. B., Callén, E., Wong, N., Malhowski, A. J., Chen, H. T., Gutierrez-Cruz, G., Sun, H., McKinnon, P. J., Wright, G. W., et al. (2013) · Cell · doi:10.1016/j.cell.2013.01.006 · Cited by 464
Self-citationRNA synthesis and histone acetylation during the course of gene activation in lymphocytes.
Pogo, B. G. T., Allfrey, V. G., & Mirsky, A. E. (1966) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.55.4.805 · Cited by 459
Relationship of CDK-activating kinase and RNA polymerase II CTD kinase TFIIH/TFIIK
Feaver, W. J., Svejstrup, J. Q., Henry, N. L., & Kornberg, R. D. (1994) · Cell · doi:10.1016/0092-8674(94)90040-x · Cited by 427
Rif1 Prevents Resection of DNA Breaks and Promotes Immunoglobulin Class Switching
Virgilio, M. D., Callén, E., Yamane, A., Zhang, W., Janković, M., Gitlin, A. D., Feldhahn, N., Resch, W., Oliveira, T. Y., Chait, B. T., et al. (2013) · Science · doi:10.1126/science.1230624 · Cited by 423
Self-citationA kinase–cyclin pair in the RNA polymerase II holoenzyme
Liao, S.-M., Zhang, J., Jeffery, D., Koleske, A. J., Thompson, C. M., Chao, D. M., Viljoen‐Bloom, M., Vuuren, H. J. J. V., & Young, R. A. (1995) · Nature · doi:10.1038/374193a0 · Cited by 419
DNA topology and a minimal set of basal factors for transcription by RNA polymerase II
Parvin, J. D., & Sharp, P. A. (1993) · Cell · doi:10.1016/0092-8674(93)90140-l · Cited by 384
Secrets of a double agent: CDK7 in cell-cycle control and transcription
Fisher, R. P. (2005) · Journal of Cell Science · doi:10.1242/jcs.02718 · Cited by 371
Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II
Goodrich, J. A., & Tjian, R. (1994) · Cell · doi:10.1016/0092-8674(94)90242-9 · Cited by 366
Gilmour, D. S., & Lis, J. T. (1986) · Molecular and Cellular Biology · doi:10.1128/mcb.6.11.3984 · Cited by 364
Transcriptional regulation and the role of diverse coactivators in animal cells
Roeder, R. G. (2004) · FEBS Letters · doi:10.1016/j.febslet.2004.12.007 · Cited by 355
Regulation of MicroRNA Expression and Abundance during Lymphopoiesis
Kuchen, S., Resch, W., Yamane, A., Kuo, N., Li, Z., Chakraborty, T., Wei, L., Laurence, A. D. J., Yasuda, T., Peng, S., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.05.009 · Cited by 324
Self-citationYamane, A., Resch, W., Kuo, N., Kuchen, S., Li, Z., Sun, H., Robbiani, D. F., McBride, K. M., Nussenzweig, M. C., & Casellas, R. C. (2010) · Nature Immunology · doi:10.1038/ni.1964 · Cited by 307
Self-citationThe functional response of upstream DNA to dynamic supercoiling in vivo
Kouzine, F., Sanford, S., Elisha-Feil, Z., & Levens, D. (2008) · Nature Structural &Molecular Biology · doi:10.1038/nsmb.1372 · Cited by 303
Self-citationMechanism of ATP-Dependent Promoter Melting by Transcription Factor IIH
Kim, T.-K., Ebright, R. H., & Reinberg, D. (2000) · Science · doi:10.1126/science.288.5470.1418 · Cited by 262
Holstege, F. C. P., van der Vliet, P. C., & Timmers, H. T. M. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00512.x · Cited by 257
RNA polymerase II elongation through chromatin
Orphanides, G., & Reinberg, D. (2000) · Nature · doi:10.1038/35035000 · Cited by 244
Radonjić, M., Andrau, J., Lijnzaad, P., Kemmeren, P., Kockelkorn, T. T. J. P., van Leenen, D., van Berkum, N. L., & Holstege, F. C. P. (2005) · Molecular Cell · doi:10.1016/j.molcel.2005.03.010 · Cited by 223
3′-End labeling of DNA with [α-32P] cordycepin-5′-triphosphate
Tu, C. D., & Cohen, S. N. (1980) · Gene · doi:10.1016/0378-1119(80)90135-3 · Cited by 221
DNA damage defines sites of recurrent chromosomal translocations in B lymphocytes
Hakim, O., Resch, W., Yamane, A., Klein, I. A., Kieffer-Kwon, K.-R., Janković, M., Oliveira, T. Y., Bothmer, A., Voss, T. C., Ansarah-Sobrinho, C., et al. (2012) · Nature · doi:10.1038/nature10909 · Cited by 204
Self-citationA Mouse Model for the Basal Transcription/DNA Repair Syndrome Trichothiodystrophy
de Boer, J., de Wit, J., STEEG, H. V., Berg, R. J. W., Morreau, H., Visser, P., Lehmann, A. R., Durán, M., Hoeijmakers, J. H. J., & Weeda, G. (1998) · Molecular Cell · doi:10.1016/s1097-2765(00)80098-2 · Cited by 194
Self-citationThree transitions in the RNA polymerase II transcription complex during initiation
Holstege, F. C. P., Fiedler, U., & Timmers, H. T. M. (1997) · The EMBO Journal · doi:10.1093/emboj/16.24.7468 · Cited by 193
Divergent transcription: A new feature of active promoters
Seila, A. C., Core, L. J., Lis, J. T., & Sharp, P. A. (2009) · Cell Cycle · doi:10.4161/cc.8.16.9305 · Cited by 177
The dynamic response of upstream DNA to transcription-generated torsional stress
Kouzine, F., Liu, J.-H., Sanford, S., Chung, H.-J., & Levens, D. (2004) · Nature Structural &Molecular Biology · doi:10.1038/nsmb848 · Cited by 165
Self-citationGenome-wide analysis reveals regulatory role of G4 DNA in gene transcriptionPreprint
Du, Z., Zhao, Y., & Li, N. (2007) · Genome Research · doi:10.1101/gr.6905408 · Cited by 165
Poised RNA Polymerase II Gives Pause for Thought
Margaritis, T., & Holstege, F. C. P. (2008) · Cell · doi:10.1016/j.cell.2008.04.027 · Cited by 157
Vermeulen, W., van Vuuren, A. J., Chipoulet, M., Schaeffer, L., Appeldoorn, E., Weeda, G., Jaspers, N. G. J., Priestley, A., Arlett, C. F., Lehmann, A. R., et al. (1994) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.1994.059.01.036 · Cited by 143
Self-citationChromatin condensation via the condensin II complex is required for peripheral T‐cell quiescence
Rawlings, J. S., Gatzka, M., Thomas, P. G., & Ihle, J. N. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.314 · Cited by 140
Sterner, D. E., Lee, J. M., Hardin, S. E., & Greenleaf, A. L. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.10.5716 · Cited by 136
Lifespans of naive, memory and effector lymphocytes
Sprent, J. (1993) · Current Opinion in Immunology · doi:10.1016/0952-7915(93)90065-z · Cited by 132
B cell activation: Three steps and their variations
Melchers, F., & Andersson, J. (1984) · Cell · doi:10.1016/0092-8674(84)90407-0 · Cited by 128
Sensitive mapping of recombination hotspots using sequencing-based detection of ssDNAPreprint
Khil, P. P., Smagulova, F. O., Brick, K., Camerini‐Otero, R. D., & Petukhova, G. V. (2012) · Genome Research · doi:10.1101/gr.130583.111 · Cited by 115
Gilmour, D. S., & Lis, J. T. (1986) · Molecular and Cellular Biology · doi:10.1128/mcb.6.11.3984-3989.1986 · Cited by 109
A temperature-sensitive disorder in basal transcription and DNA repair in humans
Vermeulen, W., Rademakers, S., Jaspers, N. G. J., Appeldoorn, E., Raams, A., Klein, B., Kleijer, W. J., Hansen, L. K., & Hoeijmakers, J. H. J. (2001) · Nature Genetics · doi:10.1038/85864 · Cited by 105
Self-citationYamane, A., Robbiani, D. F., Resch, W., Bothmer, A., Nakahashi, H., Oliveira, T. Y., Rommel, P. C., Brown, E. J., Nussenzweig, A., Nussenzweig, M. C., et al. (2013) · Cell Reports · doi:10.1016/j.celrep.2012.12.006 · Cited by 105
Self-citationSupercoil-driven DNA structures regulate genetic transactions
Kouzine, F. (2007) · Frontiers in bioscience · doi:10.2741/2398 · Cited by 103
Self-citationOhkuma, Y., Hashimoto, S., Wang, C. K., Horikoshi, M., & Roeder, R. G. (1995) · Molecular and Cellular Biology · doi:10.1128/mcb.15.9.4856 · Cited by 101
Non-B DB: a database of predicted non-B DNA-forming motifs in mammalian genomes
Cer, R. Z., Bruce, K. H., Mudunuri, U. S., Yi, M., Volfovsky, N., Luke, B. T., Bacolla, A., Collins, J., & Stephens, R. M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1170 · Cited by 98
Liu, M., Tolstorukov, M. Y., Zhurkin, V. B., Garges, S., & Adhya, S. L. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0401929101 · Cited by 95
Jaehning, J. A., Stewart, C. C., & Roeder, R. G. (1975) · Cell · doi:10.1016/0092-8674(75)90133-6 · Cited by 89
Klemsz, M. J., Justement, L. B., Palmer, E., & Cambier, J. C. (1989) · The Journal of Immunology · doi:10.4049/jimmunol.143.3.1032 · Cited by 88
Promoter escape by RNA polymerase II
Dvir, A. (2002) · Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression · doi:10.1016/s0167-4781(02)00453-0 · Cited by 83
Lutz, R. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.18.3873 · Cited by 82
Small-scale preparation of extracts from radiolabeled cells efficient in pre-mRNA splicing
Lee, K. A. W., & Green, M. R. (1990) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/0076-6879(90)81108-7 · Cited by 77
DNA structures at chromosomal translocation sites
Raghavan, S. C., & Lieber, M. R. (2006) · BioEssays · doi:10.1002/bies.20353 · Cited by 71
IL-4 protein expression and basal activation of Erk in vivo in follicular lymphoma
Calvo, K. R., Dabir, B., Kovach, A. E., Devor, C. B., Bandle, R., Bond, A., Shih, J. H., & Jaffe, E. S. (2008) · Blood · doi:10.1182/blood-2008-02-138933 · Cited by 64
Self-citationThe Analysis of Stress-Induced Duplex Destabilization in Long Genomic DNA Sequences
Benham, C. J., & Bi, C. (2004) · Journal of Computational Biology · doi:10.1089/cmb.2004.11.519 · Cited by 61
Differentiation Driven Changes in the Dynamic Organization of Basal Transcription Initiation
Giglia‐Mari, G., Theil, A. F., Mari, P., Mourgues, S., Nonnekens, J., Andrieux, L. O., de Wit, J., Miquel, C., Wijgers, N., Maas, A., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000220 · Cited by 58
Self-citationReversible G1 arrest in the cell cycle of human lymphoid cell lines by dimethyl sulfoxide
Sawai, M., Takase, K., Teraoka, H., & Tsukada, K. (1990) · Experimental Cell Research · doi:10.1016/0014-4827(90)90108-m · Cited by 58
TFIIH is an elongation factor of RNA polymerase I
Assfalg, R., Lebedev, A., Gonzalez, O. G., Schelling, A., Koch, S., & Iben, S. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr746 · Cited by 54
Pogo, B. G. T., Allfrey, V. G., & Mirsky, A. E. (1967) · The Journal of Cell Biology · doi:10.1083/jcb.35.2.477 · Cited by 45
Shklover, J., Weisman-Shomer, P., Yafe, A., & Fry, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1208 · Cited by 42
Transcription Factor TFIIH Is Required for Promoter Melting In Vivo
Guzmán, E., & Lis, J. T. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.8.5652 · Cited by 39
Zhou, Z.-X., Zhang, M., Xu, P., Takayama, Y., Xu, X., Huang, L., & Du, L. (2012) · Genome Research · doi:10.1101/gr.146357.112 · Cited by 39
Yafe, A., Shklover, J., Weisman-Shomer, P., Bengal, E., & Fry, M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn340 · Cited by 33
Mapping of RNA polymerase on mammalian genes in cells and nuclei.
Mirkovitch, J., & Darnell, J. E., Jr. (1992) · Molecular Biology of the Cell · doi:10.1091/mbc.3.10.1085 · Cited by 23
Jenne, A., & Famulok, M. (1999) · BioTechniques · doi:10.2144/99262bm15 · Cited by 13
Cited by
Sorted by citations
A survey of best practices for RNA-seq data analysis
Conesa, A., Madrigal, P., Tarazona, S., Gomez-Cabrero, D., Cervera, A., McPherson, A., Szcześniak, M. W., Gaffney, D. J., Elo, L. L., Zhang, X., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0881-8 · Cited by 2,794
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
Organization and regulation of gene transcription
Cramer, P. (2019) · Nature · doi:10.1038/s41586-019-1517-4 · Cited by 793
Selective transcriptional regulation by Myc in cellular growth control and lymphomagenesis
Sabò, A., Kress, T. R., Pelizzola, M., de Pretis, S., Gorski, M. M., Tesi, A., Morelli, M. J., Bora, P., Doni, M., Verrecchia, A., et al. (2014) · Nature · doi:10.1038/nature13537 · Cited by 496
T H 17 Cell Differentiation Is Regulated by the Circadian Clock
Yu, X., Rollins, D., Ruhn, K. A., Stubblefield, J. J., Green, C. B., Kashiwada, M., Rothman, P. B., Takahashi, J. S., & Hooper, L. V. (2013) · Science · doi:10.1126/science.1243884 · Cited by 451
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
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
