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.
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
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?
Including exogenous reference transcripts (spike-ins) is useful for quality control and for library-size normalization.
“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.
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 · see citing works
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 · see citing works
TopHat: discovering splice junctions with RNA-Seq
Trapnell, C., Pachter, L. S., & Salzberg, S. L. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp120 · Cited by 11,477 · see citing works
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 · see citing works
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× · see citing works
“(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 · see citing works
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 · see citing works
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 2,238 · see citing works
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 · see citing works
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 1,946 · see citing works
Clonal selection and learning in the antibody system
Rajewsky, K. (1996) · Nature · doi:10.1038/381751a0 · Cited by 1,701 · see citing works
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 1,498 · see citing works
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 1,396 · see citing works
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 · see citing works
Transcriptional activation by recruitment
Ptashne, M., & Gann, A. (1997) · Nature · doi:10.1038/386569a0 · Cited by 1,158 · see citing works
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 1,063 · see citing works
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 1,043 · see citing works
A high-resolution map of active promoters in the human genome
Kim, T. H., Barrera, L., Zheng, M., Qu, C.-X., Singer, M. A., Richmond, T., Wu, Y. N., Green, R. D., & Ren, B. (2005) · Nature · doi:10.1038/nature03877 · Cited by 1,019 · see citing works
Transcription of eukaryotic protein-coding genes.
Lee, T., & Young, R. (2000) · Annual Review of Genetics · doi:10.1146/annurev.genet.34.1.77 · Cited by 967 · see citing works
Regulation of plasma-cell development
Shelef, M. A., & Calame, K. L. (2005) · Nature reviews. Immunology · doi:10.1038/nri1572 · Cited by 881 · see citing works
Bentley, D. L., & Groudine, M. T. (1986) · Nature · doi:10.1038/321702a0 · Cited by 841 · see citing works
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 · see citing works
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 · see citing works
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 671 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
RNA 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 452 · see citing works
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 433 · see citing works
Self-citationRelationship 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 · see citing works
A 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 · see citing works
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 401 · see citing works
Self-citationDNA 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 · see citing works
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 · see citing works
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 365 · see citing works
Gilmour, D. S., & Lis, J. T. (1986) · Molecular and Cellular Biology · doi:10.1128/mcb.6.11.3984 · Cited by 364 · see citing works
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 340 · see citing works
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 · see citing works
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 · see citing works
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 289 · see citing works
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 · see citing works
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 · see citing works
RNA polymerase II elongation through chromatin
Orphanides, G., & Reinberg, D. (2000) · Nature · doi:10.1038/35035000 · Cited by 244 · see citing works
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 · see citing works
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 · see citing works
A 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 195 · see citing works
Self-citationDNA 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 195 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 161 · see citing works
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 151 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
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 · see citing works
Gilmour, D. S., & Lis, J. T. (1986) · Molecular and Cellular Biology · doi:10.1128/mcb.6.11.3984-3989.1986 · Cited by 109 · see citing works
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 · see citing works
Self-citationSupercoil-driven DNA structures regulate genetic transactions
Kouzine, F. (2007) · Frontiers in bioscience · doi:10.2741/2398 · Cited by 101 · see citing works
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 · see citing works
Yamane, 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 98 · see citing works
Self-citationNon-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 · see citing works
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 · see citing works
Jaehning, J. A., Stewart, C. C., & Roeder, R. G. (1975) · Cell · doi:10.1016/0092-8674(75)90133-6 · Cited by 89 · see citing works
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 · see citing works
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 · see citing works
Lutz, R. (2001) · Nucleic Acids Research · doi:10.1093/nar/29.18.3873 · Cited by 82 · see citing works
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 · see citing works
DNA structures at chromosomal translocation sites
Raghavan, S. C., & Lieber, M. R. (2006) · BioEssays · doi:10.1002/bies.20353 · Cited by 71 · see citing works
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 · see citing works
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 · see citing works
Reversible 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 · see citing works
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 57 · see citing works
Self-citationTFIIH 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 · see citing works
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 · see citing works
Zhou, Z.-X., Zhang, M.-J., Peng, X., Takayama, Y., Xu, X.-Y., Huang, L.-Z., & Du, L.-L. (2013) · Genome Research · doi:10.1101/gr.146357.112 · Cited by 44 · see citing works
Shklover, J., Weisman-Shomer, P., Yafe, A., & Fry, M. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkp1208 · Cited by 42 · see citing works
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 · see citing works
Yafe, A., Shklover, J., Weisman-Shomer, P., Bengal, E., & Fry, M. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn340 · Cited by 33 · see citing works
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 · see citing works
Jenne, A., & Famulok, M. (1999) · BioTechniques · doi:10.2144/99262bm15 · Cited by 13 · see citing works
Flagged first, then by citations
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 · see citing works
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 · see citing works
Organization and regulation of gene transcription
Cramer, P. (2019) · Nature · doi:10.1038/s41586-019-1517-4 · Cited by 732 · see citing works
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 478 · see citing works
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 445 · see citing works
Genome Organization Drives Chromosome Fragility
Canela, A., Maman, Y., Jung, S., Wong, N., Callen, E., Day, A., Kieffer-Kwon, K.-R., Pekowska, A., Zhang, H., Rao, S. S. P., et al. (2017) · Cell · doi:10.1016/j.cell.2017.06.034 · Cited by 383 · see citing works
Self-citationKieffer-Kwon, K.-R., Tang, Z., Mathé, E. A., Qian, J., Sung, M., Li, G., Resch, W., Baek, S., Pruett, N. D., Grøntved, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.039 · Cited by 326 · see citing works
Self-citationTranscription initiation complex structures elucidate DNA opening
Plaschka, C., Hantsche-Grininger, M., Dienemann, C., Burzinski, C., Plitzko, J. M., & Cramer, P. (2016) · Nature · doi:10.1038/nature17990 · Cited by 270 · see citing works
B Cell Super-Enhancers and Regulatory Clusters Recruit AID Tumorigenic Activity
Qian, J., Wang, Q., Dose, M., Pruett, N. D., Kieffer-Kwon, K.-R., Resch, W., Liang, G., Tang, Z., Mathé, E. A., Benner, C. W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.013 · Cited by 266 · see citing works
Self-citationEl Khattabi, L., Zhao, H., Kalchschmidt, J., Young, N., Jung, S., Van Blerkom, P., Kieffer-Kwon, P., Kieffer-Kwon, K.-R., Park, S., Wang, X., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.011 · Cited by 244 · see citing works
Self-citationDynamics in protein translation sustaining T cell preparedness
Wolf, T., Jin, W., Zoppi, G., Vogel, I. A., Akhmedov, M., Bleck, C. K. E., Beltraminelli, T., Rieckmann, J. C., Ramirez, N. J., Benevento, M., et al. (2020) · Nature Immunology · doi:10.1038/s41590-020-0714-5 · Cited by 220 · see citing works
Kouzine, F., Wójtowicz, D., Baranello, L., Yamane, A., Nelson, S., Resch, W., Kieffer-Kwon, K.-R., Benham, C., Casellas, R., Przytycka, T., et al. (2017) · Cell Systems · doi:10.1016/j.cels.2017.01.013 · Cited by 202 · see citing works
Self-citationTalbert, P. B., & Henikoff, S. (2020) · Experimental Cell Research · doi:10.1016/j.yexcr.2020.111895 · Cited by 218 · see citing works
Structure of a bacterial RNA polymerase holoenzyme open promoter complex
Bae, B., Feklístov, A., Lass, A., Landick, R. C., & Darst, S. A. (2015) · eLife · doi:10.7554/elife.08504 · Cited by 211 · see citing works
Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation
Kieffer-Kwon, K.-R., Nimura, K., Rao, S. S. P., Xu, J., Jung, S., Pękowska, A., Dose, M., Stevens, E., Mathé, E. A., Dong, P., et al. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.07.013 · Cited by 204 · see citing works
Self-citationRNA Polymerase II C-Terminal Domain: Tethering Transcription to Transcript and Template
Corden, J. L. (2013) · Chemical Reviews · doi:10.1021/cr400158h · Cited by 184 · see citing works
Tee, W.-W., Shen, S. S., Oksuz, O., Narendra, V., & Reinberg, D. (2014) · Cell · doi:10.1016/j.cell.2014.01.009 · Cited by 165 · see citing works
Cell of Origin and Genetic Alterations in the Pathogenesis of Multiple Myeloma
Barwick, B. G., Gupta, V. A., Vertino, P. M., & Boise, L. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.01121 · Cited by 165 · see citing works
Non-B-Form DNA Is Enriched at Centromeres
Kasinathan, S., & Henikoff, S. (2018) · Molecular biology and evolution · doi:10.1093/molbev/msy010 · Cited by 147 · see citing works
Plasma cell differentiation is coupled to division-dependent DNA hypomethylation and gene regulation
Barwick, B. G., Scharer, C. D., Bally, A. P. R., & Boss, J. M. (2016) · Nature Immunology · doi:10.1038/ni.3519 · Cited by 152 · see citing works
Structural insights into transcription initiation by RNA polymerase II
Grünberg, S., & Hahn, S. (2013) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2013.09.002 · Cited by 149 · see citing works
Establishment of DNA-DNA Interactions by the Cohesin Ring
Murayama, Y., Samora, C. P., Kurokawa, Y., Iwasaki, H., & Uhlmann, F. (2018) · Cell · doi:10.1016/j.cell.2017.12.021 · Cited by 146 · see citing works
MYC 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 · see citing works
The essential and multifunctional TFIIH complex
Rimel, J. K., & Taatjes, D. J. (2018) · Protein Science · doi:10.1002/pro.3424 · Cited by 137 · see citing works
Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory
D’Urso, A., Takahashi, Y.-H., Xiong, B., Marone, J., Coukos, R., Randise-Hinchliff, C., Wang, J.-P., Shilatifard, A., & Brickner, J. H. (2016) · eLife · doi:10.7554/elife.16691 · Cited by 133 · see citing works
Plasma cell differentiation is controlled by multiple cell division-coupled epigenetic programs
Scharer, C. D., Barwick, B. G., Guo, M., Bally, A. P. R., & Boss, J. M. (2018) · Nature Communications · doi:10.1038/s41467-018-04125-8 · Cited by 130 · see citing works
Defining the location of promoter-associated R-loops at near-nucleotide resolution using bisDRIP-seq
Dumelie, J. G., & Jaffrey, S. R. (2017) · eLife · doi:10.7554/elife.28306 · Cited by 123 · see citing works
Wu, T., Lyu, R., You, Q., & He, C. (2020) · Nature Methods · doi:10.1038/s41592-020-0797-9 · Cited by 115 · see citing works
Chen, F., Gao, X., & Shilatifard, A. (2015) · Genes & Development · doi:10.1101/gad.246173.114 · Cited by 124 · see citing works
IL-4 orchestrates STAT6-mediated DNA demethylation leading to dendritic cell differentiation
Vento‐Tormo, R., Rodríguez‐Ubreva, J., de la Rica, L., Urquiza, J., Javierre, B. M., Sabarinathan, R., Luque, A., Esteller, M., Aran, J. M., Álvarez‐Errico, D., et al. (2016) · Genome biology · doi:10.1186/s13059-015-0863-2 · Cited by 120 · see citing works
Cortini, R., Barbi, M., Caré, B. R., Lavelle, C., Lesne, A., Mozziconacci, J., & Victor, J. (2016) · Reviews of Modern Physics · doi:10.1103/revmodphys.88.025002 · Cited by 111 · see citing works
Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding
Boyaci, H., Chen, J., Jansen, R., Darst, S. A., & Campbell, E. A. (2019) · Nature · doi:10.1038/s41586-018-0840-5 · Cited by 107 · see citing works
DNA Break Mapping Reveals Topoisomerase II Activity Genome-Wide
Baranello, L., Kouzine, F., Wójtowicz, D., Cui, K., Przytycka, T. M., Zhao, K., & Levens, D. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms150713111 · Cited by 92 · see citing works
Self-citationEffects of DNA supercoiling on chromatin architecture
Corless, S., & Gilbert, N. (2016) · Biophysical Reviews · doi:10.1007/s12551-016-0242-6 · Cited by 89 · see citing works
PRMT5 is essential for B cell development and germinal center dynamics
Litzler, L. C., Zahn, A., Meli, A. P., Hébert, S., Patenaude, A., Methot, S. P., Sprumont, A., Bois, T., Kitamura, D., Costantino, S., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07884-6 · Cited by 89 · see citing works
Regulation of the RNA polymerase II pre-initiation complex by its associated coactivators
Malik, S., & Roeder, R. G. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00630-9 · Cited by 89 · see citing works
Dynamic turnover of paused Pol II complexes at human promotersPreprint
Erickson, B., Sheridan, R. M., Cortázar, M. A., & Bentley, D. L. (2018) · Genes & Development · doi:10.1101/gad.316810.118 · Cited by 90 · see citing works
Transcribing Centromeres: Noncoding RNAs and Kinetochore Assembly
Talbert, P. B., & Henikoff, S. (2018) · Trends in Genetics · doi:10.1016/j.tig.2018.05.001 · Cited by 82 · see citing works
N6-methyladenine in DNA antagonizes SATB1 in early development
Li, Z., Zhao, S., Nelakanti, R. V., Lin, K., Wu, T., Alderman, M. H., Guo, C., Wang, P., Zhang, M., Wang, M., et al. (2020) · Nature · doi:10.1038/s41586-020-2500-9 · Cited by 80 · see citing works
A novel intermediate in transcription initiation by human mitochondrial RNA polymerase
Morozov, Y. I., Agaronyan, K., Cheung, A. C. M., Anikin, M., Cramer, P., & Temiakov, D. (2014) · Nucleic Acids Research · doi:10.1093/nar/gkt1356 · Cited by 79 · see citing works
Structure of RNA polymerase II pre-initiation complex at 2.9 Å defines initial DNA opening
Schilbach, S., Aibara, S., Dienemann, C., Grabbe, F., & Cramer, P. (2021) · Cell · doi:10.1016/j.cell.2021.05.012 · Cited by 76 · see citing works
Effects of DNA supercoiling on chromatin architecture
Corless, S., & Gilbert, N. (2016) · Biophysical Reviews · doi:10.1007/s12551-016-0210-1 · Cited by 72 · see citing works
The genetics and epigenetics of satellite centromeresPreprint
Talbert, P. B., & Henikoff, S. (2022) · Genome Research · doi:10.1101/gr.275351.121 · Cited by 74 · see citing works
An early Myc‐dependent transcriptional program orchestrates cell growth during B‐cell activation
Tesi, A., de Pretis, S., Furlan, M., Filipuzzi, M., Morelli, M. J., Andronache, A., Doni, M., Verrecchia, A., Pelizzola, M., Amati, B. B., et al. (2019) · EMBO Reports · doi:10.15252/embr.201947987 · Cited by 71 · see citing works
Senataxin suppresses the antiviral transcriptional response and controls viral biogenesis
Miller, M. S., Rialdi, A., Ho, J., Tilove, M., Martínez‐Gil, L., Moshkina, N., Peralta, Z., Noel, J. C., Melegari, C., Maestre, A. M., et al. (2015) · Nature Immunology · doi:10.1038/ni.3132 · Cited by 70 · see citing works
DNA topology and transcription
Kouzine, F., Levens, D., & Baranello, L. (2014) · Nucleus · doi:10.4161/nucl.28909 · Cited by 65 · see citing works
Self-citationComplete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS
Nagy, J., Grohmann, D., Cheung, A. C. M., Schulz, S., Smollett, K. L., Werner, F., & Michaelis, J. (2015) · Nature Communications · doi:10.1038/ncomms7161 · Cited by 62 · see citing works
“Stripe” transcription factors provide accessibility to co-binding partners in mammalian genomes
Zhao, Y., Vartak, S. V., Conte, A., Wang, X., Garcia, D. A., Stevens, E., Jung, S. K., Kieffer-Kwon, K.-R., Vian, L., Stodola, T. J., et al. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.06.029 · Cited by 62 · see citing works
Self-citationGC skew is a conserved property of unmethylated CpG island promoters across vertebrates
Hartono, S. R., Korf, I. F., & Chedin, F. L. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv811 · Cited by 60 · see citing works
Torsion-Mediated Interaction between Adjacent Genes
Meyer, S., & Beslon, G. (2014) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1003785 · Cited by 67 · see citing works
Cellular MYCro Economics: Balancing MYC Function with MYC ExpressionPreprint
Levens, D. (2013) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a014233 · Cited by 60 · see citing works
Self-citationPol II Docking and Pausing at Growth and Stress Genes in C. elegans
Maxwell, C. S., Kruesi, W. S., Core, L. J., Kurhanewicz, N. A., Waters, C. T., Lewarch, C. L., Antoshechkin, I. A., Lis, J. T., Meyer, B. J., & Baugh, L. R. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.01.008 · Cited by 59 · see citing works
Nuclear pore interactions with the genome
Sood, V., & Brickner, J. H. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2013.11.018 · Cited by 58 · see citing works
Pack, unpack, bend, twist, pull, push: the physical side of gene expression
Lavelle, C. (2014) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2014.01.001 · Cited by 54 · see citing works
Sutthibutpong, T., Matek, C., Benham, C. J., Slade, G. G., Noy, A., Laughton, C. A., Doye, J. P. K., Louis, A. A., & Harris, S. A. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw815 · Cited by 50 · see citing works
The RNA polymerase II preinitiation complex
Luse, D. S. (2013) · Transcription · doi:10.4161/trns.27050 · Cited by 49 · see citing works
Cellular MYCro Economics: Balancing MYC Function with MYC ExpressionPreprint
Levens, D. (2013) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a022483 · Cited by 46 · see citing works
Self-citationMechanical determinants of chromatin topology and gene expression
Jha, R., Levens, D., & Kouzine, F. (2022) · Nucleus · doi:10.1080/19491034.2022.2038868 · Cited by 46 · see citing works
Self-citationRahmutulla, B., Matsushita, K., Satoh, M., Seimiya, M., Tsuchida, S., Kubo, S., Shimada, H., Ohtsuka, M., Miyazaki, M., & Nomura, F. (2013) · Oncotarget · doi:10.18632/oncotarget.1650 · Cited by 45 · see citing works
Dang, J., Xu, Z., Xu, A., Liu, Y., Fu, Q., Wang, J., Huang, F., Zheng, Y., Qi, G., Sun, B., et al. (2020) · Journal of Autoimmunity · doi:10.1016/j.jaut.2020.102491 · Cited by 45 · see citing works
DNA denaturation bubbles: Free-energy landscape and nucleation/closure rates
Sicard, F., Destainville, N., & Manghi, M. (2015) · The Journal of Chemical Physics · doi:10.1063/1.4905668 · Cited by 43 · see citing works
KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal–assisted labeling
Lyu, R., Wu, T., Zhu, A. C., West-Szymanski, D. C., Weng, X., Chen, M., & He, C. (2022) · Nature Protocols · doi:10.1038/s41596-021-00647-6 · Cited by 43 · see citing works
Blombach, F., Smollett, K. L., Grohmann, D., & Werner, F. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.04.016 · Cited by 42 · see citing works
Chromosomal organization of transcription: in a nutshell
Meyer, S., Reverchon, S., Nasser, W., & Muskhelishvili, G. (2017) · Current Genetics · doi:10.1007/s00294-017-0785-5 · Cited by 37 · see citing works
A 50 year history of technologies that drove discovery in eukaryotic transcription regulation
Lis, J. T. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0288-9 · Cited by 40 · see citing works
Topoisomerase II contributes to DNA secondary structure-mediated double-stranded breaks
Szlachta, K. A., Manukyan, A., Raimer, H. M., Singh, S., Salamon, A., Guo, W., Lobachev, K. S., & Wang, Y. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa483 · Cited by 42 · see citing works
Wang, X., Fan, M., Kalis, S. L., Wei, L., & Scharff, M. D. (2014) · Nature Communications · doi:10.1038/ncomms5137 · Cited by 40 · see citing works
Zhang, Z. Z., Pannunzio, N. R., Han, L., Hsieh, C., Yu, K., & Lieber, M. R. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.06.021 · Cited by 41 · see citing works
Davari, K., Lichti, J., Gallus, C., Greulich, F., Uhlenhaut, N. H., Heinig, M., Friedel, C. C., & Glasmacher, E. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.03.069 · Cited by 36 · see citing works
Essential role for the histone acetyltransferase KAT7 in T cell development, fitness, and survival
Newman, D. M., Voss, A. K., Thomas, T., & Allan, R. S. (2016) · Journal of Leukocyte Biology · doi:10.1189/jlb.1ma0816-338r · Cited by 37 · see citing works
Kumari, R., Roy, U., Desai, S. S., Nilavar, N. M., van Nieuwenhuijze, A. E. M., Paranjape, A. M., Radha, G., Bawa, P., Srivastava, M., Nambiar, M., et al. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.109390 · Cited by 38 · see citing works
Why Two? On the Role of (A-)Symmetry in Negative Supercoiling of DNA by Gyrase
Klostermeier, D. (2018) · International Journal of Molecular Sciences · doi:10.3390/ijms19051489 · Cited by 36 · see citing works
Light, W. H., & Brickner, J. H. (2013) · Nucleus · doi:10.4161/nucl.26209 · Cited by 34 · see citing works
G-quadruplexes are promoter elements controlling nucleosome exclusion and RNA polymerase II pausing
Esnault, C., Aabidine, A. Z. E., Robert, M.-C., Cucchiarini, A., Magat, T., Pigeot, A., Bouchouika, S., García-Oliver, E., Gawron, K., Basyuk, E., et al. (2023) · bioRxiv · doi:10.1038/s41588-025-02263-6 · Cited by 32 · see citing works
Anti-FIRs (PUF60) auto-antibodies are detected in the sera of early-stage colon cancer patients
Kobayashi, S., Hoshino, T., Hiwasa, T., Satoh, M., Rahmutulla, B., Tsuchida, S., Komukai, Y., Tanaka, T., Matsubara, H., Shimada, H., et al. (2016) · Oncotarget · doi:10.18632/oncotarget.12696 · Cited by 31 · see citing works
Functional interactions between gyrase subunits are optimized in a species-specific manner
Weidlich, D., & Klostermeier, D. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.010245 · Cited by 30 · see citing works
AGO2 silences mobile transposons in the nucleus of quiescent cells
Sala, L., Kumar, M., Prajapat, M. K., Chandrasekhar, S., Cosby, R. L., Rocca, G. L., Macfarlan, T. S., Awasthi, P., Chari, R., Kruhlak, M. J., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01151-z · Cited by 30 · see citing works
Self-citationSalerno, F., Howden, A. J. M., Matheson, L. S., Gizlenci, Ö., Screen, M., Lingel, H., Brunner-Weinzierl, M. C., & Turner, M. (2023) · Nature Communications · doi:10.1038/s41467-023-40621-2 · Cited by 29 · see citing works
Topoisomerase IIbeta is required for proper retinal development and survival of postmitotic cells
Li, Y., Hao, H., Tzatzalos, E., Lin, R.-K., Doh, S. T., Liu, L. F., Lyu, Y. L., & Cai, L. (2014) · Biology Open · doi:10.1242/bio.20146767 · Cited by 28 · see citing works
Divergence of transcriptional landscape occurs early in B cell activation
Fowler, T., Garruss, A. S., Ghosh, A., De, S., Becker, K. G., Wood, W. H., Weirauch, M. T., Smale, S. T., Aronow, B. J., Sen, R., et al. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0012-x · Cited by 27 · see citing works
Dissecting the Roles of Divergent and Convergent Transcription in Chromosome Instability
Pannunzio, N. R., & Lieber, M. R. (2016) · Cell Reports · doi:10.1016/j.celrep.2015.12.098 · Cited by 27 · see citing works
SIST: stress-induced structural transitions in superhelical DNA
Zhabinskaya, D., Madden, S., & Benham, C. J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu657 · Cited by 26 · see citing works
Roadmap to a plasma cell: Epigenetic and transcriptional cues that guide B cell differentiation
Wiggins, K. J., & Scharer, C. D. (2020) · Immunological Reviews · doi:10.1111/imr.12934 · Cited by 29 · see citing works
Triple-helix potential of the mouse genome
Maekawa, K., Yamada, S., Sharma, R., Chaudhuri, J., & Keeney, S. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2203967119 · Cited by 24 · see citing works
Competitive superhelical transitions involving cruciform extrusion
Zhabinskaya, D., & Benham, C. J. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt733 · Cited by 24 · see citing works
Coming to terms with chromatin structure
Even‐Faitelson, L., Hassan‐Zadeh, V., Baghestani, Z., & Bazett‐Jones, D. P. (2015) · Chromosoma · doi:10.1007/s00412-015-0534-9 · Cited by 24 · see citing works
Thomsen, I., Kunowska, N., de Souza, R. A., Moody, A.-M., Crawford, G., Wang, Y.-F., Khadayate, S. P., Whilding, C., Strid, J., Karimi, M. M., et al. (2021) · The Journal of Immunology · doi:10.4049/jimmunol.2001367 · Cited by 21 · see citing works
Pistiki, A. C., Ramoji, A., Ryabchykov, O., Thomas-Rüddel, D. O., Press, A. T., Makarewicz, O., Giamarellos‐Bourboulis, E. J., Bauer, M. W., Bocklitz, T. W., Popp, J., et al. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910481 · Cited by 20 · see citing works
George-Alexander, L.-E., Watters, J. M., Reusch, J. A., Maurin, M. M., Nepon-Sixt, B. S., Vrzalikova, K., Alexandrow, M. G., Murray, P. G., & Wright, K. L. (2017) · Molecular Immunology · doi:10.1016/j.molimm.2017.08.016 · Cited by 19 · see citing works
Single Cell Imaging of Nuclear Architecture Changes
Morrish, R. B., Hermes, M., Metz, J., Stone, N., Pagliara, S., Chahwan, R., & Palombo, F. (2019) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2019.00141 · Cited by 20 · see citing works
Dynamic Opposition of Histone Modifications
Porras, A. M. G., Chory, E. J., & Gryder, B. E. (2022) · ACS Chemical Biology · doi:10.1021/acschembio.1c01000 · Cited by 18 · see citing works
Das, S., Karmakar, S., Venkatachalapathy, H., Jha, R., Batchelor, E., & Levens, D. (2024) · Molecular Cell · doi:10.1016/j.molcel.2024.10.006 · Cited by 18 · see citing works
Self-citationInterference of viral effector proteins with chromatin, transcription, and the epigenome
Marazzi, I., & García‐Sastre, A. (2015) · Current Opinion in Microbiology · doi:10.1016/j.mib.2015.06.009 · Cited by 18 · see citing works
Herbert, A. G., Pavlov, F., Konovalov, D., & Poptsova, M. S. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054884 · Cited by 16 · see citing works
Zhang, S., Zhu, I., Deng, T., Furusawa, T., Rochman, M., Vacchio, M. S., Bosselut, R., Yamane, A., Casellas, R. C., Landsman, D., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw323 · Cited by 17 · see citing works
Self-citationCellular and chromatin dynamics of antibody‐secreting plasma cells
Bortnick, A., & Murre, C. (2015) · Wiley Interdisciplinary Reviews Developmental Biology · doi:10.1002/wdev.213 · Cited by 17 · see citing works
Krassovsky, K., Ghosh, R. P., & Meyer, B. J. (2021) · Genome Research · doi:10.1101/gr.270082.120 · Cited by 15 · see citing works
Gilbert, N., & Marenduzzo, D. (2024) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2024.102448 · Cited by 16 · see citing works
Matsushita, K., KITAMURA, K., Rahmutulla, B., Tanaka, N., Ishige, T., Satoh, M., Hoshino, T., Miyagi, S., Mori, T., Itoga, S., et al. (2014) · Oncotarget · doi:10.18632/oncotarget.3244 · Cited by 16 · see citing works
Dhx33 promotes B-cell growth and proliferation by controlling activation-induced rRNA upregulation
He, X., Zhao, J., Adilijiang, A., Hong, P., Chen, P., Lin, X., Xie, J., Du, Y., Liu, Y., Lin, L., et al. (2023) · Cellular and Molecular Immunology · doi:10.1038/s41423-022-00972-0 · Cited by 15 · see citing works
- 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