Sequence-Directed Action of RSC Remodeler and General Regulatory Factors Modulates +1 Nucleosome Position to Facilitate Transcription
Open accessAbstract
Accessible chromatin is important for RNA polymerase II recruitment and transcription initiation at eukaryotic promoters. We investigated the mechanistic links between promoter DNA sequence, nucleosome positioning, and transcription. Our results indicate that positioning of the transcription start site-associated +1 nucleosome in yeast is critical for efficient TBP binding and is driven by two key factors, the essential chromatin remodeler RSC and a small set of ubiquitous general regulatory factors (GRFs). Our findings indicate that the strength and directionality of RSC action on promoter nucleosomes depends on the arrangement and proximity of two specific DNA motifs. This, together with the effect on nucleosome position observed in double depletion experiments, suggests that, despite their widespread co-localization, RSC and GRFs predominantly act through independent signals to generate accessible chromatin. Our results provide mechanistic insight into how the promoter DNA sequence instructs trans-acting factors to control nucleosome architecture and stimulate transcription initiation.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
Recruitment of transcription machinery to promoters is restricted by nucleosomes.
“Recruitment of transcription machinery to promoters is restricted by nucleosomes19.”
From SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes (2022) · cites this paper as [19]
Histone chaperones and ATP-dependent chromatin-remodelling complexes are important for gene regulation because they regulate nucleosome dynamics at promoters, restricting or increasing promoter accessibility for recruitment of transcription factors and RNA polymerase II (Pol II).
“Histone chaperones and ATP-dependent chromatin-remodelling complexes are accordingly important for gene regulation given they regulate nucleosome dynamics at promoters, restricting or increasing promoter accessibility for recruitment of transcription factors and RNA polymerase II (Pol II)19–23.”
From SWI/SNF and the histone chaperone Rtt106 drive expression of the Pleiotropic Drug Resistance network genes (2022) · cites this paper as [19]
Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works
Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes
Clapier, C. R., Iwasa, J., Cairns, B. R., & Peterson, C. L. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.26 · Cited by 1,305 · see citing works
The DNA-encoded nucleosome organization of a eukaryotic genome
Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A., Tillo, D., Field, Y., Leproust, E., Hughes, T., Lieb, J., Widom, J., et al. (2008) · Nature · doi:10.1038/nature07667 · Cited by 1,296 · see citing works
Ordered Recruitment of Chromatin Modifying and General Transcription Factors to the IFN-β Promoter
Agalioti, T., Lomvardas, S., Parekh, B. S., Yie, J., Maniatis, T., & Thanos, D. (2000) · Cell · doi:10.1016/s0092-8674(00)00169-0 · Cited by 737 · see citing works
Identification and Distinct Regulation of Yeast TATA Box-Containing Genes
Basehoar, A. D., Zanton, S. J., & Pugh, B. F. (2004) · Cell · doi:10.1016/s0092-8674(04)00205-3 · Cited by 686 · see citing works
Determinants of nucleosome positioning
Struhl, K., & Segal, E. (2013) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2506 · Cited by 685 · see citing works
A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genomePreprint
Mavrich, T. N., Ioshikhes, I. P., Venters, B. J., Jiang, C., Tomsho, L. P., Qi, J., Schuster, S. C., Albert, I. U., & Pugh, B. F. (2008) · Genome Research · doi:10.1101/gr.078261.108 · Cited by 673 · see citing works
Lorch, Y., LaPointe, J. W., & Kornberg, R. D. (1987) · Cell · doi:10.1016/0092-8674(87)90561-7 · Cited by 605 · see citing works
The Anchor-Away Technique: Rapid, Conditional Establishment of Yeast Mutant Phenotypes
Haruki, H., Nishikawa, J., & Laemmli, U. K. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.07.020 · Cited by 547 · see citing works
Genome-wide structure and organization of eukaryotic pre-initiation complexes
Rhee, H. S., & Pugh, B. F. (2012) · Nature · doi:10.1038/nature10799 · Cited by 496 · see citing works
Understanding nucleosome dynamics and their links to gene expression and DNA replication
Lai, W. K. M., & Pugh, B. F. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.47 · Cited by 495 · see citing works
Fundamentally Different Logic of Gene Regulation in Eukaryotes and Prokaryotes
Struhl, K. (1999) · Cell · doi:10.1016/s0092-8674(00)80599-1 · Cited by 486 · see citing works
Badis, G., Chan, E. T., van Bakel, H., Peña‐Castillo, L., Tillo, D., Tsui, K., Carlson, C. D., Gossett, A. J., Hasinoff, M. J., Warren, C. L., et al. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.11.020 · Cited by 472 · see citing works
Chromatin remodelling at promoters suppresses antisense transcription
Whitehouse, I., Rando, O. J., Delrow, J., & Tsukiyama, T. (2007) · Nature · doi:10.1038/nature06391 · Cited by 456 · see citing works
Poly(dA:dT) tracts: major determinants of nucleosome organization
Segal, E., & Widom, J. (2009) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2009.01.004 · Cited by 419 · see citing works
Mechanisms that Specify Promoter Nucleosome Location and Identity
Hartley, P. D., & Madhani, H. D. (2009) · Cell · doi:10.1016/j.cell.2009.02.043 · Cited by 406 · see citing works
Struhl, K. (1985) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.82.24.8419 · Cited by 404 · see citing works
Epigenome characterization at single base-pair resolution
Henikoff, J. G., Belsky, J. A., Krassovsky, K., MacAlpine, D. M., & Henikoff, S. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110731108 · Cited by 392 · see citing works
Nucleosomes Are Context-Specific, H2A.Z-Modulated Barriers to RNA Polymerase
Weber, C. M., Ramachandran, S., & Henikoff, S. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.02.014 · Cited by 386 · see citing works
Two strategies for gene regulation by promoter nucleosomesPreprint
Tirosh, I., & Barkai, N. (2008) · Genome Research · doi:10.1101/gr.076059.108 · Cited by 383 · see citing works
High-resolution nucleosome mapping reveals transcription-dependent promoter packagingPreprint
Weiner, A., Hughes, A. L., Yassour, M., Rando, O. J., & Friedman, N. (2009) · Genome Research · doi:10.1101/gr.098509.109 · Cited by 381 · see citing works
Pioneer transcription factors, chromatin dynamics, and cell fate control
Zaret, K. S., & Mango, S. E. (2016) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2015.12.003 · Cited by 337 · see citing works
Genome-wide Nucleosome Specificity and Directionality of Chromatin Remodelers
Yen, K., Vinayachandran, V., Batta, K., Koerber, R. T., & Pugh, B. F. (2012) · Cell · doi:10.1016/j.cell.2012.04.036 · Cited by 327 · see citing works
Histone Octamer Transfer by a Chromatin-Remodeling Complex
Lorch, Y., Zhang, M., & Kornberg, R. D. (1999) · Cell · doi:10.1016/s0092-8674(00)80551-6 · Cited by 301 · see citing works
An interactive environment for agile analysis and visualization of ChIP-sequencing data
Lerdrup, M., Johansen, J. V., Singh, S. A., & Hansen, K. H. (2016) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3180 · Cited by 278 · see citing works
Kemmeren, P., Sameith, K., van de Pasch, L. A. L., Benschop, J. J., Lenstra, T. L., Margaritis, T., O’Duibhir, E., Apweiler, E., van Wageningen, S., Ko, C. W., et al. (2014) · Cell · doi:10.1016/j.cell.2014.02.054 · Cited by 277 · see citing works
Self-citationGenomic Nucleosome Organization Reconstituted with Pure Proteins
Krietenstein, N., Wal, M., Watanabe, S., Park, B., Peterson, C. L., Pugh, B. F., & Korber, P. (2016) · Cell · doi:10.1016/j.cell.2016.09.045 · Cited by 274 · see citing works
Schmid, M., Durussel, T., & Laemmli, U. K. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.09.007 · Cited by 212 · see citing works
Nucleosome Sliding via TBP DNA Binding In Vivo
Lomvardas, S., & Thanos, D. (2001) · Cell · doi:10.1016/s0092-8674(01)00490-1 · Cited by 203 · see citing works
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
Zentner, G. E., Kasinathan, S., Xin, B., Rohs, R., & Henikoff, S. (2015) · Nature Communications · doi:10.1038/ncomms9733 · Cited by 196 · see citing works
High-resolution mapping of transcription factor binding sites on native chromatin
Kasinathan, S., Orsi, G. A., Zentner, G. E., Ahmad, K., & Henikoff, S. (2013) · Nature Methods · doi:10.1038/nmeth.2766 · Cited by 183 · see citing works
RSC regulates nucleosome positioning at Pol II genes and density at Pol III genes
Parnell, T. J., Huff, J. T., & Cairns, B. R. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601946 · Cited by 183 · see citing works
Nucleosome Stability Distinguishes Two Different Promoter Types at All Protein-Coding Genes in Yeast
Kubik, S., Bruzzone, M. J., Jacquet, P., Falcone, J.-L., Rougemont, J., & Shore, D. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.10.002 · Cited by 182 · see citing works
Self-citationChromatin Remodelers: From Function to Dysfunction
Längst, G., & Manelytė, L. (2015) · Genes · doi:10.3390/genes6020299 · Cited by 174 · see citing works
A RSC/Nucleosome Complex Determines Chromatin Architecture and Facilitates Activator Binding
Floer, M., Wang, X., Prabhu, V., Berrozpe, G., Narayan, S., Spagna, D., Alvarez, D., Kendall, J., Krasnitz, A., Stepansky, A., et al. (2010) · Cell · doi:10.1016/j.cell.2010.03.048 · Cited by 165 · see citing works
Nucleosome fragility reveals novel functional states of chromatin and poises genes for activationPreprint
Xi, Y., Yao, J., Chen, R., Li, W., & He, X. (2011) · Genome Research · doi:10.1101/gr.117101.110 · Cited by 143 · see citing works
Histone Tails and the H3 αN Helix Regulate Nucleosome Mobility and Stability
Ferreira, H. C., Somers, J., Webster, R., Flaus, A., & Owen‐Hughes, T. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.02229-06 · Cited by 134 · see citing works
Molecular mechanisms of ribosomal protein gene coregulationPreprint
Reja, R., Vinayachandran, V., Ghosh, S., & Pugh, B. F. (2015) · Genes & Development · doi:10.1101/gad.268896.115 · Cited by 132 · see citing works
Histone H3 tail acetylation modulates ATP-dependent remodeling through multiple mechanisms
Chatterjee, N., Sinha, D., Dechassa, M. L., Tan, S., Shogren‐Knaak, M. A., & Bartholomew, B. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr535 · Cited by 127 · see citing works
van Bakel, H., Tsui, K., Gebbia, M., Mnaimneh, S., Hughes, T. R., & Nislow, C. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003479 · Cited by 124 · see citing works
Structure of a RSC–nucleosome complex and insights into chromatin remodeling
Chaban, Y. L., Ezeokonkwo, C., Chung, W.-H., Zhang, F., Kornberg, R. D., Maier-Davis, B., Lorch, Y., & Asturias, F. J. (2008) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1524 · Cited by 124 · see citing works
Role of DNA sequence in chromatin remodeling and the formation of nucleosome-free regionsPreprint
Lorch, Y., Maier-Davis, B., & Kornberg, R. D. (2014) · Genes & Development · doi:10.1101/gad.250704.114 · Cited by 118 · see citing works
Kent, N. A., Adams, S., Moorhouse, A. J., & Paszkiewicz, K. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1183 · Cited by 118 · see citing works
Knight, B., Kubik, S., Ghosh, B., Bruzzone, M. J., Geertz, M., Martín, V. S., Dénervaud, N., Jacquet, P., Özkan, B., Rougemont, J., et al. (2014) · Genes & Development · doi:10.1101/gad.244434.114 · Cited by 115 · see citing works
Self-citationGanapathi, M., Palumbo, M. J., Ansari, S. A., He, Q., Tsui, K., Nislow, C., & Morse, R. H. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1161 · Cited by 115 · see citing works
ChIC and ChECGenomic Mapping of Chromatin Proteins
Schmid, M., Durussel, T., & Laemmli, U. K. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00540-4 · Cited by 104 · see citing works
HTSstation: A Web Application and Open-Access Libraries for High-Throughput Sequencing Data Analysis
David, F. P. A., Delafontaine, J., Carat, S., Ross, F. J., Lefebvre, G. C., Jarosz, Y., Sinclair, L., Noordermeer, D., Rougemont, J., & Leleu, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0085879 · Cited by 101 · see citing works
Lorch, Y., Zhang, M., & Kornberg, R. D. (2001) · Molecular Cell · doi:10.1016/s1097-2765(01)00157-5 · Cited by 97 · see citing works
Asymmetric nucleosomes flank promoters in the budding yeast genomePreprint
Ramachandran, S., Zentner, G. E., & Henikoff, S. (2014) · Genome Research · doi:10.1101/gr.182618.114 · Cited by 96 · see citing works
Yeast TFIID Serves as a Coactivator for Rap1p by Direct Protein-Protein Interaction
Garbett, K. A., Tripathi, M. K., Cencki, B., Layer, J. H., & Weil, P. A. (2006) · Molecular and Cellular Biology · doi:10.1128/mcb.01558-06 · Cited by 93 · see citing works
Clapier, C. R., Kasten, M. M., Parnell, T. J., Viswanathan, R., Szerlong, H. J., Sirinakis, G., Zhang, Y., & Cairns, B. R. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.03.032 · Cited by 91 · see citing works
Godde, J. S., Nakatani, Y., & Wolffe, A. P. (1995) · Nucleic Acids Research · doi:10.1093/nar/23.22.4557 · Cited by 85 · see citing works
Yarragudi, A., Miyake, T., Li, R., & Morse, R. H. (2004) · Molecular and Cellular Biology · doi:10.1128/mcb.24.20.9152-9164.2004 · Cited by 84 · see citing works
Constitutive turnover of histone H2A.Z at yeast promoters requires the preinitiation complex
Tramantano, M., Sun, L., Au, C., Labuz, D., Liu, Z., Chou, M., Shen, C., & Luk, E. (2016) · eLife · doi:10.7554/elife.14243 · Cited by 84 · see citing works
Ganguli, D., Chereji, R. V., Iben, J., Cole, H. A., & Clark, D. J. (2014) · Genome Research · doi:10.1101/gr.177014.114 · Cited by 82 · see citing works
Nucleosome repositioning underlies dynamic gene expressionPreprint
Nocetti, N., & Whitehouse, I. (2016) · Genes & Development · doi:10.1101/gad.274910.115 · Cited by 79 · see citing works
Martínez‐Campa, C., Politis, P. K., Moreau, J.-L., Kent, N., GOODALL, J. C., Mellor, J., & Goding, C. R. (2004) · Molecular Cell · doi:10.1016/j.molcel.2004.05.022 · Cited by 77 · see citing works
The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism
Parnell, T. J., Schlichter, A., Wilson, B. G., & Cairns, B. R. (2015) · eLife · doi:10.7554/elife.06073 · Cited by 70 · see citing works
A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeastPreprint
Zaugg, J. B., & Luscombe, N. M. (2011) · Genome Research · doi:10.1101/gr.124099.111 · Cited by 52 · see citing works
Nucleosome positioning in yeasts: methods, maps, and mechanisms
Lieleg, C., Krietenstein, N., Walker, M., & Korber, P. (2014) · Chromosoma · doi:10.1007/s00412-014-0501-x · Cited by 51 · see citing works
The Sequence of Nucleosomal DNA Modulates Sliding by the Chd1 Chromatin Remodeler
Winger, J., & Bowman, G. D. (2017) · Journal of Molecular Biology · doi:10.1016/j.jmb.2017.02.002 · Cited by 51 · see citing works
Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters
de Jonge, W. J., O’Duibhir, E., Lijnzaad, P., van Leenen, D., Koerkamp, M. J. A. G., Kemmeren, P., & Holstege, F. C. P. (2016) · The EMBO Journal · doi:10.15252/embj.201695621 · Cited by 47 · see citing works
Self-citationChromatin-remodeling and the initiation of transcription
Lorch, Y., & Kornberg, R. D. (2015) · Quarterly Reviews of Biophysics · doi:10.1017/s0033583515000116 · Cited by 41 · see citing works
Wu, R., & Li, H. (2010) · Genome Research · doi:10.1101/gr.103226.109 · Cited by 40 · see citing works
Kasahara, K., Ohyama, Y., & Kokubo, T. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkq1334 · Cited by 29 · see citing works
Poly-dA:dT Tracts Form an In Vivo Nucleosomal Turnstile
de Boer, C. G., & Hughes, T. R. (2014) · PLoS ONE · doi:10.1371/journal.pone.0110479 · Cited by 21 · see citing works
The Transcriptional Repressor Activator Protein Rap1p Is a Direct Regulator of TATA-binding Protein
Bendjennat, M., & Weil, P. A. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m709436200 · Cited by 14 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Generating specificity in genome regulation through transcription factor sensitivity to chromatin
Isbel, L., Grand, R. S., & Schübeler, D. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00512-6 · Cited by 149 · see citing works
Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome
Wagner, F., Dienemann, C., Wang, H., Stützer, A., Tegunov, D., Urlaub, H., & Cramer, P. (2020) · Nature · doi:10.1038/s41586-020-2088-0 · Cited by 141 · see citing works
RSC-Associated Subnucleosomes Define MNase-Sensitive Promoters in Yeast
Brahma, S., & Henikoff, S. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.046 · Cited by 137 · see citing works
Energy-driven genome regulation by ATP-dependent chromatin remodellers
Eustermann, S., Patel, A. B., Hopfner, K., He, Y., & Korber, P. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00683-y · Cited by 139 · see citing works
Opposing chromatin remodelers control transcription initiation frequency and start site selection
Kubik, S., Bruzzone, M. J., Challal, D., Dreos, R., Mattarocci, S., Bucher, P., Libri, D., & Shore, D. (2019) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0273-3 · Cited by 126 · see citing works
Self-citationBeads on a string—nucleosome array arrangements and folding of the chromatin fiber
Baldi, S., Korber, P., & Becker, P. B. (2020) · Nature Structural & Molecular Biology · doi:10.1038/s41594-019-0368-x · Cited by 112 · see citing works
Spatiotemporal coordination of transcription preinitiation complex assembly in live cells
Nguyen, V. Q., Ranjan, A., Liu, S., Tang, X., Ling, Y. H., Wisniewski, J., Mizuguchi, G., Li, K. Y., Jou, V., Zheng, Q., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.022 · Cited by 115 · see citing works
Old cogs, new tricks: the evolution of gene expression in a chromatin context
Talbert, P. B., Meers, M. P., & Henikoff, S. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0105-7 · Cited by 108 · see citing works
Aksenova, A. Y., & Mirkin, S. M. (2019) · Genes · doi:10.3390/genes10020118 · Cited by 110 · see citing works
Chromatin Fiber Invasion and Nucleosome Displacement by the Rap1 Transcription Factor
Mivelaz, M., Cao, A.-M., Kubik, S., Zencir, S., Hovius, R., Boichenko, I., Stachowicz, A. M., Kurat, C. F., Shore, D., & Fierz, B. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.10.025 · Cited by 99 · see citing works
Self-citationImpacts of Epigenetic Processes on the Health and Productivity of Livestock
Wang, M., & Ibeagha-Awemu, E. M. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2020.613636 · Cited by 101 · see citing works
Epigenome Regulation by Dynamic Nucleosome Unwrapping
Brahma, S., & Henikoff, S. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2019.09.003 · Cited by 88 · see citing works
Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genomePreprint
Oberbeckmann, E., Wolff, M. R., Krietenstein, N., Heron, M., Ellins, J. L., Schmid, A., Krebs, S., Blum, H., Gerland, U., & Korber, P. (2019) · Genome Research · doi:10.1101/gr.253419.119 · Cited by 90 · see citing works
Klein-Brill, A., Joseph-Strauss, D., Chappleboim, A., & Friedman, N. (2019) · Cell Reports · doi:10.1016/j.celrep.2018.12.020 · Cited by 88 · see citing works
A Role for Chromatin Remodeling in Cohesin Loading onto Chromosomes
Muñoz, S., Minamino, M., Casas-Delucchi, C. S., Patel, H., & Uhlmann, F. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.027 · Cited by 88 · see citing works
Ruler elements in chromatin remodelers set nucleosome array spacing and phasing
Oberbeckmann, E., Niebauer, V., Watanabe, S., Farnung, L., Moldt, M., Schmid, A., Cramer, P., Peterson, C. L., Eustermann, S., Hopfner, K., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23015-0 · Cited by 80 · see citing works
Epigenetic pioneering by SWI/SNF family remodelers
Ahmad, K., Brahma, S., & Henikoff, S. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.10.045 · Cited by 74 · see citing works
Kim, J. M., Visanpattanasin, P., Jou, V., Liu, S., Tang, X., Zheng, Q., Li, K. Y., Snedeker, J. C., Lavis, L. D., Lionnet, T., et al. (2021) · eLife · doi:10.7554/elife.69387 · Cited by 64 · see citing works
Challal, D., Barucco, M., Kubik, S., Feuerbach, F., Candelli, T., Geoffroy, H., Benaksas, C., Shore, D., & Libri, D. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.11.037 · Cited by 60 · see citing works
Self-citationAlbert, B., Tomassetti, S., Gloor, Y. S., Dilg, D., Mattarocci, S., Kubik, S., Hafner, L., & Shore, D. (2019) · Genes & Development · doi:10.1101/gad.322040.118 · Cited by 62 · see citing works
Self-citationGenome information processing by the INO80 chromatin remodeler positions nucleosomes
Oberbeckmann, E., Krietenstein, N., Niebauer, V., Wang, Y., Schall, K., Moldt, M., Straub, T., Rohs, R., Hopfner, K., Korber, P., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23016-z · Cited by 60 · see citing works
Structure of nucleosome-bound human PBAF complex
Wang, L., Yu, J., Yu, Z., Wang, Q., Li, W., Ren, Y., Chen, Z., He, S., & Xu, Y. (2022) · Nature Communications · doi:10.1038/s41467-022-34859-5 · Cited by 59 · see citing works
Distinct patterns of histone acetyltransferase and Mediator deployment at yeast protein-coding genesPreprint
Bruzzone, M. J., Grünberg, S., Kubik, S., Zentner, G. E., & Shore, D. (2018) · Genes & Development · doi:10.1101/gad.312173.118 · Cited by 57 · see citing works
Self-citationNucleosome Positioning and Spacing: From Mechanism to Function
Singh, A. K., & Mueller‐Planitz, F. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.166847 · Cited by 54 · see citing works
Chromatin Remodelers in the 3D Nuclear Compartment
Magaña‐Acosta, M., & Valadéz-Graham, V. (2020) · Frontiers in Genetics · doi:10.3389/fgene.2020.600615 · Cited by 52 · see citing works
Mechanisms coordinating ribosomal protein gene transcription in response to stress
Zencir, S., Dilg, D., Rueda-Mejia, M. P., Shore, D., & Albert, B. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa852 · Cited by 51 · see citing works
Self-citationRepression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor
Wu, A. C. K., Patel, H., Chia, M., Moretto, F., Frith, D., Snijders, A. P., & van Werven, F. J. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.10.018 · Cited by 50 · see citing works
The biogenesis and function of nucleosome arrays
Singh, A. K., Schauer, T., Pfaller, L., Straub, T., & Mueller‐Planitz, F. (2021) · Nature Communications · doi:10.1038/s41467-021-27285-6 · Cited by 45 · see citing works
Langstein-Skora, I., Schmid, A., Huth, F., Shabani, D., Spechtenhauser, L., Likhodeeva, M., Kunert, F., Metzner, F. J., Emenecker, R. J., Richardson, M. O. G., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.02.10.480018 · Cited by 47 · see citing works
Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer
Clapier, C. R. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22115578 · Cited by 46 · see citing works
Structures of transcription preinitiation complex engaged with the +1 nucleosome
Wang, H., Schilbach, S., Ninov, M., Urlaub, H., & Cramer, P. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00865-w · Cited by 37 · see citing works
Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast
Prajapati, H. K., Ocampo, J., & Clark, D. J. (2020) · Biology · doi:10.3390/biology9080190 · Cited by 40 · see citing works
Diego‐Martin, B., Pérez-Alemany, J., Candela-Ferre, J., Corbalán-Acedo, A., Pereyra, J., Alabadı́, D., Jami‐Alahmadi, Y., Wohlschlegel, J. A., & Gallego‐Bartolomé, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac826 · Cited by 39 · see citing works
Dynamic epistasis analysis reveals how chromatin remodeling regulates transcriptional bursting
Brouwer, I., Kerklingh, E., van Leeuwen, F., & Lenstra, T. L. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-00981-1 · Cited by 38 · see citing works
Condensin-Mediated Chromosome Folding and Internal Telomeres Drive Dicentric Severing by Cytokinesis
Guérin, T. M., Béneut, C., Barinova, N., López, V., Lazar‐Stefanita, L., Deshayes, A., Thierry, A., Koszul, R., Dubrana, K., & Marcand, S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.05.021 · Cited by 32 · see citing works
DNA Double Strand Break Repair and Its Control by Nucleosome Remodeling
Karl, L., Peritore, M., Galanti, L., & Pfander, B. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2021.821543 · Cited by 37 · see citing works
Structures and implications of TBP–nucleosome complexes
Wang, H., Xiong, L., & Cramer, P. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2108859118 · Cited by 36 · see citing works
Specialization of the chromatin remodeler RSC to mobilize partially-unwrapped nucleosomes
Schlichter, A., Kasten, M. M., Parnell, T. J., & Cairns, B. R. (2020) · eLife · doi:10.7554/elife.58130 · Cited by 32 · see citing works
SWI/SNF-dependent genes are defined by their chromatin landscape
Basurto-Cayuela, L., Guerrero-Martinez, J. A., Gómez-Marín, E., Sánchez-Escabias, E., Escaño‐Maestre, M., Ceballos-Chávez, M., & Reyes, J. C. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113855 · Cited by 30 · see citing works
Fine Chromatin-Driven Mechanism of Transcription Interference by Antisense Noncoding Transcription
Gill, J. K., Maffioletti, A., García-Molinero, V., Stutz, F., & Soudet, J. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107612 · Cited by 30 · see citing works
Partitioned usage of chromatin remodelers by nucleosome-displacing factors
Chen, H., Kharerin, H., Dhasarathy, A., Kladde, M. P., & Bai, L. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111250 · Cited by 30 · see citing works
Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning
Buitrago, D., Codó, L., Illa, R., de Jorge, P., Battistini, F., Flores, O., Bayarri, G., Royo, R., del Pino, M., Heath, S. C., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz759 · Cited by 27 · see citing works
ATP-dependent remodeling of chromatin condensates reveals distinct mesoscale outcomes
Moore, C. M., Wong, E. V., Kaur, U., Chio, U. S., Zhou, Z., Ostrowski, M. S., Wu, K., Irkliyenko, I., Wang, S., Ramani, V., et al. (2025) · Science · doi:10.1126/science.adr0018 · Cited by 28 · see citing works
Hendy, O., Serebreni, L., Bergauer, K., Muerdter, F., Huber, L. A., Nemčko, F., & Stark, A. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.08.019 · Cited by 27 · see citing works
Biernat, E., Kinney, J., Dunlap, K. N., Rizza, C., & Govind, C. K. (2021) · Genetics · doi:10.1093/genetics/iyab021 · Cited by 27 · see citing works
Gnügge, R., & Symington, L. S. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa833 · Cited by 28 · see citing works
Nucleosome-directed replication origin licensing independent of a consensus DNA sequence
Li, S., Wasserman, M. R., Yurieva, O., Bai, L., O’Donnell, M. E., & Liu, S. (2022) · Nature Communications · doi:10.1038/s41467-022-32657-7 · Cited by 26 · see citing works
RSC primes the quiescent genome for hypertranscription upon cell-cycle re-entry
Cucinotta, C. E., Dell, R., Braceros, K. C. A., & Tsukiyama, T. (2021) · eLife · doi:10.7554/elife.67033 · Cited by 25 · see citing works
Managing the Steady State Chromatin Landscape by Nucleosome Dynamics
Ahmad, K., Henikoff, S., & Ramachandran, S. (2022) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-032620-104508 · Cited by 25 · see citing works
Crosstalk between chromatin structure, cohesin activity and transcription
Maya‐Miles, D., Andújar, E., Pérez-Alegre, M., Murillo-Pineda, M., Barrientos‐Moreno, M., Cabello-Lobato, M. J., Gómez-Marín, E., Morillo‐Huesca, M., & Prado, F. (2019) · Epigenetics & Chromatin · doi:10.1186/s13072-019-0293-6 · Cited by 23 · see citing works
The ACF chromatin-remodeling complex is essential for Polycomb repression
Wiles, E. T., Mumford, C. C., McNaught, K. J., Tanizawa, H., & Selker, E. U. (2022) · eLife · doi:10.7554/elife.77595 · Cited by 22 · see citing works
Distinct roles for RSC and SWI/SNF chromatin remodelers in genomic excision repairPreprint
Bohm, K. A., Hodges, A. J., Czaja, W., Selvam, K., Smerdon, M. J., Mao, P., & Wyrick, J. J. (2021) · Genome Research · doi:10.1101/gr.274373.120 · Cited by 23 · see citing works
The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo
Barnes, T., & Korber, P. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22158233 · Cited by 22 · see citing works
Pervasive transcription: a controlled risk
Villa, T., & Porrúa, O. (2022) · FEBS Journal · doi:10.1111/febs.16530 · Cited by 20 · see citing works
Dynamic 1D search and processive nucleosome translocations by RSC and ISW2 chromatin remodelers
Kim, J. M., Carcamo, C. C., Jazani, S., Xie, Z., Feng, X. A., Yamadi, M., Poyton, M. F., Holland, K. L., Grimm, J. B., Lavis, L. D., et al. (2023) · eLife · doi:10.7554/elife.91433 · Cited by 21 · see citing works
Shu, J., Ding, N., Liu, J., Cui, Y., & Chen, C. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1126 · Cited by 19 · see citing works
Peculiarities of Plasmodium falciparum Gene Regulation and Chromatin Structure
Watzlowik, M. T., Das, S., Meissner, M., & Längst, G. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22105168 · Cited by 18 · see citing works
Genome‐wide off‐rates reveal how DNA binding dynamics shape transcription factor function
de Jonge, W. J., Brok, M. O., Lijnzaad, P., Kemmeren, P., & Holstege, F. C. P. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209885 · Cited by 17 · see citing works
Self-citationNikolov, V. N., Malavia, D., & Kubota, T. (2022) · Nature Communications · doi:10.1038/s41467-022-29591-z · Cited by 16 · see citing works
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events
Allen, G., Weiss, B., Panasenko, O., Huch, S., Villányi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P. M., Liao, S. E., et al. (2022) · bioRxiv · doi:10.1186/s13059-023-02871-7 · Cited by 16 · see citing works
Self-citationChromatin remodelling comes into focus
Sundaramoorthy, R., & Owen‐Hughes, T. (2020) · F1000Research · doi:10.12688/f1000research.21933.1 · Cited by 16 · see citing works
Understanding transcription across scales: From base pairs to chromosomes
Vos, S. M. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.002 · Cited by 16 · see citing works
Langstein-Skora, I., Schmid, A., Huth, F., Shabani, D., Spechtenhauser, L., Likhodeeva, M., Kunert, F., Metzner, F. J., Emenecker, R. J., Richardson, M. O. G., et al. (2026) · Nature Cell Biology · doi:10.1038/s41556-025-01867-8 · Cited by 15 · see citing works
Kassem, S., Ferrari, P., Hughes, A. L., Soudet, J., Rando, O. J., & Strubin, M. (2020) · Science Advances · doi:10.1126/sciadv.abb0333 · Cited by 15 · see citing works
Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast
Kharerin, H., & Bai, L. (2021) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1008560 · Cited by 14 · see citing works
Engineered Chromatin Remodeling Proteins for Precise Nucleosome Positioning
Donovan, D. A., Crandall, J. G., Banks, O. G., Jensvold, Z. D., Truong, V. N., Dinwiddie, D., McKnight, L. E., & McKnight, J. N. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.10.046 · Cited by 13 · see citing works
High-resolution mapping demonstrates inhibition of DNA excision repair by transcription factors
Duan, M., Sivapragasam, S., Antony, J. S., Ulibarri, J., Hinz, J. M., Poon, G. M. K., Wyrick, J. J., & Mao, P. (2022) · eLife · doi:10.7554/elife.73943 · Cited by 13 · see citing works
Rawal, Y., Qiu, H., & Hinnebusch, A. G. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010277 · Cited by 11 · see citing works
High-Resolution Genome-Wide Occupancy in Candida spp. Using ChEC-seq
Tebbji, F., Khemiri, I., & Sellam, A. (2020) · mSphere · doi:10.1128/msphere.00646-20 · Cited by 11 · see citing works
Prasad, P., Sanyal, K., & Ghosh, S. K. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01303 · Cited by 11 · see citing works
Soudet, J., & Stutz, F. (2019) · BioEssays · doi:10.1002/bies.201900043 · Cited by 11 · see citing works
Chromatin architecture mapping by multiplex proximity tagging
Delamarre, A., Bailey, B. M., Yavid, J., Koche, R. P., Mohibullah, N., & Whitehouse, I. (2024) · Molecular Cell · doi:10.1016/j.molcel.2025.06.018 · Cited by 10 · see citing works
Interplay among transacting factors around promoter in the initial phases of transcription
Kumar, A., Chan, W. S., Taguchi, M., & Kono, H. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.04.008 · Cited by 10 · see citing works
André, K. M., Aiach, N. G., Martinez-Fernandez, V., Zeitler, L., Alberti, A., Goldar, A., Werner, M., Wilkes, C. D., & Soutourina, J. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.112465 · Cited by 10 · see citing works
ChEC-seq: a robust method to identify protein-DNA interactions genome-widePreprint
Bruzzone, M. J., Albert, B., Hafner, L., Kubik, S., Lezaja, A., Mattarocci, S., & Shore, D. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.02.18.431798 · Cited by 10 · see citing works
Self-citationThe yeast 2-micron plasmid Rep2 protein has Rep1-independent partitioning function
Mereshchuk, A., Johnstone, P. S., Chew, J. S. K., & Dobson, M. J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac810 · Cited by 9 · see citing works
VanBelzen, J., Duan, C., Brickner, D. G., & Brickner, J. H. (2024) · NAR Genomics and Bioinformatics · doi:10.1093/nargab/lqae012 · Cited by 9 · see citing works
Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription
Wu, A. C. K., & van Werven, F. J. (2019) · Transcription · doi:10.1080/21541264.2019.1608716 · Cited by 9 · see citing works
Reb1, Cbf1, and Pho4 Bias Histone Sliding and Deposition Away from Their Binding Sites
Kondalaji, S. G., & Bowman, G. D. (2021) · Molecular and Cellular Biology · doi:10.1128/mcb.00472-21 · Cited by 9 · see citing works
Barman, P., Sen, R., Kaja, A., Ferdoush, J., Guha, S., Govind, C. K., & Bhaumik, S. R. (2021) · Molecular and Cellular Biology · doi:10.1128/mcb.00368-21 · Cited by 7 · see citing works
Piwi regulates the usage of alternative transcription start sites in the Drosophila ovary
Chen, J., Liu, N., Qi, H., Neuenkirchen, N., Huang, Y., & Lin, H. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1160 · Cited by 6 · see citing works
Zencir, S., Dilg, D., Bruzzone, M. J., Stutz, F., Soudet, J., Shore, D., & Albert, B. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf276 · Cited by 6 · see citing works
Self-citationmacroH2A1 drives nucleosome dephasing and genome instability in histone humanized yeast
Haase, M. A. B., Lazar‐Stefanita, L., Ólafsson, G., Wudzinska, A. M., Shen, M. J., Truong, D. M., & Boeke, J. D. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114472 · Cited by 5 · see citing works
He, L., Zhang, P., Bai, H., Huang, J., & Yang, H. (2020) · Stem Cell Research & Therapy · doi:10.1186/s13287-020-01711-w · Cited by 6 · see citing works
Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational eventsPreprint
Allen, G. E., Weiss, B., Panasenko, O. O., Huch, S., Villányi, Z., Albert, B., Dilg, D., Zagatti, M., Schaughency, P., Liao, S. E., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.03.14.484207 · Cited by 6 · see citing works
Self-citationDynamic 1D Search and Processive Nucleosome Translocations by RSC and ISW2 Chromatin RemodelersPreprint
Kim, J. M., Carcamo, C. C., Jazani, S., Xie, Z., Feng, X. A., Yamadi, M., Poyton, M. F., Holland, K. L., Grimm, J. B., Lavis, L. D., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.06.13.544671 · Cited by 6 · see citing works
Moore, C. M., Wong, E., Kaur, U., Chio, U. S., Zhou, Z., Ostrowski, M., Wu, K., Irkliyenko, I., Wang, S., Ramani, V., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.10.611504 · Cited by 5 · see citing works
Transcriptional silencing in Saccharomyces cerevisiae: known unknowns
Dhillon, N., & Kamakaka, R. T. (2024) · Epigenetics & Chromatin · doi:10.1186/s13072-024-00553-7 · Cited by 4 · see citing works
Refined mechanism of promoter nucleosome-depleted regions resetting after replication
Zencir, S., Gill, J. K., Stutz, F., & Soudet, J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1025 · Cited by 4 · see citing works
RSC and GRFs confer promoter directionality by restricting divergent noncoding transcription
Wu, A. C. K., Vivori, C., Patel, H., Sideri, T. C., Moretto, F., & van Werven, F. J. (2022) · Life Science Alliance · doi:10.26508/lsa.202201394 · Cited by 4 · see citing works
Genome-wide regulation of Pol II, FACT, and Spt6 occupancies by RSC in Saccharomyces cerevisiae
Biernat, E., Verma, M., & Govind, C. K. (2023) · Gene · doi:10.1016/j.gene.2023.147959 · Cited by 4 · see citing works
Nucleosomal DNA has topological memory
Segura, J., Díaz‐Ingelmo, O., Martínez‐García, B., Ayats-Fraile, A., Nikolaou, C., & Roca, J. (2024) · Nature Communications · doi:10.1038/s41467-024-49023-4 · Cited by 4 · see citing works
The Avoidance of Purine Stretches by Cancer Mutations
Vikhorev, A. V., Savelev, I. V., Polesskaya, O., Rempel, M. M., Miller, R. A., Vetcher, A. A., & Myakishev-Rempel, M. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms252011050 · Cited by 4 · see citing works
Pioneers Invade the Nucleosomal Landscape
Henikoff, S., & Ramachandran, S. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.07.004 · Cited by 4 · see citing works
The Active Rather than Intrinsic Mechanism of Nucleosome Depletion by Poly(dA:dT) TractsPreprint
Barnes, T., & Korber, P. (2021) · Preprints.org · doi:10.20944/preprints202104.0579.v1 · Cited by 4 · see citing works
Biernat, E., Verma, M., Werick, M., Khan, U., Joseph, S., & Govind, C. K. (2025) · Molecular and Cellular Biology · doi:10.1080/10985549.2025.2555901 · Cited by 3 · see citing works
Cuevas-Bermúdez, A., Martinez-Fernandez, V., Garrido-Godino, A. I., Jordán‐Pla, A., Peñate, X., Martín‐Expósito, M., Gutiérrez, G., Govind, C. K., Chávez, S., Pelechano, V., et al. (2023) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2023.194995 · Cited by 3 · see citing works
Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration
Wu, K., Dhillon, N., Bajor, A., Abrahamsson, S., & Kamakaka, R. T. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113983 · Cited by 3 · see citing works
Unnatural Amino Acid Crosslinking for Increased Spatiotemporal Resolution of Chromatin Dynamics
Moleri, P., & Wilkins, B. J. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241612879 · Cited by 3 · see citing works
Lieleg, C., Novačić, A., Musladin, S., Schmid, A., Akpinar, G. G., Barbarić, S., & Korber, P. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054949 · Cited by 2 · see citing works
- Authors
- Kubik, S., O’Duibhir, E., de Jonge, W. J., Mattarocci, S., Albert, B., Falcone, J.-L., Bruzzone, M. J., Holstege, F. C. P., & Shore, D.
- Affiliations
- Institute of Genetics and Genomics in Geneva (CH)
- University Medical Center Utrecht (NL)
- University of Geneva (CH)
- Corresponding author
- Shore, David
- ORCID
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2018-07
- Volume
- 71
- Issue
- 1
- Pages
- 89-102.e5
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W2831181062
- Cited by
- 133
- References
- 67
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 19 · 2023: 23 · 2022: 21 · 2021: 22 · 2020: 17 · 2019: 17 · 2018: 5
- FWCI
- 5.42
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Swiss National Science Foundation (31003A_170153)
- Republic and Canton of Geneva
- European Research Council (671174)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Keywords
- nucleosome positioning, transcription initiation, TATA-binding protein, chromatin accessibility, RNA polymerase II recruitment, Saccharomyces cerevisiae, DNA sequence motifs, transcriptional regulation
- MeSH terms
- Nucleosomes, RNA Polymerase II, Saccharomyces cerevisiae, Transcription, Genetic, Saccharomyces cerevisiae Proteins, Chromatin Assembly and Disassembly
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