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A Pliable Mediator Acts as a Functional Rather Than an Architectural Bridge between Promoters and Enhancers
Open accessAbstract
While Mediator plays a key role in eukaryotic transcription, little is known about its mechanism of action. This study combines CRISPR-Cas9 genetic screens, degron assays, Hi-C, and cryoelectron microscopy (cryo-EM) to dissect the function and structure of mammalian Mediator (mMED). Deletion analyses in B, T, and embryonic stem cells (ESC) identified a core of essential subunits required for Pol II recruitment genome-wide. Conversely, loss of non-essential subunits mostly affects promoters linked to multiple enhancers. Contrary to current models, however, mMED and Pol II are dispensable to physically tether regulatory DNA, a topological activity requiring architectural proteins. Cryo-EM analysis revealed a conserved core, with non-essential subunits increasing structural complexity of the tail module, a primary transcription factor target. Changes in tail structure markedly increase Pol II and kinase module interactions. We propose that Mediator's structural pliability enables it to integrate and transmit regulatory signals and act as a functional, rather than an architectural bridge, between promoters and enhancers.
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“However, Promoter Capture Hi-C-based studies did not observe a significant change in enhancer–promoter contacts upon RNAP inhibition, including in cells rapidly depleted of cohesin or CTCF [349, 380].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [380]
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“However, it was shown recently that rapid removal of chromatin-bound Mediator and RNAP does not significantly affect chromosomal architecture, including enhancer–promoter interactions, in spite of triggering widespread transcriptional changes and cell cycle arrest [380].”
From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [380]
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Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,882
Wickham, H. (2016) · Use R! · doi:10.1007/978-3-319-24277-4 · Cited by 34,873
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
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
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Differential expression analysis for sequence count data
Anders, S., & Huber, W. (2010) · Genome Biology · doi:10.1186/gb-2010-11-10-r106 · Cited by 15,581
Multiplex Genome Engineering Using CRISPR/Cas Systems
Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., et al. (2013) · Science · doi:10.1126/science.1231143 · Cited by 15,339
Fast and accurate long-read alignment with Burrows-Wheeler transform.
Li, H., & Durbin, R. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp698 · Cited by 12,063
cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination
Punjani, A., Rubinstein, J. L., Fleet, D. J., & Brubaker, M. A. (2017) · Nature Methods · doi:10.1038/nmeth.4169 · Cited by 11,626
Genome engineering using the CRISPR-Cas9 system
Ran, F. A., Hsu, P. D., Wright, J., Agarwala, V., Scott, D. A., & Zhang, F. (2013) · Nature Protocols · doi:10.1038/nprot.2013.143 · Cited by 11,133
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Self-citationMotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy
Zheng, S. Q., Palovcak, E. J., Armache, J., Verba, K. A., Cheng, Y., & Agard, D. A. (2017) · Nature Methods · doi:10.1038/nmeth.4193 · Cited by 7,496
RELION: Implementation of a Bayesian approach to cryo-EM structure determination
Scheres, S. H. W. (2012) · Journal of Structural Biology · doi:10.1016/j.jsb.2012.09.006 · Cited by 5,446
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
Krueger, F., & Andrews, S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr167 · Cited by 5,275
Improved vectors and genome-wide libraries for CRISPR screening
Sanjana, N. E., Shalem, O., & Zhang, F. (2014) · Nature Methods · doi:10.1038/nmeth.3047 · Cited by 5,239
Genome-scale CRISPR-Cas9 knockout screening in human cells
Shalem, O., Sanjana, N. E., Hartenian, E., Shi, X., Scott, D. A., Mikkelsen, T. S., Heckl, D., Ebert, B. L., Root, D. E., Doench, J. G., et al. (2014) · Science · doi:10.1126/science.1247005 · Cited by 5,234
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments
Durand, N. C., Shamim, M. S., Machol, I., Rao, S. S. P., Huntley, M. H., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2016.07.002 · Cited by 3,860
Self-citationCoactivator condensation at super-enhancers links phase separation and gene control
Sabari, B. R., Dall’Agnese, A., Boija, A., Klein, I. A., Coffey, E. L., Shrinivas, K., Abraham, B. J., Hannett, N. M., Zamudio, A. V., Manteiga, J. C., et al. (2018) · Science · doi:10.1126/science.aar3958 · Cited by 2,595
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
Durand, N. C., Robinson, J., Shamim, M. S., Machol, I., Mesirov, J. P., Lander, E. S., & Aiden, E. L. (2016) · Cell Systems · doi:10.1016/j.cels.2015.07.012 · Cited by 2,421
Self-citationMediator and cohesin connect gene expression and chromatin architecture
Kagey, M. H., Newman, J. J., Bilodeau, S., Zhan, Y., Orlando, D. A., van Berkum, N. L., Ebmeier, C. C., Goossens, J., Rahl, P. B., Levine, S. S., et al. (2010) · Nature · doi:10.1038/nature09380 · Cited by 1,939
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Wu, T. D., & Nacu, S. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq057 · Cited by 1,894
Cohesin Loss Eliminates All Loop Domains
Rao, S. S. P., Huang, S.-C., Glenn St Hilaire, B., Engreitz, J. M., Perez, E. M., Kieffer-Kwon, K.-R., Sanborn, A. L., Johnstone, S. E., Bascom, G. D., Bochkov, I. D., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.026 · Cited by 1,883
Self-citationAutomated molecular microscopy: The new Leginon system
Suloway, C. J. M., Pulokas, J., Fellmann, D., Cheng, A., Guerra, F., Quispe, J. D., Stagg, S. M., Potter, C. S., & Carragher, B. O. (2005) · Journal of Structural Biology · doi:10.1016/j.jsb.2005.03.010 · Cited by 1,695
Mediator and RNA polymerase II clusters associate in transcription-dependent condensates
Cho, W.-K., Spille, J.-H., Hecht, M., Lee, C., Li, C., Grube, V., & Cisse, I. I. (2018) · Science · doi:10.1126/science.aar4199 · Cited by 1,403
Architectural protein subclasses shape 3D organization of genomes during lineage commitment
Phillips-Cremins, J. E., Sauria, M. E. G., Sanyal, A., Gerasimova, T. I., Lajoie, B. R., Bell, J. S. K., Ong, C.-T., Hookway, T. A., Guo, C., Sun, Y., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.053 · Cited by 1,187
Kim, Y.-J., Björklund, S., Li, Y., Sayre, M. H., & Kornberg, R. D. (1994) · Cell · doi:10.1016/0092-8674(94)90221-6 · Cited by 1,080
Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
Bintu, B., Mateo, L. J., Su, J.-H., Sinnott-Armstrong, N. A., Parker, M., Kinrot, S., Yamaya, K., Boettiger, A. N., & Zhuang, X. (2018) · Science · doi:10.1126/science.aau1783 · Cited by 976
BEDOPS: high-performance genomic feature operations
Neph, S. J., Kuehn, M. S., Reynolds, A. P., Haugen, E., Thurman, R. E., Johnson, A., Rynes, E., Maurano, M. T., Vierstra, J. D., Thomas, S., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts277 · Cited by 971
Imaging dynamic and selective low-complexity domain interactions that control gene transcription
Chong, S., Dugast-Darzacq, C., Liu, Z., Dong, P., Dailey, G. M., Cattoglio, C., Heckert, A., Banala, S., Lavis, L., Darzacq, X., et al. (2018) · Science · doi:10.1126/science.aar2555 · Cited by 966
The Mediator complex: a central integrator of transcription
Allen, B. L., & Taatjes, D. J. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3951 · Cited by 922
Addressing Preferred Specimen Orientation in Single-Particle Cryo-EM through Tilting
Tan, Y.-Z., Baldwin, P. R., Davis, J., Williamson, J., Potter, C., Carragher, B., & Lyumkis, D. (2017) · Nature Methods · doi:10.1038/nmeth.4347 · Cited by 920
Activating RNAs associate with Mediator to enhance chromatin architecture and transcription
Lai, F., Ørom, U. A., Cesaroni, M., Beringer, M., Taatjes, D. J., Blobel, G. A., & Shiekhattar, R. (2013) · Nature · doi:10.1038/nature11884 · Cited by 857
The metazoan Mediator co-activator complex as an integrative hub for transcriptional regulation
Malik, S., & Roeder, R. G. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2901 · Cited by 769
Deng, W., Lee, J., Wang, H., Miller, J., Reik, A., Gregory, P. D., Dean, A., & Blobel, G. A. (2012) · Cell · doi:10.1016/j.cell.2012.03.051 · Cited by 734 · cited 1×
“Experiments forcing P-E contacts demonstrate that such proximity is key to transcription (Deng et al., 2012; Morgan et al., 2017), but do not necessarily prove that stable loops are the norm.”
BackgroundHiCUP: pipeline for mapping and processing Hi-C data
Wingett, S., Ewels, P., Furlan-Magaril, M., Nagano, T., Schoenfelder, S., Fraser, P., & Andrews, S. (2015) · F1000Research · doi:10.12688/f1000research.7334.1 · Cited by 734
Enhancer Control of Transcriptional Bursting
Fukaya, T., Lim, B., & Levine, M. (2016) · Cell · doi:10.1016/j.cell.2016.05.025 · Cited by 721
Rapid protein depletion in human cells by auxin-inducible degron tagging with short homology donors
Natsume, T., Kiyomitsu, T., Saga, Y., & Kanemaki, M. T. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.03.001 · Cited by 673
Developmental enhancers and chromosome topology
Furlong, E. E. M., & Levine, M. (2018) · Science · doi:10.1126/science.aau0320 · Cited by 641
Transcription regulation by the Mediator complex
Soutourina, J. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.115 · Cited by 635
CTCF and cohesin regulate chromatin loop stability with distinct dynamics
Hansen, A. S., Pustova, I., Cattoglio, C., Tjian, R., & Darzacq, X. (2017) · eLife · doi:10.7554/elife.25776 · Cited by 613
Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells
Chen, J., Zhang, Z., Li, L., Chen, B.-C., Revyakin, A., Hajj, B., Legant, W., Dahan, M., Lionnet, T., Betzig, E., et al. (2014) · Cell · doi:10.1016/j.cell.2014.01.062 · Cited by 602
Mediator and the mechanism of transcriptional activation
Kornberg, R. D. (2005) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2005.03.011 · Cited by 595
The Energetics and Physiological Impact of Cohesin Extrusion
Vian, L., Pękowska, A., Rao, S. S. P., Kieffer-Kwon, K.-R., Jung, S., Baranello, L., Huang, S.-C., El Khattabi, L., Dose, M., Pruett, N., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.072 · Cited by 581
Self-citationVoss, N. R., Yoshioka, C., Radermacher, M., Potter, C. S., & Carragher, B. O. (2009) · Journal of Structural Biology · doi:10.1016/j.jsb.2009.01.004 · Cited by 571
The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements
Schoenfelder, S., Furlan-Magaril, M., Mifsud, B., Tavares-Cadete, F., Sugar, R., Javierre, B.-M., Nagano, T., Katsman, Y., Sakthidevi, M., Wingett, S. W., et al. (2015) · Genome Research · doi:10.1101/gr.185272.114 · Cited by 460
Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization
Finn, E. H., Pegoraro, G., Brandão, H. B., Valton, A.-L., Oomen, M. E., Dekker, J., Mirny, L., & Misteli, T. (2019) · Cell · doi:10.1016/j.cell.2019.01.020 · Cited by 459
Visualizing DNA folding and RNA in embryos at single-cell resolution
Mateo, L. J., Murphy, S. E., Hafner, A., Cinquini, I. S., Walker, C. A., & Boettiger, A. N. (2019) · Nature · doi:10.1038/s41586-019-1035-4 · Cited by 446
BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data
Guo, W., Fiziev, P. P., Yan, W., Cokus, S. J., Sun, X., Zhang, M. Q., Chen, P., & Pellegrini, M. A. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-774 · Cited by 437
CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data
Cairns, J., Freire-Pritchett, P., Wingett, S. W., Várnai, C., Dimond, A., Plagnol, V., Zerbino, D., Schoenfelder, S., Javierre, B.-M., Osborne, C., et al. (2016) · Genome Biology · doi:10.1186/s13059-016-0992-2 · Cited by 417
Human Mediator Subunit MED26 Functions as a Docking Site for Transcription Elongation Factors
Takahashi, H., Parmely, T. J., Sato, S., Tomomori‐Sato, C., Banks, C. A. S., Kong, S. E., Szutorisz, H., Swanson, S. K., Martin‐Brown, S., Washburn, M. P., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.005 · Cited by 369
CDK8 is a positive regulator of transcriptional elongation within the serum response network
Donner, A. J., Ebmeier, C. C., Taatjes, D. J., & Espinosa, J. M. (2010) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1752 · Cited by 368
Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity
Alexander, J. M., Guan, J., Li, B., Maliskova, L., Song, M., Shen, Y., Huang, B., Lomvardas, S., & Weiner, O. D. (2019) · eLife · doi:10.7554/elife.41769 · Cited by 346
Kieffer-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 337
Self-citationStructure and mechanism of the RNA polymerase II transcription machineryPreprint
Schier, A. C., & Taatjes, D. J. (2020) · Genes & Development · doi:10.1101/gad.335679.119 · Cited by 327
Architecture of the RNA polymerase II–Mediator core initiation complex
Plaschka, C., Larivière, L., Wenzeck, L., Seizl, M., Hemann, M., Tegunov, D., Petrotchenko, E. V., Borchers, C. H., Baumeister, W. P., Herzog, F., et al. (2015) · Nature · doi:10.1038/nature14229 · Cited by 325
Role of DNA Methylation in Modulating Transcription Factor Occupancy
Maurano, M. T., Wang, H., John, S., Shafer, A., Canfield, T., Lee, K., & Stamatoyannopoulos, J. A. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.07.024 · Cited by 281
Conserved Structures of Mediator and RNA Polymerase II Holoenzyme
Asturias, F. J., Jiang, Y. W., Myers, L. C., Gustafsson, C. M., & Kornberg, R. D. (1999) · Science · doi:10.1126/science.283.5404.985 · Cited by 279
Self-citationManipulation of nuclear architecture through CRISPR-mediated chromosomal looping
Morgan, S. L., Mariano, N. C., Bermudez, A., Arruda, N. L., Wu, F., Luo, Y., Shankar, G., Jia, L., Chen, H., Hu, J.-F., et al. (2017) · Nature Communications · doi:10.1038/ncomms15993 · Cited by 279
Structures of transcription pre-initiation complex with TFIIH and Mediator
Schilbach, S., Hantsche-Grininger, M., Tegunov, D., Dienemann, C., Wigge, C., Urlaub, H., & Cramer, P. (2017) · Nature · doi:10.1038/nature24282 · Cited by 271
In vivo degradation of RNA polymerase II largest subunit triggered by alpha-amanitin
Nguyen, V. T. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.15.2924 · Cited by 257
Transcription Control by E1A and MAP Kinase Pathway via Sur2 Mediator Subunit
Stevens, J. L., Cantin, G. T., Wang, G., Shevchenko, A., Shevchenko, A., & Berk, A. J. (2002) · Science · doi:10.1126/science.1068943 · Cited by 243
Iterative Stable Alignment and Clustering of 2D Transmission Electron Microscope Images
Yang, Z., Fang, J., Chittuluru, J. R., Asturias, F. J., & Penczek, P. A. (2012) · Structure · doi:10.1016/j.str.2011.12.007 · Cited by 241
Self-citationStructure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex
Robinson, P. J. J., Trnka, M. J., Bushnell, D. A., Davis, R., Matteï, P., Burlingame, A. L., & Kornberg, R. D. (2016) · Cell · doi:10.1016/j.cell.2016.08.050 · Cited by 238
Li, Y., Björklund, S., Jiang, Y. W., Kim, Y., Lane, W. S., Stillman, D. J., & Kornberg, R. D. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.24.10864 · Cited by 237
Tunable and reversible drug control of protein production via a self-excising degron
Chung, H. K., Jacobs, C. L., Huo, Y., Yang, J., Krumm, S. A., Plemper, R. K., Tsien, R. Y., & Lin, M. Z. (2015) · Nature Chemical Biology · doi:10.1038/nchembio.1869 · Cited by 233
Regulatory Enhancer–Core-Promoter Communication via Transcription Factors and Cofactors
Zabidi, M. A., & Stark, A. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.10.003 · Cited by 228
Subunit Architecture and Functional Modular Rearrangements of the Transcriptional Mediator Complex
Tsai, K.-L., Tomomori-Sato, C., Sato, S., Conaway, R. C., Conaway, J. W., & Asturias, F. J. (2014) · Cell · doi:10.1016/j.cell.2014.05.015 · Cited by 218
Self-citationMyc 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 210
Self-citationMediator-Dependent Recruitment of TFIIH Modules in Preinitiation Complex
Esnault, C., Ghavi-Helm, Y., Brun, S., Soutourina, J., van Berkum, N. L., Boschiero, C., Holstege, F. C. P., & Werner, M. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.06.021 · Cited by 194
The Mediator Complex: At the Nexus of RNA Polymerase II Transcription
Jerónimo, C., & Robert, F. (2017) · Trends in Cell Biology · doi:10.1016/j.tcb.2017.07.001 · Cited by 189
A Mechanism for Coordinating Chromatin Modification and Preinitiation Complex Assembly
Black, J. C., Choi, J. E., Lombardo, S. R., & Carey, M. (2006) · Molecular Cell · doi:10.1016/j.molcel.2006.07.018 · Cited by 168
High-resolution Single Particle Analysis from Electron Cryo-microscopy Images Using SPHIRE
Moriya, T., Saur, M., Stabrin, M., Merino, F., Voicu, H., Huang, Z. X., Penczek, P. A., Raunser, S., & Gatsogiannis, C. (2017) · Journal of Visualized Experiments · doi:10.3791/55448 · Cited by 165
Global Regulation of Promoter Melting in Naive Lymphocytes
Kouzine, F., Wojtowicz, D., Yamane, A., Resch, W., Kieffer-Kwon, K.-R., Bandle, R., Nelson, S., Nakahashi, H., Awasthi, P., Feigenbaum, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.033 · Cited by 154
Self-citationMolecular architecture of the yeast Mediator complex
Robinson, P. J., Trnka, M. J., Pellarin, R., Greenberg, C. H., Bushnell, D. A., Davis, R., Burlingame, A. L., Sali, A., & Kornberg, R. D. (2015) · eLife · doi:10.7554/elife.08719 · Cited by 150
The Mediator complex and transcription elongation
Conaway, R., & Conaway, J. W. (2012) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.08.017 · Cited by 146
A promoter interaction map for cardiovascular disease genetics
Montefiori, L. E., Sobreira, D. R., Sakabe, N. J., Aneas, I., Joslin, A. C., Hansen, G. T., Bozek, G., Moskowitz, I. P., McNally, E. M., & Nóbrega, M. A. (2018) · eLife · doi:10.7554/elife.35788 · Cited by 145
Self-citationMediator structure and rearrangements required for holoenzyme formation
Tsai, K., Yu, X., Gopalan, S., Chao, T., Zhang, Y., Florens, L. A., Washburn, M. P., Murakami, K., Conaway, R. C., Conaway, J. W., et al. (2017) · Nature · doi:10.1038/nature21393 · Cited by 141
Self-citationReconstitution of active human core Mediator complex reveals a critical role of the MED14 subunit
Cevher, M. A., Shi, Y., Li, D., Chait, B. T., Malik, S., & Roeder, R. G. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2914 · Cited by 133
Functional Association of Gdown1 with RNA Polymerase II Poised on Human Genes
Cheng, B. W., Li, T., Rahl, P. B., Adamson, T. E., Loudas, N. B., Guo, J., Varzavand, K., Cooper, J. J., Hu, X., Gnatt, A. L., et al. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.10.022 · Cited by 129
Ito, M., Okano, H. J., Darnell, R. B., & Roeder, R. G. (2002) · The EMBO Journal · doi:10.1093/emboj/cdf348 · Cited by 122
Aranda-Orgillés, B., Saldaña-Meyer, R., Wang, E., Trompouki, E., Fassl, A., Lau, S., Mullenders, J., Rocha, P. P., Raviram, R., Guillamot, M., et al. (2016) · Cell stem cell · doi:10.1016/j.stem.2016.08.004 · Cited by 111
Core Mediator structure at 3.4 Å extends model of transcription initiation complex
Nozawa, K., Schneider, T. R., & Cramer, P. (2017) · Nature · doi:10.1038/nature22328 · Cited by 108
Spaeth, J. M., Kim, N. H., & Boyer, T. (2011) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2011.07.024 · Cited by 107
Jishage, M., Malik, S., Wagner, U., Uberheide, B., Ishihama, Y., Hu, X., Chait, B. T., Gnatt, A. L., Ren, B., & Roeder, R. G. (2012) · Molecular Cell · doi:10.1016/j.molcel.2011.12.014 · Cited by 77
Russo, J. W., Nouri, M., & Balk, S. P. (2019) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-1028 · Cited by 62
Petrenko, N., Jin, Y., Wong, K. H., & Struhl, K. (2017) · eLife · doi:10.7554/elife.28447 · Cited by 54
Mediator Architecture and RNA Polymerase II Interaction
Plaschka, C., Nozawa, K., & Cramer, P. (2016) · Journal of Molecular Biology · doi:10.1016/j.jmb.2016.01.028 · Cited by 51
Eychenne, T., Novikova, E., Barrault, M., Alibert, O., Boschiero, C., Peixeiro, N., Cornu, D., Redeker, V., Kuras, L., Nicolas, P., et al. (2016) · Genes & Development · doi:10.1101/gad.285775.116 · Cited by 44
Regulatory Domains and Their MechanismsPreprint
Benabdallah, N. S., & Bickmore, W. A. (2015) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2015.80.027268 · Cited by 37
NandyMazumdar, M., Yin, S., Paranjapye, A., Kerschner, J. L., Swahn, H., Ge, A. Y., Leir, S., & Harris, A. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa089 · Cited by 34
Mediator tail subunits can form amyloid-like aggregatesin vivoand affect stress response in yeast
Zhu, X., Chen, L., Carlsten, J. O. P., Liu, Q., Yang, J., Liu, B., & Gustafsson, C. M. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv629 · Cited by 30
Ramachandran, P., Palidwor, G., Porter, C. J., & Perkins, T. J. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt001 · Cited by 29
Clock-controlled rhythmic transcription: is the clock enough and how does it work?
Beytebiere, J. R., Greenwell, B. J., Sahasrabudhe, A., & Menet, J. S. (2019) · Transcription · doi:10.1080/21541264.2019.1673636 · Cited by 25
PARP mediated chromatin unfolding is coupled to long-range enhancer activationPreprint
Benabdallah, N. S., Williamson, I., Illingworth, R. S., Boyle, S., Grimes, G. R., Therizols, P., & Bickmore, W. A. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/155325 · Cited by 24
Crystal structure of human Mediator subunit MED23
Monté, D., Clantin, B., Dewitte, F., Lens, Z., Rucktooa, P., Pardon, E., Steyaert, J., Verger, A., & Villeret, V. (2018) · Nature Communications · doi:10.1038/s41467-018-05967-y · Cited by 18
Feldmann, A., Dimitrova, E., Kenney, A., Lastuvkova, A., & Klose, R. J. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa064 · Cited by 15
Clements, F. E. (1902) · Science · doi:10.1126/science.15.386.819 · Cited by 13
Flagged first, then by citations
2 of the 102 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- Wickham, H. ggplot2: Elegant Graphics for Data Analysis, 2016, https://ggplot2-book.org/. · DOI
Cited by
Sorted by citations
Genome folding through loop extrusion by SMC complexes
Davidson, I. F., & Peters, J. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00349-7 · Cited by 531
Liquid–liquid phase separation drives cellular function and dysfunction in cancer
Mehta, S., & Zhang, J. (2022) · Nature reviews. Cancer · doi:10.1038/s41568-022-00444-7 · Cited by 464
Mechanisms of enhancer action: the known and the unknown
Panigrahi, A., & O’Malley, B. W. (2021) · Genome biology · doi:10.1186/s13059-021-02322-1 · Cited by 376
The relationship between genome structure and function
Oudelaar, A. M., & Higgs, D. R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-020-00303-x · Cited by 304
The Mediator complex as a master regulator of transcription by RNA polymerase II
Richter, W. F., Nayak, S., Iwasa, J., & Taatjes, D. J. (2022) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-022-00498-3 · Cited by 343
Metadata
- Authors
- El Khattabi, L., Zhao, H., Kalchschmidt, J., Young, N., Jung, S., Van Blerkom, P., Kieffer-Kwon, P., Kieffer-Kwon, K.-R., Park, S., Wang, X., Krebs, J., Tripathi, S., Sakabe, N., Sobreira, D. R., Huang, S.-C., Rao, S. S. P., Pruett, N., Chauss, D., Sadler, E., Lopez, A., Nóbrega, M. A., Aiden, E. L., Asturias, F. J., & Casellas, R.
- Affiliations
- University of Colorado Anschutz (US)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (US)
- University of Chicago (US)
- Baylor College of Medicine (US)
- National Institutes of Health (US)
- Corresponding author
- Asturias, Francisco J.
- Casellas, Rafael
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2019-08
- Volume
- 178
- Issue
- 5
- Pages
- 1145-1158.e20
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC7533040
- OpenAlex
- W2967977322
- Cited by
- 244
- References
- 102
- Citations by year
- 2026: 26 · 2025: 22 · 2024: 38 · 2023: 35 · 2022: 44 · 2021: 51 · 2020: 25 · 2019: 3
- FWCI
- 10.17
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- 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
- Mediator complex, RNA polymerase II recruitment, enhancers, transcriptional regulation, Hi-C, cryo-electron microscopy
- MeSH terms
- Mouse Embryonic Stem Cells, Gene Editing, Cohesins, Animals, Cells, Cultured, Chromosomal Proteins, Non-Histone, Enhancer Elements, Genetic, Humans, Male, Mice, Inbred C57BL, Promoter Regions, Genetic, RNA Polymerase II, Saccharomyces cerevisiae, CD4-Positive T-Lymphocytes, Cell Cycle Proteins, Cryoelectron Microscopy, Protein Structure, Quaternary, Saccharomyces cerevisiae Proteins, Mice, Mediator Complex, CRISPR-Cas Systems
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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.
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