- -

Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell

RiuNet: Institutional repository of the Polithecnic University of Valencia

Share/Send to

Cited by

Statistics

Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell

Show simple item record

Files in this item

dc.contributor.author Pascual-Ahuir Giner, María Desamparados es_ES
dc.contributor.author Fita-Torró, Josep es_ES
dc.contributor.author Proft, Markus Hans es_ES
dc.date.accessioned 2021-07-17T03:34:42Z
dc.date.available 2021-07-17T03:34:42Z
dc.date.issued 2020-11 es_ES
dc.identifier.uri http://hdl.handle.net/10251/169418
dc.description.abstract [EN] The regulation of gene expression is a fundamental process enabling cells to respond to internal and external stimuli or to execute developmental programs. Changes in gene expression are highly dynamic and depend on many intrinsic and extrinsic factors. In this review, we highlight the dynamic nature of transient gene expression changes to better understand cell physiology and development in general. We will start by comparing recent in vivo procedures to capture gene expression in real time. Intrinsic factors modulating gene expression dynamics will then be discussed, focusing on chromatin modifications. Furthermore, we will dissect how cell physiology or age impacts on dynamic gene regulation and especially discuss molecular insights into acquired transcriptional memory. Finally, this review will give an update on the mechanisms of heterogeneous gene expression among genetically identical individual cells. We will mainly focus on state-of-the-art developments in the yeast model but also cover higher eukaryotic systems. es_ES
dc.description.sponsorship This work was funded by Ministerio de Ciencia, Innovacion y Universidades, grant number BFU2016-75792-R. es_ES
dc.language Inglés es_ES
dc.publisher MDPI AG es_ES
dc.relation.ispartof International Journal of Molecular Sciences es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Gene expression es_ES
dc.subject Transcriptional activation es_ES
dc.subject Transcriptional memory es_ES
dc.subject Single-cell variability es_ES
dc.subject Reporter assays es_ES
dc.subject Stress adaptation es_ES
dc.subject Transcriptional dynamics es_ES
dc.subject.classification BIOQUIMICA Y BIOLOGIA MOLECULAR es_ES
dc.title Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.3390/ijms21218278 es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//BFU2016-75792-R/ES/ADAPTACION COORDINADA A ESTRES MEDIANTE LA MODULACION DE LA HOMEOSTASIS MITOCONDRIAL Y LA ACTIVACION SELECTIVA DEL TRANSPORTE MULTI-DROGA/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario Mixto de Biología Molecular y Celular de Plantas - Institut Universitari Mixt de Biologia Molecular i Cel·lular de Plantes es_ES
dc.description.bibliographicCitation Pascual-Ahuir Giner, MD.; Fita-Torró, J.; Proft, MH. (2020). Capturing and Understanding the Dynamics and Heterogeneity of Gene Expression in the Living Cell. International Journal of Molecular Sciences. 21(21):1-19. https://doi.org/10.3390/ijms21218278 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion https://doi.org/10.3390/ijms21218278 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 19 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 21 es_ES
dc.description.issue 21 es_ES
dc.identifier.eissn 1422-0067 es_ES
dc.identifier.pmid 33167354 es_ES
dc.identifier.pmcid PMC7663833 es_ES
dc.relation.pasarela S\424208 es_ES
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.description.references Murray, J. I., Whitfield, M. L., Trinklein, N. D., Myers, R. M., Brown, P. O., & Botstein, D. (2004). Diverse and Specific Gene Expression Responses to Stresses in Cultured Human Cells. Molecular Biology of the Cell, 15(5), 2361-2374. doi:10.1091/mbc.e03-11-0799 es_ES
dc.description.references Gasch, A. P., Spellman, P. T., Kao, C. M., Carmel-Harel, O., Eisen, M. B., Storz, G., … Brown, P. O. (2000). Genomic Expression Programs in the Response of Yeast Cells to Environmental Changes. Molecular Biology of the Cell, 11(12), 4241-4257. doi:10.1091/mbc.11.12.4241 es_ES
dc.description.references de-Leon, S. B.-T., & Davidson, E. H. (2007). Gene Regulation: Gene Control Network in Development. Annual Review of Biophysics and Biomolecular Structure, 36(1), 191-212. doi:10.1146/annurev.biophys.35.040405.102002 es_ES
dc.description.references Lenstra, T. L., Rodriguez, J., Chen, H., & Larson, D. R. (2016). Transcription Dynamics in Living Cells. Annual Review of Biophysics, 45(1), 25-47. doi:10.1146/annurev-biophys-062215-010838 es_ES
dc.description.references Coulon, A., Chow, C. C., Singer, R. H., & Larson, D. R. (2013). Eukaryotic transcriptional dynamics: from single molecules to cell populations. Nature Reviews Genetics, 14(8), 572-584. doi:10.1038/nrg3484 es_ES
dc.description.references Yosef, N., & Regev, A. (2011). Impulse Control: Temporal Dynamics in Gene Transcription. Cell, 144(6), 886-896. doi:10.1016/j.cell.2011.02.015 es_ES
dc.description.references Purvis, J. E., & Lahav, G. (2013). Encoding and Decoding Cellular Information through Signaling Dynamics. Cell, 152(5), 945-956. doi:10.1016/j.cell.2013.02.005 es_ES
dc.description.references Weake, V. M., & Workman, J. L. (2010). Inducible gene expression: diverse regulatory mechanisms. Nature Reviews Genetics, 11(6), 426-437. doi:10.1038/nrg2781 es_ES
dc.description.references De Nadal, E., Ammerer, G., & Posas, F. (2011). Controlling gene expression in response to stress. Nature Reviews Genetics, 12(12), 833-845. doi:10.1038/nrg3055 es_ES
dc.description.references Vihervaara, A., Duarte, F. M., & Lis, J. T. (2018). Molecular mechanisms driving transcriptional stress responses. Nature Reviews Genetics, 19(6), 385-397. doi:10.1038/s41576-018-0001-6 es_ES
dc.description.references Pérez-Ortín, J. E., Alepuz, P., Chávez, S., & Choder, M. (2013). Eukaryotic mRNA Decay: Methodologies, Pathways, and Links to Other Stages of Gene Expression. Journal of Molecular Biology, 425(20), 3750-3775. doi:10.1016/j.jmb.2013.02.029 es_ES
dc.description.references Aparicio, O., Geisberg, J. V., Sekinger, E., Yang, A., Moqtaderi, Z., & Struhl, K. (2005). Chromatin Immunoprecipitation for Determining the Association of Proteins with Specific Genomic Sequences In Vivo. Current Protocols in Molecular Biology, 69(1). doi:10.1002/0471142727.mb2103s69 es_ES
dc.description.references Wa Maina, C., Honkela, A., Matarese, F., Grote, K., Stunnenberg, H. G., Reid, G., … Rattray, M. (2014). Inference of RNA Polymerase II Transcription Dynamics from Chromatin Immunoprecipitation Time Course Data. PLoS Computational Biology, 10(5), e1003598. doi:10.1371/journal.pcbi.1003598 es_ES
dc.description.references Mason, P. B., & Struhl, K. (2005). Distinction and Relationship between Elongation Rate and Processivity of RNA Polymerase II In Vivo. Molecular Cell, 17(6), 831-840. doi:10.1016/j.molcel.2005.02.017 es_ES
dc.description.references Sato, H., Das, S., Singer, R. H., & Vera, M. (2020). Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. Annual Review of Biochemistry, 89(1), 159-187. doi:10.1146/annurev-biochem-011520-104955 es_ES
dc.description.references Janicki, S. M., Tsukamoto, T., Salghetti, S. E., Tansey, W. P., Sachidanandam, R., Prasanth, K. V., … Spector, D. L. (2004). From Silencing to Gene Expression. Cell, 116(5), 683-698. doi:10.1016/s0092-8674(04)00171-0 es_ES
dc.description.references Chao, J. A., Patskovsky, Y., Almo, S. C., & Singer, R. H. (2007). Structural basis for the coevolution of a viral RNA–protein complex. Nature Structural & Molecular Biology, 15(1), 103-105. doi:10.1038/nsmb1327 es_ES
dc.description.references Bertrand, E., Chartrand, P., Schaefer, M., Shenoy, S. M., Singer, R. H., & Long, R. M. (1998). Localization of ASH1 mRNA Particles in Living Yeast. Molecular Cell, 2(4), 437-445. doi:10.1016/s1097-2765(00)80143-4 es_ES
dc.description.references Campbell, P. D., Chao, J. A., Singer, R. H., & Marlow, F. L. (2015). Dynamic visualization of transcription and RNA subcellular localization in zebrafish. Development. doi:10.1242/dev.118968 es_ES
dc.description.references Golding, I., Paulsson, J., Zawilski, S. M., & Cox, E. C. (2005). Real-Time Kinetics of Gene Activity in Individual Bacteria. Cell, 123(6), 1025-1036. doi:10.1016/j.cell.2005.09.031 es_ES
dc.description.references Larson, D. R., Zenklusen, D., Wu, B., Chao, J. A., & Singer, R. H. (2011). Real-Time Observation of Transcription Initiation and Elongation on an Endogenous Yeast Gene. Science, 332(6028), 475-478. doi:10.1126/science.1202142 es_ES
dc.description.references Chubb, J. R., Trcek, T., Shenoy, S. M., & Singer, R. H. (2006). Transcriptional Pulsing of a Developmental Gene. Current Biology, 16(10), 1018-1025. doi:10.1016/j.cub.2006.03.092 es_ES
dc.description.references Garcia, H. G., Tikhonov, M., Lin, A., & Gregor, T. (2013). Quantitative Imaging of Transcription in Living Drosophila Embryos Links Polymerase Activity to Patterning. Current Biology, 23(21), 2140-2145. doi:10.1016/j.cub.2013.08.054 es_ES
dc.description.references Xu, H., Wang, J., Liang, Y., Fu, Y., Li, S., Huang, J., … Chen, B. (2020). TriTag: an integrative tool to correlate chromatin dynamics and gene expression in living cells. Nucleic Acids Research, 48(22), e127-e127. doi:10.1093/nar/gkaa906 es_ES
dc.description.references Niedenthal, R. K., Riles, L., Johnston, M., & Hegemann, J. H. (1996). Green fluorescent protein as a marker for gene expression and subcellular localization in budding yeast. Yeast, 12(8), 773-786. doi:10.1002/(sici)1097-0061(19960630)12:8<773::aid-yea972>3.0.co;2-l es_ES
dc.description.references Plautz, J. D., Day, R. N., Dailey, G. M., Welsh, S. B., Hall, J. C., Halpain, S., & Kay, S. A. (1996). Green fluorescent protein and its derivatives as versatile markers for gene expression in living Drosophila melanogaster, plant and mammalian cells. Gene, 173(1), 83-87. doi:10.1016/0378-1119(95)00700-8 es_ES
dc.description.references Chalfie, M., Tu, Y., Euskirchen, G., Ward, W. W., & Prasher, D. C. (1994). Green Fluorescent Protein as a Marker for Gene Expression. Science, 263(5148), 802-805. doi:10.1126/science.8303295 es_ES
dc.description.references Longo, D., & Hasty, J. (2006). Dynamics of single‐cell gene expression. Molecular Systems Biology, 2(1), 64. doi:10.1038/msb4100110 es_ES
dc.description.references Zou, F., & Bai, L. (2019). Using time-lapse fluorescence microscopy to study gene regulation. Methods, 159-160, 138-145. doi:10.1016/j.ymeth.2018.12.010 es_ES
dc.description.references Han, J., Xia, A., Huang, Y., Ni, L., Chen, W., Jin, Z., … Jin, F. (2019). Simultaneous Visualization of Multiple Gene Expression in Single Cells Using an Engineered Multicolor Reporter Toolbox and Approach of Spectral Crosstalk Correction. ACS Synthetic Biology, 8(11), 2536-2546. doi:10.1021/acssynbio.9b00223 es_ES
dc.description.references Mateus, C., & Avery, S. V. (2000). Destabilized green fluorescent protein for monitoring dynamic changes in yeast gene expression with flow cytometry. Yeast, 16(14), 1313-1323. doi:10.1002/1097-0061(200010)16:14<1313::aid-yea626>3.0.co;2-o es_ES
dc.description.references Li, X., Zhao, X., Fang, Y., Jiang, X., Duong, T., Fan, C., … Kain, S. R. (1998). Generation of Destabilized Green Fluorescent Protein as a Transcription Reporter. Journal of Biological Chemistry, 273(52), 34970-34975. doi:10.1074/jbc.273.52.34970 es_ES
dc.description.references Andersen, J. B., Sternberg, C., Poulsen, L. K., Bjørn, S. P., Givskov, M., & Molin, S. (1998). New Unstable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria. Applied and Environmental Microbiology, 64(6), 2240-2246. doi:10.1128/aem.64.6.2240-2246.1998 es_ES
dc.description.references He, L., Binari, R., Huang, J., Falo-Sanjuan, J., & Perrimon, N. (2019). In vivo study of gene expression with an enhanced dual-color fluorescent transcriptional timer. eLife, 8. doi:10.7554/elife.46181 es_ES
dc.description.references Allen, M. S., Wilgus, J. R., Chewning, C. S., Sayler, G. S., & Simpson, M. L. (2006). A destabilized bacterial luciferase for dynamic gene expression studies. Systems and Synthetic Biology, 1(1), 3-9. doi:10.1007/s11693-006-9001-5 es_ES
dc.description.references Yasunaga, M., Murotomi, K., Abe, H., Yamazaki, T., Nishii, S., Ohbayashi, T., … Nakajima, Y. (2015). Highly sensitive luciferase reporter assay using a potent destabilization sequence of calpain 3. Journal of Biotechnology, 194, 115-123. doi:10.1016/j.jbiotec.2014.12.004 es_ES
dc.description.references Leclerc, G. M., Boockfor, F. R., Faught, W. J., & Frawley, L. S. (2000). Development of a Destabilized Firefly Luciferase Enzyme for Measurement of Gene Expression. BioTechniques, 29(3), 590-601. doi:10.2144/00293rr02 es_ES
dc.description.references Rienzo, A., Pascual-Ahuir, A., & Proft, M. (2012). The use of a real-time luciferase assay to quantify gene expression dynamics in the living yeast cell. Yeast, 29(6), 219-231. doi:10.1002/yea.2905 es_ES
dc.description.references Robertson, J. B., Stowers, C. C., Boczko, E., & Hirschie Johnson, C. (2008). Real-time luminescence monitoring of cell-cycle and respiratory oscillations in yeast. Proceedings of the National Academy of Sciences, 105(46), 17988-17993. doi:10.1073/pnas.0809482105 es_ES
dc.description.references Deng, L., Sugiura, R., Takeuchi, M., Suzuki, M., Ebina, H., Takami, T., … Kuno, T. (2006). Real-Time Monitoring of Calcineurin Activity in Living Cells: Evidence for Two Distinct Ca2+-dependent Pathways in Fission Yeast. Molecular Biology of the Cell, 17(11), 4790-4800. doi:10.1091/mbc.e06-06-0526 es_ES
dc.description.references Mazo-Vargas, A., Park, H., Aydin, M., & Buchler, N. E. (2014). Measuring fast gene dynamics in single cells with time-lapse luminescence microscopy. Molecular Biology of the Cell, 25(22), 3699-3708. doi:10.1091/mbc.e14-07-1187 es_ES
dc.description.references Liu, Z., & Tjian, R. (2018). Visualizing transcription factor dynamics in living cells. Journal of Cell Biology, 217(4), 1181-1191. doi:10.1083/jcb.201710038 es_ES
dc.description.references Jin, X., Hapsari, N. D., Lee, S., & Jo, K. (2020). DNA binding fluorescent proteins as single-molecule probes. The Analyst, 145(12), 4079-4095. doi:10.1039/d0an00218f es_ES
dc.description.references Dolz-Edo, L., Rienzo, A., Poveda-Huertes, D., Pascual-Ahuir, A., & Proft, M. (2013). Deciphering Dynamic Dose Responses of Natural Promoters and Single cis Elements upon Osmotic and Oxidative Stress in Yeast. Molecular and Cellular Biology, 33(11), 2228-2240. doi:10.1128/mcb.00240-13 es_ES
dc.description.references Pascual-Ahuir, A., González-Cantó, E., Juyoux, P., Pable, J., Poveda-Huertes, D., Saiz-Balbastre, S., … Proft, M. (2019). Dose dependent gene expression is dynamically modulated by the history, physiology and age of yeast cells. Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, 1862(4), 457-471. doi:10.1016/j.bbagrm.2019.02.009 es_ES
dc.description.references Pelet, S., Rudolf, F., Nadal-Ribelles, M., de Nadal, E., Posas, F., & Peter, M. (2011). Transient Activation of the HOG MAPK Pathway Regulates Bimodal Gene Expression. Science, 332(6030), 732-735. doi:10.1126/science.1198851 es_ES
dc.description.references Paliwal, S., Iglesias, P. A., Campbell, K., Hilioti, Z., Groisman, A., & Levchenko, A. (2007). MAPK-mediated bimodal gene expression and adaptive gradient sensing in yeast. Nature, 446(7131), 46-51. doi:10.1038/nature05561 es_ES
dc.description.references Zhang, Q., Yoon, Y., Yu, Y., Parnell, E. J., Garay, J. A. R., Mwangi, M. M., … Bai, L. (2013). Stochastic expression and epigenetic memory at the yeastHOpromoter. Proceedings of the National Academy of Sciences, 110(34), 14012-14017. doi:10.1073/pnas.1306113110 es_ES
dc.description.references Gutin, J., Joseph‐Strauss, D., Sadeh, A., Shalom, E., & Friedman, N. (2019). Genetic screen of the yeast environmental stress response dynamics uncovers distinct regulatory phases. Molecular Systems Biology, 15(8). doi:10.15252/msb.20198939 es_ES
dc.description.references Rajkumar, A. S., Liu, G., Bergenholm, D., Arsovska, D., Kristensen, M., Nielsen, J., … Keasling, J. D. (2016). Engineering of synthetic, stress-responsive yeast promoters. Nucleic Acids Research, 44(17), e136-e136. doi:10.1093/nar/gkw553 es_ES
dc.description.references Duveau, F., Yuan, D. C., Metzger, B. P. H., Hodgins-Davis, A., & Wittkopp, P. J. (2017). Effects of mutation and selection on plasticity of a promoter activity inSaccharomyces cerevisiae. Proceedings of the National Academy of Sciences, 114(52), E11218-E11227. doi:10.1073/pnas.1713960115 es_ES
dc.description.references Redden, H., Morse, N., & Alper, H. S. (2014). The synthetic biology toolbox for tuning gene expression in yeast. FEMS Yeast Research, n/a-n/a. doi:10.1111/1567-1364.12188 es_ES
dc.description.references Brouwer, I., & Lenstra, T. L. (2019). Visualizing transcription: key to understanding gene expression dynamics. Current Opinion in Chemical Biology, 51, 122-129. doi:10.1016/j.cbpa.2019.05.031 es_ES
dc.description.references Rodriguez, J., & Larson, D. R. (2020). Transcription in Living Cells: Molecular Mechanisms of Bursting. Annual Review of Biochemistry, 89(1), 189-212. doi:10.1146/annurev-biochem-011520-105250 es_ES
dc.description.references Tunnacliffe, E., & Chubb, J. R. (2020). What Is a Transcriptional Burst? Trends in Genetics, 36(4), 288-297. doi:10.1016/j.tig.2020.01.003 es_ES
dc.description.references Hornung, G., Bar-Ziv, R., Rosin, D., Tokuriki, N., Tawfik, D. S., Oren, M., & Barkai, N. (2012). Noise-mean relationship in mutated promoters. Genome Research, 22(12), 2409-2417. doi:10.1101/gr.139378.112 es_ES
dc.description.references Dadiani, M., van Dijk, D., Segal, B., Field, Y., Ben-Artzi, G., Raveh-Sadka, T., … Segal, E. (2013). Two DNA-encoded strategies for increasing expression with opposing effects on promoter dynamics and transcriptional noise. Genome Research, 23(6), 966-976. doi:10.1101/gr.149096.112 es_ES
dc.description.references Raveh-Sadka, T., Levo, M., Shabi, U., Shany, B., Keren, L., Lotan-Pompan, M., … Segal, E. (2012). Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nature Genetics, 44(7), 743-750. doi:10.1038/ng.2305 es_ES
dc.description.references Van Dijk, D., Sharon, E., Lotan-Pompan, M., Weinberger, A., Segal, E., & Carey, L. B. (2016). Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators. Genome Research, 27(1), 87-94. doi:10.1101/gr.212316.116 es_ES
dc.description.references Mehta, G. D., Ball, D. A., Eriksson, P. R., Chereji, R. V., Clark, D. J., McNally, J. G., & Karpova, T. S. (2018). Single-Molecule Analysis Reveals Linked Cycles of RSC Chromatin Remodeling and Ace1p Transcription Factor Binding in Yeast. Molecular Cell, 72(5), 875-887.e9. doi:10.1016/j.molcel.2018.09.009 es_ES
dc.description.references Ball, D. A., Mehta, G. D., Salomon-Kent, R., Mazza, D., Morisaki, T., Mueller, F., … Karpova, T. S. (2016). Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin. Nucleic Acids Research, 44(21), e160-e160. doi:10.1093/nar/gkw744 es_ES
dc.description.references Karpova, T. S., Kim, M. J., Spriet, C., Nalley, K., Stasevich, T. J., Kherrouche, Z., … McNally, J. G. (2008). Concurrent Fast and Slow Cycling of a Transcriptional Activator at an Endogenous Promoter. Science, 319(5862), 466-469. doi:10.1126/science.1150559 es_ES
dc.description.references Donovan, B. T., Huynh, A., Ball, D. A., Patel, H. P., Poirier, M. G., Larson, D. R., … Lenstra, T. L. (2019). Live‐cell imaging reveals the interplay between transcription factors, nucleosomes, and bursting. The EMBO Journal, 38(12). doi:10.15252/embj.2018100809 es_ES
dc.description.references Lenstra, T. L., Coulon, A., Chow, C. C., & Larson, D. R. (2015). Single-Molecule Imaging Reveals a Switch between Spurious and Functional ncRNA Transcription. Molecular Cell, 60(4), 597-610. doi:10.1016/j.molcel.2015.09.028 es_ES
dc.description.references Senecal, A., Munsky, B., Proux, F., Ly, N., Braye, F. E., Zimmer, C., … Darzacq, X. (2014). Transcription Factors Modulate c-Fos Transcriptional Bursts. Cell Reports, 8(1), 75-83. doi:10.1016/j.celrep.2014.05.053 es_ES
dc.description.references Stavreva, D. A., Garcia, D. A., Fettweis, G., Gudla, P. R., Zaki, G. F., Soni, V., … Hager, G. L. (2019). Transcriptional Bursting and Co-bursting Regulation by Steroid Hormone Release Pattern and Transcription Factor Mobility. Molecular Cell, 75(6), 1161-1177.e11. doi:10.1016/j.molcel.2019.06.042 es_ES
dc.description.references Nelson, D. E., Ihekwaba, A. E. C., Elliott, M., Johnson, J. R., Gibney, C. A., Foreman, B. E., … White, M. R. H. (2004). Oscillations in NF-κB Signaling Control the Dynamics of Gene Expression. Science, 306(5696), 704-708. doi:10.1126/science.1099962 es_ES
dc.description.references Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A. J., Elowitz, M. B., & Alon, U. (2004). Dynamics of the p53-Mdm2 feedback loop in individual cells. Nature Genetics, 36(2), 147-150. doi:10.1038/ng1293 es_ES
dc.description.references Izeddin, I., Récamier, V., Bosanac, L., Cissé, I. I., Boudarene, L., Dugast-Darzacq, C., … Darzacq, X. (2014). Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus. eLife, 3. doi:10.7554/elife.02230 es_ES
dc.description.references Suter, D. M., Molina, N., Gatfield, D., Schneider, K., Schibler, U., & Naef, F. (2011). Mammalian Genes Are Transcribed with Widely Different Bursting Kinetics. Science, 332(6028), 472-474. doi:10.1126/science.1198817 es_ES
dc.description.references Keller, S. H., Jena, S. G., Yamazaki, Y., & Lim, B. (2020). Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar. Proceedings of the National Academy of Sciences, 117(26), 15096-15103. doi:10.1073/pnas.1917040117 es_ES
dc.description.references Ochiai, H., Hayashi, T., Umeda, M., Yoshimura, M., Harada, A., Shimizu, Y., … Nikaido, I. (2020). Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. Science Advances, 6(25). doi:10.1126/sciadv.aaz6699 es_ES
dc.description.references Hoppe, C., Bowles, J. R., Minchington, T. G., Sutcliffe, C., Upadhyai, P., Rattray, M., & Ashe, H. L. (2020). Modulation of the Promoter Activation Rate Dictates the Transcriptional Response to Graded BMP Signaling Levels in the Drosophila Embryo. Developmental Cell, 54(6), 727-741.e7. doi:10.1016/j.devcel.2020.07.007 es_ES
dc.description.references Bakker, R., Mani, M., & Carthew, R. W. (2020). The Wg and Dpp morphogens regulate gene expression by modulating the frequency of transcriptional bursts. eLife, 9. doi:10.7554/elife.56076 es_ES
dc.description.references Klemm, S. L., Shipony, Z., & Greenleaf, W. J. (2019). Chromatin accessibility and the regulatory epigenome. Nature Reviews Genetics, 20(4), 207-220. doi:10.1038/s41576-018-0089-8 es_ES
dc.description.references Nocetti, N., & Whitehouse, I. (2016). Nucleosome repositioning underlies dynamic gene expression. Genes & Development, 30(6), 660-672. doi:10.1101/gad.274910.115 es_ES
dc.description.references Cosma, M. P., Tanaka, T., & Nasmyth, K. (1999). Ordered Recruitment of Transcription and Chromatin Remodeling Factors to a Cell Cycle– and Developmentally Regulated Promoter. Cell, 97(3), 299-311. doi:10.1016/s0092-8674(00)80740-0 es_ES
dc.description.references Govind, C. K., Yoon, S., Qiu, H., Govind, S., & Hinnebusch, A. G. (2005). Simultaneous Recruitment of Coactivators by Gcn4p Stimulates Multiple Steps of Transcription In Vivo. Molecular and Cellular Biology, 25(13), 5626-5638. doi:10.1128/mcb.25.13.5626-5638.2005 es_ES
dc.description.references Biggar, S. R. (1999). Continuous and widespread roles for the Swi-Snf complex in transcription. The EMBO Journal, 18(8), 2254-2264. doi:10.1093/emboj/18.8.2254 es_ES
dc.description.references Rando, O. J., & Winston, F. (2012). Chromatin and Transcription in Yeast. Genetics, 190(2), 351-387. doi:10.1534/genetics.111.132266 es_ES
dc.description.references Shen, C.-H., Leblanc, B. P., Alfieri, J. A., & Clark, D. J. (2001). Remodeling of Yeast CUP1 Chromatin Involves Activator-Dependent Repositioning of Nucleosomes over the Entire Gene and Flanking Sequences. Molecular and Cellular Biology, 21(2), 534-547. doi:10.1128/mcb.21.2.534-547.2001 es_ES
dc.description.references Shen, C.-H., & Clark, D. J. (2001). DNA Sequence Plays a Major Role in Determining Nucleosome Positions in Yeast CUP1 Chromatin. Journal of Biological Chemistry, 276(37), 35209-35216. doi:10.1074/jbc.m104733200 es_ES
dc.description.references Erkina, T. Y., Zou, Y., Freeling, S., Vorobyev, V. I., & Erkine, A. M. (2009). Functional interplay between chromatin remodeling complexes RSC, SWI/SNF and ISWI in regulation of yeast heat shock genes. Nucleic Acids Research, 38(5), 1441-1449. doi:10.1093/nar/gkp1130 es_ES
dc.description.references Mitra, D., Parnell, E. J., Landon, J. W., Yu, Y., & Stillman, D. J. (2006). SWI/SNF Binding to the HO Promoter Requires Histone Acetylation and Stimulates TATA-Binding Protein Recruitment. Molecular and Cellular Biology, 26(11), 4095-4110. doi:10.1128/mcb.01849-05 es_ES
dc.description.references Sudarsanam, P. (1999). The nucleosome remodeling complex, Snf/Swi, is required for the maintenance of transcription invivo and is partially redundant with the histone acetyltransferase, Gcn5. The EMBO Journal, 18(11), 3101-3106. doi:10.1093/emboj/18.11.3101 es_ES
dc.description.references Barbaric, S., Luckenbach, T., Schmid, A., Blaschke, D., Hörz, W., & Korber, P. (2007). Redundancy of Chromatin Remodeling Pathways for the Induction of the Yeast PHO5 Promoter in Vivo. Journal of Biological Chemistry, 282(38), 27610-27621. doi:10.1074/jbc.m700623200 es_ES
dc.description.references Proft, M., & Struhl, K. (2002). Hog1 Kinase Converts the Sko1-Cyc8-Tup1 Repressor Complex into an Activator that Recruits SAGA and SWI/SNF in Response to Osmotic Stress. Molecular Cell, 9(6), 1307-1317. doi:10.1016/s1097-2765(02)00557-9 es_ES
dc.description.references Lemieux, K., & Gaudreau, L. (2004). Targeting of Swi/Snf to the yeast GAL1 UASG requires the Mediator, TAFIIs, and RNA polymerase II. The EMBO Journal, 23(20), 4040-4050. doi:10.1038/sj.emboj.7600416 es_ES
dc.description.references Rienzo, A., Poveda-Huertes, D., Aydin, S., Buchler, N. E., Pascual-Ahuir, A., & Proft, M. (2015). Different Mechanisms Confer Gradual Control and Memory at Nutrient- and Stress-Regulated Genes in Yeast. Molecular and Cellular Biology, 35(21), 3669-3683. doi:10.1128/mcb.00729-15 es_ES
dc.description.references Kundu, S., Horn, P. J., & Peterson, C. L. (2007). SWI/SNF is required for transcriptional memory at the yeast GAL gene cluster. Genes & Development, 21(8), 997-1004. doi:10.1101/gad.1506607 es_ES
dc.description.references Dhasarathy, A., & Kladde, M. P. (2005). Promoter Occupancy Is a Major Determinant of Chromatin Remodeling Enzyme Requirements. Molecular and Cellular Biology, 25(7), 2698-2707. doi:10.1128/mcb.25.7.2698-2707.2005 es_ES
dc.description.references Acar, M., Becskei, A., & van Oudenaarden, A. (2005). Enhancement of cellular memory by reducing stochastic transitions. Nature, 435(7039), 228-232. doi:10.1038/nature03524 es_ES
dc.description.references Vanacloig-Pedros, E., Lozano-Pérez, C., Alarcón, B., Pascual-Ahuir, A., & Proft, M. (2019). Live-cell assays reveal selectivity and sensitivity of the multidrug response in budding yeast. Journal of Biological Chemistry, 294(35), 12933-12946. doi:10.1074/jbc.ra119.009291 es_ES
dc.description.references Thakur, J. K., Arthanari, H., Yang, F., Pan, S.-J., Fan, X., Breger, J., … Näär, A. M. (2008). A nuclear receptor-like pathway regulating multidrug resistance in fungi. Nature, 452(7187), 604-609. doi:10.1038/nature06836 es_ES
dc.description.references Hao, N., Budnik, B. A., Gunawardena, J., & O’Shea, E. K. (2013). Tunable Signal Processing Through Modular Control of Transcription Factor Translocation. Science, 339(6118), 460-464. doi:10.1126/science.1227299 es_ES
dc.description.references Hansen, A. S., & O’Shea, E. K. (2016). Encoding four gene expression programs in the activation dynamics of a single transcription factor. Current Biology, 26(7), R269-R271. doi:10.1016/j.cub.2016.02.058 es_ES
dc.description.references Hao, N., & O’Shea, E. K. (2011). Signal-dependent dynamics of transcription factor translocation controls gene expression. Nature Structural & Molecular Biology, 19(1), 31-39. doi:10.1038/nsmb.2192 es_ES
dc.description.references Babazadeh, R., Lahtvee, P.-J., Adiels, C. B., Goksör, M., Nielsen, J. B., & Hohmann, S. (2017). The yeast osmostress response is carbon source dependent. Scientific Reports, 7(1). doi:10.1038/s41598-017-01141-4 es_ES
dc.description.references Vanacloig-Pedros, E., Bets-Plasencia, C., Pascual-Ahuir, A., & Proft, M. (2015). Coordinated Gene Regulation in the Initial Phase of Salt Stress Adaptation. Journal of Biological Chemistry, 290(16), 10163-10175. doi:10.1074/jbc.m115.637264 es_ES
dc.description.references Nikopoulou, C., Parekh, S., & Tessarz, P. (2019). Ageing and sources of transcriptional heterogeneity. Biological Chemistry, 400(7), 867-878. doi:10.1515/hsz-2018-0449 es_ES
dc.description.references Feser, J., Truong, D., Das, C., Carson, J. J., Kieft, J., Harkness, T., & Tyler, J. K. (2010). Elevated Histone Expression Promotes Life Span Extension. Molecular Cell, 39(5), 724-735. doi:10.1016/j.molcel.2010.08.015 es_ES
dc.description.references Hu, Z., Chen, K., Xia, Z., Chavez, M., Pal, S., Seol, J.-H., … Tyler, J. K. (2014). Nucleosome loss leads to global transcriptional up-regulation and genomic instability during yeast aging. Genes & Development, 28(4), 396-408. doi:10.1101/gad.233221.113 es_ES
dc.description.references Sen, P., Dang, W., Donahue, G., Dai, J., Dorsey, J., Cao, X., … Berger, S. L. (2015). H3K36 methylation promotes longevity by enhancing transcriptional fidelity. Genes & Development, 29(13), 1362-1376. doi:10.1101/gad.263707.115 es_ES
dc.description.references Feser, J., & Tyler, J. (2010). Chromatin structure as a mediator of aging. FEBS Letters, 585(13), 2041-2048. doi:10.1016/j.febslet.2010.11.016 es_ES
dc.description.references Liu, P., Song, R., Elison, G. L., Peng, W., & Acar, M. (2017). Noise reduction as an emergent property of single-cell aging. Nature Communications, 8(1). doi:10.1038/s41467-017-00752-9 es_ES
dc.description.references Işıldak, U., Somel, M., Thornton, J. M., & Dönertaş, H. M. (2020). Temporal changes in the gene expression heterogeneity during brain development and aging. Scientific Reports, 10(1). doi:10.1038/s41598-020-60998-0 es_ES
dc.description.references Wiley, C. D., Flynn, J. M., Morrissey, C., Lebofsky, R., Shuga, J., Dong, X., … Campisi, J. (2017). Analysis of individual cells identifies cell-to-cell variability following induction of cellular senescence. Aging Cell, 16(5), 1043-1050. doi:10.1111/acel.12632 es_ES
dc.description.references Enge, M., Arda, H. E., Mignardi, M., Beausang, J., Bottino, R., Kim, S. K., & Quake, S. R. (2017). Single-Cell Analysis of Human Pancreas Reveals Transcriptional Signatures of Aging and Somatic Mutation Patterns. Cell, 171(2), 321-330.e14. doi:10.1016/j.cell.2017.09.004 es_ES
dc.description.references Bahar, R., Hartmann, C. H., Rodriguez, K. A., Denny, A. D., Busuttil, R. A., Dollé, M. E. T., … Vijg, J. (2006). Increased cell-to-cell variation in gene expression in ageing mouse heart. Nature, 441(7096), 1011-1014. doi:10.1038/nature04844 es_ES
dc.description.references Angelidis, I., Simon, L. M., Fernandez, I. E., Strunz, M., Mayr, C. H., Greiffo, F. R., … Schiller, H. B. (2019). An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics. Nature Communications, 10(1). doi:10.1038/s41467-019-08831-9 es_ES
dc.description.references Koohy, H., Bolland, D. J., Matheson, L. S., Schoenfelder, S., Stellato, C., Dimond, A., … Varga-Weisz, P. D. (2018). Genome organization and chromatin analysis identify transcriptional downregulation of insulin-like growth factor signaling as a hallmark of aging in developing B cells. Genome Biology, 19(1). doi:10.1186/s13059-018-1489-y es_ES
dc.description.references Bochkis, I. M., Przybylski, D., Chen, J., & Regev, A. (2014). Changes in Nucleosome Occupancy Associated with Metabolic Alterations in Aged Mammalian Liver. Cell Reports, 9(3), 996-1006. doi:10.1016/j.celrep.2014.09.048 es_ES
dc.description.references Cheung, P., Vallania, F., Warsinske, H. C., Donato, M., Schaffert, S., Chang, S. E., … Kuo, A. J. (2018). Single-Cell Chromatin Modification Profiling Reveals Increased Epigenetic Variations with Aging. Cell, 173(6), 1385-1397.e14. doi:10.1016/j.cell.2018.03.079 es_ES
dc.description.references Booth, L. N., & Brunet, A. (2016). The Aging Epigenome. Molecular Cell, 62(5), 728-744. doi:10.1016/j.molcel.2016.05.013 es_ES
dc.description.references Martinez-Jimenez, C. P., Eling, N., Chen, H.-C., Vallejos, C. A., Kolodziejczyk, A. A., Connor, F., … Odom, D. T. (2017). Aging increases cell-to-cell transcriptional variability upon immune stimulation. Science, 355(6332), 1433-1436. doi:10.1126/science.aah4115 es_ES
dc.description.references Frenk, S., & Houseley, J. (2018). Gene expression hallmarks of cellular ageing. Biogerontology, 19(6), 547-566. doi:10.1007/s10522-018-9750-z es_ES
dc.description.references Riera, C. E., Merkwirth, C., De Magalhaes Filho, C. D., & Dillin, A. (2016). Signaling Networks Determining Life Span. Annual Review of Biochemistry, 85(1), 35-64. doi:10.1146/annurev-biochem-060815-014451 es_ES
dc.description.references Guan, Q., Haroon, S., Bravo, D. G., Will, J. L., & Gasch, A. P. (2012). Cellular Memory of Acquired Stress Resistance in Saccharomyces cerevisiae. Genetics, 192(2), 495-505. doi:10.1534/genetics.112.143016 es_ES
dc.description.references Ben Meriem, Z., Khalil, Y., Hersen, P., & Fabre, E. (2019). Hyperosmotic Stress Response Memory is Modulated by Gene Positioning in Yeast. Cells, 8(6), 582. doi:10.3390/cells8060582 es_ES
dc.description.references D’Urso, A., & Brickner, J. H. (2016). Epigenetic transcriptional memory. Current Genetics, 63(3), 435-439. doi:10.1007/s00294-016-0661-8 es_ES
dc.description.references Avramova, Z. (2015). Transcriptional ‘memory’ of a stress: transient chromatin and memory (epigenetic) marks at stress-response genes. The Plant Journal, 83(1), 149-159. doi:10.1111/tpj.12832 es_ES
dc.description.references Gialitakis, M., Arampatzi, P., Makatounakis, T., & Papamatheakis, J. (2010). Gamma Interferon-Dependent Transcriptional Memory via Relocalization of a Gene Locus to PML Nuclear Bodies. Molecular and Cellular Biology, 30(8), 2046-2056. doi:10.1128/mcb.00906-09 es_ES
dc.description.references Ding, Y., Liu, N., Virlouvet, L., Riethoven, J.-J., Fromm, M., & Avramova, Z. (2013). Four distinct types of dehydration stress memory genes in Arabidopsis thaliana. BMC Plant Biology, 13(1). doi:10.1186/1471-2229-13-229 es_ES
dc.description.references Liu, N., Ding, Y., Fromm, M., & Avramova, Z. (2014). Different gene-specific mechanisms determine the ‘revised-response’ memory transcription patterns of a subset of A. thaliana dehydration stress responding genes. Nucleic Acids Research, 42(9), 5556-5566. doi:10.1093/nar/gku220 es_ES
dc.description.references Ding, Y., Fromm, M., & Avramova, Z. (2012). Multiple exposures to drought «train» transcriptional responses in Arabidopsis. Nature Communications, 3(1). doi:10.1038/ncomms1732 es_ES
dc.description.references Brickner, D. G., Cajigas, I., Fondufe-Mittendorf, Y., Ahmed, S., Lee, P.-C., Widom, J., & Brickner, J. H. (2007). H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State. PLoS Biology, 5(4), e81. doi:10.1371/journal.pbio.0050081 es_ES
dc.description.references Sood, V., Cajigas, I., D’Urso, A., Light, W. H., & Brickner, J. H. (2017). Epigenetic Transcriptional Memory of GAL Genes Depends on Growth in Glucose and the Tup1 Transcription Factor in Saccharomyces cerevisiae. Genetics, 206(4), 1895-1907. doi:10.1534/genetics.117.201632 es_ES
dc.description.references Kundu, S., & Peterson, C. L. (2010). Dominant Role for Signal Transduction in the Transcriptional Memory of Yeast GAL Genes. Molecular and Cellular Biology, 30(10), 2330-2340. doi:10.1128/mcb.01675-09 es_ES
dc.description.references Zacharioudakis, I., Gligoris, T., & Tzamarias, D. (2007). A Yeast Catabolic Enzyme Controls Transcriptional Memory. Current Biology, 17(23), 2041-2046. doi:10.1016/j.cub.2007.10.044 es_ES
dc.description.references Lavy, T., Yanagida, H., & Tawfik, D. S. (2015). Gal3 Binds Gal80 Tighter than Gal1 Indicating Adaptive Protein Changes Following Duplication. Molecular Biology and Evolution, 33(2), 472-477. doi:10.1093/molbev/msv240 es_ES
dc.description.references Sood, V., & Brickner, J. H. (2017). Genetic and Epigenetic Strategies Potentiate Gal4 Activation to Enhance Fitness in Recently Diverged Yeast Species. Current Biology, 27(23), 3591-3602.e3. doi:10.1016/j.cub.2017.10.035 es_ES
dc.description.references D’Urso, A., Takahashi, Y., Xiong, B., Marone, J., Coukos, R., Randise-Hinchliff, C., … Brickner, J. H. (2016). Set1/COMPASS and Mediator are repurposed to promote epigenetic transcriptional memory. eLife, 5. doi:10.7554/elife.16691 es_ES
dc.description.references Light, W. H., Freaney, J., Sood, V., Thompson, A., D’Urso, A., Horvath, C. M., & Brickner, J. H. (2013). A Conserved Role for Human Nup98 in Altering Chromatin Structure and Promoting Epigenetic Transcriptional Memory. PLoS Biology, 11(3), e1001524. doi:10.1371/journal.pbio.1001524 es_ES
dc.description.references Light, W. H., Brickner, D. G., Brand, V. R., & Brickner, J. H. (2010). Interaction of a DNA Zip Code with the Nuclear Pore Complex Promotes H2A.Z Incorporation and INO1 Transcriptional Memory. Molecular Cell, 40(1), 112-125. doi:10.1016/j.molcel.2010.09.007 es_ES
dc.description.references Fabrizio, P., Garvis, S., & Palladino, F. (2019). Histone Methylation and Memory of Environmental Stress. Cells, 8(4), 339. doi:10.3390/cells8040339 es_ES
dc.description.references Lämke, J., Brzezinka, K., Altmann, S., & Bäurle, I. (2015). A hit‐and‐run heat shock factor governs sustained histone methylation and transcriptional stress memory. The EMBO Journal, 35(2), 162-175. doi:10.15252/embj.201592593 es_ES
dc.description.references Bevington, S. L., Cauchy, P., Piper, J., Bertrand, E., Lalli, N., Jarvis, R. C., … Cockerill, P. N. (2016). Inducible chromatin priming is associated with the establishment of immunological memory in T cells. The EMBO Journal, 35(5), 515-535. doi:10.15252/embj.201592534 es_ES
dc.description.references To, T. K., & Kim, J. M. (2014). Epigenetic regulation of gene responsiveness in Arabidopsis. Frontiers in Plant Science, 4. doi:10.3389/fpls.2013.00548 es_ES
dc.description.references Maxwell, C. S., Kruesi, W. S., Core, L. J., Kurhanewicz, N., Waters, C. T., Lewarch, C. L., … Baugh, L. R. (2014). Pol II Docking and Pausing at Growth and Stress Genes in C. elegans. Cell Reports, 6(3), 455-466. doi:10.1016/j.celrep.2014.01.008 es_ES
dc.description.references Elowitz, M. B., Levine, A. J., Siggia, E. D., & Swain, P. S. (2002). Stochastic Gene Expression in a Single Cell. Science, 297(5584), 1183-1186. doi:10.1126/science.1070919 es_ES
dc.description.references Rogers, K. W., & Schier, A. F. (2011). Morphogen Gradients: From Generation to Interpretation. Annual Review of Cell and Developmental Biology, 27(1), 377-407. doi:10.1146/annurev-cellbio-092910-154148 es_ES
dc.description.references Losick, R., & Desplan, C. (2008). Stochasticity and Cell Fate. Science, 320(5872), 65-68. doi:10.1126/science.1147888 es_ES
dc.description.references Natoli, G., Saccani, S., Bosisio, D., & Marazzi, I. (2005). Interactions of NF-κB with chromatin: the art of being at the right place at the right time. Nature Immunology, 6(5), 439-445. doi:10.1038/ni1196 es_ES
dc.description.references Kellogg, R. A., & Tay, S. (2015). Noise Facilitates Transcriptional Control under Dynamic Inputs. Cell, 160(3), 381-392. doi:10.1016/j.cell.2015.01.013 es_ES
dc.description.references Wheat, J. C., Sella, Y., Willcockson, M., Skoultchi, A. I., Bergman, A., Singer, R. H., & Steidl, U. (2020). Single-molecule imaging of transcription dynamics in somatic stem cells. Nature, 583(7816), 431-436. doi:10.1038/s41586-020-2432-4 es_ES
dc.description.references Swain, P. S., Elowitz, M. B., & Siggia, E. D. (2002). Intrinsic and extrinsic contributions to stochasticity in gene expression. Proceedings of the National Academy of Sciences, 99(20), 12795-12800. doi:10.1073/pnas.162041399 es_ES
dc.description.references Kærn, M., Elston, T. C., Blake, W. J., & Collins, J. J. (2005). Stochasticity in gene expression: from theories to phenotypes. Nature Reviews Genetics, 6(6), 451-464. doi:10.1038/nrg1615 es_ES
dc.description.references Acar, M., Mettetal, J. T., & van Oudenaarden, A. (2008). Stochastic switching as a survival strategy in fluctuating environments. Nature Genetics, 40(4), 471-475. doi:10.1038/ng.110 es_ES
dc.description.references Balaban, N. Q., Merrin, J., Chait, R., Kowalik, L., & Leibler, S. (2004). Bacterial Persistence as a Phenotypic Switch. Science, 305(5690), 1622-1625. doi:10.1126/science.1099390 es_ES
dc.description.references Schmutzer, M., & Wagner, A. (2020). Gene expression noise can promote the fixation of beneficial mutations in fluctuating environments. PLOS Computational Biology, 16(10), e1007727. doi:10.1371/journal.pcbi.1007727 es_ES
dc.description.references Levy, S. F., Ziv, N., & Siegal, M. L. (2012). Bet Hedging in Yeast by Heterogeneous, Age-Correlated Expression of a Stress Protectant. PLoS Biology, 10(5), e1001325. doi:10.1371/journal.pbio.1001325 es_ES
dc.description.references Levy, S. F. (2016). Cellular Heterogeneity: Benefits Besides Bet-Hedging. Current Biology, 26(9), R355-R357. doi:10.1016/j.cub.2016.03.034 es_ES
dc.description.references Gefen, O., & Balaban, N. Q. (2009). The importance of being persistent: heterogeneity of bacterial populations under antibiotic stress. FEMS Microbiology Reviews, 33(4), 704-717. doi:10.1111/j.1574-6976.2008.00156.x es_ES
dc.description.references Sharma, S. V., Lee, D. Y., Li, B., Quinlan, M. P., Takahashi, F., Maheswaran, S., … Settleman, J. (2010). A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations. Cell, 141(1), 69-80. doi:10.1016/j.cell.2010.02.027 es_ES
dc.description.references Roesch, A., Fukunaga-Kalabis, M., Schmidt, E. C., Zabierowski, S. E., Brafford, P. A., Vultur, A., … Herlyn, M. (2010). A Temporarily Distinct Subpopulation of Slow-Cycling Melanoma Cells Is Required for Continuous Tumor Growth. Cell, 141(4), 583-594. doi:10.1016/j.cell.2010.04.020 es_ES
dc.description.references Shaffer, S. M., Dunagin, M. C., Torborg, S. R., Torre, E. A., Emert, B., Krepler, C., … Raj, A. (2017). Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance. Nature, 546(7658), 431-435. doi:10.1038/nature22794 es_ES
dc.description.references Raser, J. M., & O’Shea, E. K. (2004). Control of Stochasticity in Eukaryotic Gene Expression. Science, 304(5678), 1811-1814. doi:10.1126/science.1098641 es_ES
dc.description.references Lidstrom, M. E., & Konopka, M. C. (2010). The role of physiological heterogeneity in microbial population behavior. Nature Chemical Biology, 6(10), 705-712. doi:10.1038/nchembio.436 es_ES
dc.description.references Brown, R., Curry, E., Magnani, L., Wilhelm-Benartzi, C. S., & Borley, J. (2014). Poised epigenetic states and acquired drug resistance in cancer. Nature Reviews Cancer, 14(11), 747-753. doi:10.1038/nrc3819 es_ES
dc.description.references Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M., O’Shea, E., Pilpel, Y., & Barkai, N. (2006). Noise in protein expression scales with natural protein abundance. Nature Genetics, 38(6), 636-643. doi:10.1038/ng1807 es_ES
dc.description.references Barroso, G. V., Puzovic, N., & Dutheil, J. Y. (2018). The Evolution of Gene-Specific Transcriptional Noise Is Driven by Selection at the Pathway Level. Genetics, 208(1), 173-189. doi:10.1534/genetics.117.300467 es_ES
dc.description.references Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006). Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature, 441(7095), 840-846. doi:10.1038/nature04785 es_ES
dc.description.references Gasch, A. P., Yu, F. B., Hose, J., Escalante, L. E., Place, M., Bacher, R., … McClean, M. N. (2017). Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress. PLOS Biology, 15(12), e2004050. doi:10.1371/journal.pbio.2004050 es_ES
dc.description.references Charlebois, D. A., Abdennur, N., & Kaern, M. (2011). Gene Expression Noise Facilitates Adaptation and Drug Resistance Independently of Mutation. Physical Review Letters, 107(21). doi:10.1103/physrevlett.107.218101 es_ES
dc.description.references Charlebois, D. A. (2015). Effect and evolution of gene expression noise on the fitness landscape. Physical Review E, 92(2). doi:10.1103/physreve.92.022713 es_ES
dc.description.references Jones, D. L., Brewster, R. C., & Phillips, R. (2014). Promoter architecture dictates cell-to-cell variability in gene expression. Science, 346(6216), 1533-1536. doi:10.1126/science.1255301 es_ES
dc.description.references Sanchez, A., & Golding, I. (2013). Genetic Determinants and Cellular Constraints in Noisy Gene Expression. Science, 342(6163), 1188-1193. doi:10.1126/science.1242975 es_ES
dc.description.references Sanchez, A., Choubey, S., & Kondev, J. (2013). Regulation of Noise in Gene Expression. Annual Review of Biophysics, 42(1), 469-491. doi:10.1146/annurev-biophys-083012-130401 es_ES
dc.description.references Sánchez, Á., & Kondev, J. (2008). Transcriptional control of noise in gene expression. Proceedings of the National Academy of Sciences, 105(13), 5081-5086. doi:10.1073/pnas.0707904105 es_ES
dc.description.references Das, D., Dey, S., Brewster, R. C., & Choubey, S. (2017). Effect of transcription factor resource sharing on gene expression noise. PLOS Computational Biology, 13(4), e1005491. doi:10.1371/journal.pcbi.1005491 es_ES
dc.description.references Engl, C., Jovanovic, G., Brackston, R. D., Kotta-Loizou, I., & Buck, M. (2020). The route to transcription initiation determines the mode of transcriptional bursting in E. coli. Nature Communications, 11(1). doi:10.1038/s41467-020-16367-6 es_ES
dc.description.references Brown, C. R., & Boeger, H. (2014). Nucleosomal promoter variation generates gene expression noise. Proceedings of the National Academy of Sciences, 111(50), 17893-17898. doi:10.1073/pnas.1417527111 es_ES
dc.description.references Brown, C. R., Mao, C., Falkovskaia, E., Jurica, M. S., & Boeger, H. (2013). Linking Stochastic Fluctuations in Chromatin Structure and Gene Expression. PLoS Biology, 11(8), e1001621. doi:10.1371/journal.pbio.1001621 es_ES
dc.description.references Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., … Greenleaf, W. J. (2015). Single-cell chromatin accessibility reveals principles of regulatory variation. Nature, 523(7561), 486-490. doi:10.1038/nature14590 es_ES
dc.description.references Wu, S., Li, K., Li, Y., Zhao, T., Li, T., Yang, Y.-F., & Qian, W. (2017). Independent regulation of gene expression level and noise by histone modifications. PLOS Computational Biology, 13(6), e1005585. doi:10.1371/journal.pcbi.1005585 es_ES
dc.description.references Lagha, M., Bothma, J. P., Esposito, E., Ng, S., Stefanik, L., Tsui, C., … Levine, M. S. (2013). Paused Pol II Coordinates Tissue Morphogenesis in the Drosophila Embryo. Cell, 153(5), 976-987. doi:10.1016/j.cell.2013.04.045 es_ES
dc.description.references Buettner, F., Natarajan, K. N., Casale, F. P., Proserpio, V., Scialdone, A., Theis, F. J., … Stegle, O. (2015). Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells. Nature Biotechnology, 33(2), 155-160. doi:10.1038/nbt.3102 es_ES
dc.description.references Battich, N., Stoeger, T., & Pelkmans, L. (2015). Control of Transcript Variability in Single Mammalian Cells. Cell, 163(7), 1596-1610. doi:10.1016/j.cell.2015.11.018 es_ES
dc.description.references Ansel, J., Bottin, H., Rodriguez-Beltran, C., Damon, C., Nagarajan, M., Fehrmann, S., … Yvert, G. (2008). Cell-to-Cell Stochastic Variation in Gene Expression Is a Complex Genetic Trait. PLoS Genetics, 4(4), e1000049. doi:10.1371/journal.pgen.1000049 es_ES
dc.description.references You, S.-T., Jhou, Y.-T., Kao, C.-F., & Leu, J.-Y. (2019). Experimental evolution reveals a general role for the methyltransferase Hmt1 in noise buffering. PLOS Biology, 17(10), e3000433. doi:10.1371/journal.pbio.3000433 es_ES


This item appears in the following Collection(s)

Show simple item record