Single-RNA counting reveals alternative modes of gene expression in yeast

Zenklusen, Daniel, Larson, Daniel R, Singer, Robert H·2008·Nature Structural & Molecular Biology

Cited by (683)

Items 201–300 of 683

  1. Noise and Information Transmission in Promoters with Multiple Internal States
    Georg Rieckh, Gašper Tkačik · 2014 · Biophysical Journal
  2. Theory in Biology: Figure 1 or Figure 7?
    Rob Phillips · 2015 · Trends in Cell Biology
  3. Promoter-specific dynamics of TATA-binding protein association with the human genome
    Yuko Hasegawa, Jason D. Lieb, Kevin Struhl · 2019 · Genome Research
  4. Estimating selection on synonymous codon usage from noisy experimental data
    Wallace, Edward W.J., Airoldi, Edoardo M., Drummond, D. Allan · 2013 · Molecular Biology and Evolution
  5. Quantifying the contribution of chromatin dynamics to stochastic gene expression reveals long, locus-dependent periods between transcriptional bursts
    José Viñuelas, Gaël Kaneko, Antoine Coulon, Elodie Vallin, Valérie Morin, Camila Mejia-Pous, Jean-Jacques Kupiec, Guillaume Beslon, Olivier Gandrillon · 2013 · BMC Biology
  6. The extent of ribosome queuing in budding yeast
    Alon Diament, Anna Feldman, Elisheva Schochet, Martin Kupiec, Yoav Arava, Tamir Tuller · 2018 · PLoS Computational Biology
  7. Measuring transcription at a single gene copy reveals hidden drivers of bacterial individuality
    Mengyu Wang, Jing Zhang, Heng Xu, Ido Golding · 2019 · Nature Microbiology
  8. Stochastic expression dynamics of a transcription factor revealed by single-molecule noise analysis
    Zach Hensel, Haidong Feng, Bo Han, Christine L. Hatem, Jin Wang, Jie Xiao · 2012 · Nature Structural & Molecular Biology
  9. Two steps forward—one step back: Advances in affinity purification mass spectrometry of macromolecular complexes
    Marlene Oeffinger · 2012 · PROTEOMICS
  10. RiboSys, a high-resolution, quantitative approach to measure the in vivo kinetics of pre-mRNA splicing and 3′-end processing in Saccharomyces cerevisiae
    Ross D. Alexander, J. David Barrass, Beatriz Solange Dichtl, Martin Koš, Tomasz Obtułowicz, Marie-Cécile Robert, Michał Koper, Iwona Karkusiewicz, Luisa Mariconti, David W. Tollervey et al. · 2010 · RNA
  11. BayFish: Bayesian inference of transcription dynamics from population snapshots of single-molecule RNA FISH in single cells
    Mariana Gómez-Schiavon, Liangfu Chen, Anne E. West, Nicolas E. G. Buchler · 2017 · Genome biology
  12. Antisense transcription‐dependent chromatin signature modulates sense transcript dynamics
    Tom Brown, Françoise S. Howe, Struan C. Murray, Meredith Wouters, Philipp Lorenz, Emily Seward, Scott Rata, Andrew Angel, Jane Mellor · 2018 · Molecular Systems Biology
  13. Modeling the dynamic behavior of biochemical regulatory networks
    John J. Tyson, Teeraphan Laomettachit, Pavel Kraikivski · 2018 · Journal of Theoretical Biology
  14. A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast
    Judith B. Zaugg, Nicholas M. Luscombe · 2011 · Genome Research
  15. Analyzing mRNA Expression Using Single mRNA Resolution Fluorescent In Situ Hybridization
    Daniel R. Zenklusen, Robert H. Singer · 2010 · Methods in enzymology on CD-ROM/Methods in enzymology
  16. Single molecule approaches for quantifying transcription and degradation rates in intact mammalian tissues
    Keren Bahar Halpern, Shalev Itzkovitz · 2015 · Methods
  17. Single-cell differences in matrix gene expression do not predict matrix deposition
    Allison Coté, Claire M. McLeod, Megan J. Farrell, Patrick D. McClanahan, Margaret C. Dunagin, Arjun Raj, Robert L. Mauck · 2016 · Nature Communications
  18. Shadow enhancers can suppress input transcription factor noise through distinct regulatory logic
    Rachel Waymack, Alvaro Fletcher, Germán Enciso, Zeba Wunderlich · 2020 · eLife
  19. Coverage-dependent bias creates the appearance of binary splicing in single cells
    Carlos F. Buen Abad Najar, Nir Yosef, Liana F. Lareau · 2020 · eLife
  20. Frequency Domain Analysis of Fluctuations of mRNA and Protein Copy Numbers within a Cell Lineage: Theory and Experimental Validation
    Chen Jia, Ramon Grima · 2021 · Physical Review X
  21. Elimination of cap structures generated by mRNA decay involves the new scavenger mRNA decapping enzyme Aph1/FHIT together with DcpS
    Valério Taverniti, Bertrand Séraphin · 2014 · Nucleic Acids Research
  22. Transimulation - Protein Biosynthesis Web Service
    Siwiak, Marlena, Zielenkiewicz, Piotr · 2013 · PLoS ONE
  23. Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei
    Veit Schubert, Klaus Weißhart · 2015 · Journal of Experimental Botany
  24. The architecture of eukaryotic translation
    Dominique Chu, Tobias von der Haar · 2012 · Nucleic Acids Research
  25. Single molecule fluorescence in situ hybridisation for quantitating post-transcriptional regulation in Drosophila brains
    Lu Yang, Josh Titlow, Darragh Ennis, Carlas Smith, Jessica H. Mitchell, Florence L. Young, Scott Waddell, David Ish‐Horowicz, Ilan Davis · 2017 · Methods
  26. Interactions between HIV-1 Gag and Viral RNA Genome Enhance Virion Assembly
    Kari A. Dilley, Olga A. Nikolaitchik, Andrea Galli, Ryan C. Burdick, Louis Levine, Kelvin Li, Alan R. Rein, Vinay K. Pathak, Wei-Shau Hu · 2017 · Journal of Virology
  27. Transcriptional Regulation of Lineage Commitment - A Stochastic Model of Cell Fate Decisions
    Jose Teles, Cristina Pina, Patrik Edén, Mattias Ohlsson, Tariq Enver, Carsten Peterson · 2013 · PLoS Computational Biology
  28. Complex dynamics of transcription regulation
    Diana A. Stavreva, Lyuba Varticovski, Gordon L. Hager · 2012 · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
  29. Discriminating cellular heterogeneity using microwell-based RNA cytometry
    Ivan K. Dimov, Rong Lu, Eric P. Lee, Jun Seita, Debashis Sahoo, Seung-min Park, Irving L. Weissman, Luke P. Lee · 2014 · Nature Communications
  30. Genome architecture and the role of transcription
    Argyris Papantonis, Peter R. Cook · 2010 · Current Opinion in Cell Biology
  31. Quantitative analysis of the transcription control mechanism
    Changhui Mao, Christopher R. Brown, Elena Falkovskaia, Shawfeng Dong, Eva Hrabeta‐Robinson, Lauren Wenger, Hinrich Boeger · 2010 · Molecular Systems Biology
  32. Exploring transcription regulation through cell-to-cell variability
    Ruty Rinott, Ariel Jaimovich, Nir Friedman · 2011 · Proceedings of the National Academy of Sciences
  33. Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions
    Xiaoming Fu, Heta Patel, Stefano Coppola, Libin Xu, Zhixing Cao, Tineke Laura Lenstra, Ramon Grima · 2022 · eLife
  34. Oscillatory control of signalling molecules
    Pawel Paszek, Dean Andrew Jackson, Michael White · 2010 · Current Opinion in Genetics & Development
  35. Subnuclear positioning and interchromosomal clustering of the GAL1-10 locus are controlled by separable, interdependent mechanisms
    Donna Garvey Brickner, Varun Sood, Evelina Tutucci, Robert Coukos, Kayla Viets, Robert H. Singer, Jason H. Brickner · 2016 · Molecular Biology of the Cell
  36. Genome-wide inference reveals that feedback regulations constrain promoter-dependent transcriptional burst kinetics
    Songhao Luo, Zihao Wang, Zhenquan Zhang, Tianshou Zhou, Jiajun Zhang · 2022 · Nucleic Acids Research
  37. A Nutrient-Responsive Pathway that Determines M Phase Timing through Control of B-Cyclin mRNA Stability
    Vincent Messier, Daniel Zenklusen, Stephen W. Michnick · 2013 · Cell
  38. Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control
    Sarah A. Peck Justice, Katlyn D. Hughes, Jose F. Victorino, Amber L. Mosley · 2019 · Wiley Interdisciplinary Reviews - RNA
  39. Visualizing the translation and packaging of HIV-1 full-length RNA
    Jianbo Chen, Yang Liu, Bin Wu, Olga A. Nikolaitchik, Preeti R. Mohan, Jiji Chen, Vinay K. Pathak, Wei-Shau Hu · 2020 · Proceedings of the National Academy of Sciences
  40. Transcriptional bursting: stochasticity in deterministic development
    Emilia A. Leyes Porello, Robert T. Trudeau, Bomyi Lim · 2023 · Development
  41. What have single-molecule studies taught us about gene expression?
    Huimin Chen, Daniel R. Larson · 2016 · Genes & Development
  42. Mov10 and APOBEC3G Localization to Processing Bodies Is Not Required for Virion Incorporation and Antiviral Activity
    Taisuke Izumi, Ryan C. Burdick, Mayu Shigemi, Sergey Y. Plisov, Wei-Shau Hu, Vinay K. Pathak · 2013 · Journal of Virology
  43. The Interleaved Genome
    Jane Mellor, Ronja Woloszczuk, Françoise S. Howe · 2015 · Trends in Genetics
  44. Multiple Transcript Properties Related to Translation Affect mRNA Degradation Rates in Saccharomyces cerevisiae
    Benjamin Neymotin, Victoria M. Ettorre, David Gresham · 2016 · G3 Genes Genomes Genetics
  45. Dynamics of RNA polymerase II and elongation factor Spt4/5 recruitment during activator-dependent transcription
    Grace A. Rosen, Inwha Baek, Larry J. Friedman, Yoo Jin Joo, Stephen Buratowski, Jeff Gelles · 2020 · Proceedings of the National Academy of Sciences
  46. Inferring gene regulation from stochastic transcriptional variation across single cells at steady state
    Anika Gupta, Jorge Diego Martin-Rufino, Thouis R. Jones, Vidya Subramanian, Xiaojie Qiu, Emanuelle I. Grody, Alex Bloemendal, Chen Weng, Sheng-Yong Niu, Kyung Hoi Min et al. · 2022 · Proceedings of the National Academy of Sciences
  47. Single-cell new RNA sequencing reveals principles of transcription at the resolution of individual bursts
    Daniel Ramsköld, Gert‐Jan Hendriks, Anton J. M. Larsson, Juliane V. Mayr, Christoph Ziegenhain, Michael Hagemann-Jensen, Leonard Hartmanis, Rickard Sandberg · 2024 · Nature Cell Biology
  48. Digital nature of the immediate-early transcriptional response
    Michelle Stevense, Tetsuya Muramoto, Iris I. Müller, Jonathan Robert Chubb · 2010 · Development
  49. Dynamics of HIV-1 RNA Near the Plasma Membrane during Virus Assembly
    Luca Sardo, Steven C. Hatch, Jianbo Chen, Olga A. Nikolaitchik, Ryan C. Burdick, De Chen, Christopher J. Westlake, Stephen Lockett, Vinay K. Pathak, Wei-Shau Hu · 2015 · Journal of Virology
  50. Distribution Modes and Their Corresponding Parameter Regions in Stochastic Gene Transcription
    Feng Jiao, Qiwen Sun, Moxun Tang, Jianshe Yu, Bo Zheng · 2015 · SIAM Journal on Applied Mathematics
  51. Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus
    Yinjia Li, Sheng Zuo, Zhiliang Zhang, Zhanjie Li, Jinlei Han, Zhaoqing Chu, Robert Hasterok, Kai Wang · 2018 · The Plant Journal
  52. Origins and consequences of transcriptional discontinuity
    David M. Suter, Nacho Molina, Félix Naef, Ueli Schibler · 2011 · Current Opinion in Cell Biology
  53. Using variability in gene expression as a tool for studying gene regulation
    Olivia M. Padovan-Merhar, Arjun Raj · 2013 · WIREs Systems Biology and Medicine
  54. The Chemical Fluctuation Theorem governing gene expression
    Seong Jun Park, Sanggeun Song, Gil‐Suk Yang, Philip M. Kim, Sangwoon Yoon, Ji‐Hyun Kim, Jaeyoung Sung · 2018 · Nature Communications
  55. HIV-1 uncoating requires long double-stranded reverse transcription products
    Ryan C. Burdick, Michael Morse, Ioulia F. Rouzina, Mark C. Williams, Wei-Shau Hu, Vinay K. Pathak · 2024 · Science Advances
  56. Transcription by the numbers redux: experiments and calculations that surprise
    Hernán G. García, Álvaro Sánchez, Thomas E. Kuhlman, Jané Kondev, Rob Phillips · 2010 · Trends in Cell Biology
  57. Hybrid modeling and simulation of stochastic effects on progression through the eukaryotic cell cycle
    Zhen Liu, Pu Yang, Fei Li, Clifford A. Shaffer, Stefan Hoops, John J. Tyson, Yang Cao · 2012 · The Journal of Chemical Physics
  58. Exploiting Natural Fluctuations to Identify Kinetic Mechanisms in Sparsely Characterized Systems
    Andreas Hilfinger, Thomas M. Norman, Johan Paulsson · 2016 · Cell Systems
  59. Architecture and dynamics of overlapped RNA regulatory networks
    Christopher P. Lapointe, Melanie A. Preston, Daniel Wilinski, Harriet A. J. Saunders, Zachary T. Campbell, Marvin Wickens · 2017 · RNA
  60. Sensitivity of mRNA Translation
    Gilad Poker, Michael Margaliot A, Tamir Tuller · 2015 · Scientific Reports
  61. Analytical Time-Dependent Distributions for Gene Expression Models With Complex Promoter Switching Mechanisms
    Chen Jia, Youming Li · 2023 · SIAM Journal on Applied Mathematics
  62. Transcriptional Bursting Diversifies the Behaviour of a Toggle Switch: Hybrid Simulation of Stochastic Gene Expression
    Pavol Bokes, John R. King, Andrew T. A. Wood, Matthew Loose · 2013 · Bulletin of Mathematical Biology
  63. A Stochastic Model of the Yeast Cell Cycle Reveals Roles for Feedback Regulation in Limiting Cellular Variability
    Debashis Barik, David A. Ball, Jean Peccoud, John J. Tyson · 2016 · PLoS Computational Biology
  64. Stochastic transcription in the p53‐mediated response to DNA damage is modulated by burst frequency
    Dhana Friedrich, Laura Friedel, Ana Finzel, Andreas Herrmann, Stephan Preibisch, Alexander Loewer · 2019 · Molecular Systems Biology
  65. The minimal intrinsic stochasticity of constitutively expressed eukaryotic genes is sub-Poissonian
    Douglas E. Weidemann, James Holehouse, Abhyudai Singh, Ramon Grima, Silke Hauf · 2023 · Science Advances
  66. Single-Molecule Resolution Fluorescent In Situ Hybridization (smFISH) in the Yeast S. cerevisiae
    Samir Rahman, Daniel Zenklusen · 2013 · Methods in molecular biology
  67. Quantifying the Effect of Ribosomal Density on mRNA Stability
    Shlomit Edri, Tamir Tuller · 2014 · PLoS ONE
  68. Population density approach for discrete mRNA distributions in generalized switching models for stochastic gene expression
    Adam R. Stinchcombe, Charles S. Peskin, Daniel Tranchina · 2012 · Physical Review E
  69. Distinguishing between models of mammalian gene expression: telegraph-like models versus mechanistic models
    Braichenko, Svitlana, Holehouse, James, Grima, Ramon · 2021 · Journal of The Royal Society Interface
  70. APOBEC3 proteins can copackage and comutate HIV-1 genomes
    Belete Ayele Desimmie, Ryan C. Burdick, Taisuke Izumi, Hibiki Doi, Wei Shao, W. Gregory Alvord, Kei Sato, Yoshio Koyanagi, Sara Jones, Eleanor M. P. Wilson et al. · 2016 · Nucleic Acids Research
  71. Modelling and measuring intracellular competition for finite resources during gene expression
    Renana Sabi, Tamir Tuller · 2019 · Journal of The Royal Society Interface
  72. m-TAG: a PCR-based genomic integration method to visualize the localization of specific endogenous mRNAs in vivo in yeast
    Liora Haim-Vilmovsky, Jeffrey E. Gerst · 2009 · Nature Protocols
  73. Polysome collapse and RNA condensation fluidize the cytoplasm
    Ying Xie, Tong Shu, Tiewei Liu, Marie-Christin Spindler, Julia Mahamid, Glen M. Hocky, David Gresham, Liam J. Holt · 2024 · Molecular Cell
  74. The Low Noise Limit in Gene Expression
    Roy D. Dar, Brandon S. Razooky, Leor S. Weinberger, Chris D. Cox, Michael L. Simpson · 2015 · PLoS ONE
  75. Why Dom34 Stimulates Growth of Cells with Defects of 40S Ribosomal Subunit Biosynthesis
    Arpita Bhattacharya, Kerri B. McIntosh, Ian M. Willis, Jonathan R. Warner · 2010 · Molecular and Cellular Biology
  76. Biophysical modeling with variational autoencoders for bimodal, single-cell RNA sequencing data
    Maria Carilli, Gennady Gorin, Yongin Choi, Tara Chari, Lior S. Pachter · 2024 · Nature Methods
  77. Differential context-specific impact of individual core promoter elements on transcriptional dynamics
    Oliver Hendy, John A. Campbell, Jocelyn D. Weissman, Daniel R. Larson, Dinah S. Singer · 2017 · Molecular Biology of the Cell
  78. Detecting RNA base methylations in single cells by in situ hybridization
    Rohan T. Ranasinghe, Martin R. Challand, Kristina A. Ganzinger, Benjamin W. Lewis, Charlotte A. Softley, Wolfgang Hellmut Schmied, Mathew H. Horrocks, Nadia Shivji, Jason W. Chin, JAMES M. SPENCER et al. · 2018 · Nature Communications
  79. Co-translational control of protein complex formation: a fundamental pathway of cellular organization?
    Neal K. Williams, Bernhard Dichtl · 2018 · Biochemical Society Transactions
  80. Concentration fluctuations in growing and dividing cells: Insights into the emergence of concentration homeostasis
    Chen Jia, Abhyudai Singh, Ramon Grima · 2022 · PLoS Computational Biology
  81. Quantifying and correcting bias in transcriptional parameter inference from single-cell data
    Ramon Grima, Pierre-Marie Esmenjaud · 2023 · Biophysical Journal
  82. Resource Sharing Controls Gene Expression Bursting
    Patrick M. Caveney, Sarah Elizabeth Norred, Charles W. J. Chin, Jonathan B. Boreyko, Brandon S. Razooky, Scott T. Retterer, Charles Patrick Collier, Michael L. Simpson · 2016 · ACS Synthetic Biology
  83. Homeostasis in the Central Dogma of molecular biology: the importance of mRNA instability
    Pérez-Ortín, José E., Tordera, Vicente, Chávez, Sebastián · 2019 · RNA Biology
  84. Replicative aging as a source of cell heterogeneity in budding yeast
    Дмитрий Алексеевич Кнорре, Aglaia V. Azbarova, Kseniia V. Galkina, Boris A. Feniouk, Fedor F. Severin · 2018 · Mechanisms of Ageing and Development
  85. Quantitative 3D Tracing of Gene-delivery Viral Vectors in Human Cells and Animal Tissues
    Xiao, Ping-Jie, Li, Chengwen, Neumann, Aaron, Samulski, R Jude · 2012 · Molecular Therapy
  86. Quantitative measurement of single cell dynamics
    Denise Bakstad, Antony D. Adamson, David G. Spiller, Michael White · 2011 · Current Opinion in Biotechnology
  87. Geometry-Induced Bursting Dynamics in Gene Expression
    B. Meyer, Olivier Bénichou, Yariv Kafri, Raphaël Voituriez · 2012 · Biophysical Journal
  88. Unbiased Quantitative Models of Protein Translation Derived from Ribosome Profiling Data
    Alexey A. Gritsenko, Marc Hulsman, Marcel J. T. Reinders, Dick de Ridder · 2015 · PLoS Computational Biology
  89. Uniform gene expression in embryos is achieved by temporal averaging of transcription noise
    L. Carine Stapel, Christoph Zechner, Nadine L. Vastenhouw · 2017 · Genes & Development
  90. Data normalization for addressing the challenges in the analysis of single-cell transcriptomic datasets
    Raquel Cuevas‐Díaz Durán, Haichao Wei, Jiaqian Wu · 2024 · BMC Genomics
  91. Transcriptional refractoriness is dependent on core promoter architecture
    François Cesbron, Michael Oehler, Nati Ha, Gencer Sancar, Michael Brunner · 2015 · Nature Communications
  92. Quantifying the transcriptional output of single alleles in single living mammalian cells
    Sharon Yunger, Liat Rosenfeld, Yuval Garini, Yaron Shav‐Tal · 2013 · Nature Protocols
  93. Global and targeted approaches to single-cell transcriptome characterization
    Aleksandra A. Kolodziejczyk, Tapio Lönnberg · 2017 · Briefings in Functional Genomics
  94. Gene promoters dictate histone occupancy within genes
    Roberto Perales, Benjamin Erickson, Lian Zhang, Hyunmin Kim, Elan Valiquett, David L. Bentley · 2013 · The EMBO Journal
  95. Identification of a Plant Viral RNA Genome in the Nucleus
    Ruimin Gao, Peng Liu, Sek‐Man Wong · 2012 · PLoS ONE
  96. A nucleoporin, Nup60p, affects the nuclear and cytoplasmic localization of ASH1 mRNA in S. cerevisiae
    Erin A. Powrie, Daniel Zenklusen, Robert H. Singer · 2010 · RNA
  97. Nuclear Retention Prevents Premature Cytoplasmic Appearance of mRNA
    Thomas Beuchert Kallehauge, Marie-Cécile Robert, Édouard Bertrand, Torben Heick Jensen · 2012 · Molecular Cell
  98. Balancing noise and plasticity in eukaryotic gene expression
    Djordje Bajić, Juan F. Poyatos · 2012 · BMC Genomics
  99. Measuring Transcription Dynamics in Living Cells Using Fluctuation Analysis
    Matthew Ferguson, Daniel R. Larson · 2013 · Methods in molecular biology
  100. Nascent RNA kinetics: Transient and steady state behavior of models of transcription
    Sandeep Choubey · 2018 · Physical review. E