Single-allele analysis of transcription kinetics in living mammalian cells

Yunger, Sharon, Rosenfeld, Liat, Garini, Yuval, Shav-Tal, Yaron·2010·Nature Methods

Cited by (176)

Items 101–176 of 176

  1. Stochastic allelic expression as trigger for contractile imbalance in hypertrophic cardiomyopathy
    Judith Montag, Theresia Kraft · 2020 · Biophysical Reviews
  2. Exact results for gene-expression models with general waiting-time distributions
    Jinqiang Zhang, Aimin Chen, Huahai Qiu, Jiajun Zhang, Tianhai Tian, Tianshou Zhou · 2024 · Physical review. E
  3. CD-tagging-MS2: detecting allelic expression of endogenous mRNAs and their protein products in single cells
    Jonathan Sheinberger, Hodaya Hochberg-Laufer, Erez Lavi, Itamar Kanter, Shira Avivi-Mintz, Gita Reinitz, Avital Schwed-Gross, Yuval Aizler, Eli Varon, Noa Kinor et al. · 2017 · Biology Methods and Protocols
  4. Seeing Is Believing: Visualizing Transcriptional Dynamics in Single Cells
    Alyshia Newhart, Susan M. Janicki · 2013 · Journal of Cellular Physiology
  5. Single-site transcription rates through fitting of ensemble-averaged data from fluorescence recovery after photobleaching: A fat-tailed distribution
    Liat Rosenfeld, Eldad Kepten, Sharon Yunger, Yaron Shav‐Tal, Yuval Garini · 2015 · Physical Review E
  6. Acting on impulse: dissecting the dynamics of the NFAT transcriptional response
    Alon Kalo, Yaron Shav‐Tal · 2013 · Genome biology
  7. Direct visualization of transcriptional activation by physical enhancer–promoter proximity
    Hongtao Chen, Miki Fujioka, James B. Jaynes, Thomas Gregor · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  8. Patient-specific hiPSC-derived cardiomyocytes indicate allelic and contractile imbalance as pathogenic factor in early-stage Hypertrophic Cardiomyopathy
    Natalie Weber, Judith Montag, Kathrin Kowalski, Bogdan I. Iorga, Jeanne de la Roche, Tim Holler, Daniel Wojciechowski, Meike Wendland, Ante Radocaj, Anne Kathrin Mayer et al. · 2024 · Journal of Molecular and Cellular Cardiology
  9. Modeling stochastic gene expression: From Markov to non-Markov models
    Zhenquan Zhang, Junhao Liang, Zihao Wang, Jiajun Zhang, Tianshou Zhou · 2020 · Mathematical Biosciences & Engineering
  10. Incorporating spatial diffusion into models of bursty stochastic transcription
    Christopher E. Miles · 2025 · Journal of The Royal Society Interface
  11. A role for Rtt109 in buffering gene-dosage imbalance during DNA replication
    Yoav Voichek, Raz Bar‐Ziv, Naama Barkai · 2016 · Nucleus
  12. Discontinuous transcription
    Evgeny Smirnov, Matúš Hornáček, Tomáš Vacı́k, Dušan Cmarko, Ivan Raška · 2017 · Nucleus
  13. Decoding the grammar of transcriptional regulation from RNA polymerase measurements: models and their applications
    Md Zulfikar Ali, Sandeep Choubey · 2019 · Physical Biology
  14. Methods for spatial and temporal imaging of the different steps involved in RNA processing at single‐molecule resolution
    Fatu Badiane Markey, Vijay Parashar, Mona Batish · 2020 · Wiley Interdisciplinary Reviews - RNA
  15. On the right track
    Amir Mor, Rakefet Ben-Yishay, Yaron Shav‐Tal · 2010 · Nucleus
  16. RNA polymerase II transcription on the fast lane
    Alessandro Marcello · 2012 · Transcription
  17. Regulatory Mechanisms for Transcriptional Bursting Revealed by an Event-Based Model
    Renjie Wu, Bangyan Zhou, Wei Wang, Feng Liu · 2023 · Research
  18. Real-Time Temporal Dynamics of Bicistronic Expression Mediated by Internal Ribosome Entry Site and 2A Cleaving Sequence.
    Soomin Lee, Jeong-Ah Kim, Hee-Dae Kim, Sooyoung Chung, Kyungjin Kim, Han Kyoung Choe · 2019 · Europe PMC (PubMed Central)
  19. Single-cell, single-mRNA analysis of Ccnb1 promoter regulation
    Nidhi Vishnoi, Jie Yao · 2017 · Scientific Reports
  20. Advancing towards a global mammalian gene regulation model through single-cell analysis and synthetic biology
    Josh Tycko, Mike V. Van, Michael B. Elowitz, Lacramioara Bintu · 2017 · Current Opinion in Biomedical Engineering
  21. Transcription factor residence time dominates over concentration in transcription activation
    Achim P. Popp, Johannes Hettich, J. Christof M. Gebhardt · 2020 · bioRxiv (Cold Spring Harbor Laboratory)
  22. Time-resolved analysis of transcription kinetics in single live mammalian cells
    Hongyoung Choi, Byung Hun Lee, Hye Yoon Park · 2022 · Frontiers in Physics
  23. Measuring the Kinetics of mRNA Transcription in Single Living Cells
    Yehuda Brody, Yaron Shav‐Tal · 2011 · Journal of Visualized Experiments
  24. Dynamical analysis of mCAT2 gene models with CTN-RNA nuclear retention
    Qianliang Wang, Tianshou Zhou · 2015 · Physical Biology
  25. Zooming in on single active genes in living mammalian cells
    Sharon Yunger, Alon Kalo, Pinhas Kafri, Jonathan Sheinberger, Erez Lavi, Noa Neufeld, Yaron Shav‐Tal · 2013 · Histochemistry and Cell Biology
  26. S-phase transcriptional buffering quantified on two different promoters
    Sharon Yunger, Pinhas Kafri, Liat Rosenfeld, Eliraz Greenberg, Noa Kinor, Yuval Garini, Yaron Shav‐Tal · 2018 · Life Science Alliance
  27. Bursting through the cell cycle
    Shani Ben‐Moshe, Shalev Itzkovitz · 2016 · eLife
  28. Rapid Transcriptional Pulsing Dynamics of High Expressing Retroviral Transgenes in Embryonic Stem Cells
    Mandy Lo, Sylvie Rival‐Gervier, Peter Pasceri, James Ellis · 2012 · PLoS ONE
  29. Quantitative measurement of transcription dynamics in living cells
    Adam M. Corrigan, Jonathan Robert Chubb · 2015 · Methods in cell biology
  30. Pol II caught speeding by single gene imaging
    Danielle Cannon, Jonathan Robert Chubb · 2011 · EMBO Reports
  31. Measuring transcription dynamics in living cells using a photobleaching approach
    Hodaya Hochberg-Laufer, Yehuda Brody, Yaron Shav‐Tal · 2017 · Methods
  32. Single-Molecule Imaging of RNA Splicing in Live Cells
    José Rino, Robert M. Martin, Célia Carvalho, Ana C. de Jesus, Maria Carmo‐Fonseca · 2015 · Methods in enzymology on CD-ROM/Methods in enzymology
  33. Imaging mRNAs in Living Mammalian Cells
    Sharon Yunger, Yaron Shav‐Tal · 2011 · Methods in molecular biology
  34. The delicate relationship between DNA replication timing and gene expression
    Avraham Greenberg, Britny Blumenfeld, Itamar Simon · 2020 · Current Opinion in Systems Biology
  35. An emerging paradigm in epigenetic marking: coordination of transcription and replication
    Tyler K. Fenstermaker, Svetlana Petruk, Alexander Mazo · 2024 · Transcription
  36. Fluorescence Amplification Tags for Single‐Molecule Imaging and Tracking of Proteins, RNA, and DNA in Live Cells
    Yifan Bao, Tianle Xiong, Arnaud Gautier, Murat Sünbül, Lu Wang · 2026 · Angewandte Chemie International Edition
  37. How Transcription Factor Clusters Shape the Transcriptional Landscape
    Rahul Munshi · 2024 · Biomolecules
  38. Transcription, one allele at a time
    Timothée Lionnet, Robert H. Singer · 2010 · Genome biology
  39. Dynamics and Transport of Nuclear RNA
    Jonathan Sheinberger, Yaron Shav‐Tal · 2016 · Springer eBooks
  40. Lessons from (pre-)mRNA Imaging.
    Srivathsan Adivarahan, Daniel Zenklusen · 2019 · Advances in Experimental Medicine and Biology
  41. Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo Development
    César Nieto, Zahra Vahdat, Bomyi Lim, Abhyudai Singh · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
  42. Visualizing genetic information flow in space and time
    Kaijin Chen, Kun Zhao, Yihan Wan · 2025 · Science China Life Sciences
  43. Interpreting Gene-Expression Profiles in Transplantation: A Critical Appraisal
    Nicolas Pallet, Éric Thervet, Michel Desjardins · 2011 · Frontiers in Genetics
  44. Different effects of fast and slow input fluctuations on output in gene regulation
    Huahai Qiu, Zhanjiang Yuan, Tianshou Zhou, Luonan Chen · 2020 · Chaos An Interdisciplinary Journal of Nonlinear Science
  45. Exact burst-size distributions for gene-expression models with complex promoter structure
    Liying Zhou, Wenhao Chen, Jinqiang Zhang, Jiajun Zhang, Huahai Qiu, Tianshou Zhou · 2024 · Biosystems
  46. RNA-Based Imaging System
    Phei Er Saw, Erwei Song · 2025 · Springer eBooks
  47. Transcriptional pulsing of a nucleolar transgene
    Viola Vaňková Hausnerová, Pavel Křížek, Guy M. Hagen, Christian Lanctôt · 2016 · bioRxiv (Cold Spring Harbor Laboratory)
  48. CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNP export in developing embryos
    Youkui Huang, Bao‐Qing Gao, Quan Meng, Liang-Zhong Yang, Xu-Kai Ma, Hao Wu, Yu-Hang Pan, Li Chun Yang, Dong Li, Ling‐Ling Chen · 2022 · Research Square
  49. A Microarray Analysis of Parkinson’s Disease: New Clues and Evaluation
    Lirong Huo, Xibin Liang, Yi He, Xiaomin Wang · 2015 · Journal of Biosciences and Medicines
  50. Watching a gene at work
    Brendan Borrell · 2010 · Nature
  51. Design (and) principles of nuclear dynamics in Stockholm
    Yaron Shav‐Tal, Jan Lammerding · 2015 · Nucleus
  52. Imaging Nascent RNA Dynamics in Dictyostelium
    Jonathan Robert Chubb, Michelle Stevense, Danielle Cannon, Tetsuya Muramoto, Adam M. Corrigan · 2013 · Methods in molecular biology
  53. Data Integration of High-Throughput Proteomic and Transcriptomic Data based on Public Database Knowledge
    Astrid Wachter · 2017
  54. Regulatory mechanisms are revealed by the distribution of transcription initiation times in single microbial cells
    Sandeep Choubey, Jané Kondev, Álvaro Sánchez · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
  55. Autoregulation of pre-mRNA processing for buffering noisy gene expression
    Madeline E. Smith, Khem Raj Ghusinga, Abhyudai Singh · 2019 · bioRxiv (Cold Spring Harbor Laboratory)
  56. Author response: Kinetic competition during the transcription cycle results in stochastic RNA processing
    Antoine Coulon, Matthew Ferguson, Valeria de Turris, Murali Palangat, Carson C. Chow, Daniel R. Larson · 2014 · eLife
  57. The Energy as a Determinant Factor in the Ethiopathogeny of Chromosomal Abnormalities. The Unsuspected Bioenergetic Role of Melanin
    Arturo Solís Herrera · 2020 · IntechOpen eBooks
  58. Quantitative models for transcriptional dynamics monitored using an MS2-GFP system
    Hongyoung Choi, Byung Hun Lee, Hye Yoon Park · 2021 · Journal of the Korean Physical Society
  59. Study and Modeling of Biological Noise-Filtering Properties of Conserved Gene Regulatory Networks Motifs in Animal Development
    Lina Marcela Ruiz Galvis, Gloria Machado, Boris A. Rodríguez · 2022 · bioRxiv (Cold Spring Harbor Laboratory)
  60. In Situ Hybridization as a Method to Examine Gene Regulatory Activity In Vivo
    Rhea R. Datta, Pınar Önal · 2022 · Methods in molecular biology
  61. Additional file 4 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
    Youkui Huang, Bao‐Qing Gao, Quan Meng, Liang-Zhong Yang, Xu-Kai Ma, Hao Wu, Yu-Hang Pan, Li Chun Yang, Dong Li, Ling‐Ling Chen · 2023 · Figshare
  62. Additional file 6 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
    Youkui Huang, Bao‐Qing Gao, Quan Meng, Liang-Zhong Yang, Xu-Kai Ma, Hao Wu, Yu-Hang Pan, Li Chun Yang, Dong Li, Ling‐Ling Chen · 2023 · Figshare
  63. Additional file 3 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
    Youkui Huang, Bao‐Qing Gao, Quan Meng, Liang-Zhong Yang, Xu-Kai Ma, Hao Wu, Yu-Hang Pan, Li Chun Yang, Dong Li, Ling‐Ling Chen · 2023 · Figshare
  64. Additional file 5 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
    Youkui Huang, Bao‐Qing Gao, Quan Meng, Liang-Zhong Yang, Xu-Kai Ma, Hao Wu, Yu-Hang Pan, Li Chun Yang, Dong Li, Ling‐Ling Chen · 2023 · Figshare
  65. Additional file 2 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
    Youkui Huang, Bao‐Qing Gao, Quan Meng, Liang-Zhong Yang, Xu-Kai Ma, Hao Wu, Yu-Hang Pan, Li Chun Yang, Dong Li, Ling‐Ling Chen · 2023 · Figshare
  66. Exact Burst-Size Distributions for Gene-Expression Models with Complex Promoter Structure
    Tianshou Zhou, Liying Zhou, Haowen Chen, Jinqiang Zhang, Jiajun Zhang, Huahai Qiu · 2024 · SSRN Electronic Journal
  67. Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo Development
    César Nieto, Zahra Vahdat, Bomyi Lim, Abhyudai Singh · 2025 · eLife
  68. Regulation of Transcriptional Bursting and Spatial Patterning in Early Drosophila Embryo Development
    César Nieto, Zahra Vahdat, Bomyi Lim, Abhyudai Singh · 2025 · eLife
  69. Additional file 8 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
    Huang, Youkui, Gao, Bao-Qing, Meng, Quan, Yang, Liang-Zhong, Ma, Xu-Kai, Wu, Hao, Pan, Yu-Hang, Yang, Li, Dong Li, Chen, Ling-Ling · 2023 · Figshare
  70. Additional file 1 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
    Huang, Youkui, Gao, Bao-Qing, Meng, Quan, Yang, Liang-Zhong, Ma, Xu-Kai, Wu, Hao, Pan, Yu-Hang, Yang, Li, Dong Li, Chen, Ling-Ling · 2023 · Figshare
  71. Additional file 7 of CRISPR-dCas13-tracing reveals transcriptional memory and limited mRNA export in developing zebrafish embryos
    Huang, Youkui, Gao, Bao-Qing, Meng, Quan, Yang, Liang-Zhong, Ma, Xu-Kai, Wu, Hao, Pan, Yu-Hang, Yang, Li, Dong Li, Chen, Ling-Ling · 2023 · Figshare
  72. Fluorescence Amplification Tags for Single‐Molecule Imaging and Tracking of Proteins, RNA, and DNA in Live Cells
    Yifan Bao, Tianle Xiong, Arnaud Gautier, Murat Sünbül, Lu Wang · 2026 · Angewandte Chemie
  73. Architecture chromosomique du locus Xic : implications pour la régulation de l'inactivation du chromosome X
    Elphège Pierre Nora · 2011 · theses.fr (ABES)
  74. Etude des mécanismes de la régulation transcriptionnelle et développement d'outils bioinformatiques pour le traitement des données de séquençage haut débit
    Romain Fenouil · 2013 · theses.fr (ABES)
  75. Study of Polycomb target genes architecture in Drosophila using multiplexed optical microscopy
    Julian Gurgo · 2021
  76. Measuring the Proximity of Nuclear lncRNAs to Nuclear Bodies
    Sarah E. Hasenson, Yaron Shav‐Tal · 2026 · Methods in molecular biology