A single molecule view of gene expression
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TLDR
The view that has emerged is rooted in a probabilistic understanding of cellular processes that quantitatively explains both the mean and the variation observed in gene-expression patterns among single cells.About:
This article is published in Trends in Cell Biology.The article was published on 2009-11-01 and is currently open access. It has received 225 citations till now. The article focuses on the topics: Regulation of gene expression & Systems biology.read more
Citations
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Spatially resolved, highly multiplexed RNA profiling in single cells
Kok Hao Chen,Alistair N. Boettiger,Jeffrey R. Moffitt,Siyuan Wang,Xiaowei Zhuang,Xiaowei Zhuang +5 more
TL;DR: This report reports multiplexed error-robust FISH (MERFISH), a single-molecule imaging method that allows thousands of RNA species to be imaged in single cells by using combinatorial FISH labeling with encoding schemes capable of detecting and/or correcting errors.
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Mammalian genes are transcribed with widely different bursting kinetics
David M. Suter,Nacho Molina,David Gatfield,David Gatfield,Kim Schneider,Ueli Schibler,Felix Naef +6 more
TL;DR: This work established various gene trap cell lines and transgenic cell lines expressing a short-lived luciferase protein from an unstable mRNA, and recorded bioluminescence in real time in single cells, demonstrating that bursting kinetics are highly gene-specific.
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Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells
Samuel Marguerat,M Alexander Schmidt,Sandra Codlin,Wei-Wei Chen,Ruedi Aebersold,Ruedi Aebersold,Jürg Bähler +6 more
TL;DR: This rich resource provides the first comprehensive reference for all RNA and most protein concentrations in a eukaryote under two key physiological conditions: cellular proliferation and quiescence.
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The RelA/SpoT homolog (RSH) superfamily: distribution and functional evolution of ppGpp synthetases and hydrolases across the tree of life.
TL;DR: High-throughput sensitive sequence searching of over 1000 genomes from across the tree of life is performed in combination with phylogenetic analyses to consolidate previous ad hoc identification of diverse RSHs in different organisms and provide a much-needed unifying terminology for the field.
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Real-time quantification of single RNA translation dynamics in living cells
Tatsuya Morisaki,Kenneth Lyon,Keith F. DeLuca,Jennifer G. DeLuca,Brian P. English,Zhengjian Zhang,Luke D. Lavis,Jonathan B. Grimm,Sarada Viswanathan,Loren L. Looger,Timothée Lionnet,Timothy J. Stasevich +11 more
TL;DR: NCT, a technique that uses multi-epitope tags and antibody-based fluorescent probes to quantify protein synthesis dynamics at the single-mRNA level, reveals the stochastic nature of single mRNA translation.
References
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RNA-Seq: a revolutionary tool for transcriptomics
TL;DR: The RNA-Seq approach to transcriptome profiling that uses deep-sequencing technologies provides a far more precise measurement of levels of transcripts and their isoforms than other methods.
Book
Stochastic processes in physics and chemistry
TL;DR: In this article, the authors introduce the Fokker-planck equation, the Langevin approach, and the diffusion type of the master equation, as well as the statistics of jump events.
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Stochastic Gene Expression in a Single Cell
TL;DR: This work constructed strains of Escherichia coli that enable detection of noise and discrimination between the two mechanisms by which it is generated and reveals how low intracellular copy numbers of molecules can fundamentally limit the precision of gene regulation.
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Global analysis of protein expression in yeast
Sina Ghaemmaghami,Won-Ki Huh,Kiowa Bower,Russell W. Howson,Archana Belle,Noah Dephoure,Erin K. O'Shea,Jonathan S. Weissman +7 more
TL;DR: A Saccharomyces cerevisiae fusion library is created where each open reading frame is tagged with a high-affinity epitope and expressed from its natural chromosomal location, and it is found that about 80% of the proteome is expressed during normal growth conditions.