Literature DB >> 22410830

Transcription goes digital.

Timothée Lionnet1, Robert H Singer.   

Abstract

Transcription is a complex process that integrates the state of the cell and its environment to generate adequate responses for cell fitness and survival. Recent microscopy experiments have been able to monitor transcription from single genes in individual cells. These observations have revealed two striking features: transcriptional activity can vary markedly from one cell to another, and is subject to large changes over time, sometimes within minutes. How the chromatin structure, transcription machinery assembly and signalling networks generate such patterns is still unclear. In this review, we present the techniques used to investigate transcription from single genes, introduce quantitative modelling tools, and discuss transcription mechanisms and their implications for gene expression regulation.

Mesh:

Year:  2012        PMID: 22410830      PMCID: PMC3321162          DOI: 10.1038/embor.2012.31

Source DB:  PubMed          Journal:  EMBO Rep        ISSN: 1469-221X            Impact factor:   8.807


  89 in total

1.  Single-allele analysis of transcription kinetics in living mammalian cells.

Authors:  Sharon Yunger; Liat Rosenfeld; Yuval Garini; Yaron Shav-Tal
Journal:  Nat Methods       Date:  2010-07-18       Impact factor: 28.547

2.  Digital nature of the immediate-early transcriptional response.

Authors:  Michelle Stevense; Tetsuya Muramoto; Iris Müller; Jonathan R Chubb
Journal:  Development       Date:  2010-02       Impact factor: 6.868

3.  Methylation of H3K4 Is required for inheritance of active transcriptional states.

Authors:  Tetsuya Muramoto; Iris Müller; Giles Thomas; Andrew Melvin; Jonathan R Chubb
Journal:  Curr Biol       Date:  2010-02-25       Impact factor: 10.834

4.  Transcriptional memory: staying in the loop.

Authors:  Jason H Brickner
Journal:  Curr Biol       Date:  2010-01-12       Impact factor: 10.834

5.  Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.

Authors:  Yuichi Taniguchi; Paul J Choi; Gene-Wei Li; Huiyi Chen; Mohan Babu; Jeremy Hearn; Andrew Emili; X Sunney Xie
Journal:  Science       Date:  2010-07-30       Impact factor: 47.728

6.  Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing.

Authors:  Savaş Tay; Jacob J Hughey; Timothy K Lee; Tomasz Lipniacki; Stephen R Quake; Markus W Covert
Journal:  Nature       Date:  2010-06-27       Impact factor: 49.962

Review 7.  FRAP and kinetic modeling in the analysis of nuclear protein dynamics: what do we really know?

Authors:  Florian Mueller; Davide Mazza; Timothy J Stasevich; James G McNally
Journal:  Curr Opin Cell Biol       Date:  2010-04-21       Impact factor: 8.382

8.  Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle.

Authors:  Lu Bai; Gilles Charvin; Eric D Siggia; Frederick R Cross
Journal:  Dev Cell       Date:  2010-04-20       Impact factor: 12.270

9.  Transcript counting in single cells reveals dynamics of rDNA transcription.

Authors:  Rui Zhen Tan; Alexander van Oudenaarden
Journal:  Mol Syst Biol       Date:  2010-04-13       Impact factor: 11.429

10.  Variability in gene expression underlies incomplete penetrance.

Authors:  Arjun Raj; Scott A Rifkin; Erik Andersen; Alexander van Oudenaarden
Journal:  Nature       Date:  2010-02-18       Impact factor: 49.962

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  39 in total

Review 1.  Imaging the Life and Death of mRNAs in Single Cells.

Authors:  Jeffrey A Chao; Timothée Lionnet
Journal:  Cold Spring Harb Perspect Biol       Date:  2018-12-03       Impact factor: 10.005

2.  Diverse Spatial Expression Patterns Emerge from Unified Kinetics of Transcriptional Bursting.

Authors:  Benjamin Zoller; Shawn C Little; Thomas Gregor
Journal:  Cell       Date:  2018-10-18       Impact factor: 41.582

3.  Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos.

Authors:  Jacques P Bothma; Hernan G Garcia; Emilia Esposito; Gavin Schlissel; Thomas Gregor; Michael Levine
Journal:  Proc Natl Acad Sci U S A       Date:  2014-07-03       Impact factor: 11.205

4.  Reinitiation enhances reliable transcriptional responses in eukaryotes.

Authors:  Bo Liu; Zhanjiang Yuan; Kazuyuki Aihara; Luonan Chen
Journal:  J R Soc Interface       Date:  2014-08-06       Impact factor: 4.118

Review 5.  Single molecule fluorescence approaches shed light on intracellular RNAs.

Authors:  Sethuramasundaram Pitchiaya; Laurie A Heinicke; Thomas C Custer; Nils G Walter
Journal:  Chem Rev       Date:  2014-01-08       Impact factor: 60.622

Review 6.  Single-Cell and Single-Molecule Analysis of Gene Expression Regulation.

Authors:  Maria Vera; Jeetayu Biswas; Adrien Senecal; Robert H Singer; Hye Yoon Park
Journal:  Annu Rev Genet       Date:  2016-11-23       Impact factor: 16.830

7.  Cell-to-cell variability in the propensity to transcribe explains correlated fluctuations in gene expression.

Authors:  Marc S Sherman; Kim Lorenz; M Hunter Lanier; Barak A Cohen
Journal:  Cell Syst       Date:  2015-11-25       Impact factor: 10.304

Review 8.  RNP transport in cell biology: the long and winding road.

Authors:  Carolina Eliscovich; Robert H Singer
Journal:  Curr Opin Cell Biol       Date:  2017-03-01       Impact factor: 8.382

Review 9.  Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression.

Authors:  Hanae Sato; Sulagna Das; Robert H Singer; Maria Vera
Journal:  Annu Rev Biochem       Date:  2020-03-16       Impact factor: 23.643

Review 10.  Coupling mRNA processing with transcription in time and space.

Authors:  David L Bentley
Journal:  Nat Rev Genet       Date:  2014-02-11       Impact factor: 53.242

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