Single cell gene expression linkfest

Gene regulation is an old field, but gene regulation at the single cell level is a whole new ball of wax. Some of us in the lab are trying to get up to speed in this field, and I need to pick out five good papers for consideration.

The place to begin is with this great review, and then work through the references:

Central dogma at the single-molecule level in living cells, Gene-Wei Li and X. Sunney Xie, Nature 475, 308–315 (21 July 2011)

Picking selectively, I ended up with the list below, and unfortunately I need to somehow narrow this down to five… and preferably all five won’t be from Sunney Xie’s group. Any suggestions?

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells, Yuichi Taniguchi, Paul J. Choi, Gene-Wei Li, Huiyi Chen, Mohan Babu, Jeremy Hearn, Andrew Emili and X. Sunney Xie, Science 30 July 2010: Vol. 329 no. 5991 pp. 533-538

Probing Gene Expression in Live Cells, One Protein Molecule at a Time, Ji Yu, Jie Xiao, Xiaojia Ren, Kaiqin Lao and X. Sunney Xie, Science 17 March 2006:Vol. 311 no. 5767 pp. 1600-1603

Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell, Johan Elf, Gene-Wei Li, and X. Sunney Xie, Science 25 May 2007:Vol. 316 no. 5828 pp. 1191-1194

Diffusion controlled reaction rates in spheroidal geometry: Application to repressor-operator association and membrane bound enzymes, Peter H. Richter, Manfred Eigen, Biophysical Chemistry, Volume 2, Issue 3, October 1974, Pages 255–263

Tumor Suppressor p53 Slides on DNA with Low Friction and High Stability, Anahita Tafvizi, Fang Huang, Jason S. Leith, Alan R. Fersht, Leonid A. Mirny, and Antoine M. van Oijen, Biophys J. 2008 July 1; 95(1): L01–L03.

Effects of macromolecular crowding and DNA looping on gene regulation kinetics, Gene-Wei Li, Otto G. Berg and Johan Elf, Nature Physics 5, 294 – 297 (2009)

Real-Time Kinetics of Gene Activity in Individual Bacteria, Ido Golding, Johan Paulsson, Scott M. Zawilski and Edward C. Cox, Cell, Volume 123, Issue 6, 1025-1036, 16 December 2005

Stochastic mRNA Synthesis in Mammalian Cells, Raj A, Peskin CS, Tranchina D, Vargas DY, Tyagi S, PLoS Biol 4(10): e309 (2006).

Imaging intracellular RNA distribution and dynamics in living cells, Sanjay Tyagi, Nature Methods 6, 331 – 338 (2009)

Analytical distributions for stochastic gene expression, Vahid Shahrezaei and Peter S. Swain, PNAS November 11, 2008 vol. 105 no. 45 17256-17261

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise, John R. S. Newman, Sina Ghaemmaghami, Jan Ihmels, David K. Breslow, Matthew Noble, Joseph L. DeRisi, and Jonathan S. Weissman Nature 441, 840-846 (15 June 2006)

Intrinsic and extrinsic contributions to stochasticity in gene expression, Peter S. Swain, Michael B. Elowitz, and Eric D. Siggia, PNAS October 1, 2002 vol. 99 no. 20 12795-12800

Visualization of Single RNA Transcripts in Situ, Andrea M. Femino, Fredric S. Fay†, Kevin Fogarty and Robert H. Singer, Science 24 April 1998:Vol. 280 no. 5363 pp. 585-590

Noise in Gene Expression Determines Cell Fate in Bacillus subtilis, Hédia Maamar, Arjun Raj, and David Dubnau, Science 27 July 2007:Vol. 317 no. 5837 pp. 526-529

Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling, Darren M. Gowers and Stephen E. Halford, The EMBO Journal (2003) 22, 1410 – 1418

Eukaryotic transcription: what does it mean for a gene to be ‘on’?, Golding I, Cox EC, Curr Biol. 2006 May 23;16(10):R371-3.

Transcriptional pulsing of a developmental gene, Chubb JR, Trcek T, Shenoy SM, Singer RH, Curr Biol. 2006 May 23;16(10):1018-25.

Quantitative transcription factor binding kinetics at the single-molecule level, Wang Y, Guo L, Golding I, Cox EC, Ong NP, Biophys J. 2009 Jan;96(2):609-20.

Author: Mike White

Genomes, Books, and Science Fiction

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