Literature DB >> 24089448

Positional information, in bits.

Julien O Dubuis1, Gasper Tkacik, Eric F Wieschaus, Thomas Gregor, William Bialek.   

Abstract

Cells in a developing embryo have no direct way of "measuring" their physical position. Through a variety of processes, however, the expression levels of multiple genes come to be correlated with position, and these expression levels thus form a code for "positional information." We show how to measure this information, in bits, using the gap genes in the Drosophila embryo as an example. Individual genes carry nearly two bits of information, twice as much as would be expected if the expression patterns consisted only of on/off domains separated by sharp boundaries. Taken together, four gap genes carry enough information to define a cell's location with an error bar of ~1 along the anterior/posterior axis of the embryo. This precision is nearly enough for each cell to have a unique identity, which is the maximum information the system can use, and is nearly constant along the length of the embryo. We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network.

Entities:  

Keywords:  embryonic development; gene regulatory networks; optimization

Mesh:

Substances:

Year:  2013        PMID: 24089448      PMCID: PMC3799327          DOI: 10.1073/pnas.1315642110

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  33 in total

1.  Adaptive rescaling maximizes information transmission.

Authors:  N Brenner; W Bialek; R de Ruyter van Steveninck
Journal:  Neuron       Date:  2000-06       Impact factor: 17.173

2.  Regulation of noise in the expression of a single gene.

Authors:  Ertugrul M Ozbudak; Mukund Thattai; Iren Kurtser; Alan D Grossman; Alexander van Oudenaarden
Journal:  Nat Genet       Date:  2002-04-22       Impact factor: 38.330

3.  Noise in eukaryotic gene expression.

Authors:  William J Blake; Mads KAErn; Charles R Cantor; J J Collins
Journal:  Nature       Date:  2003-04-10       Impact factor: 49.962

4.  Stochastic gene expression in a single cell.

Authors:  Michael B Elowitz; Arnold J Levine; Eric D Siggia; Peter S Swain
Journal:  Science       Date:  2002-08-16       Impact factor: 47.728

5.  Dynamic interpretation of maternal inputs by the Drosophila segmentation gene network.

Authors:  Feng Liu; Alexander H Morrison; Thomas Gregor
Journal:  Proc Natl Acad Sci U S A       Date:  2013-04-11       Impact factor: 11.205

6.  Positional information and the spatial pattern of cellular differentiation.

Authors:  L Wolpert
Journal:  J Theor Biol       Date:  1969-10       Impact factor: 2.691

7.  slam encodes a developmental regulator of polarized membrane growth during cleavage of the Drosophila embryo.

Authors:  Thomas Lecuit; Reba Samanta; Eric Wieschaus
Journal:  Dev Cell       Date:  2002-04       Impact factor: 12.270

8.  A self-organizing system of repressor gradients establishes segmental complexity in Drosophila.

Authors:  Dorothy E Clyde; Maria S G Corado; Xuelin Wu; Adam Paré; Dmitri Papatsenko; Stephen Small
Journal:  Nature       Date:  2003-12-18       Impact factor: 49.962

Review 9.  Seeing is believing: the bicoid morphogen gradient matures.

Authors:  Anne Ephrussi; Daniel St Johnston
Journal:  Cell       Date:  2004-01-23       Impact factor: 41.582

10.  Mutations affecting segment number and polarity in Drosophila.

Authors:  C Nüsslein-Volhard; E Wieschaus
Journal:  Nature       Date:  1980-10-30       Impact factor: 49.962

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  44 in total

1.  Information processing in the adaptation of Saccharomyces cerevisiae to osmotic stress: an analysis of the phosphorelay system.

Authors:  Friedemann Uschner; Edda Klipp
Journal:  Syst Synth Biol       Date:  2014-04-19

2.  Maternal origins of developmental reproducibility.

Authors:  Mariela D Petkova; Shawn C Little; Feng Liu; Thomas Gregor
Journal:  Curr Biol       Date:  2014-05-22       Impact factor: 10.834

3.  Robustness, Accuracy, and Cell State Heterogeneity in Biological Systems.

Authors:  Roy Wollman
Journal:  Curr Opin Syst Biol       Date:  2017-12-15

4.  Positional information, positional error, and readout precision in morphogenesis: a mathematical framework.

Authors:  Gašper Tkačik; Julien O Dubuis; Mariela D Petkova; Thomas Gregor
Journal:  Genetics       Date:  2014-10-31       Impact factor: 4.562

5.  Distributed and dynamic intracellular organization of extracellular information.

Authors:  Alejandro A Granados; Julian M J Pietsch; Sarah A Cepeda-Humerez; Iseabail L Farquhar; Gašper Tkačik; Peter S Swain
Journal:  Proc Natl Acad Sci U S A       Date:  2018-05-21       Impact factor: 11.205

6.  The Berg-Purcell limit revisited.

Authors:  Kazunari Kaizu; Wiet de Ronde; Joris Paijmans; Koichi Takahashi; Filipe Tostevin; Pieter Rein ten Wolde
Journal:  Biophys J       Date:  2014-02-18       Impact factor: 4.033

7.  Noise and information transmission in promoters with multiple internal States.

Authors:  Georg Rieckh; Gašper Tkačik
Journal:  Biophys J       Date:  2014-03-04       Impact factor: 4.033

8.  Morphogenesis at criticality.

Authors:  Dmitry Krotov; Julien O Dubuis; Thomas Gregor; William Bialek
Journal:  Proc Natl Acad Sci U S A       Date:  2014-02-10       Impact factor: 11.205

Review 9.  Cellular noise and information transmission.

Authors:  Andre Levchenko; Ilya Nemenman
Journal:  Curr Opin Biotechnol       Date:  2014-06-09       Impact factor: 9.740

10.  Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network.

Authors:  Erik Clark; Michael Akam
Journal:  Elife       Date:  2016-08-15       Impact factor: 8.140

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