Literature DB >> 17875664

Rational design of memory in eukaryotic cells.

Caroline M Ajo-Franklin1, David A Drubin, Julian A Eskin, Elaine P S Gee, Dirk Landgraf, Ira Phillips, Pamela A Silver.   

Abstract

The ability to logically engineer novel cellular functions promises a deeper understanding of biological systems. Here we demonstrate the rational design of cellular memory in yeast that employs autoregulatory transcriptional positive feedback. We built a set of transcriptional activators and quantitatively characterized their effects on gene expression in living cells. Modeling in conjunction with the quantitative characterization of the activator-promoter pairs accurately predicts the behavior of the memory network. This study demonstrates the power of taking advantage of components with measured quantitative parameters to specify eukaryotic regulatory networks with desired properties.

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Year:  2007        PMID: 17875664      PMCID: PMC1973140          DOI: 10.1101/gad.1586107

Source DB:  PubMed          Journal:  Genes Dev        ISSN: 0890-9369            Impact factor:   11.361


  30 in total

1.  Construction of a genetic toggle switch in Escherichia coli.

Authors:  T S Gardner; C R Cantor; J J Collins
Journal:  Nature       Date:  2000-01-20       Impact factor: 49.962

2.  A positive-feedback-based bistable 'memory module' that governs a cell fate decision.

Authors:  Wen Xiong; James E Ferrell
Journal:  Nature       Date:  2003-11-27       Impact factor: 49.962

3.  Highly specific zinc finger proteins obtained by directed domain shuffling and cell-based selection.

Authors:  Jessica A Hurt; Stacey A Thibodeau; Andrew S Hirsh; Carl O Pabo; J Keith Joung
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-03       Impact factor: 11.205

4.  Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli.

Authors:  Mariette R Atkinson; Michael A Savageau; Jesse T Myers; Alexander J Ninfa
Journal:  Cell       Date:  2003-05-30       Impact factor: 41.582

5.  Epigenetic properties of white-opaque switching in Candida albicans are based on a self-sustaining transcriptional feedback loop.

Authors:  Rebecca E Zordan; David J Galgoczy; Alexander D Johnson
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-09       Impact factor: 11.205

6.  Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans.

Authors:  Guanghua Huang; Huafeng Wang; Song Chou; Xinyi Nie; Jiangye Chen; Haoping Liu
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-11       Impact factor: 11.205

Review 7.  Designing biological systems.

Authors:  David A Drubin; Jeffrey C Way; Pamela A Silver
Journal:  Genes Dev       Date:  2007-02-01       Impact factor: 11.361

8.  Positive-feedback loops as a flexible biological module.

Authors:  Nicholas T Ingolia; Andrew W Murray
Journal:  Curr Biol       Date:  2007-03-29       Impact factor: 10.834

9.  A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications.

Authors:  Takeharu Nagai; Keiji Ibata; Eun Sun Park; Mie Kubota; Katsuhiko Mikoshiba; Atsushi Miyawaki
Journal:  Nat Biotechnol       Date:  2002-01       Impact factor: 54.908

10.  Single-cell quantification of molecules and rates using open-source microscope-based cytometry.

Authors:  Andrew Gordon; Alejandro Colman-Lerner; Tina E Chin; Kirsten R Benjamin; Richard C Yu; Roger Brent
Journal:  Nat Methods       Date:  2007-01-21       Impact factor: 28.547

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  96 in total

1.  Synthetic biology. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations.

Authors:  Fahim Farzadfard; Timothy K Lu
Journal:  Science       Date:  2014-11-14       Impact factor: 47.728

2.  Emergent bistability: effects of additive and multiplicative noise.

Authors:  S Ghosh; S Banerjee; I Bose
Journal:  Eur Phys J E Soft Matter       Date:  2012-02-23       Impact factor: 1.890

3.  The sensitivity of memory consolidation and reconsolidation to inhibitors of protein synthesis and kinases: computational analysis.

Authors:  Yili Zhang; Paul Smolen; Douglas A Baxter; John H Byrne
Journal:  Learn Mem       Date:  2010-08-24       Impact factor: 2.460

Review 4.  Building synthetic memory.

Authors:  Mara C Inniss; Pamela A Silver
Journal:  Curr Biol       Date:  2013-09-09       Impact factor: 10.834

Review 5.  Harnessing nature's toolbox: regulatory elements for synthetic biology.

Authors:  Patrick M Boyle; Pamela A Silver
Journal:  J R Soc Interface       Date:  2009-03-04       Impact factor: 4.118

6.  Rewritable digital data storage in live cells via engineered control of recombination directionality.

Authors:  Jerome Bonnet; Pakpoom Subsoontorn; Drew Endy
Journal:  Proc Natl Acad Sci U S A       Date:  2012-05-21       Impact factor: 11.205

7.  Robust, tunable genetic memory from protein sequestration combined with positive feedback.

Authors:  Tatenda Shopera; William R Henson; Andrew Ng; Young Je Lee; Kenneth Ng; Tae Seok Moon
Journal:  Nucleic Acids Res       Date:  2015-09-17       Impact factor: 16.971

Review 8.  Role of chromatin states in transcriptional memory.

Authors:  Sharmistha Kundu; Craig L Peterson
Journal:  Biochim Biophys Acta       Date:  2009-02-21

9.  Bottom-up approaches in synthetic biology and biomaterials for tissue engineering applications.

Authors:  Mitchell S Weisenberger; Tara L Deans
Journal:  J Ind Microbiol Biotechnol       Date:  2018-03-19       Impact factor: 3.346

10.  Synthetic metabolic computation in a bioluminescence-sensing system.

Authors:  Natalia Barger; Phyana Litovco; Ximing Li; Mouna Habib; Ramez Daniel
Journal:  Nucleic Acids Res       Date:  2019-11-04       Impact factor: 16.971

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