Literature DB >> 22475987

Single-molecule dynamics of transcription of the lar promoter.

M Kandhavelu1, A Häkkinen, O Yli-Harja, A S Ribeiro.   

Abstract

We measured the in vivo production of RNA molecules tagged with MS2d-GFP in Escherichia coli, driven by the lar promoter, under weak and medium induction. The distributions of intervals between consecutive productions of RNAs are found to be sub-exponential, and the process of RNA production is found to be sub-Poissonian. We discuss possible models of transcription initiation and, based on our results and previous in vitro measurements, find that a sequential two-step model of transcription initiation at the promoter region explains the results well.

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Year:  2012        PMID: 22475987     DOI: 10.1088/1478-3975/9/2/026004

Source DB:  PubMed          Journal:  Phys Biol        ISSN: 1478-3967            Impact factor:   2.583


  10 in total

1.  In vivo kinetics of segregation and polar retention of MS2-GFP-RNA complexes in Escherichia coli.

Authors:  Abhishekh Gupta; Jason Lloyd-Price; Ramakanth Neeli-Venkata; Samuel M D Oliveira; Andre S Ribeiro
Journal:  Biophys J       Date:  2014-05-06       Impact factor: 4.033

2.  Origins of transcriptional transition: balance between upstream and downstream regulatory gene sequences.

Authors:  Adrien Sala; Muhammad Shoaib; Olga Anufrieva; Gnanavel Mutharasu; Olli Yli-Harja; Meenakshisundaram Kandhavelu
Journal:  MBio       Date:  2015-01-27       Impact factor: 7.867

3.  Multiplex Eukaryotic Transcription (In)activation: Timing, Bursting and Cycling of a Ratchet Clock Mechanism.

Authors:  Katja N Rybakova; Frank J Bruggeman; Aleksandra Tomaszewska; Martijn J Moné; Carsten Carlberg; Hans V Westerhoff
Journal:  PLoS Comput Biol       Date:  2015-04-24       Impact factor: 4.475

4.  Temperature-Dependent Model of Multi-step Transcription Initiation in Escherichia coli Based on Live Single-Cell Measurements.

Authors:  Samuel M D Oliveira; Antti Häkkinen; Jason Lloyd-Price; Huy Tran; Vinodh Kandavalli; Andre S Ribeiro
Journal:  PLoS Comput Biol       Date:  2016-10-28       Impact factor: 4.475

5.  Single-cell measurement of plasmid copy number and promoter activity.

Authors:  Bin Shao; Jayan Rammohan; Daniel A Anderson; Nina Alperovich; David Ross; Christopher A Voigt
Journal:  Nat Commun       Date:  2021-03-05       Impact factor: 14.919

6.  In vivo single-molecule kinetics of activation and subsequent activity of the arabinose promoter.

Authors:  Jarno Mäkelä; Meenakshisundaram Kandhavelu; Samuel M D Oliveira; Jerome G Chandraseelan; Jason Lloyd-Price; Juha Peltonen; Olli Yli-Harja; Andre S Ribeiro
Journal:  Nucleic Acids Res       Date:  2013-05-03       Impact factor: 16.971

7.  Deciphering Transcriptional Dynamics In Vivo by Counting Nascent RNA Molecules.

Authors:  Sandeep Choubey; Jane Kondev; Alvaro Sanchez
Journal:  PLoS Comput Biol       Date:  2015-11-06       Impact factor: 4.475

8.  Effects of multimerization on the temporal variability of protein complex abundance.

Authors:  Antti Häkkinen; Huy Tran; Olli Yli-Harja; Brian Ingalls; Andre S Ribeiro
Journal:  BMC Syst Biol       Date:  2013-08-12

9.  Effects of rate-limiting steps in transcription initiation on genetic filter motifs.

Authors:  Antti Häkkinen; Huy Tran; Olli Yli-Harja; Andre S Ribeiro
Journal:  PLoS One       Date:  2013-08-05       Impact factor: 3.240

10.  Untangling statistical and biological models to understand network inference: the need for a genomics network ontology.

Authors:  Frank Emmert-Streib; Matthias Dehmer; Benjamin Haibe-Kains
Journal:  Front Genet       Date:  2014-08-29       Impact factor: 4.599

  10 in total

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