Literature DB >> 27667861

Stochastic Kinetics of Nascent RNA.

Heng Xu1, Samuel O Skinner1, Anna Marie Sokac2, Ido Golding1.   

Abstract

The stochastic kinetics of transcription is typically inferred from the distribution of RNA numbers in individual cells. However, cellular RNA reflects additional processes downstream of transcription, hampering this analysis. In contrast, nascent (actively transcribed) RNA closely reflects the kinetics of transcription. We present a theoretical model for the stochastic kinetics of nascent RNA, which we solve to obtain the probability distribution of nascent RNA per gene. The model allows us to evaluate the kinetic parameters of transcription from single-cell measurements of nascent RNA. The model also predicts surprising discontinuities in the distribution of nascent RNA, a feature which we verify experimentally.

Entities:  

Year:  2016        PMID: 27667861      PMCID: PMC5033037          DOI: 10.1103/PhysRevLett.117.128101

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  47 in total

1.  A structural model of transcription elongation.

Authors:  N Korzheva; A Mustaev; M Kozlov; A Malhotra; V Nikiforov; A Goldfarb; S A Darst
Journal:  Science       Date:  2000-07-28       Impact factor: 47.728

2.  Real-time observation of transcription initiation and elongation on an endogenous yeast gene.

Authors:  Daniel R Larson; Daniel Zenklusen; Bin Wu; Jeffrey A Chao; Robert H Singer
Journal:  Science       Date:  2011-04-22       Impact factor: 47.728

3.  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

4.  The finite state projection algorithm for the solution of the chemical master equation.

Authors:  Brian Munsky; Mustafa Khammash
Journal:  J Chem Phys       Date:  2006-01-28       Impact factor: 3.488

5.  Measurement of gene regulation in individual cells reveals rapid switching between promoter states.

Authors:  Leonardo A Sepúlveda; Heng Xu; Jing Zhang; Mengyu Wang; Ido Golding
Journal:  Science       Date:  2016-03-10       Impact factor: 47.728

6.  Mechanism of transcriptional bursting in bacteria.

Authors:  Shasha Chong; Chongyi Chen; Hao Ge; X Sunney Xie
Journal:  Cell       Date:  2014-07-17       Impact factor: 41.582

7.  Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner.

Authors:  Eric A Galburt; Stephan W Grill; Anna Wiedmann; Lucyna Lubkowska; Jason Choy; Eva Nogales; Mikhail Kashlev; Carlos Bustamante
Journal:  Nature       Date:  2007-03-14       Impact factor: 49.962

8.  Single-RNA counting reveals alternative modes of gene expression in yeast.

Authors:  Daniel Zenklusen; Daniel R Larson; Robert H Singer
Journal:  Nat Struct Mol Biol       Date:  2008-11-16       Impact factor: 15.369

9.  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

10.  Allele-specific detection of single mRNA molecules in situ.

Authors:  Clinton H Hansen; Alexander van Oudenaarden
Journal:  Nat Methods       Date:  2013-08-11       Impact factor: 28.547

View more
  22 in total

1.  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

2.  Statistics of Nascent and Mature RNA Fluctuations in a Stochastic Model of Transcriptional Initiation, Elongation, Pausing, and Termination.

Authors:  Tatiana Filatova; Nikola Popovic; Ramon Grima
Journal:  Bull Math Biol       Date:  2020-12-22       Impact factor: 1.758

3.  A Stochastic Model of Gene Expression with Polymerase Recruitment and Pause Release.

Authors:  Zhixing Cao; Tatiana Filatova; Diego A Oyarzún; Ramon Grima
Journal:  Biophys J       Date:  2020-08-03       Impact factor: 4.033

4.  Distribution of Initiation Times Reveals Mechanisms of Transcriptional Regulation in Single Cells.

Authors:  Sandeep Choubey; Jane Kondev; Alvaro Sanchez
Journal:  Biophys J       Date:  2018-05-08       Impact factor: 4.033

5.  Effects of mRNA Degradation and Site-Specific Transcriptional Pausing on Protein Expression Noise.

Authors:  Sangjin Kim; Christine Jacobs-Wagner
Journal:  Biophys J       Date:  2018-04-10       Impact factor: 4.033

6.  Modeling bursty transcription and splicing with the chemical master equation.

Authors:  Gennady Gorin; Lior Pachter
Journal:  Biophys J       Date:  2022-02-07       Impact factor: 4.033

7.  Pathway dynamics can delineate the sources of transcriptional noise in gene expression.

Authors:  Lucy Ham; Marcel Jackson; Michael Ph Stumpf
Journal:  Elife       Date:  2021-10-12       Impact factor: 8.140

8.  RNA velocity unraveled.

Authors:  Gennady Gorin; Meichen Fang; Tara Chari; Lior Pachter
Journal:  PLoS Comput Biol       Date:  2022-09-12       Impact factor: 4.779

9.  Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction.

Authors:  Jingyao Wang; Shihe Zhang; Hongfang Lu; Heng Xu
Journal:  Nat Commun       Date:  2022-05-17       Impact factor: 17.694

Review 10.  Transcriptional precision and accuracy in development: from measurements to models and mechanisms.

Authors:  Lital Bentovim; Timothy T Harden; Angela H DePace
Journal:  Development       Date:  2017-11-01       Impact factor: 6.868

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.