Transcription by the numbers redux: Experiments and calculations that surprise

Hernan G. Garcia, Alvaro Sanchez, Thomas Kuhlman, Jane Kondev, Rob Phillips

Research output: Contribution to journalReview article

Abstract

The study of transcription has witnessed an explosion of quantitative effort both experimentally and theoretically. In this article we highlight some of the exciting recent experimental efforts in the study of transcription with an eye to the demands that such experiments put on theoretical models of transcription. From a modeling perspective, we focus on two broad classes of models: the so-called thermodynamic models that use statistical mechanics to reckon the level of gene expression as probabilities of promoter occupancy, and rate-equation treatments that focus on the temporal evolution of the activity of a given promoter and that make it possible to compute the distributions of messenger RNA and proteins. We consider several appealing case studies to illustrate how quantitative models have been used to dissect transcriptional regulation.

Original languageEnglish (US)
Pages (from-to)723-733
Number of pages11
JournalTrends in Cell Biology
Volume20
Issue number12
DOIs
StatePublished - Dec 1 2010

Fingerprint

Dexfenfluramine
Explosions
Statistical Models
Mechanics
Thermodynamics
Theoretical Models
Gene Expression
Messenger RNA
Proteins

ASJC Scopus subject areas

  • Cell Biology

Cite this

Garcia, H. G., Sanchez, A., Kuhlman, T., Kondev, J., & Phillips, R. (2010). Transcription by the numbers redux: Experiments and calculations that surprise. Trends in Cell Biology, 20(12), 723-733. https://doi.org/10.1016/j.tcb.2010.07.002

Transcription by the numbers redux : Experiments and calculations that surprise. / Garcia, Hernan G.; Sanchez, Alvaro; Kuhlman, Thomas; Kondev, Jane; Phillips, Rob.

In: Trends in Cell Biology, Vol. 20, No. 12, 01.12.2010, p. 723-733.

Research output: Contribution to journalReview article

Garcia, HG, Sanchez, A, Kuhlman, T, Kondev, J & Phillips, R 2010, 'Transcription by the numbers redux: Experiments and calculations that surprise', Trends in Cell Biology, vol. 20, no. 12, pp. 723-733. https://doi.org/10.1016/j.tcb.2010.07.002
Garcia, Hernan G. ; Sanchez, Alvaro ; Kuhlman, Thomas ; Kondev, Jane ; Phillips, Rob. / Transcription by the numbers redux : Experiments and calculations that surprise. In: Trends in Cell Biology. 2010 ; Vol. 20, No. 12. pp. 723-733.
@article{a29008813a014fc0966f5ea9ee0b445c,
title = "Transcription by the numbers redux: Experiments and calculations that surprise",
abstract = "The study of transcription has witnessed an explosion of quantitative effort both experimentally and theoretically. In this article we highlight some of the exciting recent experimental efforts in the study of transcription with an eye to the demands that such experiments put on theoretical models of transcription. From a modeling perspective, we focus on two broad classes of models: the so-called thermodynamic models that use statistical mechanics to reckon the level of gene expression as probabilities of promoter occupancy, and rate-equation treatments that focus on the temporal evolution of the activity of a given promoter and that make it possible to compute the distributions of messenger RNA and proteins. We consider several appealing case studies to illustrate how quantitative models have been used to dissect transcriptional regulation.",
author = "Garcia, {Hernan G.} and Alvaro Sanchez and Thomas Kuhlman and Jane Kondev and Rob Phillips",
year = "2010",
month = "12",
day = "1",
doi = "10.1016/j.tcb.2010.07.002",
language = "English (US)",
volume = "20",
pages = "723--733",
journal = "Trends in Cell Biology",
issn = "0962-8924",
publisher = "Elsevier Limited",
number = "12",

}

TY - JOUR

T1 - Transcription by the numbers redux

T2 - Experiments and calculations that surprise

AU - Garcia, Hernan G.

AU - Sanchez, Alvaro

AU - Kuhlman, Thomas

AU - Kondev, Jane

AU - Phillips, Rob

PY - 2010/12/1

Y1 - 2010/12/1

N2 - The study of transcription has witnessed an explosion of quantitative effort both experimentally and theoretically. In this article we highlight some of the exciting recent experimental efforts in the study of transcription with an eye to the demands that such experiments put on theoretical models of transcription. From a modeling perspective, we focus on two broad classes of models: the so-called thermodynamic models that use statistical mechanics to reckon the level of gene expression as probabilities of promoter occupancy, and rate-equation treatments that focus on the temporal evolution of the activity of a given promoter and that make it possible to compute the distributions of messenger RNA and proteins. We consider several appealing case studies to illustrate how quantitative models have been used to dissect transcriptional regulation.

AB - The study of transcription has witnessed an explosion of quantitative effort both experimentally and theoretically. In this article we highlight some of the exciting recent experimental efforts in the study of transcription with an eye to the demands that such experiments put on theoretical models of transcription. From a modeling perspective, we focus on two broad classes of models: the so-called thermodynamic models that use statistical mechanics to reckon the level of gene expression as probabilities of promoter occupancy, and rate-equation treatments that focus on the temporal evolution of the activity of a given promoter and that make it possible to compute the distributions of messenger RNA and proteins. We consider several appealing case studies to illustrate how quantitative models have been used to dissect transcriptional regulation.

UR - http://www.scopus.com/inward/record.url?scp=78650216734&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=78650216734&partnerID=8YFLogxK

U2 - 10.1016/j.tcb.2010.07.002

DO - 10.1016/j.tcb.2010.07.002

M3 - Review article

C2 - 20801657

AN - SCOPUS:78650216734

VL - 20

SP - 723

EP - 733

JO - Trends in Cell Biology

JF - Trends in Cell Biology

SN - 0962-8924

IS - 12

ER -