共 61 条
Using variability in gene expression as a tool for studying gene regulation
被引:18
作者:

Padovan-Merhar, Olivia
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Penn, Dept Phys, Philadelphia, PA 19104 USA Univ Penn, Dept Phys, Philadelphia, PA 19104 USA

Raj, Arjun
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Penn, Dept Bioengn, Philadelphia, PA 19104 USA Univ Penn, Dept Phys, Philadelphia, PA 19104 USA
机构:
[1] Univ Penn, Dept Phys, Philadelphia, PA 19104 USA
[2] Univ Penn, Dept Bioengn, Philadelphia, PA 19104 USA
基金:
美国国家卫生研究院;
关键词:
DYNAMIC PROTEOMICS;
PROTEIN EXPRESSION;
NONCODING RNAS;
CELL FATE;
SINGLE;
NOISE;
TRANSCRIPTION;
MOLECULE;
REVEALS;
HETEROGENEITY;
D O I:
10.1002/wsbm.1243
中图分类号:
R-3 [医学研究方法];
R3 [基础医学];
学科分类号:
1001 ;
摘要:
With the advent of quantitative tools for measuring gene expression in single cells, researchers have made the discovery that in many contexts, messenger RNA and protein levels can vary widely from cell to cell, often because of inherently stochastic events associated with gene expression. The study of this cellular individuality has become a field of study in its own right, characterized by a blend of technological development, theoretical analysis, and, more recently, applications to biological phenomena. In this review, we focus on the use of the variability inherent to gene expression as a tool to understand gene regulation. We discuss the use of variability as a natural systems-level perturbation, its use in quantitatively characterizing the biological processes underlying transcription, and its application to the discovery of new gene regulatory interactions. We believe that use of variability can provide new biological insights into different aspects of transcriptional control and can provide a powerful complementary approach to that of existing techniques. (C) 2013 Wiley Periodicals, Inc.
引用
收藏
页码:751 / 759
页数:9
相关论文
共 61 条
[1]
Cellular Decision Making and Biological Noise: From Microbes to Mammals
[J].
Balazsi, Gabor
;
van Oudenaarden, Alexander
;
Collins, James J.
.
CELL,
2011, 144 (06)
:910-925

Balazsi, Gabor
论文数: 0 引用数: 0
h-index: 0
机构:
Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Unit 950, Houston, TX 77054 USA Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Boston, MA 02215 USA

van Oudenaarden, Alexander
论文数: 0 引用数: 0
h-index: 0
机构:
MIT, Dept Phys, Cambridge, MA 02139 USA
MIT, Dept Biol, Cambridge, MA 02139 USA Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Boston, MA 02215 USA

Collins, James J.
论文数: 0 引用数: 0
h-index: 0
机构:
Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Boston, MA 02215 USA
Boston Univ, Ctr BioDynam, Boston, MA 02215 USA
Harvard Univ, Wyss Inst Biol Inspired Engn, Boston, MA 02215 USA Boston Univ, Howard Hughes Med Inst, Dept Biomed Engn, Boston, MA 02215 USA
[2]
Noise in protein expression scales with natural protein abundance
[J].
Bar-Even, Arren
;
Paulsson, Johan
;
Maheshri, Narendra
;
Carmi, Miri
;
O'Shea, Erin
;
Pilpel, Yitzhak
;
Barkai, Naama
.
NATURE GENETICS,
2006, 38 (06)
:636-643

Bar-Even, Arren
论文数: 0 引用数: 0
h-index: 0
机构: Harvard Univ, Dept Syst Biol, Boston, MA 02115 USA

Paulsson, Johan
论文数: 0 引用数: 0
h-index: 0
机构: Harvard Univ, Dept Syst Biol, Boston, MA 02115 USA

Maheshri, Narendra
论文数: 0 引用数: 0
h-index: 0
机构: Harvard Univ, Dept Syst Biol, Boston, MA 02115 USA

Carmi, Miri
论文数: 0 引用数: 0
h-index: 0
机构: Harvard Univ, Dept Syst Biol, Boston, MA 02115 USA

O'Shea, Erin
论文数: 0 引用数: 0
h-index: 0
机构: Harvard Univ, Dept Syst Biol, Boston, MA 02115 USA

论文数: 引用数:
h-index:
机构:

论文数: 引用数:
h-index:
机构:
[3]
MicroRNAs: Target Recognition and Regulatory Functions
[J].
Bartel, David P.
.
CELL,
2009, 136 (02)
:215-233

Bartel, David P.
论文数: 0 引用数: 0
h-index: 0
机构:
MIT, Howard Hughes Med Inst, Cambridge, MA 02139 USA
MIT, Dept Biol, Cambridge, MA 02139 USA
Whitehead Inst Biomed Res, Cambridge, MA 02142 USA MIT, Howard Hughes Med Inst, Cambridge, MA 02139 USA
[4]
Phenotypic consequences of promoter-mediated transcriptional noise
[J].
Blake, William J.
;
Balazsi, Gbor
;
Kohanski, Michael A.
;
Isaacs, Farren J.
;
Murphy, Kevin F.
;
Kuang, Yina
;
Cantor, Charles R.
;
Walt, David R.
;
Collins, James J.
.
MOLECULAR CELL,
2006, 24 (06)
:853-865

Blake, William J.
论文数: 0 引用数: 0
h-index: 0
机构: Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

Balazsi, Gbor
论文数: 0 引用数: 0
h-index: 0
机构: Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

Kohanski, Michael A.
论文数: 0 引用数: 0
h-index: 0
机构: Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

Isaacs, Farren J.
论文数: 0 引用数: 0
h-index: 0
机构: Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

Murphy, Kevin F.
论文数: 0 引用数: 0
h-index: 0
机构: Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

Kuang, Yina
论文数: 0 引用数: 0
h-index: 0
机构: Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

Cantor, Charles R.
论文数: 0 引用数: 0
h-index: 0
机构: Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

Walt, David R.
论文数: 0 引用数: 0
h-index: 0
机构: Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA

Collins, James J.
论文数: 0 引用数: 0
h-index: 0
机构:
Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA Boston Univ, Dept Biomed Engn, Boston, MA 02215 USA
[5]
Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase
[J].
Buganim, Yosef
;
Faddah, Dina A.
;
Cheng, Albert W.
;
Itskovich, Elena
;
Markoulaki, Styliani
;
Ganz, Kibibi
;
Klemm, Sandy L.
;
van Oudenaarden, Alexander
;
Jaenisch, Rudolf
.
CELL,
2012, 150 (06)
:1209-1222

Buganim, Yosef
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge, MA 02142 USA Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

Faddah, Dina A.
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge, MA 02142 USA
MIT, Dept Biol, Cambridge, MA 02139 USA Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

Cheng, Albert W.
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge, MA 02142 USA
MIT, Dept Computat & Syst Biol, Cambridge, MA 02139 USA Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

Itskovich, Elena
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge, MA 02142 USA Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

Markoulaki, Styliani
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge, MA 02142 USA Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

Ganz, Kibibi
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge, MA 02142 USA Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

Klemm, Sandy L.
论文数: 0 引用数: 0
h-index: 0
机构:
MIT, Dept Elect Engn & Comp Sci, Cambridge, MA 02139 USA Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

van Oudenaarden, Alexander
论文数: 0 引用数: 0
h-index: 0
机构:
MIT, Dept Biol, Cambridge, MA 02139 USA
MIT, Dept Phys, Cambridge, MA 02139 USA
Royal Netherlands Acad Arts & Sci, Hubrecht Inst, NL-3584 CT Utrecht, Netherlands
Univ Med Ctr Utrecht, NL-3584 CT Utrecht, Netherlands Whitehead Inst Biomed Res, Cambridge, MA 02142 USA

Jaenisch, Rudolf
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge, MA 02142 USA
MIT, Dept Biol, Cambridge, MA 02139 USA Whitehead Inst Biomed Res, Cambridge, MA 02142 USA
[6]
Single-Cell Analysis Reveals that Noncoding RNAs Contribute to Clonal Heterogeneity by Modulating Transcription Factor Recruitment
[J].
Bumgarner, Stacie L.
;
Neuert, Gregor
;
Voight, Benjamin F.
;
Symbor-Nagrabska, Anna
;
Grisafi, Paula
;
van Oudenaarden, Alexander
;
Fink, Gerald R.
.
MOLECULAR CELL,
2012, 45 (04)
:470-482

Bumgarner, Stacie L.
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge Ctr 9, Cambridge, MA 02142 USA MIT, Dept Phys, Cambridge, MA 02139 USA

Neuert, Gregor
论文数: 0 引用数: 0
h-index: 0
机构:
MIT, Dept Phys, Cambridge, MA 02139 USA MIT, Dept Phys, Cambridge, MA 02139 USA

Voight, Benjamin F.
论文数: 0 引用数: 0
h-index: 0
机构:
Broad Inst Harvard & MIT, Cambridge Ctr 7, Cambridge, MA 02142 USA
Univ Penn, Perelman Sch Med, Dept Pharmacol, Philadelphia, PA 19104 USA MIT, Dept Phys, Cambridge, MA 02139 USA

Symbor-Nagrabska, Anna
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge Ctr 9, Cambridge, MA 02142 USA MIT, Dept Phys, Cambridge, MA 02139 USA

Grisafi, Paula
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge Ctr 9, Cambridge, MA 02142 USA MIT, Dept Phys, Cambridge, MA 02139 USA

van Oudenaarden, Alexander
论文数: 0 引用数: 0
h-index: 0
机构:
MIT, Dept Phys, Cambridge, MA 02139 USA MIT, Dept Phys, Cambridge, MA 02139 USA

Fink, Gerald R.
论文数: 0 引用数: 0
h-index: 0
机构:
Whitehead Inst Biomed Res, Cambridge Ctr 9, Cambridge, MA 02142 USA MIT, Dept Phys, Cambridge, MA 02139 USA
[7]
Stochastic protein expression in individual cells at the single molecule level
[J].
Cai, L
;
Friedman, N
;
Xie, XS
.
NATURE,
2006, 440 (7082)
:358-362

Cai, L
论文数: 0 引用数: 0
h-index: 0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA

Friedman, N
论文数: 0 引用数: 0
h-index: 0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA

Xie, XS
论文数: 0 引用数: 0
h-index: 0
机构:
Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA Harvard Univ, Dept Chem & Biol Chem, Cambridge, MA 02138 USA
[8]
Transcriptome-wide noise controls lineage choice in mammalian progenitor cells
[J].
Chang, Hannah H.
;
Hemberg, Martin
;
Barahona, Mauricio
;
Ingber, Donald E.
;
Huang, Sui
.
NATURE,
2008, 453 (7194)
:544-U10

Chang, Hannah H.
论文数: 0 引用数: 0
h-index: 0
机构:
Childrens Hosp, Vasc Biol Programme, Dept Pathol & Surg, Boston, MA 02115 USA
Harvard Univ, Sch Med, Boston, MA 02115 USA
Harvard Univ, Sch Med, Program Biophys, Boston, MA 02115 USA
Harvard Univ, Sch Med, MD PhD Programme, Boston, MA 02115 USA Childrens Hosp, Vasc Biol Programme, Dept Pathol & Surg, Boston, MA 02115 USA

Hemberg, Martin
论文数: 0 引用数: 0
h-index: 0
机构:
Univ London Imperial Coll Sci Technol & Med, Dept Bioengn, London SW7 2AZ, England
Univ London Imperial Coll Sci Technol & Med, Inst Math Sci, London SW7 2AZ, England Childrens Hosp, Vasc Biol Programme, Dept Pathol & Surg, Boston, MA 02115 USA

Barahona, Mauricio
论文数: 0 引用数: 0
h-index: 0
机构:
Univ London Imperial Coll Sci Technol & Med, Dept Bioengn, London SW7 2AZ, England
Univ London Imperial Coll Sci Technol & Med, Inst Math Sci, London SW7 2AZ, England Childrens Hosp, Vasc Biol Programme, Dept Pathol & Surg, Boston, MA 02115 USA

Ingber, Donald E.
论文数: 0 引用数: 0
h-index: 0
机构:
Childrens Hosp, Vasc Biol Programme, Dept Pathol & Surg, Boston, MA 02115 USA
Harvard Univ, Sch Med, Boston, MA 02115 USA
Harvard Inst Biol Inspired Engn, Cambridge, MA 02139 USA Childrens Hosp, Vasc Biol Programme, Dept Pathol & Surg, Boston, MA 02115 USA

Huang, Sui
论文数: 0 引用数: 0
h-index: 0
机构:
Childrens Hosp, Vasc Biol Programme, Dept Pathol & Surg, Boston, MA 02115 USA
Harvard Univ, Sch Med, Boston, MA 02115 USA Childrens Hosp, Vasc Biol Programme, Dept Pathol & Surg, Boston, MA 02115 USA
[9]
A stochastic single-molecule event triggers phenotype switching of a bacterial cell
[J].
Choi, Paul J.
;
Cai, Long
;
Frieda, Kirsten
;
Xie, Sunney
.
SCIENCE,
2008, 322 (5900)
:442-446

Choi, Paul J.
论文数: 0 引用数: 0
h-index: 0
机构:
Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA

Cai, Long
论文数: 0 引用数: 0
h-index: 0
机构:
Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA

Frieda, Kirsten
论文数: 0 引用数: 0
h-index: 0
机构:
Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA

Xie, Sunney
论文数: 0 引用数: 0
h-index: 0
机构:
Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA Harvard Univ, Dept Chem & Chem Biol, Cambridge, MA 02138 USA
[10]
Transcriptional pulsing of a developmental gene
[J].
Chubb, JR
;
Trcek, T
;
Shenoy, SM
;
Singer, RH
.
CURRENT BIOLOGY,
2006, 16 (10)
:1018-1025

Chubb, JR
论文数: 0 引用数: 0
h-index: 0
机构: Yeshiva Univ Albert Einstein Coll Med, Dept Anat & Struct Biol, Bronx, NY 10461 USA

Trcek, T
论文数: 0 引用数: 0
h-index: 0
机构: Yeshiva Univ Albert Einstein Coll Med, Dept Anat & Struct Biol, Bronx, NY 10461 USA

Shenoy, SM
论文数: 0 引用数: 0
h-index: 0
机构: Yeshiva Univ Albert Einstein Coll Med, Dept Anat & Struct Biol, Bronx, NY 10461 USA

Singer, RH
论文数: 0 引用数: 0
h-index: 0
机构: Yeshiva Univ Albert Einstein Coll Med, Dept Anat & Struct Biol, Bronx, NY 10461 USA