Open Access

Molecular Systems Biology, volume 11, issue 1, pages 775

Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes

LI Xu ¹

Wang Wenqi ¹

Wang Jiadong ¹

Malovannaya Anna ²

Xi Yuanxin ^{2, 3}

Li Wei ^{2, 3}

Guerra Rudy ⁴

Hawke David H ⁵

Qin Jun ²

Chen Junjie ¹

Hide authors affiliations Show authors affiliations: 5 affiliations

Department of Experimental Radiation Oncology The University of Texas MD Anderson Cancer Center Houston TX USA |

Department of Molecular and Cellular Biology Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA |

Division of Biostatistics Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA |

⁴

Department of Statistics Rice University Houston TX USA |

⁵

Proteomics Facility Department of Pathology The University of Texas MD Anderson Cancer Center Houston TX USA |

Publication type: Journal Article

Publication date: 2015-01-22

Wiley

Journal: Molecular Systems Biology

Quartile SCImago

Quartile WOS

Impact factor: 9.9

ISSN: 17444292

DOI: 10.15252/msb.20145504

Copy DOI

PubMed ID: 25609649

General Biochemistry, Genetics and Molecular Biology

General Agricultural and Biological Sciences

General Immunology and Microbiology

Computational Theory and Mathematics

Information Systems

Applied Mathematics

Abstract

The current knowledge on how transcription factors (TFs), the ultimate targets and executors of cellular signalling pathways, are regulated by protein–protein interactions remains limited. Here, we performed proteomics analyses of soluble and chromatin‐associated complexes of 56 TFs, including the targets of many signalling pathways involved in development and cancer, and 37 members of the Forkhead box (FOX) TF family. Using tandem affinity purification followed by mass spectrometry (TAP/MS), we performed 214 purifications and identified 2,156 high‐confident protein–protein interactions. We found that most TFs form very distinct protein complexes on and off chromatin. Using this data set, we categorized the transcription‐related or unrelated regulators for general or specific TFs. Our study offers a valuable resource of protein–protein interaction networks for a large number of TFs and underscores the general principle that TFs form distinct location‐specific protein complexes that are associated with the different regulation and diverse functions of these TFs.

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Citations by journals

	1 2 3 4 5
Nucleic Acids Research	Nucleic Acids Research, 5, 4.55% Nucleic Acids Research 5 publications, 4.55%
Scientific Reports	Scientific Reports, 5, 4.55% Scientific Reports 5 publications, 4.55%
Journal of Biological Chemistry	Journal of Biological Chemistry, 5, 4.55% Journal of Biological Chemistry 5 publications, 4.55%
International Journal of Molecular Sciences	International Journal of Molecular Sciences, 4, 3.64% International Journal of Molecular Sciences 4 publications, 3.64%
Molecular and Cellular Proteomics	Molecular and Cellular Proteomics, 4, 3.64% Molecular and Cellular Proteomics 4 publications, 3.64%
Cells	Cells, 3, 2.73% Cells 3 publications, 2.73%
Cell Reports	Cell Reports, 3, 2.73% Cell Reports 3 publications, 2.73%
Molecular Cell	Molecular Cell, 2, 1.82% Molecular Cell 2 publications, 1.82%
Genes	Genes, 2, 1.82% Genes 2 publications, 1.82%
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Nature Communications	Nature Communications, 2, 1.82% Nature Communications 2 publications, 1.82%
Molecular Systems Biology	Molecular Systems Biology, 2, 1.82% Molecular Systems Biology 2 publications, 1.82%
Physiological Genomics	Physiological Genomics, 2, 1.82% Physiological Genomics 2 publications, 1.82%
eLife	eLife, 2, 1.82% eLife 2 publications, 1.82%
British Journal of Radiology	British Journal of Radiology, 1, 0.91% British Journal of Radiology 1 publication, 0.91%
Development (Cambridge)	Development (Cambridge), 1, 0.91% Development (Cambridge) 1 publication, 0.91%
Medical Oncology	Medical Oncology, 1, 0.91% Medical Oncology 1 publication, 0.91%
Molecular Syndromology	Molecular Syndromology, 1, 0.91% Molecular Syndromology 1 publication, 0.91%
Molecules	Molecules, 1, 0.91% Molecules 1 publication, 0.91%
Journal of Personalized Medicine	Journal of Personalized Medicine, 1, 0.91% Journal of Personalized Medicine 1 publication, 0.91%
Frontiers in Oncology	Frontiers in Oncology, 1, 0.91% Frontiers in Oncology 1 publication, 0.91%
Frontiers in Molecular Neuroscience	Frontiers in Molecular Neuroscience, 1, 0.91% Frontiers in Molecular Neuroscience 1 publication, 0.91%
Journal of Neurodevelopmental Disorders	Journal of Neurodevelopmental Disorders, 1, 0.91% Journal of Neurodevelopmental Disorders 1 publication, 0.91%
Science China Life Sciences	Science China Life Sciences, 1, 0.91% Science China Life Sciences 1 publication, 0.91%
Cancer Cell International	Cancer Cell International, 1, 0.91% Cancer Cell International 1 publication, 0.91%
Journal of Experimental and Clinical Cancer Research	Journal of Experimental and Clinical Cancer Research, 1, 0.91% Journal of Experimental and Clinical Cancer Research 1 publication, 0.91%
Cerebellum	Cerebellum, 1, 0.91% Cerebellum 1 publication, 0.91%
Cell Death and Differentiation	Cell Death and Differentiation, 1, 0.91% Cell Death and Differentiation 1 publication, 0.91%
Microsystem Technologies	Microsystem Technologies, 1, 0.91% Microsystem Technologies 1 publication, 0.91%
	1 2 3 4 5

Citations by publishers

	2 4 6 8 10 12 14 16 18
Springer Nature	Springer Nature, 17, 15.45% Springer Nature 17 publications, 15.45%
Elsevier	Elsevier, 15, 13.64% Elsevier 15 publications, 13.64%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 14, 12.73% Multidisciplinary Digital Publishing Institute (MDPI) 14 publications, 12.73%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 9, 8.18% American Society for Biochemistry and Molecular Biology 9 publications, 8.18%
Oxford University Press	Oxford University Press, 6, 5.45% Oxford University Press 6 publications, 5.45%
Wiley	Wiley, 6, 5.45% Wiley 6 publications, 5.45%
Frontiers Media S.A.	Frontiers Media S.A., 2, 1.82% Frontiers Media S.A. 2 publications, 1.82%
American Society for Microbiology	American Society for Microbiology, 2, 1.82% American Society for Microbiology 2 publications, 1.82%
American Physiological Society	American Physiological Society, 2, 1.82% American Physiological Society 2 publications, 1.82%
eLife Sciences Publications	eLife Sciences Publications, 2, 1.82% eLife Sciences Publications 2 publications, 1.82%
British Institute of Radiology	British Institute of Radiology, 1, 0.91% British Institute of Radiology 1 publication, 0.91%
The Company of Biologists	The Company of Biologists, 1, 0.91% The Company of Biologists 1 publication, 0.91%
S. Karger AG	S. Karger AG, 1, 0.91% S. Karger AG 1 publication, 0.91%
Federation of American Societies for Experimental Biology (FASEB)	Federation of American Societies for Experimental Biology (FASEB), 1, 0.91% Federation of American Societies for Experimental Biology (FASEB) 1 publication, 0.91%
American Chemical Society (ACS)	American Chemical Society (ACS), 1, 0.91% American Chemical Society (ACS) 1 publication, 0.91%
Pleiades Publishing	Pleiades Publishing, 1, 0.91% Pleiades Publishing 1 publication, 0.91%
EMBO press	EMBO press, 1, 0.91% EMBO press 1 publication, 0.91%
Dove Medical Press	Dove Medical Press, 1, 0.91% Dove Medical Press 1 publication, 0.91%
BMJ	BMJ, 1, 0.91% BMJ 1 publication, 0.91%
Zhejiang University Press	Zhejiang University Press, 1, 0.91% Zhejiang University Press 1 publication, 0.91%
Annual Reviews	Annual Reviews, 1, 0.91% Annual Reviews 1 publication, 0.91%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 1, 0.91% Cold Spring Harbor Laboratory 1 publication, 0.91%
Almazov National Medical Research Centre	Almazov National Medical Research Centre, 1, 0.91% Almazov National Medical Research Centre 1 publication, 0.91%
American Society for Cell Biology (ASCB)	American Society for Cell Biology (ASCB), 1, 0.91% American Society for Cell Biology (ASCB) 1 publication, 0.91%
Society for Neuroscience	Society for Neuroscience, 1, 0.91% Society for Neuroscience 1 publication, 0.91%
American Thoracic Society	American Thoracic Society, 1, 0.91% American Thoracic Society 1 publication, 0.91%
Bentham Science	Bentham Science, 1, 0.91% Bentham Science 1 publication, 0.91%
	2 4 6 8 10 12 14 16 18

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LI Xu et al. Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes // Molecular Systems Biology. 2015. Vol. 11. No. 1. p. 775.

GOST all authors (up to 50) Copy

LI Xu, Wang W., Wang J., Malovannaya A., Xi Y., Li W., Guerra R., Hawke D. H., Qin J., Chen J. Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes // Molecular Systems Biology. 2015. Vol. 11. No. 1. p. 775.

RIS |

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RIS Copy

TY - JOUR

DO - 10.15252/msb.20145504

UR - https://doi.org/10.15252%2Fmsb.20145504

TI - Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes

T2 - Molecular Systems Biology

AU - LI Xu

AU - Wang, Wenqi

AU - Wang, Jiadong

AU - Malovannaya, Anna

AU - Xi, Yuanxin

AU - Li, Wei

AU - Guerra, Rudy

AU - Hawke, David H

AU - Qin, Jun

AU - Chen, Junjie

PY - 2015

DA - 2015/01/22 00:00:00

PB - Wiley

SP - 775

IS - 1

VL - 11

PMID - 25609649

SN - 1744-4292

ER -

BibTex |

Cite this

BibTex Copy

@article{2015_LI Xu,

author = {LI Xu and Wenqi Wang and Jiadong Wang and Anna Malovannaya and Yuanxin Xi and Wei Li and Rudy Guerra and David H Hawke and Jun Qin and Junjie Chen},

title = {Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes},

journal = {Molecular Systems Biology},

year = {2015},

volume = {11},

publisher = {Wiley},

month = {jan},

url = {https://doi.org/10.15252%2Fmsb.20145504},

number = {1},

pages = {775},

doi = {10.15252/msb.20145504}

}

MLA

Cite this

MLA Copy

LI Xu, et al. “Proteomic analyses reveal distinct chromatin‐associated and soluble transcription factor complexes.” Molecular Systems Biology, vol. 11, no. 1, Jan. 2015, p. 775. https://doi.org/10.15252%2Fmsb.20145504.

Found error?

Publisher

Wiley

Journal

Molecular Systems Biology

Quartile SCImago

Quartile WOS

Impact factor

9.9

ISSN

17444292 (Print)