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A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification

Aurine Verkest, Thomas Abeel, Ken Heyndrickx, Jelle Van Leene UGent, Christa Lanz, Eveline Van De Slijke UGent, Nancy De Winne UGent, Dominique Eeckhout UGent, Geert Persiau UGent, Frank Van Breusegem UGent, et al. (2014) PLANT PHYSIOLOGY. 164(3). p.1122-1133
abstract
Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation, this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis (Arabidopsis thaliana) cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional chromatin immunoprecipitation and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and coexpression network analyses demonstrates the quality of the E2Fa TChAP sequencing data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
SEQ, EXPRESSION, NETWORK, VIVO CROSS-LINKING, GENOME-WIDE ANALYSIS, PLANT DEVELOPMENT, PROTEIN-DNA INTERACTIONS, EMBRYONIC STEM-CELLS, TANDEM AFFINITY PURIFICATION, CHROMATIN IMMUNOPRECIPITATION CHIP
journal title
PLANT PHYSIOLOGY
Plant Physiol.
volume
164
issue
3
pages
1122 - 1133
Web of Science type
Article
Web of Science id
000332475000002
JCR category
PLANT SCIENCES
JCR impact factor
6.841 (2014)
JCR rank
8/204 (2014)
JCR quartile
1 (2014)
ISSN
0032-0889
DOI
10.1104/pp.113.229617
project
Bioinformatics: from nucleotids to networks (N2N)
project
Biotechnology for a sustainable economy (Bio-Economy)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
4388319
handle
http://hdl.handle.net/1854/LU-4388319
date created
2014-05-19 13:27:54
date last changed
2016-12-19 15:43:02
@article{4388319,
  abstract     = {Genome-wide identification of transcription factor (TF) binding sites is pivotal to our understanding of gene expression regulation. Although much progress has been made in the determination of potential binding regions of proteins by chromatin immunoprecipitation, this method has some inherent limitations regarding DNA enrichment efficiency and antibody necessity. Here, we report an alternative strategy for assaying in vivo TF-DNA binding in Arabidopsis (Arabidopsis thaliana) cells by tandem chromatin affinity purification (TChAP). Evaluation of TChAP using the E2Fa TF and comparison with traditional chromatin immunoprecipitation and single chromatin affinity purification illustrates the suitability of TChAP and provides a resource for exploring the E2Fa transcriptional network. Integration with transcriptome, cis-regulatory element, functional enrichment, and coexpression network analyses demonstrates the quality of the E2Fa TChAP sequencing data and validates the identification of new direct E2Fa targets. TChAP enhances both TF target mapping throughput, by circumventing issues related to antibody availability, and output, by improving DNA enrichment efficiency.},
  author       = {Verkest, Aurine and Abeel, Thomas and Heyndrickx, Ken and Van Leene, Jelle and Lanz, Christa and Van De Slijke, Eveline and De Winne, Nancy and Eeckhout, Dominique and Persiau, Geert and Van Breusegem, Frank and Inz{\'e}, Dirk and Vandepoele, Klaas and De Jaeger, Geert},
  issn         = {0032-0889},
  journal      = {PLANT PHYSIOLOGY},
  keyword      = {SEQ,EXPRESSION,NETWORK,VIVO CROSS-LINKING,GENOME-WIDE ANALYSIS,PLANT DEVELOPMENT,PROTEIN-DNA INTERACTIONS,EMBRYONIC STEM-CELLS,TANDEM AFFINITY PURIFICATION,CHROMATIN IMMUNOPRECIPITATION CHIP},
  language     = {eng},
  number       = {3},
  pages        = {1122--1133},
  title        = {A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification},
  url          = {http://dx.doi.org/10.1104/pp.113.229617},
  volume       = {164},
  year         = {2014},
}

Chicago
Verkest, Aurine, Thomas Abeel, Ken Heyndrickx, Jelle Van Leene, Christa Lanz, Eveline Van De Slijke, Nancy De Winne, et al. 2014. “A Generic Tool for Transcription Factor Target Gene Discovery in Arabidopsis Cell Suspension Cultures Based on Tandem Chromatin Affinity Purification.” Plant Physiology 164 (3): 1122–1133.
APA
Verkest, A., Abeel, T., Heyndrickx, K., Van Leene, J., Lanz, C., Van De Slijke, E., De Winne, N., et al. (2014). A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification. PLANT PHYSIOLOGY, 164(3), 1122–1133.
Vancouver
1.
Verkest A, Abeel T, Heyndrickx K, Van Leene J, Lanz C, Van De Slijke E, et al. A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification. PLANT PHYSIOLOGY. 2014;164(3):1122–33.
MLA
Verkest, Aurine, Thomas Abeel, Ken Heyndrickx, et al. “A Generic Tool for Transcription Factor Target Gene Discovery in Arabidopsis Cell Suspension Cultures Based on Tandem Chromatin Affinity Purification.” PLANT PHYSIOLOGY 164.3 (2014): 1122–1133. Print.