A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification
- Author
- Aurine Verkest, Thomas Abeel (UGent) , Ken Heyndrickx (UGent) , 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) , Dirk Inzé (UGent) , Klaas Vandepoele (UGent) and Geert De Jaeger (UGent)
- Organization
- Project
- 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.
- Keywords
- SEQ, EXPRESSION, NETWORK, VIVO CROSS-LINKING, GENOME-WIDE ANALYSIS, PLANT DEVELOPMENT, PROTEIN-DNA INTERACTIONS, EMBRYONIC STEM-CELLS, TANDEM AFFINITY PURIFICATION, CHROMATIN IMMUNOPRECIPITATION CHIP
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-4388319
- MLA
- Verkest, Aurine, et al. “A Generic Tool for Transcription Factor Target Gene Discovery in Arabidopsis Cell Suspension Cultures Based on Tandem Chromatin Affinity Purification.” PLANT PHYSIOLOGY, vol. 164, no. 3, 2014, pp. 1122–33, doi:10.1104/pp.113.229617.
- APA
- Verkest, A., Abeel, T., Heyndrickx, K., Van Leene, J., Lanz, C., Van De Slijke, E., … De Jaeger, G. (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. https://doi.org/10.1104/pp.113.229617
- Chicago author-date
- 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): 1122–33. https://doi.org/10.1104/pp.113.229617.
- Chicago author-date (all authors)
- Verkest, Aurine, Thomas Abeel, Ken Heyndrickx, Jelle Van Leene, Christa Lanz, Eveline Van De Slijke, Nancy De Winne, Dominique Eeckhout, Geert Persiau, Frank Van Breusegem, Dirk Inzé, Klaas Vandepoele, and Geert De Jaeger. 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. doi:10.1104/pp.113.229617.
- 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.
- IEEE
- [1]A. Verkest et al., “A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification,” PLANT PHYSIOLOGY, vol. 164, no. 3, pp. 1122–1133, 2014.
@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 Inzé, Dirk and Vandepoele, Klaas and De Jaeger, Geert}},
issn = {{0032-0889}},
journal = {{PLANT PHYSIOLOGY}},
keywords = {{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://doi.org/10.1104/pp.113.229617}},
volume = {{164}},
year = {{2014}},
}
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