Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)
- 18 February 2010
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Protocols
- Vol. 5 (3), 457-472
- https://doi.org/10.1038/nprot.2009.244
Abstract
Chromatin immunoprecipitation (ChIP) is a powerful technique to study interactions between transcription factors (TFs) and DNA in vivo. For genome-wide de novo discovery of TF-binding sites, the DNA that is obtained in ChIP experiments needs to be processed for sequence identification. The sequences can be identified by direct sequencing (ChIP-SEQ) or hybridization to microarrays (ChIP-CHIP). Given the small amounts of DNA that are usually obtained in ChIP experiments, successful and reproducible sample processing is challenging. Here we provide a detailed procedure for ChIP of plant TFs, as well as protocols for sample preparation for ChIP-SEQ and for ChIP-CHIP. Our ChIP procedure is optimized for high signal-to-noise ratio starting with tissue fixation, followed by nuclei isolation, immunoprecipitation, DNA amplification and purification. We also provide a guide for primary data analysis of ChIP-SEQ data. The complete protocol for ChIP-SEQ/ChIP-CHIP sample preparation starting from plant harvest takes ∼7 d.Keywords
This publication has 40 references indexed in Scilit:
- A Systems Approach Reveals Regulatory Circuitry for Arabidopsis Trichome Initiation by the GL3 and GL1 SelectorsPLoS Genetics, 2009
- Genome‐scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5The Plant Journal, 2008
- Mapping short DNA sequencing reads and calling variants using mapping quality scoresGenome Research, 2008
- Substantial biases in ultra-short read data sets from high-throughput DNA sequencingNucleic Acids Research, 2008
- Serial ChIP as a tool to investigate the co-localization or exclusion of proteins on plant genesPlant Methods, 2008
- Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencingNature Methods, 2007
- Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of DevelopmentTHE PLANT CELL ONLINE, 2007
- Genomic Approach for the Understanding of Dynamic Aspect of Chromosome BehaviorMethods in Enzymology, 2006
- A chromatin immunoprecipitation (ChIP) approach to isolate genes regulated by AGL15, a MADS domain protein that preferentially accumulates in embryosThe Plant Journal, 2002
- A Serine/Threonine Protein Kinase Gene Isolated by an in vivo Binding Procedure Using the Arabidopsis Floral Homeotic Gene Product, AGAMOUSPlant and Cell Physiology, 1997