Protocol abstract
Nature Protocols 3, - 698 - 709 (2008)
Published online: 3 April 2008 | doi:10.1038/nprot.2008.38
Subject Categories: Biochemistry and protein analysis | Cell and developmental biology | Immunological techniques | Isolation, purification and separation | Model organisms
Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans
Arnab Mukhopadhyay1, Bart Deplancke1, Albertha J M Walhout1 & Heidi A Tissenbaum1
Abstract
In order to determine how signaling pathways differentially regulate gene expression, it is necessary to identify the interactions between transcription factors (TFs) and their cognate cis-regulatory DNA elements. Here, we have outlined a chromatin immunoprecipitation (ChIP) protocol for use in whole Caenorhabditis elegans extracts. We discuss optimization of the procedure, including growth and harvesting of the worms, formaldehyde fixation, TF immunoprecipitation and analysis of bound sequences through real-time PCR. It takes 
10–12 d to obtain the worm culture for ChIP; the ChIP procedure is spaced out over a period of 2.5 d with two overnight incubations.
- Program in Gene Function and Expression, Program in Molecular Medicine, Aaron Lazare Research Building, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA.
Correspondence to: Heidi A Tissenbaum1 e-mail: Heidi.Tissenbaum@umassmed.edu
nature-products
A-Z product listing
- 7-ml Glass homogenizer(Kontes Glass)
- 7500 Real-Time PCR system(Applied Biosystems)
- Agar(Fisher)
- Bactopeptone(Becton Dickinson)
- Blotting grade blocker nonfat dry milk(Bio-Rad)
- CaCl2 (Fisher)
