title: PROTOCOLS: Chromatin Immunoprecipitation from Arabidopsis Tissues.
abstract: The ability of proteins to associate with genomic DNA in the context of chromatin is critical for many nuclear processes including transcription, replication, recombination, and DNA repair. Chromatin immunoprecipication (ChIP) is a practical and useful technique for characterizing protein / DNA association in vivo. The procedure generally includes six steps: (1) crosslinking the protein to the DNA; (2) isolating the chromatin; (3) chromatin fragmentation; (4) imunoprecipitation with antibodies against the protein of interest; (5) DNA recovery; and (6) PCR identification of factor associated DNA sequences. In this protocol, we describe guidelines, experimental setup, and conditions for ChIP in intact Arabidopsis tissues. This protocol has been used to study association of histone modifications, of chromatin remodeling ATPases, as well as of sequence-specific transcription factors with the genomic DNA in various Arabidopsis thaliana tissues. The protocol described focuses on ChIP-qPCR, but can readily be adapted for use in ChIP-chip or ChIP-seq experiments. The entire procedure can be completed within 3 days.
authors.affiliation: Department of Biology, University of Pennsylvania, 415 S. University Avenue, Philadelphia, PA, USA 19104.
authors.forename: Nobutoshi
authors.initials: N
authors.lastname: Yamaguchi
authors.affiliation: Department of Biology, University of Pennsylvania, 415 S. University Avenue, Philadelphia, PA, USA 19104 ; Department of Biology and Duke Center for Systems Biology, 4128 French Family Science Center, Duke University, Durham, NC 27708.
authors.forename: Cara M
authors.initials: CM
authors.lastname: Winter
authors.affiliation: Department of Biology, University of Pennsylvania, 415 S. University Avenue, Philadelphia, PA, USA 19104.
authors.forename: Miin-Feng
authors.initials: MF
authors.lastname: Wu
authors.affiliation: Department of Biology, University of Pennsylvania, 415 S. University Avenue, Philadelphia, PA, USA 19104.
authors.forename: Chang Seob
authors.initials: CS
authors.lastname: Kwon
authors.affiliation: Department of Biology, University of Pennsylvania, 415 S. University Avenue, Philadelphia, PA, USA 19104.
authors.forename: Dilusha A
authors.initials: DA
authors.lastname: William
authors.affiliation: Department of Biology, University of Pennsylvania, 415 S. University Avenue, Philadelphia, PA, USA 19104.
authors.forename: Doris
authors.initials: D
authors.lastname: Wagner