title: Optimization of a method for chromatin immunoprecipitation assays in the marine invertebrate chordate Ciona.
abstract: Chromatin immunoprecipitation (ChIP) assays allow the efficient characterization of the in vivo occupancy of genomic regions by DNA-binding proteins and thus facilitate the prediction of cis-regulatory sequences in silico and guide their validation in vivo. For these reasons, these assays and their permutations (e.g., ChIP-on-chip and ChIP-sequencing) are currently being extended to several non-mainstream model organisms, as the availability of specific antibodies increases. Here, we describe the development of a polyclonal antibody against the Brachyury protein of the marine invertebrate chordate Ciona intestinalis and provide a detailed ChIP protocol that should be easily adaptable to other marine organisms.
authors.affiliation: Department of Cell and Developmental Biology, Weill Medical College of Cornell University, 1300 York Avenue, Box 60, New York, NY 10065, USA.
authors.forename: Hitoshi
authors.initials: H
authors.lastname: Aihara
authors.forename: Lavanya
authors.initials: L
authors.lastname: Katikala
authors.forename: Robert W
authors.initials: RW
authors.lastname: Zeller
authors.forename: Anna
authors.initials: A
authors.lastname: Di Gregorio
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Nibu
mesh_terms: D000818:Animals; D000906:Antibodies / Q000235:genetics; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002938:Ciona intestinalis / Q000737:chemistry*; D017931:DNA Primers / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics; D004268:DNA-Binding Proteins / Q000032:analysis*; D007150:Immunohistochemistry; D047468:Immunoprecipitation; D008386:Marine Biology / Q000379:methods; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*
chemical_list: D000906:Antibodies; D017931:DNA Primers; D018076:DNA, Complementary; D004268:DNA-Binding Proteins