title: ChIP-seq Analysis of Condensin Complex in Cultured Mammalian Cells.
abstract: ChIP-seq, or chromatin immunoprecipitation combined with massively parallel DNA sequencing, is a powerful technique to investigate in vivo protein-DNA interactions on a genome-wide scale at high resolution. Here we describe a ChIP-seq protocol optimized for analysis of condensin I complex on human mitotic chromosomes. The protocol includes procedures of intensive cell fixation by two cross-linking reagents and thorough chromatin shearing by nuclease and sonication treatments, both of which contribute to improving the signal-to-noise ratio of condensin I ChIP-seq profiles. The optimized protocol may also be helpful to explore chromosomal binding sites of other "hard-to-see" proteins by ChIP-seq.
authors: Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
authors: Toyonori
authors: T
authors: Sakata
authors: Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan. kshirahi@iam.u-tokyo.ac.jp.|CREST, Japan Science and Technology Agency (JST), K's Gobancho 6F, 7 Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan. kshirahi@iam.u-tokyo.ac.jp.
authors: Katsuhiko
authors: K
authors: Shirahige
authors: Laboratory of Genome Structure and Function, Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032, Japan.
authors: Takashi
authors: T
authors: Sutani
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics* / Q000378:metabolism; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D002875:Chromosomes / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D046912:Multiprotein Complexes / Q000235:genetics* / Q000378:metabolism; D011485:Protein Binding
chemical_list: D002843:Chromatin; D004268:DNA-Binding Proteins; D046912:Multiprotein Complexes; C108312:condensin complexes; D000251:Adenosine Triphosphatases
keywords: ChIP-seq; Chromatin immunoprecipitation; Chromosome condensation; Condensin; High-throughput sequencing; Mitosis