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.
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Acknowledgment
We thank Y. Katou, R. Nakato, M. Bando, and all other members of the Shirahige laboratory for support and discussion. This work was supported in part by CREST from JST (K.S.), by Grants-in-aid for Scientific Research (A) (K.S.), Grants-in-aid for Scientific Research (C) (T.Su.), and Grants-in-aid for Scientific Research on Innovative Areas (K.S.) from JSPS (KAKENHI grant numbers 15H02369, 24570006, and 15H05976, respectively). T.Sa. is supported by JSPS research fellowship for young scientists.
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Sakata, T., Shirahige, K., Sutani, T. (2017). ChIP-seq Analysis of Condensin Complex in Cultured Mammalian Cells. In: Yokomori, K., Shirahige, K. (eds) Cohesin and Condensin. Methods in Molecular Biology, vol 1515. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6545-8_16
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DOI: https://doi.org/10.1007/978-1-4939-6545-8_16
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