Protocol for fractionation-assisted native ChIP (fanChIP) to capture protein-protein/DNA interactions on chromatin

Ryo Miyamoto; Akihiko Yokoyama

doi:10.1016/j.xpro.2021.100404

Protocol for fractionation-assisted native ChIP (fanChIP) to capture protein-protein/DNA interactions on chromatin

STAR Protoc. 2021 Mar 23;2(2):100404. doi: 10.1016/j.xpro.2021.100404. eCollection 2021 Jun 18.

Authors

Ryo Miyamoto¹, Akihiko Yokoyama^{1

2}

Affiliations

¹ Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata 997-0052, Japan.
² Division of Hematological Malignancy, National Cancer Center Research Institute, Chuo-ku, Tokyo 104-0045, Japan.

Abstract

Conventional chromatin immunoprecipitation (ChIP) includes many steps that need to be optimized. Here, we have described a protocol of fractionation-assisted native ChIP (fanChIP) which combines subfractionation and native ChIP to purify protein/chromatin complexes applicable for analyses of both protein-protein and protein-DNA interactions within a short period of time. fanChIP is advantageous as subcellular fractionation removes chromatin-unbound materials before immunoprecipitation, and the chromatin fragmentation by micrococcal nuclease (MNase) in a mild condition enables one-step purification of intact protein/chromatin complexes. For complete details on the use and execution of this protocol, please refer to Miyamoto et al. (2020).

Keywords: Chromatin immunoprecipitation (ChIP); Genomics; Molecular Biology.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin Immunoprecipitation / methods*
Chromatin* / genetics
Chromatin* / metabolism
DNA* / analysis
DNA* / chemistry
DNA* / metabolism
HEK293 Cells
High-Throughput Nucleotide Sequencing
Humans
Sequence Analysis, DNA
Sequence Analysis, Protein

Substances

Chromatin
DNA