Understanding RNA-Chromatin Interactions Using Chromatin Isolation by RNA Purification (ChIRP)

  • Ci Chu
  • Howard Y. ChangEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1480)


ChIRP is a novel and easy-to-use technique for studying long noncoding RNA (lncRNA)-chromatin interactions. RNA and chromatin are cross-linked in vivo using formaldehyde or glutaraldehyde, and purified using biotinylated antisense oligonucleotides that hybridize to the target RNA. Co-precipitated DNA is then purified and analyzed by quantitative PCR (qPCR) or high-throughput sequencing.

Key words

lncRNA Chromatin High-throughput sequencing Cross-linking 



This work was supported by the Singapore Agency for Science, Technology, and Research (A*STAR to C.C.) and the US National Institutes of Healthy (H.Y.C.). H.Y.C. is an Early Career Scientist of the Howard Hughes Medical Institute.


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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  1. 1.Center for Personal Dynamic RegulomesStanford UniversityStanfordUSA

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