I am planning to do RNA-ChIP (chromatin immunoprecipitation) recently. Here I have a question about the sonication condition. For the conventional ChIP, sonication could break DNA and the protein binding site on the chromatin could be precisely mapped. Will the RNA be effectively cleaved under the same sonication condition as ChIP, or the RNA need further fragmentation? Surprisingly I read one paper published on Mol.Cel.Bio. 2008 Sep;28(18):5811-24. In this paper, the author suggested that the Pol II associated RNA is not fragmented by sonication as showed in Fig S4.. What do you think? Is that possible the crosslinked RNA is still kept intact after sonication? If it is true, then why and how? Is that because the mRNP formed in the nascent RNA could protect it from breaking? Any suggestion or idea would be greatly appreciated!
Does sonication break down RNA in RNA-ChIP
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