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It is now estimated that the human genome encodes thousands of long noncoding (lnc)RNAs. These novel molecules are causing a paradigm shift in the field of molecular biology as a number of lncRNAs have been shown to be involved in a wide range of biological functions including regulation of gene expression. Also, misregulation of lncRNAs has been observed in human diseases such as cancer and neurological disorders. These findings have spurred a huge interest in elucidating the functions and mechanisms of lncRNAs; and therefore, the need for new methods to do so. In this chapter, we discuss RIP-Seq, a method that is utilized to discover the lncRNA partners of a specific protein. This procedure involves immunoprecipitation of a protein from cross-linked cell lysate followed by reverse-cross-linking, isolation, and deep sequencing of RNAs, leading to the identification of all lncRNAs that are associated with a specific protein complex.


Victoria A Moran, Courtney N Niland, Ahmad M Khalil. Co-Immunoprecipitation of long noncoding RNAs. Methods in molecular biology (Clifton, N.J.). 2012;925:219-28

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PMID: 22907501

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