Chromatin immunoprecipitation approaches to determine co-transcriptional nature of splicing

Chromatin immunoprecipitation (ChIP) is a common method used to determine the position along DNA where an antigen is found. The method was initially devised for protein antigens that come in direct contact with genomic DNA, such as components of the transcriptional machinery and histones. However, ChIP can also be extended to antigens that bind RNA, as demonstrated by the specific localization of spliceosomal components to particular gene regions that correlate with when and where introns and exons are transcribed. The activities of any RNA binding protein can in principle be monitored using ChIP, and RNA dependency of binding can also be assessed through RNase treatment. Combined with qPCR or high-throughput sequencing, this method allows the detection of RNA bound proteins at individual genes or genome-wide. Here, we present a detailed protocol for "splicing factor ChIP" in tissue culture cells.