Binding factors of RNAPII isolated from the HeLa cell nuclei

RNA polymerase II (RNAPII) is a major transcription protein that transcribes the genomic DNA packaged into chromatin. To reveal the RNAPII structures during transcription in the human genome, we extracted the RNAPII molecules inside the HeLa cell nuclei and determined the structures of transcribing RNAPII molecules associated with/without the transcription elongation factors and nucleosome. Our LC-MS/MS analysis revealed that the preinitiation complex components, such as Mediator, TFIIH, and TFIID, the elongation complex subunits, such as SPT4/5, SPT6, and ELOF1, and histones exist in the immunopurified fraction of RNAPII from HeLa cell nuclei.