Distinctive Interactomes of RNA polymerase II phosphorylation during different stages of transcription

We have discovered distinctive protein interactomes for Ser2 and Ser5 phosphorylation of the C-terminal domain (CTD) of RNA Pol II. Calcium Homeostasis Endoplasmic reticulum (CHERP) was identified in our pulldown to directly interact with Ser2 phosphomarks on the CTD of Pol II. As Pol II is a chromatin-associated protein, we sought to identify genomic regions that CHERP, a Pol II binding protein, occupy through ChIP-seq analysis. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for HA-tagged CHERP in WT HEK293 cells and for HA-tagged CHERP in HEK293 cells that have decreased levels of Ser2 phosphorylation on the C-terminal domain of Pol II.