Genome-wide mapping of UPF1 and Pol II [ChIP-seq]

ChIP with NMD core componenet UPF1 antibody in normal S2 cells and ChIP with Pol II Ser2 antibodies in S2 cells. UPF1 is an ATP-driven RNA helicase required for efficient nonsense mediated mRNA decay in eukaryotes. Although it is currently understood that UPF1 primarily acts on the 3’UTR of translating mRNAs in the cytoplasm, our data indicates that this is a highly dynamic protein that is rapidly shuttling between nucleus and cytoplasm in Drosophila. Additionally, ChIP-seq analysis in different cell types demonstrates genome-wide association of UPF1 with nascent RNAs at most of the active Pol II transcription sites, and at some specific Pol III genes. Notably, intron recognition appears to interfere with association and translocation of UPF1 on nascent transcripts. Cells depleted of UPF1 show defects in nuclear processes such as mRNA export and transcription site retention. These data, thus redefine UPF1 as a global player in mRNA based processes in the nucleus as well as the cytoplasm. To examine the presence of UPF1 RNA helicase on chromosomes, replicates of UPF1 ChIP DNA were sequenced by using Illumina HiSeq4000. Input was sequenced as ChIP control. Role of UPF1 in transcription regulation was examined by Pol II Ser2 or Pol II ChIP in control and UPF1 depleted cells. All the experiments were done using Drosophila embryonic S2 cells.