Nascent RNA and Poly(A) RNA Seq from S2 cells [RNA-seq]

Nascent RNA and Poly(A) RNA Seq from 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. Overall design: Nascent RNA were isolated from Histone-DNA-Pol II-RNA fraction of S2 cells and poly(A) RNA were isolated from cytoplasmic fraction of S2 Cells. Sequencing was performed using sequenced by using Illumina HiSeq4000.