BioProject

We report transcripts of which stabilities are regulated by human Pumilio proteins (PUM). More...

We report transcripts of which stabilities are regulated by human Pumilio proteins (PUM). PUM is an RNA-binding protein that binds specifically to 5'-UGUAHAUA-3' sequence and is a degradation factor of cytoplasmic mRNA by recruiting CCR4-NOT deadenylase. Although many RIP-seq, RIP-chip, CLIP-seq identified mRNAs bound to PUM, we still do not know which mRNAs are degraded by PUM. Here we identify bona-fide target mRNAs of PUM in a human cell line. Bona-fide targets of the RBP are defined by two criteria. One criterion is mRNAs bound to the PUM, which are determined by RNA immunoprecipitation sequencing (RIP-seq). The other criterion is mRNAs degraded by the PUM, which are determined by 5'-bromo-uridine (BrU) immunoprecipitation chase-deep sequencing analysis (BRIC-seq). BRIC-seq enables the determination of genome-wide RNA stability by chasing chronological decreases of BrU-labeled RNAs under physiologically non-disturbed condition. An RNA half-life of each transcript is calculated from the decreasing BrU-labeled RNA. By comparing the RNA half-lives between in normal cells and in the PUM KD cells, we can identify mRNA of which stability is regulated by the PUM. Merging the results of RIP-seq and BRIC-seq will yield the bona-fide targets of the PUM. Less...