Systematic characterization of the composition and dynamics of processing body-associated mRNAs [dataset 3]

Processing bodies (PBs) are dynamic, membraneless organelles consisting of RNAs and proteins. While PB proteins have been extensively characterized, the methods for systematically profiling PB-associated RNAs are limited. To address this, we developed PB-TRIBE-STAMP, a new tool based on two orthogonal RNA editing enzymes. Simultaneously applying APOBEC1-DDX6 and LSM14A-ADAR2dd, PB-TRIBE-STAMP identified 1,639 and 2,577 PB-associated mRNAs in HCT116 and HEK293T cells, respectively. Further biochemical isolation of PBs followed by RNA-seq validated that edited transcripts of these mRNAs were indeed enriched in PBs. Integration of PB-TRIBE-STAMP with long-read sequencing revealed that the PB-associated transcripts possessed shorter poly(A)-tails and mRNA isoforms with longer 3' UTRs were more likely to be associated with PBs than those with shorter ones. Moreover, we established a TRIBE-ID-based tool to characterize the mRNA-PB association at high temporal resolution and unveiled a higher splicing efficiency of PB-associated XBP1 transcripts during unfolded protein response (UPR). Finally, based on single-cell LSM14A-TRIBE-ID (sc-LSM14A-TRIBE-ID), we demonstrated the dynamic pattern of mRNA-PB association during cell cycle progression. Overall design: To identify PB-associated mRNAs and investigate the PB-mediated RNA regulation, we established STAMP, HyperTRIBE, PB-TRIBE-STAMP, LSM14A-TRIBE-ID, and DDX6-KO cells. We then performed mRNA-seq, ONT long-read sequencing, and polysome-seq.