Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1214217 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32076759_1.fastq.gz | Fastqsanger.gz | |||
| SRR32076759_2.fastq.gz | Fastqsanger.gz |
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Project description: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 genetic perturbation demonstrated that these transcripts were translationally repressed by PBs. Next, integration of PB-TRIBE-STAMP with long-read sequencing revealed that the PB-associated transcripts possessed shorter poly(A)-tails. 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 sc-LSM14A-TRIBE-ID, we demonstrated the dynamic pattern of mRNA-PB interaction during cell cycle progression.
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