Source 1primary paper2025MED
Toolkit/PB-TRIBE-STAMP
PB-TRIBE-STAMP
Taxonomy: Mechanism Branch / Architecture. Workflows sit above the mechanism and technique branches rather than replacing them.
Summary
we developed PB-TRIBE-STAMP, a tool based on two orthogonal RNA editing enzymes
Usefulness & Problems
No literature-backed usefulness or problem-fit explainer has been materialized for this record yet.
Published Workflows
Systematic characterization of the composition and dynamics of processing body-associated mRNAs.
2025Objective: Systematically characterize the composition and dynamics of processing body-associated mRNAs using orthogonal RNA editing-based profiling and orthogonal sequencing validation.
Why it works: The workflow uses two orthogonal RNA editing enzyme fusions to identify PB-associated mRNAs and then applies orthogonal sequencing-based analyses to validate enrichment and characterize transcript features and dynamics.
orthogonal RNA editing to mark PB-associated transcriptsLSM14A/PB association dynamicsdual RNA editing-based profilingbiochemical isolation followed by RNA-seqlong-read sequencingsingle-cell RNA editing-based profiling
Stages
- 1.PB-TRIBE-STAMP profiling(broad_screen)
To systematically identify PB-associated mRNAs in cell lines using orthogonal RNA editing enzymes.
Selection: Edited transcripts detected after simultaneous application of APOBEC1-DDX6 and LSM14A-ADAR2dd were used to identify PB-associated mRNAs.
- 2.Biochemical PB isolation and RNA-seq validation(confirmatory_validation)
To orthogonally validate that edited transcripts identified by PB-TRIBE-STAMP are enriched in PBs.
Selection: Enrichment of edited transcripts in biochemically isolated PBs.
- 3.Long-read sequencing characterization(secondary_characterization)
To characterize transcript features of PB-associated RNAs beyond initial identification.
Selection: Long-read sequencing analysis of PB-associated transcripts.
- 4.Temporal LSM14A-TRIBE-ID analysis(functional_characterization)
To resolve mRNA-LSM14A/PB association at high temporal resolution.
Selection: TRIBE-ID-based temporal characterization of mRNA-LSM14A/PB association.
- 5.Single-cell dynamic analysis(secondary_characterization)
To examine dynamic mRNA-LSM14A/PB association during cell cycle progression at single-cell resolution.
Selection: Single-cell LSM14A-TRIBE-ID analysis across cell-cycle progression.
Taxonomy & Function
Primary hierarchy
Mechanism Branch
Architecture: A composed arrangement of multiple parts that instantiates one or more mechanisms.
Techniques
Sequence VerificationTarget processes
editingInput: Chemical
Validation
Cell-freeBacteriaMammalianMouseHumanTherapeuticIndep. Replication
Supporting Sources
Ranked Claims
LSM14A-associated XBP1 transcripts showed higher splicing efficiency during unfolded protein response.
unveiled a higher splicing efficiency of LSM14A-associated XBP1 transcripts during unfolded protein response (UPR)
PB-TRIBE-STAMP identified 1639 PB-associated mRNAs in HCT116 cells and 2577 PB-associated mRNAs in HEK293T cells.
PB-TRIBE-STAMP identified 1,639 and 2,577 PB-associated mRNAs in HCT116 and HEK293T cells, respectively.
PB-associated mRNAs identified in HCT116 1639PB-associated mRNAs identified in HEK293T 2577
Many mRNA 3' UTR isoforms exhibited isoform-specific processing body association patterns.
Many mRNA 3' UTR isoforms exhibited isoform-specific PB association patterns.
Biochemical isolation of processing bodies followed by RNA-seq validated that edited transcripts of PB-TRIBE-STAMP-identified mRNAs were enriched in processing bodies.
Further biochemical isolation of PBs followed by RNA-seq validated that edited transcripts of these mRNAs were indeed enriched in PBs.
sc-LSM14A-TRIBE-ID demonstrated a dynamic pattern of mRNA-LSM14A/processing body association during cell cycle progression.
based on single-cell LSM14A-TRIBE-ID (sc-LSM14A-TRIBE-ID), we demonstrated the dynamic pattern of mRNA-LSM14A/PB association during cell cycle progression.
The study developed PB-TRIBE-STAMP as a tool based on two orthogonal RNA editing enzymes for systematic profiling of processing body-associated RNAs.
To address this, we developed PB-TRIBE-STAMP, a tool based on two orthogonal RNA editing enzymes.
The study established an LSM14A-TRIBE-ID-based tool to characterize mRNA-LSM14A/processing body association at high temporal resolution.
we established a TRIBE-ID-based tool to characterize the mRNA-LSM14A/PB association at high temporal resolution
Integration of PB-TRIBE-STAMP with long-read sequencing revealed that PB-associated transcripts had shorter poly(A) tails.
Integration of PB-TRIBE-STAMP with long-read sequencing revealed that the PB-associated transcripts possessed shorter poly(A)-tails.
Approval Evidence
1 source5 linked approval claimsfirst-pass slug pb-tribe-stamp
we developed PB-TRIBE-STAMP, a tool based on two orthogonal RNA editing enzymes
Source:
identification resultsupports
PB-TRIBE-STAMP identified 1639 PB-associated mRNAs in HCT116 cells and 2577 PB-associated mRNAs in HEK293T cells.
PB-TRIBE-STAMP identified 1,639 and 2,577 PB-associated mRNAs in HCT116 and HEK293T cells, respectively.
Source:
isoform specificitysupports
Many mRNA 3' UTR isoforms exhibited isoform-specific processing body association patterns.
Many mRNA 3' UTR isoforms exhibited isoform-specific PB association patterns.
Source:
orthogonal validationsupports
Biochemical isolation of processing bodies followed by RNA-seq validated that edited transcripts of PB-TRIBE-STAMP-identified mRNAs were enriched in processing bodies.
Further biochemical isolation of PBs followed by RNA-seq validated that edited transcripts of these mRNAs were indeed enriched in PBs.
Source:
tool developmentsupports
The study developed PB-TRIBE-STAMP as a tool based on two orthogonal RNA editing enzymes for systematic profiling of processing body-associated RNAs.
To address this, we developed PB-TRIBE-STAMP, a tool based on two orthogonal RNA editing enzymes.
Source:
transcript feature associationsupports
Integration of PB-TRIBE-STAMP with long-read sequencing revealed that PB-associated transcripts had shorter poly(A) tails.
Integration of PB-TRIBE-STAMP with long-read sequencing revealed that the PB-associated transcripts possessed shorter poly(A)-tails.
Source:
Comparisons
No literature-backed comparison notes have been materialized for this record yet.
Ranked Citations
- 1.