Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human andDrosophilacells
Open Access
- 11 May 2023
- journal article
- research article
- Published by Cold Spring Harbor Laboratory in RNA
- Vol. 29 (8), 1230-1242
- https://doi.org/10.1261/rna.079608.123
Abstract
RNA binding proteins (RBPs) perform a myriad of functions and are implicated in numerous neurological diseases. To identify the targets of RBPs in small numbers of cells, we developed TRIBE, in which the catalytic domain of the RNA editing enzyme ADAR (ADARcd) is fused to a RBP. When the RBP binds to a mRNA, ADAR catalyzes A to G modifications in the target mRNA that can be easily identified in standard RNA-sequencing. In STAMP, the concept is the same except the ADARcd is replaced by the RNA editing enzyme APOBEC. Here we compared TRIBE and STAMP side-by-side in human and Drosophila cells. The goal is to learn the pros and cons of each method so that researchers can choose the method best suited to their RBP and system. In human cells, TRIBE and STAMP were performed using the RBP TDP-43. Although they both identified TDP-43 target mRNAs, combining the two methods more successfully identified high confidence targets. In Drosophila cells, RBP-APOBEC fusions generated only low numbers of editing sites, comparable to the level of control editing. This was true for two different RBPs, Hrp48 and Thor (Drosophila EIF4E-BP), indicating that STAMP does not work well in Drosophila.Keywords
Funding Information
- Howard Hughes Medical Institute
- NIH (R01 (DA037721))
This publication has 54 references indexed in Scilit:
- Mechanistic insights into editing-site specificity of ADARsProceedings of the National Academy of Sciences of the United States of America, 2012
- STAR: ultrafast universal RNA-seq alignerBioinformatics, 2012
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and explorationBriefings in Bioinformatics, 2012
- Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43Nature Neuroscience, 2011
- Characterizing the RNA targets and position-dependent splicing regulation by TDP-43Nature Neuroscience, 2011
- Transcriptome-wide sequencing reveals numerous APOBEC1 mRNA-editing targets in transcript 3′ UTRsNature Structural & Molecular Biology, 2011
- Integrative genomics viewerNature Biotechnology, 2011
- TDP-43 regulates its mRNA levels through a negative feedback loopThe EMBO Journal, 2010
- RNA Processing and ExportCold Spring Harbor Perspectives in Biology, 2010
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression dataBioinformatics, 2009