ArticleNature communications2023
PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing.
Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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Who cites it
5 citing papers in PubMed, 7 citations in OpenAlex.
- Systematic characterization of the composition and dynamics of processing body-associated mRNAs.Nature communications · 2025Article
- Sequencing technologies to measure translation in single cells.Nature reviews. Molecular cell biology · 2025Review
- Harnessing RNA base editing for diverse applications in RNA biology and RNA therapeutics.Advanced biotechnology · 2025Review
- Infernape uncovers cell type-specific and spatially resolved alternative polyadenylation in the brain.Genome research · 2023Article
- Revealing the hidden RBP-RNA interactions with RNA modification enzyme-based strategies.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
3 authors at 1 institution in 2 countries.
Funding
Abstract
RNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. We benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.