Massively Parallel Dissection of RNA in RNA-protein interactions in vivo
Hass, E. P.; Lee, Y. H.; Campodonico, W.; Lee, Y. K.; Lasda, E.; Shah, J. S.; Rinn, J.; Hwang, T.
Show abstract
Many of the biological functions performed by RNA are mediated by RNA-binding proteins (RBPs), and understanding the molecular basis of these interactions is fundamental to molecular biology. Here, we present MPRNA-immunoprecipitation (MPRNA-IP), an adaptation of the previously developed massively parallel RNA assay (MPRNA), and a new avenue for in vivo high-throughput dissection of RNA-protein interactions. By using custom pools of tens of thousands of RNA sequences containing systematically designed truncations and mutations, we are able to identify RNA domains, sequences, and secondary structures necessary and sufficient for protein binding in a single experiment. We show that this approach is successful for multiple RNAs of interest including NORAD, MS2, and human telomerase RNA, and we describe statistical models for identifying RNA domains and parsing the structural contributions of RNA in these interactions. By blending modern and classical approaches, MPRNA-IP provides a novel high-throughput way to elucidate RNA-based mechanisms behind RNA-protein interactions.
Matching journals
The top 5 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Learning cis-regulatory principles of ADAR-based RNA editing from CRISPR-mediated mutagenesis 97%
- Expanded palette of RNA base editors for comprehensive RBP-RNA interactome studies 97%
- Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct and long-read sequencing 97%
Similar papers in this journal
- ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing 97%
- DeepCLIP: Predicting the effect of mutations on protein-RNA binding with Deep Learning 96%
- New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity 96%
Similar papers in this journal
Similar papers in this journal
- Functional classification of noncoding RNAs associated with distinct histone modifications by PIRCh-seq 95%
- ZetaSuite, A Computational Method for Analyzing Multi-dimensional High-throughput Data, Reveals Genes with Opposite Roles in Cancer Dependency 94%
- Mapping snoRNA-target RNA interactions in an RNA binding protein-dependent manner with chimeric eCLIP 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.