ArticleMethods (San Diego, Calif.)2017
Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS).
Article in Methods (San Diego, Calif.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- CisBP-RNA: a web resource for eukaryotic RNA-binding proteins and their motifs.Nucleic acids research · 2026Article
- caRBP-Pred: Leveraging Protein Language Models for the Prediction of Chromatin-Associated RNA-Binding Proteins.Computational and structural biotechnology journal · 2026Article
- Deaminase-based RNA recording enables high throughput mutational profiling of protein-RNA interactions.bioRxiv : the preprint server for biology · 2025Article
- PRIESSTESS: interpretable, high-performing models of the sequence and structure preferences of RNA-binding proteins.Nucleic acids research · 2022Article
- Generative and interpretable machine learning for aptamer design and analysis of in vitro sequence selection.PLoS computational biology · 2022Article
- Methods for the directed evolution of biomolecular interactions.Trends in biochemical sciences · 2022Review
- Expanding the binding specificity for RNA recognition by a PUF domain.Nature communications · 2021Article
- Principles of mRNA control by human PUM proteins elucidated from multimodal experiments and integrative data analysis.RNA (New York, N.Y.) · 2020Article
- High throughput approaches to study RNA-protein interactions in vitro.Methods (San Diego, Calif.) · 2020Review
- Molecular entrapment by RNA: an emerging tool for disrupting protein-RNA interactionsRNA biology · 2020Article
- Unique repression domains of Pumilio utilize deadenylation and decapping factors to accelerate destruction of target mRNAs.Nucleic acids research · 2020Article
- Linking RNA Sequence, Structure, and Function on Massively Parallel High-Throughput Sequencers.Cold Spring Harbor perspectives in biology · 2019Review
- Article
- The target specificity of the RNA binding protein Pumilio is determined by distinct co-factors.Bioscience reports · 2019Article
- Preparation of cooperative RNA recognition complexes for crystallographic structural studies.Methods in enzymology · 2019Article
- Global pairwise RNA interaction landscapes reveal core features of protein recognition.Nature communications · 2018Article
- Inhibition of Poly(A)-binding protein with a synthetic RNA mimic reduces pain sensitization in mice.Nature communications · 2018Article
- Combinatorial control of messenger RNAs by Pumilio, Nanos and Brain Tumor Proteins.RNA biology · 2017Article
- The contribution of the C5 protein subunit ofRNA (New York, N.Y.) · 2017Article
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Authors and funding
6 authors.
Funding
Abstract
RNA-binding proteins (RBPs) collaborate to control virtually every aspect of RNA function. Tremendous progress has been made in the area of global assessment of RBP specificity using next-generation sequencing approaches both in vivo and in vitro. Understanding how protein-protein interactions enable precise combinatorial regulation of RNA remains a significant problem. Addressing this challenge requires tools that can quantitatively determine the specificities of both individual proteins and multimeric complexes in an unbiased and comprehensive way. One approach utilizes in vitro selection, high-throughput sequencing, and sequence-specificity landscapes (SEQRS). We outline a SEQRS experiment focused on obtaining the specificity of a multi-protein complex between Drosophila RBPs Pumilio (Pum) and Nanos (Nos). We discuss the necessary controls in this type of experiment and examine how the resulting data can be complemented with structural and cell-based reporter assays. Additionally, SEQRS data can be integrated with functional genomics data to uncover biological function. Finally, we propose extensions of the technique that will enhance our understanding of multi-protein regulatory complexes assembled onto RNA.
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Registered trials
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