Endo-bind-n-seq: identifying RNA motifs of RNA binding proteins isolated from endogenous sources.

ABSTRACT: RNA binding proteins (RBPs) are crucial regulators of gene expression and critically depend on the specific recognition of their target RNAs. Accordingly, a selection of methods to analyze RBP specificities has been developed, including protein-RNA crosslinking and sequencing (CLIP) and in vitro selection methods such as SELEX, RNA compete or RNA bind-n-seq. However, limitations like the availability for purified recombinant proteins and custom microarray platforms (RNAcompete) or extensive sequencing depth and sophisticated bioinformatic data processing (CLIP) may limit a broader implementation of these methods. Here, we present an RNA bind-n-seq method that uses short random RNA pools and enables multiple rounds of selection. This results in strong motif enrichment with low positional va

SUBMITTER: Hanelt TN 

PROVIDER: S-EPMC11612968 | biostudies-literature | 2025 Feb

REPOSITORIES: biostudies-literature