RAP-RNA: A Methodological Approach to Study Base-Pairing Between Endogenous RNAs.

RISC-bound small RNA sequencing provides insights into guide-strand selection and siRNA trimming and tailing following insecticidal dsRNA delivery

RNA interference (RNAi) offers a sequence-specific approach to pest control. In insects, Dicer-2 processes double-stranded RNA (dsRNA) into small interfering RNA (siRNA) duplexes, from which the RNA-induced silencing complex (RISC) retains a guide strand. However, how the sequence of delivered dsRNA shapes the RISC-bou...

Knocking Down Long Noncoding RNAs Using Antisense Oligonucleotide Gapmers.

Detection of Long Non-Coding RNA Localization by RNA Fluorescence In Situ Hybridization (FISH).

This work presents a robust RNA FISH protocol for detecting the lncRNA Xist, a chromatin-associated master regulator of X chromosome inactivation (XCI) that serves as a paradigm for lncRNA biology and demonstrates the effectiveness of this method for investigating lncRNA localization and chromatin-associated function.

Complementary Approaches for Accurate Detection of tRNA-Derived Small RNAs (tsRNAs): Small RNA Northern Blotting and Dumbbell PCR.

Two complementary methods for tsRNA validation are presented, small RNA northern blotting, which allows direct visualization of RNA size and abundance, and dumbbell PCR, which enables isoform-specific quantification with single-nucleotide resolution, which provide robust tools to validate tsRNA expression and facilitat...

Identification of RNA Targets of Classical and Non-Canonical RNA-binding Proteins by soniCLIP

By combining reduced input requirements, high reproducibility, a shortened 3.5-day workflow and the elimination of gel-based purification, soniCLIP provides an efficient and robust approach for the identification of RNA targets of canonical and non-canonical RBPs.

LncRNA Knockdown Using Gapmer Antisense Oligonucleotides.