Dec 1, 2023 · We present a new method, TargetRNA3, for predicting targets of small RNA regulators and show that it outperforms existing approaches. TargetRNA3 is available at https://cs.wellesley.edu/~btjaden/TargetRNA3. Small regulatory RNAs (sRNAs) are widespread in …

Feb 28, 2023 · Regulation of porin expression in bacteria is complex and often involves small-RNA regulators. Several small-RNA regulators have been described for Burkholderia cenocepacia, and this study aimed to characterize the biological role of the conserved small RNA NcS25 and its cognate target, outer membrane protein BCAL3473.

In bacteria and archaea, small RNAs (sRNAs) regulate complex networks through antisense interactions with target mRNAs in trans, and riboswitches regulate gene expression in cis based on the ability to bind small-molecule ligands.

Two decades after the first genome-wide screens showed small RNAs (sRNAs) to be a widespread feature of bacterial genomes, these short noncoding transcripts remain enigmatic. High-throughput RNA sequencing (RNA-seq)-based approaches now routinely find hundreds of potential sRNAs in any bacterium examined (1).

Jan 7, 2025 · RNA-free Arabidopsis AGO1 interacts with the autophagy cargo receptor ATI1 by direct contact with specific N-coil amino acid residues whose mutation reduces the degradation rate of RNA-free...

We focus on two case studies (1) sRNA-mRNA annealing with Hfq protein and (2) structural rearrangements within an mRNA upon sRNA binding. These protocols can be easily adapted for studying other systems.

Mar 22, 2018 · We have developed a method, termed target-enrichment of sRNAs (TEsR), that enables targeted sequencing of rare sRNAs and diverse precursor and mature forms of sRNAs not detectable by current...

May 6, 2015 · Here, we provide a simple benchmark for bacterial sRNA target prediction based on trusted E. coli sRNA/target pairs. We use this benchmark to assess the most recent RNA target predictors as well as earlier programs for RNA-RNA hybrid prediction.

Feb 20, 2012 · We successfully applied INTARNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs....

May 4, 2022 · Hundreds of bacterial small RNAs (sRNAs) require the Hfq chaperone to regulate mRNA expression. Hfq is limiting, thus competition among sRNAs for binding to Hfq shapes the proteomes of individual...