
Annotating RNA motifs in sequences and alignments
Dec 17, 2014 · We present a bioinformatic approach to characterize RNA motifs, which are critical components of many RNA structure–function relationships. These motifs can, in some instances, provide researchers with functional hypotheses for uncharacterized RNAs.
Global Mapping of Small RNA-Target Interactions in Bacteria
Sep 1, 2016 · Small RNAs (sRNAs) associated with the RNA chaperon protein Hfq are key posttranscriptional regulators of gene expression in bacteria. Deciphering the sRNA-target interactome is an essential step toward understanding the roles of sRNAs in the cellular networks.
A comparative study of sequence- and structure-based features of …
Nov 13, 2017 · Here, we present a statistical analysis of different sequence- and structure-related features of bacterial sRNAs to identify the descriptors that could discriminate sRNAs from other bacterial RNAs.
RNA motif - Wikipedia
An RNA motif is a description of a group of RNAs that have a related structure. RNA motifs consist of a pattern of features within the primary sequence and secondary structure of related RNAs. Thus, it extends the concept of a sequence motif to include RNA secondary structure.
RNA motif discovery: a computational overview - PMC
Here, we give a detailed review of the various computational techniques proposed in literature attempting to solve this general motif discovery problem. We also give empirical comparisons of some of the current state of the art methods and point out future directions of research.
Hfq CLASH uncovers sRNA-target interaction networks linked to …
May 1, 2020 · We demonstrate that Hfq CLASH robustly captures bona fide RNA-RNA interactions. We identified hundreds of novel sRNA base-pairing interactions, including many sRNA-sRNA interactions and involving 3’UTR-derived sRNAs. We rediscovered known and identified novel sRNA seed sequences.
Positional Effects of AAN Motifs in rpoS Regulation by sRNAs and …
Jan 23, 2014 · The AAN motif in rpoS mRNA is ≥ 60 nt upstream of the sRNA binding site. These examples suggest that sequence elements within each mRNA may fine-tune interactions between Hfq and the sRNA target region, potentially influencing the regulatory outcome.
A conserved RNA seed‐pairing domain directs small …
Aug 8, 2019 · Small regulatory RNAs (sRNAs) are crucial components of many stress response systems. The envelope stress response (ESR) of Gram‐negative bacteria is a paradigm for sRNA‐mediated stress management and involves, among other factors, the alternative sigma factor E (σ E) and one or more sRNAs.
Kink turn sRNA folding upon L7Ae binding using molecular
Nov 14, 2013 · The kink-turn sRNA motif in archaea, whose combination with protein L7Ae initializes the assembly of small ribonucleoprotein particles (sRNPs), plays a key role in ribosome maturation and the translation process.
Small RNAs and Hfq capture unfolded RNA target sites during ...
May 4, 2023 · Small ribonucleoproteins (sRNPs) target nascent precursor RNAs to guide folding, modification, and splicing during transcription. Yet, rapid co-transcriptional folding of the RNA can mask sRNP sites, impeding target recognition and regulation.