Prevalence of small base-pairing RNAs derived from diverse genomic loci

PP Adams, G Storz - Biochimica Et Biophysica Acta (BBA)-Gene …, 2020 - Elsevier
Small RNAs (sRNAs) that act by base-pairing have been shown to play important roles in
fine-tuning the levels and translation of their target transcripts across a variety of model and …

Physical and functional analysis of viral RNA genomes by SHAPE

MA Boerneke, JE Ehrhardt… - Annual review of …, 2019 - annualreviews.org
RNA viruses encode the information required to usurp cellular metabolism and gene
regulation and to enable their own replication in two ways: in the linear sequence of their …

Using SHAPE-MaP to model RNA secondary structure and identify 3′ UTR variation in Chikungunya virus

EA Madden, KS Plante, CR Morrison… - Journal of …, 2020 - Am Soc Microbiol
Chikungunya virus (CHIKV) is a mosquito-borne alphavirus associated with debilitating
arthralgia in humans. RNA secondary structure in the viral genome plays an important role …

Structural divergence creates new functional features in alphavirus genomes

KM Kutchko, EA Madden, C Morrison… - Nucleic acids …, 2018 - academic.oup.com
Alphaviruses are mosquito-borne pathogens that cause human diseases ranging from
debilitating arthritis to lethal encephalitis. Studies with Sindbis virus (SINV), which causes …

Structural and functional annotation of long noncoding RNAs

MA Smith, JS Mattick - Bioinformatics: Volume II: Structure, Function, and …, 2017 - Springer
Protein-coding RNAs represent only a small fraction of the transcriptional output in higher
eukaryotes. The remaining RNA species encompass a broad range of molecular functions …

T1TAdb: the database of type I toxin–antitoxin systems

NJ Tourasse, F Darfeuille - Rna, 2021 - rnajournal.cshlp.org
Type I toxin–antitoxin (T1TA) systems constitute a large class of genetic modules with
antisense RNA (asRNA)-mediated regulation of gene expression. They are widespread in …

Adaptive evolution at mRNA editing sites in soft-bodied cephalopods

M Moldovan, Z Chervontseva, G Bazykin, MS Gelfand - PeerJ, 2020 - peerj.com
Background The bulk of variability in mRNA sequence arises due to mutation—change in
DNA sequence which is heritable if it occurs in the germline. However, variation in mRNA …

ORFans in Mitochondrial Genomes of Marine Polychaete Polydora

M Selifanova, O Demianchenko… - Genome Biology and …, 2023 - academic.oup.com
Most characterized metazoan mitochondrial genomes are compact and encode a small set
of proteins that are essential for oxidative phosphorylation, as well as rRNA and tRNA for …

Role of pre-mRNA secondary structures in the regulation of alternative splicing

PM Rubtsov - Molecular Biology, 2016 - Springer
Alternative splicing of pre-mRNA is one of the main mechanisms regulating gene expression
that generates multiple transcripts from one gene. The review considers the specific role that …

Conserved RNA structures in the intergenic regions of ambisense viruses

M Kiening, F Weber, D Frishman - Scientific Reports, 2017 - nature.com
Ambisense viruses are negative-sense single-stranded RNA viruses that use a unique
expression strategy. Their genome contains at least one ambisense RNA segment that …