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View article: The <scp>RNA</scp> ‐Puzzles Assessments of <scp>RNA</scp> ‐Only Targets in <scp>CASP16</scp>
The <span>RNA</span> ‐Puzzles Assessments of <span>RNA</span> ‐Only Targets in <span>CASP16</span> Open
RNA‐Puzzles was launched in 2011 as a collaborative effort dedicated to advancing and improving RNA 3D structure prediction. The automatic evaluation protocols for comparisons between prediction and experiment developed within RNA‐Puzzles …
View article: <i>Doublesex</i> gene in <i>Bombyx mori</i>: <scp>CRISPR</scp>‐mediated female‐to‐male sex reversal through exon skipping
<i>Doublesex</i> gene in <i>Bombyx mori</i>: <span>CRISPR</span>‐mediated female‐to‐male sex reversal through exon skipping Open
BACKGROUND Sex control technology has great potential to improve the efficiency of economic insect utilization and integrated pest management by enabling targeted population suppression or elimination. The silkworm ( Bombyx mori ), a lepid…
View article: The Biology of tRNA t6A Modification and Hypermodifications—Biogenesis and Disease Relevance
The Biology of tRNA t6A Modification and Hypermodifications—Biogenesis and Disease Relevance Open
The structure and function of transfer RNAs (tRNAs) are highly dependent on post-transcriptional chemical modifications that attach distinct chemical groups to various nucleobase atoms at selected tRNA positions via enzymatic reactions. In…
View article: RNA-Puzzles Round V: blind predictions of 23 RNA structures
RNA-Puzzles Round V: blind predictions of 23 RNA structures Open
RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication …
View article: Multiple independent origins of the female W chromosome in moths and butterflies
Multiple independent origins of the female W chromosome in moths and butterflies Open
Lepidoptera, the most diverse group of insects, exhibit female heterogamy (Z0 or ZW), which is different from most other insects (male heterogamy, XY). Previous studies suggest a single origin of the Z chromosome. However, the origin of th…
View article: RNA Dynamics from Experimental and Computational Approaches
RNA Dynamics from Experimental and Computational Approaches Open
Ribonucleic acids (RNA) are unique in that they can store genetic information, replicate and perform catalysis. Importantly, RNA molecules are highly dynamic, and thus determining the ensemble of conformations that they populate is crucial…
View article: Marc van Regenmortel, personal recollections on a forward‐thinking editor
Marc van Regenmortel, personal recollections on a forward‐thinking editor Open
Marc van Regenmortel was the Editor‐in‐Chief of the Journal of Molecular Recognition for the last 25 years. Without attempting to summarize Marc's exceptional career and achievements, we would like to tell the story of the tortuous and con…
View article: Contribution of tRNA sequence and modifications to the decoding preferences of <i>E. coli</i> and <i>M. mycoides</i> tRNAGlyUCC for synonymous glycine codons
Contribution of tRNA sequence and modifications to the decoding preferences of <i>E. coli</i> and <i>M. mycoides</i> tRNAGlyUCC for synonymous glycine codons Open
tRNA superwobbling, used by certain bacteria and organelles, is an intriguing decoding concept in which a single tRNA isoacceptor is used to decode all synonymous codons of a four-fold degenerate codon box. While Escherichia coli relies on…
View article: SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data
SilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data Open
The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic divers…
View article: Assessment of three‐dimensional RNA structure prediction in CASP15
Assessment of three‐dimensional RNA structure prediction in CASP15 Open
The prediction of RNA three‐dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first CASP exercise that involved RNA structure modeling. Forty‐two predictor groups su…
View article: SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome
SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome Open
In severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the non-structural protein NSP1 inhibits translation of host mRNAs by binding to the mRNA entry channel of the ribosome and, together with the 5′-untranslated region (UTR) of…
View article: Assessment of three-dimensional RNA structure prediction in CASP15
Assessment of three-dimensional RNA structure prediction in CASP15 Open
The prediction of RNA three-dimensional structures remains an unsolved problem. Here, we report assessments of RNA structure predictions in CASP15, the first CASP exercise that involved RNA structure modeling. Forty two predictor groups su…
View article: Anionic G•U pairs in bacterial ribosomal rRNAs
Anionic G•U pairs in bacterial ribosomal rRNAs Open
Wobble GU pairs (or G•U) occur frequently within double-stranded RNA helices interspersed between standard G=C and A-U Watson–Crick pairs. Another type of G•U pair interacting via their Watson–Crick edges has been observed in the A site of…
View article: Identification of U<sup>p</sup>47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium
Identification of U<sup>p</sup>47 in three thermophilic archaea, one mesophilic archaeon, and one hyperthermophilic bacterium Open
Analysis of the profile of the tRNA modifications in several Archaea allowed us to observe a novel modified uridine in the V-loop of several tRNAs from two species: Pyrococcus furiosus and Sulfolobus acidocaldarius . Recently, Ohira and co…
View article: Brief considerations on targeting RNA with small molecules
Brief considerations on targeting RNA with small molecules Open
For more than three decades, RNA has been known to be a relevant and attractive macromolecule to target but figuring out which RNA should be targeted and how remains challenging. Recent years have seen the confluence of approaches for scre…
View article: Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models
Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models Open
RNA is a unique biomolecule that is involved in a variety of fundamental biological functions, all of which depend solely on its structure and dynamics. Since the experimental determination of crystal RNA structures is laborious, computati…
View article: Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures
Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures Open
Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. …
View article: Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses
Correlated sequence signatures are present within the genomic 5′UTR RNA and NSP1 protein in coronaviruses Open
The 5′UTR part of coronavirus genomes plays key roles in the viral replication cycle and translation of viral mRNAs. The first 75–80 nt, also called the leader sequence, are identical for genomic mRNA and subgenomic mRNAs. Recently, it was…
View article: Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions
Structure prediction of the druggable fragments in SARS-CoV-2 untranslated regions Open
The outbreak of the COVID-19 pandemic has led to intensive studies of both the structure and replication mechanism of SARS-CoV-2. In spite of some secondary structure experiments being carried out, the 3D structure of the key function regi…
View article: Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions Open
In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models…
View article: Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationships
Reference genomes of 545 silkworms enable high-throughput exploring genotype-phenotype relationships Open
The silkworm Bombyx mori is a domestic insect for silk production and a lepidopteran model. The currently available genomes limit a full understanding of its genetic and phenotypic diversity. Here we assembled long-read genomes of 545 dome…
View article: Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions
Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions Open
In silico prediction is a well-established approach to derive a general shape of an RNA molecule based on its sequence or secondary structure. This paper reports an analysis of the stereochemical quality of the RNA three-dimensional models…
View article: Bacterial translation machinery for deliberate mistranslation of the genetic code
Bacterial translation machinery for deliberate mistranslation of the genetic code Open
Significance Aminoacyl-transfer RNA (tRNA) synthetases (aaRSs) are essential enzymes that mediate accurate expression of the genetic code. More than 96% of analyzed species possess duplicated aaRSs genes, which are presumed to encode canon…
View article: Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant, and a thermophilic bacterium
Comparative study on tertiary contacts and folding of RNase P RNAs from a psychrophilic, a mesophilic/radiation-resistant, and a thermophilic bacterium Open
In most bacterial type A RNase P RNAs (P RNAs), two major loop-helix tertiary contacts (L8–P4 and L18–P8) help to orient the two independently folding S- and C-domains for concerted recognition of precursor tRNA substrates. Here, we analyz…