25 papers · ranked by Valyu relevance
Jingjing Sun, Junzhou Wu, Yifeng Yuan, Leon Fan + 8 more
Transfer RNA (tRNA) modifications have emerged as critical posttranscriptional regulators of gene expression affecting diverse biological and disease processes. While there is extensive knowledge about the enzymes installing the dozens of post-transcriptional tRNA modifications – the tRNA epitranscriptome – very little…
Simon Grelet, Ariel McShane, Eveline Hok, Jensen Tomberlin + 3 more
'Philip H. Howe' 'Renaud Geslain' 'Baochuan Lin'] Recent studies have placed transfer RNA (tRNA), a housekeeping molecule, in the heart of fundamental cellular processes such as embryonic development and tumor progression. Such discoveries were contingent on the concomitant development of methods able to deliver…
Phillipe Loher, Aristeidis G. Telonis, Isidore Rigoutsos
Transfer RNA fragments (tRFs) are an established class of constitutive regulatory molecules that arise from precursor and mature tRNAs. RNA deep sequencing (RNA-seq) has greatly facilitated the study of tRFs. However, the repeat nature of the tRNA templates and the idiosyncrasies of tRNA sequences necessitate the…
Cédric Gobet, Benjamin Weger, Julien Marquis, Eva Martin + 2 more
Protein translation depends on mRNA-specific initiation, elongation and termination rates. While the regulation of ribosome elongation is well studied in bacteria and yeast, less is known in higher eukaryotes. Here, we combined ribosome and tRNA profiling to investigate the relations between ribosome elongation rates…
Yuko Nakano, Howard Gamper, Henri McGuigan, Sunita Maharjan + 8 more
Monitoring the dynamic changes of cellular tRNA pools is challenging, due to the extensive post-transcriptional modifications of individual species. The most critical component in tRNAseq is a processive reverse transcriptase (RT) that can read through each modification with high efficiency. Here we show that the…
Kevin Van Bortle, Douglas H. Phanstiel, Michael P. Snyder
Background The human genome is hierarchically organized into local and long-range structures that help shape cell-type-specific transcription patterns. Transfer RNA (tRNA) genes (tDNAs), which are transcribed by RNA polymerase III (RNAPIII) and encode RNA molecules responsible for translation, are dispersed throughout…
Rodrigo Alarcon, Daniel Köster, Stine Behrmann, Zoya Ignatova
Transfer RNAs (tRNAs) play an essential role in protein synthesis and cellular homeostasis, with their dysregulation associated with various human pathologies. Recent advances in direct RNA sequencing by the Nanopore platform have enabled simultaneous profiling of tRNA abundance, modifications, and aminoacylation…
Marius Külp, Halvard Bonig, Michael A. Rieger
Codons function as translation units in open-reading-frames (ORF) of genes to encode for proteins. Transfer RNAs (tRNAs) mediate the connection of every codon to its cognate amino acid. Despite the cooperation between messenger and transfer RNA during translation, approaches to integrate codon usage and tRNA quantities…
Jose R. Jaramillo-Ponce, Philippe Wolff, Virginie Marchand, Yuri Motorin + 12 more
Transfer RNAs play a critical role in protein synthesis by matching mRNA codons to their corresponding amino acids. Their post-transcriptional modifications, shaping structure, stability, and codon decoding, are now recognized as key regulators of translation and cellular adaptation, including in bacterial pathogens.…
Daisuke Ando, Sherif Rashad, Thomas J Begley, Hidenori Endo + 3 more
The tRNA epitranscriptome has been recognized as an important player in mRNA translation regulation. tRNA modifications, tRNA expression, and tRNA derived small RNAs (tsRNAs) all play important roles in physiology as well as in multiple pathologies. While the decoding capacity of tRNA is generally understood, there…
Michael Lanzillotti, Jennifer Brodbelt
Mass spectrometry has proven to be a highly effective tool for characterization of RNA post-transcriptional modifications. For both synthetic RNAs and ones from biological sources, mass spectrometry can interrogate multiple, co-occurring covalent modifications at the nucleotide level simultaneously. To expand the…
Ryota Yamagami, Hiroyuki Hori
Transfer RNAs undergo diverse posttranscriptional modifications to regulate a myriad of cellular events including translation, stress response, and viral replication. These posttranscriptional modifications are synthesized by site-specific modification enzymes. Recent RNA-seq techniques have revealed multiple features…
Michael Lanzillotti, Jennifer Brodbelt
Broad interest in nucleic acids – both their therapeutic capabilities and understanding the nuances of their structure and resulting function – has increased in recent years. Post-transcriptional modifications in particular have become an important analysis target, as these covalent modifications to the sugars…
Katherine C. H. Amrine, Wesley D. Swingley, David H. Ardell
Phylogenomic analyses are subject to bias from convergence in macromolecular compositions and noise from horizontal gene transfer (HGT). Accordingly, compositional convergence leads to contradictory results on the phylogeny of taxa such as the ecologically dominant SAR11 group of Alphaproteobacteria, which have…
Guillaume Hummel, David Pflieger, Alexandre Berr, Laurence Drouard
Transfer RNAs (tRNAs) are universal adaptors of the genetic code, yet their evolutionary dynamics across photosynthetic eukaryotes remain underexplored. Here, we present the largest comparative re-analysis integrating the PlantRNA database with published data to explore tRNA gene evolution. We find that tRNA gene…
Q Li, Manda Riehl
Profiling is a process that finds similarities between different RNA secondary structures by extracting signals from the Boltzmann sampling. The reproducibility of profiling can be identified by the standard deviation of number of features among Boltzmann samples. We found a strong relationship between the frequency of…
Jing Zhao, Bo Qin, Rainer Nikolay, Christian M. T. Spahn + 1 more
'Gong Zhang'] In all kingdoms of life, proteins are synthesized by ribosomes in a process referred to as translation. The amplitude of translational regulation exceeds the sum of transcription, mRNA degradation and protein degradation. Therefore, it is essential to investigate translation in a global scale. Like the…
Sarah K. Schultz, Ute Kothe
Transfer RNAs (tRNAs) are the most highly modified cellular RNAs, both with respect to the proportion of nucleotides that are modified within the tRNA sequence and with respect to the extraordinary diversity in tRNA modification chemistry. However, the functions of many different tRNA modifications are only beginning…
Eleonora de Klerk, Johan T. den Dunnen, Peter A. C. ‘t Hoen
Technological advances in the sequencing field support in-depth characterization of the transcriptome. Here, we review genome-wide RNA sequencing methods used to investigate specific aspects of gene expression and its regulation, from transcription to RNA processing and translation. We discuss tag-based methods for…
Michael Lanzillotti, Jennifer Brodbelt
Recent progress in top-down mass spectrometry analysis of progressively larger nucleic acids has enabled in-depth characterization of intact, modified RNA molecules. Development of methods for desalting and MS/MS fragmentation allows rapid acquisition of high-quality top-down MS/MS spectra of nucleic acids up to 100…
Binil Shyam T.V., Rati Sharma
mRNA translation is a crucial process that leads to protein synthesis in living cells. Therefore, it is a process that needs to work optimally for a cell to stay healthy and alive. With advancements in microscopy and novel experimental techniques, a lot of the intricate details about the translation mechanism are now…
Authors not listed
Therapeutic oligonucleotides (ONs) are short synthetic DNA or RNA strands used to modulate protein expression in disease treatment. Besides the full-length product (FLP), ON samples contain many closely related impurities that must be profiled to ensure drug quality. Separation techniques, such as ion-pairing…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Emmajay Sutherland, Christopher Harding, Clarissa Czekster
Cyclodipeptide synthases (CDPSs) are a growing family of enzymes capable of producing a large variety of cyclodipetide products using aminoacylated tRNA. Histidine-containing cyclic dipeptides have important biological activities as anticancer and neuroprotective molecules. Out of the 120 experimentally validated CDPS…
Shuhao Zhang, Zhen Wang, Jie Qiao, Wenbing Zhang
The ribosome ensures translational accuracy by monitoring codon-anticodon interactions at the A site decoding center. However, the mechanism by which conserved nucleotide A1493 contributes to this process remains controversial. To address this, we performed molecular dynamics simulations initiated from ribosomal…