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…
Jingjing Sun, Junzhou Wu, Yifeng Yuan, Leon Fan + 9 more
'Wei\xa0Lin\xa0Patrina Chua' 'Yan\xa0Han\xa0Sharon Ling' 'Seetharamsing Balamkundu' 'Dwijapriya' 'Hazel\xa0Suen\xa0Suen Chay' 'Thomas\xa0J Begley' 'Valérie de\xa0Crécy-Lagard' 'Agnieszka Dziergowska' 'Peter\xa0C Dedon'] Title: Abstract Transfer RNA (tRNA) modifications have emerged as critical post-transcriptional…
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…
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…
Jesse S. Leavitt, Henry Moore, Thomas J. Santangelo, Todd M. Lowe
Transfer RNA (tRNA) modifications are essential for structural integrity, decoding fidelity, and stress adaptation, yet their evolutionary dynamics remain poorly understood. Here, we apply Ordered Two-Template Relay sequencing (OTTR-seq) to comprehensively profile tRNA modifications across nine archaeal species…
Herbert Guimaraes de Sousa Silva, Janaina de Freitas Nascimento, Marilene Souza Braga, Ana Paula de Jesus Menezes + 5 more
Trypanosoma cruzi, the etiological agent of Chagas disease, infects millions of people in the Americas. This parasite undergoes drastic changes in its morphology and metabolism between infective and noninfective forms through global remodeling of its proteome. Chemical modification of tRNA (tRNA modification)…
María Martha Sainz, Mariana Sotelo-Silveira, Carla V. Filippi, Sofía Zardo
'Sofía Zardo'] Title: Abstract Leguminous plants can establish endosymbiotic relationships with nitrogen-fixing soil rhizobacteria. Bacterial infection and nodule organogenesis are two independent but highly coordinated genetic programs that are active during this interaction. These genetic programs can be regulated…
Lexi Gao, Andrew Behrens, Geraldine Rodschinka, Sergio Forcelloni + 3 more
'Sascha Wani' 'Katrin Strasser' 'Danny D. Nedialkova'] Transfer RNAs are essential for translating genetic information into proteins. The human genome contains hundreds of predicted tRNA genes, many in multiple copies. How their expression is regulated to control tRNA repertoires is unknown. Here we combined…
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…
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…
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…
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…
Qiuyi Wang, Yuanhui Mao
Ribosome profiling has revolutionized our understanding of gene expression regulation by providing a snapshot of global translation in vivo. This powerful technique enables the investigation of the dynamics of translation initiation, elongation, and termination, and has provided insights into the regulation of protein…
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…
Mengyi Tang, Kumbit Hwang, Sung Ha Kang
We propose a new deterministic methodology to predict RNA sequence and protein folding. Is stem enough for structure prediction? The main idea is to consider all possible stem formation in the given sequence. With the stem loop energy and the strength of stem, we explore how to deterministically utilize stem…
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…
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…
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…
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…