The tRNA identity landscape for aminoacylation and beyond

R Giegé, G Eriani - Nucleic Acids Research, 2023 - academic.oup.com
Abstract tRNAs are key partners in ribosome-dependent protein synthesis. This process is
highly dependent on the fidelity of tRNA aminoacylation by aminoacyl-tRNA synthetases …

Genome-wide analysis of the in vivo tRNA structurome reveals RNA structural and modification dynamics under heat stress

R Yamagami, JP Sieg, SM Assmann… - Proceedings of the …, 2022 - National Acad Sciences
RNA structure plays roles in myriad cellular events including transcription, translation, and
RNA processing. Genome-wide analyses of RNA secondary structure in vivo by chemical …

Developing community resources for nucleic acid structures

HM Berman, CL Lawson, B Schneider - Life, 2022 - mdpi.com
In this review, we describe the creation of the Nucleic Acid Database (NDB) at Rutgers
University and how it became a testbed for the current infrastructure of the RCSB Protein …

Self-assembly and condensation of intermolecular poly (UG) RNA quadruplexes

S Roschdi, EJ Montemayor, R Vivek… - Nucleic Acids …, 2024 - academic.oup.com
Abstract Poly (UG) or 'pUG'dinucleotide repeats are highly abundant sequences in
eukaryotic RNAs. In Caenorhabditis elegans, pUGs are added to RNA 3′ ends to direct …

RNA folding studies inside peptide-rich droplets reveal roles of modified nucleosides at the origin of life

MCO Meyer, R Yamagami, S Choi, CD Keating… - Science …, 2023 - science.org
Compartmentalization of RNA in biopolymer-rich membraneless organelles is now
understood to be pervasive and critical for the function of extant biology and has been …

Application of mutational profiling: New functional analyses reveal the tRNA recognition mechanism of tRNA m1A22 methyltransferase

R Yamagami, H Hori - Journal of Biological Chemistry, 2023 - ASBMB
Transfer RNAs undergo diverse posttranscriptional modifications to regulate a myriad of
cellular events including translation, stress response, and viral replication. These …

Deciphering the conformational stability of MazE7 antitoxin in Mycobacterium tuberculosis from molecular dynamics simulation study

R Saha, G Bhattacharje, S De… - Journal of Biomolecular …, 2025 - Taylor & Francis
MazEF Toxin-antitoxin (TA) systems are associated with the persistent phenotype of the
pathogen, Mycobacterium tuberculosis (Mtb), aiding their survival. Though extensively …

Lead-seq: transcriptome-wide structure probing in vivo using lead(II) ions

C Twittenhoff, VB Brandenburg, F Righetti… - Nucleic Acids …, 2020 - academic.oup.com
The dynamic conformation of RNA molecules within living cells is key to their function.
Recent advances in probing the RNA structurome in vivo, including the use of SHAPE …

Trans-editing by aminoacyl-tRNA synthetase-like editing domains

ABK Nagy, M Bakhtina, K Musier-Forsyth - The Enzymes, 2020 - Elsevier
Aminoacyl-tRNA synthetases (aaRS) are ubiquitous enzymes responsible for aminoacyl-
tRNA (aa-tRNA) synthesis. Correctly formed aa-tRNAs are necessary for proper decoding of …

Asterix/Gtsf1 links tRNAs and piRNA silencing of retrotransposons

JJ Ipsaro, PA O'Brien, S Bhattacharya, AG Palmer… - Cell reports, 2021 - cell.com
Summary The Piwi-interacting RNA (piRNA) pathway safeguards genomic integrity by
silencing transposable elements (transposons) in the germline. While Piwi is the central …