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MetabolomicsElucidation of the epitranscriptomic RNA modification landscape of chikungunya virus

The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus to study the landscape of viral RNA modification in infected human cells. ...

2024-06-11 | MTBLS8697 | MetaboLights
MetabolomicsNeuronal tRNA modifications in Aplysia californica are repatterned during behavioral habituation
Transfer RNA (tRNA) modifications have been increasingly implicated as post-transcriptional regulators of basic neuronal functions. However, characterizing tRNA modification profiles in specific neural circuits that control well-defined behaviors is notoriously difficult due to the complexity of con...
2026-09-01 | MTBLS15420 | MetaboLights
MetabolomicsN6-methyladenosine modification is not a general trait of positive-sense RNA viral genomes

Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these findings are mostly based on m6A-seq, an antibody-dependent technique with...

2024-01-25 | MTBLS6978 | MetaboLights
MetabolomicsIdentification of the modifications in artificial E. coli rRNAs
Ribosome biogenesis is pivotal in the self-replication of life. In Escherichia coli, three ribosomal RNAs and 54 ribosomal proteins are synthesized and subjected to cooperative hierarchical assembly facilitated by numerous accessory factors. Realizing ribosome biogenesis in vitro is a critical miles...
2024-12-09 | MTBLS7425 | MetaboLights
MetabolomicsRNA modification dynamics during Enterococcus faecalis OG1RF growth
Quantitative analysis of relative levels of RNA modifications in small (primarily tRNA) and large (primarily 16S/23S rRNA) RNAs isolated from Enterococcus faecalis OG1RF across a growth time course in BHI media.
2026-08-20 | MTBLS14602 | MetaboLights
MetabolomicsTranslational repression of viral RNA mediates arbovirus persistence in mosquitoes

Persistent infection of mosquito vectors is essential for the transmission of arboviruses, yet how these viruses produce sufficient progeny without compromising host cell fitness remains unclear. Arbovirus genomes exhibit suboptimal codon usage for both human and mosquito hosts, raising questions...

2026-02-12 | MTBLS12760 | MetaboLights
MetabolomicsGut Commensal Bacteria-Derived Methionine is Required for Host Reproduction by Modulating RNA m6A Methylation of the Insulin Receptor_targeted metabolites

Gut commensal bacteria promote host reproduction by modulating metabolism and nutrition, but the molecular mechanisms by which microbes regulate reproduction remain unclear. Here, we show that gut commensal bacteria promote host reproduction by providing amino-acid methionine, which controls the ...

2025-06-22 | MTBLS12470 | MetaboLights
TranscriptomicsChemical modifications mark alternatively spliced and actively degrading messenger RNAs in Arabidopsis and humans
Post-transcriptional chemical modification of RNA bases is a widespread and physiologically relevant regulator of RNA maturation, stability, and function. While modifications are best characterized in short, noncoding RNAs such as transfer RNAs (tRNAs), growing evidence indicates that messenger RNAs...
ORGANISM(S): Homo sapiens 
2015-10-31 | E-GEOD-66224 | biostudies-arrayexpress
ProteomicsComprehensive Nucleoside Analysis of Archaeal RNA Modification Profiles Reveals a m7G in the Conserved P-loop of 23S rRNA
Extremophilic archaea employ diverse chemical RNA modifications, providing a rich source of new enzymes for biotechnologically valuable RNA manipulations. Our understanding of the modified nucleoside profiles in Archaea, as well as the functions and dynamic regulation of specific RNA modifications i...
ORGANISM(S): Thermococcus kodakarensis 
2025-02-12 | PXD060644 | Pride
Rna modifications Archaea Lc-ms/ms 
ProteomicsRNA oligomers training set for the Pytheas scoring function
Mass spectrometry remains an important method for analysis of modified nucleosides ubiquitously present in cellular RNAs, in particular for ribosomal and transfer RNAs that play crucial roles in mRNA translation and decoding. Furthermore, modifications have effect on the lifetimes of nucleic acids i...
ORGANISM(S): Escherichia coli 
2022-05-04 | PXD030435 | Pride
Training set Scoring function Rna Pytheas 
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