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Article
Open AccessN1-methylation of adenosine (m1A) in ND5 mRNA leads to complex I dysfunction in Alzheimer’s disease
One mechanism of particular interest to regulate mRNA fate post-transcriptionally is mRNA modification. Especially the extent of m1A mRNA methylation is highly discussed due to methodological differences. However...
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Article
Open AccessQuantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing
Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacki...
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Article
Open AccessMETTL1 promotes tumorigenesis through tRNA-derived fragment biogenesis in prostate cancer
Newly growing evidence highlights the essential role that epitranscriptomic marks play in the development of many cancers; however, little is known about the role and implications of altered epitranscriptome d...
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Article
Open AccessFUS regulates a subset of snoRNA expression and modulates the level of rRNA modifications
FUS is a multifunctional protein involved in many aspects of RNA metabolism, including transcription, splicing, translation, miRNA processing, and replication-dependent histone gene expression. In this work, w...
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Chapter
Methods to Analyze Post-transcriptional Modifications Applied to Stable RNAs in Staphylococcus aureus
RNA modifications contribute to the various functions of RNAs in all living organisms. Some of these modifications are dynamic and contribute to the regulation of gene expression. In bacteria, their roles in s...
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Protocol
Data Analysis Pipeline for Detection and Quantification of Pseudouridine (ψ) in RNA by HydraPsiSeq
Pseudouridine, a modified RNA residue formed by the isomerization of its parental U nucleotide, is prevalent in a majority of cellular RNAs; its presence was reported in tRNA, rRNA, and sn/snoRNA as well as in...
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Article
Open AccessFTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell
Cancer stem cells (CSCs) are a small but critical cell population for cancer biology since they display inherent resistance to standard therapies and give rise to metastases. Despite accruing evidence establis...
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Article
Open AccessCell culture NAIL-MS allows insight into human tRNA and rRNA modification dynamics in vivo
Recently, studies about RNA modification dynamics in human RNAs are among the most controversially discussed. As a main reason, we identified the unavailability of a technique which allows the investigation of...
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Protocol
Quantitative and Qualitative Assessment of Small RNA Preparations
Recent advances in high-throughput sequencing have shed new light on the diversity of small noncoding RNA (sncRNA) classes and their crucial roles in gene regulation and disease. One key step in sncRNA profili...
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Protocol
AlkAniline-Seq: A Highly Sensitive and Specific Method for Simultaneous Map** of 7-Methyl-guanosine (m7G) and 3-Methyl-cytosine (m3C) in RNAs by High-Throughput Sequencing
Epitranscriptomics is an emerging field where the development of high-throughput analytical technologies is essential to profile the dynamics of RNA modifications under different conditions. Despite important ...
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Protocol
Isolation, Extraction and Deep-Sequencing Analysis of Extracellular RNAs (exRNAs) from Human Plasma
Extracellular RNAs (exRNAs) are secreted by nearly all cell types and are now known to play multiple physiological roles. Human plasma, a readily available sample for biomedical analysis, was reported to conta...
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Article
Open Access2,6-Diaminopurine as a highly potent corrector of UGA nonsense mutations
Nonsense mutations cause about 10% of genetic disease cases, and no treatments are available. Nonsense mutations can be corrected by molecules with nonsense mutation readthrough activity. An extract of the mus...
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Article
Open AccessLimited antibody specificity compromises epitranscriptomic analyses
A controversial discussion on the occurrence of the RNA modification m1A in mRNA takes a new turn, as an antibody with a central role in modification map** was shown to also bind mRNA cap structures.
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Protocol
Map** and Quantification of tRNA 2′-O-Methylation by RiboMethSeq
Current development of epitranscriptomics field requires efficient experimental protocols for precise map** and quantification of various modified nucleotides in RNA. Despite important advances in the field ...
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Article
FTSJ3 is an RNA 2′-O-methyltransferase recruited by HIV to avoid innate immune sensing
In mammals, 2′-O-methylation of RNA is a molecular signature by which the cellular innate immune system distinguishes endogenous from exogenous messenger RNA1–3. However, the molecular functions of RNA 2′-O-methy...
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Article
Open AccessContribution of protein Gar1 to the RNA-guided and RNA-independent rRNA:Ψ-synthase activities of the archaeal Cbf5 protein
Archaeal RNA:pseudouridine-synthase (PUS) Cbf5 in complex with proteins L7Ae, Nop10 and Gar1, and guide box H/ACA sRNAs forms ribonucleoprotein (RNP) catalysts that insure the conversion of uridines into pseud...
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Article
Open AccessPublisher Correction: A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients
The original version of this Article contained an error in the title, which was incorrectly given as 'APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients'. This has now been corrected in b...
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Article
Open AccessA PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients
To date, epimutations reported in man have been somatic and erased in germlines. Here, we identify a cause of the autosomal recessive cblC class of inborn errors of vitamin B12 metabolism that we name “epi-cblC”....
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Protocol
Quantification of 2′-O-Me Residues in RNA Using Next-Generation Sequencing (Illumina RiboMethSeq Protocol)
RNA 2′-O-methylation is one of the ubiquitous nucleotide modifications found in many RNA types from bacteria, archaea, and eukarya. We and others have recently published accurate and sensitive detection of these ...
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Article
Open AccessIdentification of sites of 2′-O-methylation vulnerability in human ribosomal RNAs by systematic map**
Ribosomal RNA modifications are important in optimizing ribosome function. Sugar 2′-O-methylation performed by fibrillarin-associated box C/D antisense guide snoRNAs impacts all steps of translation, playing a...
