Mass spectrometry of the fifth nucleoside: a review of the identification of pseudouridine in nucleic acids

Research progress of RNA pseudouridine modification in nervous system

Recent advances of pseudouridine (Ψ, 5-ribosyluracil) modification highlight its crucial role as a post-transcriptional regulator in gene expression and its impact on various RNA processes. Ψ synthase (PUS), a category of RNA-modifying enzymes, orchestrates the pseudouridylation reaction. It can specifically recognize conserved sequences or structural motifs within substrates, thereby regulating the biological function of various RNA molecules accurately. Our comprehensive review underscored the close association of PUS1, PUS3, PUS7, PUS10, and dyskerin PUS1 with various nervous system disorders, including neurodevelopmental disorders, nervous system tumors, mitochondrial myopathy, lactic acidosis and sideroblastic anaemia (MLASA) syndrome, peripheral nervous system disorders, and type II myotonic dystrophy. In light of these findings, this study elucidated how Ψ strengthened RNA structures and contributed to RNA function, thereby providing valuable insights into the intricate molecular mechanisms underlying nervous system diseases. However, the detailed effects and mechanisms of PUS on neuron remain elusive. This lack of mechanistic understanding poses a substantial obstacle to the development of therapeutic approaches for various neurological disorders based on Ψ modification.

In-Gel Cyanoethylation for Pseudouridines Mass Spectrometry Detection of Bacterial Regulatory RNA

Regulatory RNAs, as well as many RNA families, contain chemically modified nucleotides, including pseudouridines (ψ). To map nucleotide modifications, approaches based on enzymatic digestion of RNA followed by nano liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) analysis were implemented several years ago. However, detection of ψ by mass spectrometry (MS) is challenging as ψ exhibits the same mass as uridine. Thus, a chemical labeling strategy using acrylonitrile was developed to detect this mass-silent modification. Acrylonitrile reacts specifically to ψ to form 1-cyanoethylpseudouridine (Ceψ), resulting in a mass shift of ψ detectable by MS. Here, a protocol detailing the steps from the purification of RNA by polyacrylamide gel electrophoresis, including in-gel labeling of ψ, to MS data interpretation to map ψ and other modifications is proposed. To demonstrate its efficiency, the protocol was applied to bacterial regulatory RNAs from E. coli: 6S RNA and transfer-messenger RNA (tmRNA, also known as 10Sa RNA). Moreover, ribonuclease P (RNase P) was also mapped using this approach. This method enabled the detection of several ψ at single nucleotide resolution.

H/ACA snRNP-dependent ribosome biogenesis regulates translation of polyglutamine proteins

Stem cells in many systems, including Drosophila germline stem cells (GSCs), increase ribosome biogenesis and translation during terminal differentiation. Here, we show that the H/ACA small nuclear ribonucleoprotein (snRNP) complex that promotes pseudouridylation of ribosomal RNA (rRNA) and ribosome biogenesis is required for oocyte specification. Reducing ribosome levels during differentiation decreased the translation of a subset of messenger RNAs that are enriched for CAG trinucleotide repeats and encode polyglutamine-containing proteins, including differentiation factors such as RNA-binding Fox protein 1. Moreover, ribosomes were enriched at CAG repeats within transcripts during oogenesis. Increasing target of rapamycin (TOR) activity to elevate ribosome levels in H/ACA snRNP complex-depleted germlines suppressed the GSC differentiation defects, whereas germlines treated with the TOR inhibitor rapamycin had reduced levels of polyglutamine-containing proteins. Thus, ribosome biogenesis and ribosome levels can control stem cell differentiation via selective translation of CAG repeat-containing transcripts.

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 mRNA/lncRNA. Multiple analytical deep sequencing-based approaches have been proposed for pseudouridine detection and quantification, among which the most popular relies on the use of soluble carbodiimide (termed CMCT). Recently, we developed an alternative protocol for pseudouridine mapping and quantification. The principle is based on protection of pseudouridine against random RNA cleavage by hydrazine/aniline treatment (HydraPsiSeq protocol). This "negative" detection mode requires higher sequencing depth and provides a precise quantification of the pseudouridine content. All "wet-lab" technical details of the HydraPsiSeq protocol have been described in recent publications. Here, we describe all bioinformatics analysis steps required for data processing from raw reads to the pseudouridylation profile of known or unknown RNA.

Ribosomal RNA Pseudouridylation: Will Newly Available Methods Finally Define the Contribution of This Modification to Human Ribosome Plasticity?

In human rRNA, at least 104 specific uridine residues are modified to pseudouridine. Many of these pseudouridylation sites are located within functionally important ribosomal domains and can influence ribosomal functional features. Until recently, available methods failed to reliably quantify the level of modification at each specific rRNA site. Therefore, information obtained so far only partially explained the degree of regulation of pseudouridylation in different physiological and pathological conditions. In this focused review, we provide a summary of the methods that are now available for the study of rRNA pseudouridylation, discussing the perspectives that newly developed approaches are offering.

General Principles for the Detection of Modified Nucleotides in RNA by Specific Reagents

Epitranscriptomics heavily rely on chemical reagents for the detection, quantification, and localization of modified nucleotides in transcriptomes. Recent years have seen a surge in mapping methods that use innovative and rediscovered organic chemistry in high throughput approaches. While this has brought about a leap of progress in this young field, it has also become clear that the different chemistries feature variegated specificity and selectivity. The associated error rates, e.g., in terms of false positives and false negatives, are in large part inherent to the chemistry employed. This means that even assuming technically perfect execution, the interpretation of mapping results issuing from the application of such chemistries are limited by intrinsic features of chemical reactivity. An important but often ignored fact is that the huge stochiometric excess of unmodified over-modified nucleotides is not inert to any of the reagents employed. Consequently, any reaction aimed at chemical discrimination of modified versus unmodified nucleotides has optimal conditions for selectivity that are ultimately anchored in relative reaction rates, whose ratio imposes intrinsic limits to selectivity. Here chemical reactivities of canonical and modified ribonucleosides are revisited as a basis for an understanding of the limits of selectivity achievable with chemical methods.

Epitranscriptomic Signatures in lncRNAs and Their Possible Roles in Cancer

In contrast to the amazing exponential growth in knowledge related to long non-coding RNAs (lncRNAs) involved in cell homeostasis or dysregulated pathological states, little is known so far about the links between the chemical modifications occurring in lncRNAs and their function. Generally, ncRNAs are post-transcriptional regulators of gene expression, but RNA modifications occurring in lncRNAs generate an additional layer of gene expression control. Chemical modifications that have been reported in correlation with lncRNAs include m⁶A, m⁵C and pseudouridylation. Up to date, several chemically modified long non-coding transcripts have been identified and associated with different pathologies, including cancers. This review presents the current level of knowledge on the most studied cancer-related lncRNAs, such as the metastasis associated lung adenocarcinoma transcript 1 (MALAT1), the Hox transcript antisense intergenic RNA (HOTAIR), or the X-inactive specific transcript (XIST), as well as more recently discovered forms, and their potential roles in different types of cancer. Understanding how these RNA modifications occur, and the correlation between lncRNA changes in structure and function, may open up new therapeutic possibilities in cancer.

Total synthesis of pseudouridineviaHeck-typeC-glycosylation

Pseudouridine (1) was synthesized by functional group interconversions of the Heck adduct11from 2,4-dimethoxy-5-iodopyrimidine (8) and ribofuranoid glycal4.

The Dark Side of the Epitranscriptome: Chemical Modifications in Long Non-Coding RNAs

The broad application of next-generation sequencing technologies in conjunction with improved bioinformatics has helped to illuminate the complexity of the transcriptome, both in terms of quantity and variety. In humans, 70–90% of the genome is transcribed, but only ~2% carries the blueprint for proteins. Hence, there is a huge class of non-translated transcripts, called long non-coding RNAs (lncRNAs), which have received much attention in the past decade. Several studies have shown that lncRNAs are involved in a plethora of cellular signaling pathways and actively regulate gene expression via a broad selection of molecular mechanisms. Only recently, sequencing-based, transcriptome-wide studies have characterized different types of post-transcriptional chemical modifications of RNAs. These modifications have been shown to affect the fate of RNA and further expand the variety of the transcriptome. However, our understanding of their biological function, especially in the context of lncRNAs, is still in its infancy. In this review, we will focus on three epitranscriptomic marks, namely pseudouridine (Ψ), N⁶-methyladenosine (m⁶A) and 5-methylcytosine (m⁵C). We will introduce writers, readers, and erasers of these modifications, and we will present methods for their detection. Finally, we will provide insights into the distribution and function of these chemical modifications in selected, cancer-related lncRNAs.

Pseudouridine in the Anticodon of Escherichia coli tRNATyr(QΨA) Is Catalyzed by the Dual Specificity Enzyme RluF

Pseudouridine is found in almost all cellular ribonucleic acids (RNAs). Of the multiple characteristics attributed to pseudouridine, making messenger RNAs (mRNAs) highly translatable and non-immunogenic is one such feature that directly implicates this modification in protein synthesis. We report the existence of pseudouridine in the anticodon of Escherichia coli tyrosine transfer RNAs (tRNAs) at position 35. Pseudouridine was verified by multiple detection methods, which include pseudouridine-specific chemical derivatization and gas phase dissociation of RNA during liquid chromatography tandem mass spectrometry (LC-MS/MS). Analysis of total tRNA isolated from E. coli pseudouridine synthase knock-out mutants identified RluF as the enzyme responsible for this modification. Furthermore, the absence of this modification compromises the translational ability of a luciferase reporter gene coding sequence when it is preceded by multiple tyrosine codons. This effect has implications for the translation of mRNAs that are rich in tyrosine codons in bacterial expression systems.

Sequence mapping of transfer RNA chemical modifications by liquid chromatography tandem mass spectrometry

Mass spectrometry is a powerful analytical tool for identifying and characterizing structural modifications to the four canonical bases in RNA, information that is lost when using techniques such as PCR for RNA analysis. Here we described an updated method for sequence mapping of modified nucleosides in transfer RNA. This modification mapping approach utilizes knowledge of the modified nucleosides present in the sample along with the genome-derived tRNA sequence to readily locate modifications site-specifically in the tRNA sequence. The experimental approach involves isolation of the tRNA of interest followed by separate enzymatic digestion to nucleosides and oligonucleotides. Both samples are analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) and the data sets are then combined to yield the modification profile of the tRNA. Data analysis is facilitated by the use of unmodified sequence exclusion lists and new developments in software that can automate MS/MS spectral annotation. The method is illustrated using tRNA-Asn isolated from Thermus thermophilus.

A mass spectrometry-based method for direct determination of pseudouridine in RNA

Pseudouridine (5-ribosyluracil, Ψ) is the only ‘mass-silent’ nucleoside produced by post-transcriptional RNA modification. We describe here a novel mass spectrometry (MS)-based method for direct determination of Ψ in RNA. The method assigns a Ψ-containing nucleolytic RNA fragment by an accurate measurement of a signature doubly dehydrated nucleoside anion ([C₉H₇N₂O₄]¹⁻, m/z 207.04) produced by collision-induced dissociation MS, and it determines the Ψ-containing nucleotide sequence by pseudo-MS³, i.e. in-source fragmentation followed by MS². By applying this method, we identified all of the known Ψs in the canonical human spliceosomal snRNAs and, unexpectedly, found two previously unknown Ψs in the U5 and U6 snRNAs. Because the method allows direct determination of Ψ in a subpicomole quantity of RNA, it will serve as a useful tool for the structure/function studies of a wide variety of non-coding RNAs.

The emerging epitranscriptomics of long noncoding RNAs

The pervasive transcription of genomes into long noncoding RNAs has been amply demonstrated in recent years and garnered much attention. Similarly, emerging 'epitranscriptomics' research has shown that chemically modified nucleosides, thought to be largely the domain of tRNAs and other infrastructural RNAs, are far more widespread and can exert unexpected influence on RNA utilization. Both areas are characterized by the often-ephemeral nature of the subject matter in that few individual examples have been fully assessed for their molecular or cellular function, and effects might often be subtle and cumulative. Here we review available information at the intersection of these two exciting areas of biology, by focusing on four RNA modifications that have been mapped transcriptome-wide: 5-methylcytidine, N6-methyladenosine, pseudouridine as well as adenosine to inosine (A-to-I) editing, and their incidence and function in long noncoding RNAs. This article is part of a Special Issue entitled: Clues to long noncoding RNA taxonomy, edited by Dr. Tetsuro Hirose and Dr. Shinichi Nakagawa.

The identification and characterization of non-coding and coding RNAs and their modified nucleosides by mass spectrometry

The analysis of ribonucleic acids (RNA) by mass spectrometry has been a valuable analytical approach for more than 25 years. In fact, mass spectrometry has become a method of choice for the analysis of modified nucleosides from RNA isolated out of biological samples. This review summarizes recent progress that has been made in both nucleoside and oligonucleotide mass spectral analysis. Applications of mass spectrometry in the identification, characterization and quantification of modified nucleosides are discussed. At the oligonucleotide level, advances in modern mass spectrometry approaches combined with the standard RNA modification mapping protocol enable the characterization of RNAs of varying lengths ranging from low molecular weight short interfering RNAs (siRNAs) to the extremely large 23 S rRNAs. New variations and improvements to this protocol are reviewed, including top-down strategies, as these developments now enable qualitative and quantitative measurements of RNA modification patterns in a variety of biological systems.

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined 'variable sequencing', which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing.

Small nucleolar RNAs and RNA-guided post-transcriptional modification

snoRNAs (small nucleolar RNAs) constitute one of the largest and best-studied classes of non-coding RNAs that confer enzymatic specificity. With associated proteins, these snoRNAs form ribonucleoprotein complexes that can direct 2'-O-methylation or pseudouridylation of target non-coding RNAs. Aided by computational methods and high-throughput sequencing, new studies have expanded the diversity of known snoRNA functions. Complexes incorporating snoRNAs have dynamic specificity, and include diverse roles in RNA silencing, telomerase maintenance and regulation of alternative splicing. Evidence that dysregulation of snoRNAs can cause human disease, including cancer, indicates that the full scope of snoRNA roles remains an unfinished story. The diversity in structure, genomic origin and function between snoRNAs found in different complexes and among different phyla illustrates the surprising plasticity of snoRNAs in evolution. The ability of snoRNAs to direct highly specific interactions with other RNAs is a consistent thread in their newly discovered functions. Because they are ubiquitous throughout Eukarya and Archaea, it is likely they were a feature of the last common ancestor of these two domains, placing their origin over two billion years ago. In the present chapter, we focus on recent advances in our understanding of these ancient, but functionally dynamic RNA-processing machines.

Pseudouridine: still mysterious, but never a fake (uridine)!

Pseudouridine (Ψ) is the most abundant of >150 nucleoside modifications in RNA. Although Ψ was discovered as the first modified nucleoside more than half a century ago, neither the enzymatic mechanism of its formation, nor the function of this modification are fully elucidated. We present the consistent picture of Ψ synthases, their substrates and their substrate positions in model organisms of all domains of life as it has emerged to date and point out the challenges that remain concerning higher eukaryotes and the elucidation of the enzymatic mechanism.

A personal perspective on chemistry-driven RNA research

In this mini review, we discuss how our understanding of ribonucleic acid (RNA) properties becomes significantly deepened when a broad range of modern chemical and biophysical methods is applied. We span our perspective from RNA solid-phase synthesis and site-specific labeling to single-molecule fluorescence-resonance-energy-transfer imaging and NMR spectroscopy approaches to explore the dynamics of RNA over a broad timescale. We then move on to Fourier-transform-ion-cyclotron-resonance mass spectrometry (FT-ICR-MS) as a powerful technique for RNA sequencing and modification analysis. The novel methodological developments are discussed for selected biological systems that include the thiamine-pyrophosphate riboswitch, HIV and ribosomal A-site RNA, and transfer RNA.

Mass spectrometry-based quantification of pseudouridine in RNA

Direct detection of pseudouridine (ψ), an isomer of uridine, in RNA is challenging. The most popular method requires chemical derivatization using N-cyclohexyl-N'-β-(4-methylmorpholinum ethyl) carbodiimide p-tosylate (CMCT) followed by radiolabeled primer extension mediated by reverse transcriptase. More recently, mass spectrometry (MS)-based approaches for sequence placement of pseudouridine in RNA have been developed. Nearly all of these approaches, however, only yield qualitative information regarding the presence or absence of pseudouridine in a given RNA population. Here, we have extended a previously developed liquid chromatography tandem mass spectrometry (LC-MS/MS) method to enable both the qualitative and quantitative analysis of pseudouridine. Quantitative selected reaction monitoring (SRM) assays were developed using synthetic oligonucleotides, with or without pseudouridine, and the results yielded a linear relationship between the ion abundance of the pseudouridine-specific fragment ion and the amount of pseudouridine-containing oligonucleotide present in the original sample. Using this quantitative SRM assay, the extent of pseudouridine hypomodification in the conserved T-loop of tRNA isolated from two different Escherichia coli strains was established.

Identification, localization, and relative quantitation of pseudouridine in RNA by tandem mass spectrometry of hydrolysis products

The constitutional isomers uridine (U) and pseudouridine (Ψ) cannot be distinguished from each other by simple mass measurements of RNA or its fragments because the conversion of U into Ψ is a "mass-silent" post-transcriptional modification. Here we propose a new mass spectrometry based method for identification, localization, and relative quantitation of Ψ in RNA consisting of ∼20 nucleotides that does not require chemical labeling. Our approach takes advantage of the different fragmentation behavior of uridine (N-glycosidic bond) and pseudouridine (C-glycosidic bond) residues in RNA upon collisionally activated dissociation.

Use of specific chemical reagents for detection of modified nucleotides in RNA

Naturally occurring cellular RNAs contain an impressive number of chemically distinct modified residues which appear posttranscriptionally, as a result of specific action of the corresponding RNA modification enzymes. Over 100 different chemical modifications have been identified and characterized up to now. Identification of the chemical nature and exact position of these modifications is typically based on 2D-TLC analysis of nucleotide digests, on HPLC coupled with mass spectrometry, or on the use of primer extension by reverse transcriptase. However, many modified nucleotides are silent in reverse transcription, since the presence of additional chemical groups frequently does not change base-pairing properties. In this paper, we give a summary of various chemical approaches exploiting the specific reactivity of modified nucleotides in RNA for their detection.

Characterization of oligodeoxynucleotides and modifications by 193 nm photodissociation and electron photodetachment dissociation

Ultraviolet photodissociation (UVPD) at 193 nm is compared to collision induced dissociation (CID) for sequencing and determination of modifications of multideprotonated 6-20-mer oligodeoxynucleotides. UVPD at 193 nm causes efficient charge reduction of the deprotonated oligodeoxynucleotides via electron detachment, in addition to extensive backbone cleavages to yield sequence ions of relatively low abundance, including w, x, y, z, a, a-B, b, c, and d ions. Although internal ions populate UVPD spectra, base loss ions from the precursor are absent. Subsequent CID of the charge-reduced oligodeoxynucleotides formed upon electron detachment, in a net process called electron photodetachment dissociation (EPD), results in abundant sequence ions in terms of w, z, a, a-B, and d products, with a marked decrease in the abundance of precursor base loss ions and internal fragments. Complete sequencing was possible for virtually all oligodeoxynucleotides studied. EPD of three modified oligodeoxynucleotides, a methylated oligodeoxynucleotide, a phosphorothioate-modified oligodeoxynucleotide, and an ethylated-oligodeoxynucleotide, resulted in specific and extensive backbone cleavages, specifically, w, z, a, a-B, and d products, which allowed the modification site(s) to be pinpointed to a more specific location than by conventional CID.

Hybrid activation methods for elucidating nucleic acid modifications

Hybrid tandem mass spectrometry (MS/MS) techniques combining electron transfer (ET) and collision activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), or ultraviolet photodissociation (UVPD) were implemented and evaluated for the characterization of a series of oligonucleotides and oligoribonucleotides, including both native single strands and single strands containing platinated, phosphorothioated, and 2'-O-methylated modification sites. ET-IRMPD and ET-UVPD of oligodeoxynucleotides and oligoribonucleotides resulted in rich fragmentation with respect to production of w, a, z, and d ions for DNA, and c, y, w, a-B, d, and z ions for RNA, with many product ions retaining the modification and thus allowing site specific identification. ET-IRMPD caused more extensive secondary dissociation of the ions, in addition to a broader distribution of detectable sequence ions attributed to using a lower mass cutoff. ET-UVPD promoted higher energy fragmentation pathways and created the most diverse MS/MS spectra. The numerous products generated by the hybrid MS/MS techniques resulted in specific and extensive backbone cleavages which allowed the modification sites of multiply modified oligonucleotides to be elucidated.

Frontiers of mass spectrometry in nucleic acids analysis

Nucleic acids research is a highly competitive field of research. A number of well established methods are available. The current output of high throughput ("next generation") sequencing technologies is impressive, and still technologies are continuing to make progress regarding read lengths, bp per second, accuracy and costs. Although in the 1990s MS was considered as an analytical platform for sequencing, it was soon realized that MS will never be competitive. Thus, the focus shifted from de novo sequencing towards other areas of application where MS has proven to be a powerful analytical tool. Potential niches for the application of MS in nucleic acids research include genotyping of genetic markers (single nucleotide polymorphisms, short tandem repeats, and combinations thereof), quality control of synthetic oligonucleotides, metabolic profiling of therapeutics, characterization of modified nucleobases in DNA and RNA molecules, and the study of non covalent interactions among nucleic acids as well as interactions of nucleic acids with drugs and proteins. The diversity of possible applications for MS highlights its significance for nucleic acid research.

Matrix-assisted laser desorption/ionization mass spectrometry screening for pseudouridine in mixtures of small RNAs by chemical derivatization, RNase digestion and signature products

We have developed a method to screen for pseudouridines in complex mixtures of small RNAs using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). First, the unfractionated crude mixture of tRNAs is digested to completion with an endoribonuclease, such as RNase T1, and the digestion products are examined using MALDI-MS. Individual RNAs are identified by their signature digestion products, which arise through the detection of unique mass values after nuclease digestion. Next, the endonuclease digest is derivatized using N-cyclohexyl-N'-(2-morpholinoethyl)carbodiimide metho-p-toluenesulfonate (CMCT), which selectively modifies all pseudouridine, thiouridine and 2-methylthio-6-isopentenyladenosine nucleosides. MALDI-MS determination of the CMCT-derivatized endonuclease digest reveals the presence of pseudouridine through a 252 Da mass increase over the underivatized digest. Proof-of-concept experiments were conducted using a mixture of Escherichia coli transfer RNAs and endoribonucleases T1 and A. More than 80% of the expected pseudouridines from this mixture were detected using this screening approach, even on an unfractionated sample of tRNAs. This approach should be particularly useful in the identification of putative pseudouridine synthases through detection of their target RNAs and can provide insight into specific small RNAs that may contain pseudouridine.