Perspectives on topology of the human m1A methylome at single nucleotide resolution

Role of RNA modifications in blood development and regeneration

Blood development and regeneration require rapid turnover of cells, and ribonucleic acid (RNA) modifications play a key role in it via regulating stemness and cell fate regulation. RNA modifications affect gene activity via posttranscriptional and translation-mediated mechanisms. Diverse molecular players involved in RNA-modification processes are abundantly expressed by hematopoietic stem cells and lineages. Close to 150 RNA chemical modifications have been reported, but only N6-methyl adenosine (m6A), inosine (I), pseudouridine (Ψ), and m1A-a handful-have been studied in-cell fate regulation. The role of RNA modification in blood diseases and disorders is an emerging field and offers potential for therapeutic interventions. Knowledge of RNA-modification and enzymatic activities could be used to design therapies in the future. Here, we summarized the recent advances in RNA modification and the epitranscriptome field and discussed their regulation of blood development and regeneration.

The physiological and pathological roles of RNA modifications in T cells

RNA molecules undergo dynamic chemical modifications in response to various external or cellular stimuli. Some of those modifications have been demonstrated to post-transcriptionally modulate the RNA transcription, localization, stability, translation, and degradation, ultimately tuning the fate decisions and function of mammalian cells, particularly T cells. As a crucial part of adaptive immunity, T cells play fundamental roles in defending against infections and tumor cells. Recent findings have illuminated the importance of RNA modifications in modulating T cell survival, proliferation, differentiation, and functional activities. Therefore, understanding the epi-transcriptomic control of T cell biology enables a potential avenue for manipulating T cell immunity. This review aims to elucidate the physiological and pathological roles of internal RNA modifications in T cell development, differentiation, and functionality drawn from current literature, with the goal of inspiring new insights for future investigations and providing novel prospects for T cell-based immunotherapy.

New directions for Ψ and m1A decoding in mRNA: deciphering the stoichiometry and function

Over the past decade, advancements in epitranscriptomics have significantly enhanced our understanding of mRNA metabolism and its role in human development and diseases. This period has witnessed breakthroughs in sequencing technologies and the identification of key proteins involved in RNA modification processes. Alongside the well-studied m6A, Ψ and m1A have emerged as key epitranscriptomic markers. Initially identified through transcriptome-wide profiling, these modifications are now recognized for their broad impact on RNA metabolism and gene expression. In this Perspective, we focus on the detections and functions of Ψ and m1A modifications in mRNA and discuss previous discrepancies and future challenges. We summarize recent advances and highlight the latest sequencing technologies for stoichiometric detection and their mechanistic investigations for functional unveiling in mRNA as the new research directions.

Regulation and functions of non-m6A mRNA modifications

Nucleobase modifications are prevalent in eukaryotic mRNA and their discovery has resulted in the emergence of epitranscriptomics as a research field. The most abundant internal (non-cap) mRNA modification is N6-methyladenosine (m6A), the study of which has revolutionized our understanding of post-transcriptional gene regulation. In addition, numerous other mRNA modifications are gaining great attention because of their major roles in RNA metabolism, immunity, development and disease. In this Review, we focus on the regulation and function of non-m6A modifications in eukaryotic mRNA, including pseudouridine (Ψ), N6,2'-O-dimethyladenosine (m6Am), N1-methyladenosine (m1A), inosine, 5-methylcytidine (m5C), N4-acetylcytidine (ac4C), 2'-O-methylated nucleotide (Nm) and internal N7-methylguanosine (m7G). We highlight their regulation, distribution, stoichiometry and known roles in mRNA metabolism, such as mRNA stability, translation, splicing and export. We also discuss their biological consequences in physiological and pathological processes. In addition, we cover research techniques to further study the non-m6A mRNA modifications and discuss their potential future applications.

Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine

Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.

Navigating the pitfalls of mapping DNA and RNA modifications

Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.

N1-Methyladenosine modification of mRNA regulates neuronal gene expression and oxygen glucose deprivation/reoxygenation induction

N¹-Methyladenosine (m1A) is an abundant modification of transcripts, plays important roles in regulating mRNA structure and translation efficiency, and is dynamically regulated under stress. However, the characteristics and functions of mRNA m1A modification in primary neurons and oxygen glucose deprivation/reoxygenation (OGD/R) induced remain unclear. We first constructed a mouse cortical neuron OGD/R model and then used methylated RNA immunoprecipitation (MeRIP) and sequencing technology to demonstrate that m1A modification is abundant in neuron mRNAs and dynamically regulated during OGD/R induction. Our study suggests that Trmt10c, Alkbh3, and Ythdf3 may be m1A-regulating enzymes in neurons during OGD/R induction. The level and pattern of m1A modification change significantly during OGD/R induction, and differential methylation is closely associated with the nervous system. Our findings show that m1A peaks in cortical neurons aggregate at both the 5' and 3' untranslated regions. m1A modification can regulate gene expression, and peaks in different regions have different effects on gene expression. By analysing m1A-seq and RNA-seq data, we show a positive correlation between differentially methylated m1A peaks and gene expression. The correlation was verified by using qRT-PCR and MeRIP-RT-PCR. Moreover, we selected human tissue samples from Parkinson's disease (PD) and Alzheimer's disease (AD) patients from the Gene Expression Comprehensive (GEO) database to analyse the selected differentially expressed genes (DEGs) and differential methylation modification regulatory enzymes, respectively, and found similar differential expression results. We highlight the potential relationship between m1A modification and neuronal apoptosis following OGD/R induction. Furthermore, by mapping mouse cortical neurons and OGD/R-induced modification characteristics, we reveal the important role of m1A modification in OGD/R and gene expression regulation, providing new ideas for research on neurological damage.

Development of Mild Chemical Catalysis Conditions for m1A-to-m6A Rearrangement on RNA

The conversion of N¹-methyladenosine (m¹A) to N⁶-methyladenosine (m⁶A) on RNA is an important step for both allowing efficient reverse transcription read-though for sequencing analysis and mapping modifications in the transcriptome. Enzymatic transformation is often used, but the efficiency of the removal can depend on local sequence context. Chemical conversion through the application of the Dimroth rearrangement, in which m¹A rearranges into m⁶A under heat and alkaline conditions, is an alternative, but the required alkaline conditions result in significant RNA degradation by hydrolysis of the phosphodiester backbone. Here, we report novel, mild pH conditions that catalyze m¹A-to-m⁶A arrangement using 4-nitrothiophenol as a catalyst. We demonstrate the efficient rearrangement in mononucleosides, synthetic RNA oligonucleotides, and RNAs isolated from human cell lines, thereby validating a new approach for converting m¹A-to-m⁶A in RNA samples for sequencing analyses.

RNA nucleotide methylation: 2021 update

Among RNA modifications, transfer of methylgroups from the typical cofactor S-adenosyl-l-methionine by methyltransferases (MTases) to RNA is by far the most common reaction. Since our last review about a decade ago, the field has witnessed the re-emergence of mRNA methylation as an important mechanism in gene regulation. Attention has then spread to many other RNA species; all being included into the newly coined concept of the "epitranscriptome." The focus moved from prokaryotes and single cell eukaryotes as model organisms to higher eukaryotes, in particular to mammals. The perception of the field has dramatically changed over the past decade. A previous lack of phenotypes in knockouts in single cell organisms has been replaced by the apparition of MTases in numerous disease models and clinical investigations. Major driving forces of the field include methylation mapping techniques, as well as the characterization of the various MTases, termed "writers." The latter term has spilled over from DNA modification in the neighboring epigenetics field, along with the designations "readers," applied to mediators of biological effects upon specific binding to a methylated RNA. Furthermore "eraser" enzymes effect the newly discovered oxidative removal of methylgroups. A sense of reversibility and dynamics has replaced the older perception of RNA modification as a concrete-cast, irreversible part of RNA maturation. A related concept concerns incompletely methylated residues, which, through permutation of each site, lead to inhomogeneous populations of numerous modivariants. This review recapitulates the major developments of the past decade outlined above, and attempts a prediction of upcoming trends. This article is categorized under: RNA Processing > RNA Editing and Modification.

Chemical methods and advanced sequencing technologies for deciphering mRNA modifications

RNA modification, like other epigenetic modifications such as DNA modification and histone modification, is an emerging player in the field of the posttranscriptional regulation of gene expression. More than 160 kinds of RNA modifications have been identified, and they are widely distributed in different types of RNA. Recently, researchers have increasingly used advanced technologies to study modified nucleic acids in order to elucidate their biological functions and expand the understanding of the central laws of epigenetics. In this tutorial review, we comprehensively outline current advanced techniques for decoding RNA modifications, highlighting some of the bottlenecks in existing approaches as well as new opportunities that may lead to innovations. With this review, we expect to provide chemistry and biology students and researchers with ideas for solving some challenging problems, such as how to simultaneously detect multiple types of modifications within the same system. Moreover, some low-coverage modifications that may act as 'candidates' in important transcriptional processes need to be further explored. These novel approaches have the potential to lay a foundation for understanding the nuanced complexities of the biological functions of RNA modification.

Repurposing RNA sequencing for discovery of RNA modifications in clinical cohorts

The study of RNA modifications in large clinical cohorts can reveal relationships between the epitranscriptome and human diseases, although this is especially challenging. We developed ModTect (https://github.com/ktan8/ModTect), a statistical framework to identify RNA modifications de novo by standard RNA-sequencing with deletion and mis-incorporation signals. We show that ModTect can identify both known (N ¹-methyladenosine) and previously unknown types of mRNA modifications (N ²,N ²-dimethylguanosine) at nucleotide-resolution. Applying ModTect to 11,371 patient samples and 934 cell lines across 33 cancer types, we show that the epitranscriptome was dysregulated in patients across multiple cancer types and was additionally associated with cancer progression and survival outcomes. Some types of RNA modification were also more disrupted than others in patients with cancer. Moreover, RNA modifications contribute to multiple types of RNA-DNA sequence differences, which unexpectedly escape detection by Sanger sequencing. ModTect can thus be used to discover associations between RNA modifications and clinical outcomes in patient cohorts.

Mapping messenger RNA methylations at single base resolution

The messenger RNA (mRNA) methylations in mammalian cells have been found to contain N⁶-methyladenosine (m⁶A), N⁶-2'-O-dimethyladenosine (m⁶Am), 7-methylguanosine (m⁷G), 1-methyladenosine (m¹A), 5-methylcytosine (m⁵C), and 2'-O-methylation (2'-OMe). Their regulatory functions in control of mRNA fate and gene expression are being increasingly uncovered. To unambiguously understand the critical roles of mRNA methylations in physiological and pathological processes, mapping these methylations at single base resolution is highly required. Here, we will review the progresses made in methylation sequencing methodologies developed mainly in recent two years, with an emphasis on chemical labeling-assisted single base resolution methods, and discuss the problems and prospects as well.

Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update

The precise mapping and quantification of the numerous RNA modifications that are present in tRNAs, rRNAs, ncRNAs/miRNAs, and mRNAs remain a major challenge and a top priority of the epitranscriptomics field. After the keystone discoveries of massive m⁶A methylation in mRNAs, dozens of deep sequencing-based methods and protocols were proposed for the analysis of various RNA modifications, allowing us to considerably extend the list of detectable modified residues. Many of the currently used methods rely on the particular reverse transcription signatures left by RNA modifications in cDNA; these signatures may be naturally present or induced by an appropriate enzymatic or chemical treatment. The newest approaches also include labeling at RNA abasic sites that result from the selective removal of RNA modification or the enhanced cleavage of the RNA ribose-phosphate chain (perhaps also protection from cleavage), followed by specific adapter ligation. Classical affinity/immunoprecipitation-based protocols use either antibodies against modified RNA bases or proteins/enzymes, recognizing RNA modifications. In this survey, we review the most recent achievements in this highly dynamic field, including promising attempts to map RNA modifications by the direct single-molecule sequencing of RNA by nanopores.

Mapping the epigenetic modifications of DNA and RNA

Over 17 and 160 types of chemical modifications have been identified in DNA and RNA, respectively. The interest in understanding the various biological functions of DNA and RNA modifications has lead to the cutting-edged fields of epigenomics and epitranscriptomics. Developing chemical and biological tools to detect specific modifications in the genome or transcriptome has greatly facilitated their study. Here, we review the recent technological advances in this rapidly evolving field. We focus on high-throughput detection methods and biological findings for these modifications, and discuss questions to be addressed as well. We also summarize third-generation sequencing methods, which enable long-read and single-molecule sequencing of DNA and RNA modification.

Comprehensive review and assessment of computational methods for predicting RNA post-transcriptional modification sites from RNA sequences

RNA post-transcriptional modifications play a crucial role in a myriad of biological processes and cellular functions. To date, more than 160 RNA modifications have been discovered; therefore, accurate identification of RNA-modification sites is fundamental for a better understanding of RNA-mediated biological functions and mechanisms. However, due to limitations in experimental methods, systematic identification of different types of RNA-modification sites remains a major challenge. Recently, more than 20 computational methods have been developed to identify RNA-modification sites in tandem with high-throughput experimental methods, with most of these capable of predicting only single types of RNA-modification sites. These methods show high diversity in their dataset size, data quality, core algorithms, features extracted and feature selection techniques and evaluation strategies. Therefore, there is an urgent need to revisit these methods and summarize their methodologies, in order to improve and further develop computational techniques to identify and characterize RNA-modification sites from the large amounts of sequence data. With this goal in mind, first, we provide a comprehensive survey on a large collection of 27 state-of-the-art approaches for predicting N1-methyladenosine and N6-methyladenosine sites. We cover a variety of important aspects that are crucial for the development of successful predictors, including the dataset quality, operating algorithms, sequence and genomic features, feature selection, model performance evaluation and software utility. In addition, we also provide our thoughts on potential strategies to improve the model performance. Second, we propose a computational approach called DeepPromise based on deep learning techniques for simultaneous prediction of N1-methyladenosine and N6-methyladenosine. To extract the sequence context surrounding the modification sites, three feature encodings, including enhanced nucleic acid composition, one-hot encoding, and RNA embedding, were used as the input to seven consecutive layers of convolutional neural networks (CNNs), respectively. Moreover, DeepPromise further combined the prediction score of the CNN-based models and achieved around 43% higher area under receiver-operating curve (AUROC) for m1A site prediction and 2–6% higher AUROC for m6A site prediction, respectively, when compared with several existing state-of-the-art approaches on the independent test. In-depth analyses of characteristic sequence motifs identified from the convolution-layer filters indicated that nucleotide presentation at proximal positions surrounding the modification sites contributed most to the classification, whereas those at distal positions also affected classification but to different extents. To maximize user convenience, a web server was developed as an implementation of DeepPromise and made publicly available at http://DeepPromise.erc.monash.edu/, with the server accepting both RNA sequences and genomic sequences to allow prediction of two types of putative RNA-modification sites.

Reading Chemical Modifications in the Transcriptome

Diverse chemical modifications have been identified in the transcriptome, leading to the emerging field of epitranscriptomics. In eukaryotic mRNA, the 5' cap and 3' poly(A) tail play important roles in regulation, and multiple internal modifications have also been revealed to participate in RNA metabolism. In this review, we focus on internal modifications in eukaryotic mRNA, including modifications to A/U/C/G bases and to ribose as well. We provide an overview of their biogenesis, high-throughput detection methods, biological functions, and regulatory mechanisms, with an emphasis on their reported reader proteins (RNA-binding proteins that specifically bind to modified RNA). We also briefly discuss the current problems in the investigation of mRNA modifications that need to be solved.

Evolution of a reverse transcriptase to map N1-methyladenosine in human messenger RNA

Chemical modifications to messenger RNA are increasingly recognized as a critical regulatory layer in the flow of genetic information, but quantitative tools to monitor RNA modifications in a whole-transcriptome and site-specific manner are lacking. Here we describe a versatile platform for directed evolution that rapidly selects for reverse transcriptases that install mutations at sites of a given type of RNA modification during reverse transcription, allowing for site-specific identification of the modification. To develop and validate the platform, we evolved the HIV-1 reverse transcriptase against N¹-methyladenosine (m¹A). Iterative rounds of selection yielded reverse transcriptases with both robust read-through and high mutation rates at m¹A sites. The optimal evolved reverse transcriptase enabled detection of well-characterized m¹A sites and revealed hundreds of m¹A sites in human mRNA. This work develops and validates the reverse transcriptase evolution platform, and provides new tools, analysis methods and datasets to study m¹A biology.

Methods for RNA Modification Mapping Using Deep Sequencing: Established and New Emerging Technologies

New analytics of post-transcriptional RNA modifications have paved the way for a tremendous upswing of the biological and biomedical research in this field. This especially applies to methods that included RNA-Seq techniques, and which typically result in what is termed global scale modification mapping. In this process, positions inside a cell’s transcriptome are receiving a status of potential modification sites (so called modification calling), typically based on a score of some kind that issues from the particular method applied. The resulting data are thought to represent information that goes beyond what is contained in typical transcriptome data, and hence the field has taken to use the term “epitranscriptome”. Due to the high rate of newly published mapping techniques, a significant number of chemically distinct RNA modifications have become amenable to mapping, albeit with variegated accuracy and precision, depending on the nature of the technique. This review gives a brief overview of known techniques, and how they were applied to modification calling.