-
Molecular Cell Feb 2022N-methyladenosine (mA) is an abundant RNA modification that plays critical roles in RNA regulation and cellular function. Global mA profiling has revealed important...
N-methyladenosine (mA) is an abundant RNA modification that plays critical roles in RNA regulation and cellular function. Global mA profiling has revealed important aspects of mA distribution and function, but to date such studies have been restricted to large populations of cells. Here, we develop a method to identify mA sites transcriptome-wide in single cells. We uncover surprising heterogeneity in the presence and abundance of mA sites across individual cells and identify differentially methylated mRNAs across the cell cycle. Additionally, we show that cellular subpopulations can be distinguished based on their RNA methylation signatures, independent from gene expression. These studies reveal fundamental features of mA that have been missed by mA profiling of bulk cells and suggest the presence of cell-intrinsic mechanisms for mA deposition.
Topics: Adenosine; Gene Expression Profiling; HEK293 Cells; Humans; Methylation; RNA Processing, Post-Transcriptional; RNA, Messenger; Sequence Analysis, RNA; Single-Cell Analysis; Transcriptome
PubMed: 35081365
DOI: 10.1016/j.molcel.2021.12.038 -
Nature Genetics Aug 2021The most prevalent post-transcriptional mRNA modification, N-methyladenosine (mA), plays diverse RNA-regulatory roles, but its genetic control in human tissues remains...
The most prevalent post-transcriptional mRNA modification, N-methyladenosine (mA), plays diverse RNA-regulatory roles, but its genetic control in human tissues remains uncharted. Here we report 129 transcriptome-wide mA profiles, covering 91 individuals and 4 tissues (brain, lung, muscle and heart) from GTEx/eGTEx. We integrate these with interindividual genetic and expression variation, revealing 8,843 tissue-specific and 469 tissue-shared mA quantitative trait loci (QTLs), which are modestly enriched in, but mostly orthogonal to, expression QTLs. We integrate mA QTLs with disease genetics, identifying 184 GWAS-colocalized mA QTL, including brain mA QTLs underlying neuroticism, depression, schizophrenia and anxiety; lung mA QTLs underlying expiratory flow and asthma; and muscle/heart mA QTLs underlying coronary artery disease. Last, we predict novel mA regulators that show preferential binding in mA QTLs, protein interactions with known mA regulators and expression correlation with the mA levels of their targets. Our results provide important insights and resources for understanding both cis and trans regulation of epitranscriptomic modifications, their interindividual variation and their roles in human disease.
Topics: Adenosine; Brain; Genome-Wide Association Study; Heart; Humans; Lung; Methylation; Muscle, Skeletal; Organ Specificity; Polymorphism, Single Nucleotide; Quantitative Trait Loci; RNA Processing, Post-Transcriptional; RNA-Binding Proteins; Reproducibility of Results
PubMed: 34211177
DOI: 10.1038/s41588-021-00890-3 -
Profiles of Drug Substances,... 2022Ticagrelor is one of the most recent antiplatelet agents used to inhibit platelet aggregation via blocking the ADP receptors of the subtype P2Y. It belongs to the... (Review)
Review
Ticagrelor is one of the most recent antiplatelet agents used to inhibit platelet aggregation via blocking the ADP receptors of the subtype P2Y. It belongs to the non-thienopyridine class. The drug was first discovered by Astra Zeneca and approved for use in 2011 by the FDA. Ticagrelor is usually used for the prevention and treatment of thromboembolism in adult patients with acute coronary syndrome. This chapter include an overview on the physical properties, chemical properties, mode of action, pharmacokinetics and common uses of ticagrelor. In addition, the reported methods of ticagrelor assay will be discussed briefly in order to help analysts to find the most convenient method for its estimation in routine analysis. The methods of synthesis used for the preparation of ticagrelor will also be covered in this chapter. Moreover, the analytical and characterization techniques used to characterize ticagrelor row material are summarized herein.
Topics: Acute Coronary Syndrome; Adenosine; Adult; Humans; Platelet Aggregation; Platelet Aggregation Inhibitors; Purinergic P2Y Receptor Antagonists; Ticagrelor
PubMed: 35396017
DOI: 10.1016/bs.podrm.2021.10.003 -
Nature Methods Dec 2019N-methyladenosine (mA) is a widespread RNA modification that influences nearly every aspect of the messenger RNA lifecycle. Our understanding of mA has been facilitated...
N-methyladenosine (mA) is a widespread RNA modification that influences nearly every aspect of the messenger RNA lifecycle. Our understanding of mA has been facilitated by the development of global mA mapping methods, which use antibodies to immunoprecipitate methylated RNA. However, these methods have several limitations, including high input RNA requirements and cross-reactivity to other RNA modifications. Here, we present DART-seq (deamination adjacent to RNA modification targets), an antibody-free method for detecting mA sites. In DART-seq, the cytidine deaminase APOBEC1 is fused to the mA-binding YTH domain. APOBEC1-YTH expression in cells induces C-to-U deamination at sites adjacent to mA residues, which are detected using standard RNA-seq. DART-seq identifies thousands of mA sites in cells from as little as 10 ng of total RNA and can detect mA accumulation in cells over time. Additionally, we use long-read DART-seq to gain insights into mA distribution along the length of individual transcripts.
Topics: APOBEC-1 Deaminase; Adenosine; Base Sequence; Deamination; HEK293 Cells; Humans; Transcriptome
PubMed: 31548708
DOI: 10.1038/s41592-019-0570-0 -
Nature Biotechnology Jun 2022Current methods for programmed RNA editing using endogenous ADAR enzymes and engineered ADAR-recruiting RNAs (arRNAs) suffer from low efficiency and bystander off-target...
Current methods for programmed RNA editing using endogenous ADAR enzymes and engineered ADAR-recruiting RNAs (arRNAs) suffer from low efficiency and bystander off-target editing. Here, we describe LEAPER 2.0, an updated version of LEAPER that uses covalently closed circular arRNAs, termed circ-arRNAs. We demonstrate on average ~3.1-fold higher editing efficiency than their linear counterparts when expressed in cells or delivered as in vitro-transcribed circular RNA oligonucleotides. To lower off-target editing we deleted pairings of uridines with off-target adenosines, which almost completely eliminated bystander off-target adenosine editing. Engineered circ-arRNAs enhanced the efficiency and fidelity of editing endogenous CTNNB1 and mutant TP53 transcripts in cell culture. Delivery of circ-arRNAs using adeno-associated virus in a mouse model of Hurler syndrome corrected the pathogenic point mutation and restored α-L-iduronidase catalytic activity, lowering glycosaminoglycan accumulation in the liver. LEAPER 2.0 provides a new design of arRNA that enables more precise, efficient RNA editing with broad applicability for therapy and basic research.
Topics: Adenosine; Adenosine Deaminase; Animals; Hydrolases; Mice; RNA; RNA Editing; RNA, Circular; RNA-Binding Proteins
PubMed: 35145313
DOI: 10.1038/s41587-021-01180-3 -
Current Opinion in Genetics &... Aug 2022Remarkable technological progress has led to breakthrough discoveries in epitranscriptomics, reshaping our understanding of modifications decorating RNA. The past decade... (Review)
Review
Remarkable technological progress has led to breakthrough discoveries in epitranscriptomics, reshaping our understanding of modifications decorating RNA. The past decade has seen a tremendous endeavor to describe the nature, functions, and biological roles of messenger RNA (mRNA) modifications, positioning epitranscriptomics as a crucial pillar in tumor biology. Like DNA and histone modifications, mRNA marks have been increasingly linked to cancer pathogenesis. Here, we summarize the latest research in cancer epitranscriptomics with emphasis on N6-methyladenosine, untangling its contribution to five prime oncogenic features: tumor growth, activating invasion and metastasis, stemness, metabolic reprogramming, and tumor microenvironment. We discuss mRNA-modifying enzymes, their impact on biological processes, and contribution to cancer hallmarks. We spotlight epitranscriptomics as a promising bonanza for forthcoming targeting approaches in cancer therapy.
Topics: Adenosine; DNA; Humans; Neoplasms; RNA; RNA, Messenger; Tumor Microenvironment
PubMed: 35679814
DOI: 10.1016/j.gde.2022.101924 -
Genes Dec 2022Chronic lung diseases are highly prevalent worldwide and cause significant mortality. Lung cancer is the end stage of many chronic lung diseases. RNA epigenetics can... (Review)
Review
Chronic lung diseases are highly prevalent worldwide and cause significant mortality. Lung cancer is the end stage of many chronic lung diseases. RNA epigenetics can dynamically modulate gene expression and decide cell fate. Recently, studies have confirmed that RNA epigenetics plays a crucial role in the developing of chronic lung diseases. Further exploration of the underlying mechanisms of RNA epigenetics in chronic lung diseases, including lung cancer, may lead to a better understanding of the diseases and promote the development of new biomarkers and therapeutic strategies. This article reviews basic information on RNA modifications, including methylation of adenosine (mA), methylation of adenosine (mA), -methylguanosine (mG), 5-methylcytosine (mC), 2'O-methylation (2'-O-Me or Nm), pseudouridine (5-ribosyl uracil or Ψ), and adenosine to inosine RNA editing (A-to-I editing). We then show how they relate to different types of lung disease. This paper hopes to summarize the mechanisms of RNA modification in chronic lung disease and finds a new way to develop early diagnosis and treatment of chronic lung disease.
Topics: Humans; RNA; Methylation; Epigenesis, Genetic; Adenosine; Lung Neoplasms
PubMed: 36553648
DOI: 10.3390/genes13122381 -
Clinical and Translational Medicine Jun 2024Dysregulated RNA modifications, stemming from the aberrant expression and/or malfunction of RNA modification regulators operating through various pathways, play pivotal... (Review)
Review
Dysregulated RNA modifications, stemming from the aberrant expression and/or malfunction of RNA modification regulators operating through various pathways, play pivotal roles in driving the progression of haematological malignancies. Among RNA modifications, N-methyladenosine (mA) RNA modification, the most abundant internal mRNA modification, stands out as the most extensively studied modification. This prominence underscores the crucial role of the layer of epitranscriptomic regulation in controlling haematopoietic cell fate and therefore the development of haematological malignancies. Additionally, other RNA modifications (non-mA RNA modifications) have gained increasing attention for their essential roles in haematological malignancies. Although the roles of the mA modification machinery in haematopoietic malignancies have been well reviewed thus far, such reviews are lacking for non-mA RNA modifications. In this review, we mainly focus on the roles and implications of non-mA RNA modifications, including N-acetylcytidine, pseudouridylation, 5-methylcytosine, adenosine to inosine editing, 2'-O-methylation, N-methyladenosine and N-methylguanosine in haematopoietic malignancies. We summarise the regulatory enzymes and cellular functions of non-mA RNA modifications, followed by the discussions of the recent studies on the biological roles and underlying mechanisms of non-mA RNA modifications in haematological malignancies. We also highlight the potential of therapeutically targeting dysregulated non-mA modifiers in blood cancer.
Topics: Humans; Hematologic Neoplasms; RNA Processing, Post-Transcriptional; RNA; Adenosine
PubMed: 38880983
DOI: 10.1002/ctm2.1666 -
Current Drug Targets 2022Epilepsy, a complex neurological syndrome with dominant symptoms and various comorbidities, affects over 70 million people worldwide. Epilepsy-related comorbidities,... (Review)
Review
Epilepsy, a complex neurological syndrome with dominant symptoms and various comorbidities, affects over 70 million people worldwide. Epilepsy-related comorbidities, including cognitive and psychiatric disorders, can impede therapy for epilepsy patients, leading to heavy burdens on patients and society. Adenosine has an anti-epileptic and anticonvulsive function in the brain. Several studies have shown that, through adenosine receptor-dependent and -independent mechanisms, adenosine can influence the development and progression (epileptogenesis) of epilepsy and its associated comorbidities. As the key enzyme for adenosine clearance, adenosine kinase (ADK) can exacerbate epileptic seizures not only by accelerating adenosine clearance, but also by increasing global DNA methylation through the transmethylation pathway. Therefore, adenosine augmentation therapies for epilepsy can have dual functions in the inhibition of epileptic seizures and the prevention of its overall progress. This review has three main purposes. First, we discuss how maladaptive changes in the adenosine pathway affect the development and progress of epilepsy in both receptor-dependent and receptor-independent ways. Second, we highlight the important influence of associated comorbidities on the prognosis of epilepsy and explore the role of adenosine in these comorbidities. Finally, we emphasize the potential of adenosine augmentation therapies in restoring normal adenosine signaling in the epileptic brain. Such treatments could effectively improve the prognosis of patients who are resistant to most antiepileptic drugs (AEDs), and thus bring new challenges and opportunities in the treatment of epilepsy patients.
Topics: Adenosine; Adenosine Kinase; Anticonvulsants; Epilepsy; Humans; Seizures
PubMed: 34602036
DOI: 10.2174/1389450122666210928145258 -
American Journal of Physiology. Cell... Jun 2022Fibroblasts play an important role in the pathogenic mechanisms of several socially significant diseases, including pulmonary and cardiovascular fibrosis, liver... (Review)
Review
Fibroblasts play an important role in the pathogenic mechanisms of several socially significant diseases, including pulmonary and cardiovascular fibrosis, liver cirrhosis, systemic sclerosis, progressive kidney disease. The alterations of the epitranscriptome, including more than 170 distinct posttranscriptional RNA modifications or editing events, justified their investigation as an important modulator of fibrosis. Recent development of high-throughput methods allows the identification of RNA modification sites and their mechanistic aspect in the fibrosis development. The most common RNA modification is methylation of N-adenosine deposited by the mA methyltransferase complex (METTL3/14/16, WTAP, KIAA1429, and RBM15/15B), erased by demethylases (FTO and ALKBH5), and recognized by binding proteins (e.g., YTHDF1/2/3, YTHDC1/2, IGF2BP1/2/3, etc.). Adenosine to inosine (A-to-I) RNA editing is another abundant editing event converting adenosine to inosine in double-stranded RNA regions through the action of the adenosine deaminase (ADAR) proteins. Last but not least, 5-methylcytosine (mC) regulates the stability and translation of mRNAs. All those RNA modifications have been observed in mRNA as well as the noncoding regions of pre-mRNA and noncoding RNAs (ncRNAs) and demonstrated to be involved in fibrosis in different cellular and animal models. This Mini-Review focuses on the latest research on epitranscriptomic marks related to fibroblast biology and fibrosis as well as elucidates the future research directions in this context.
Topics: Adenosine; Animals; Fibroblasts; Fibrosis; Inosine; RNA; RNA, Messenger
PubMed: 35508185
DOI: 10.1152/ajpcell.00121.2022