RNA Methylation in ncRNA: Classes, Detection, and Molecular Associations

Global DNA and RNA Methylation Signature in Response to Antipsychotic Treatment in First-Episode Schizophrenia Patients

Background

Schizophrenia is a heterogeneous chronic psychiatric disorder influenced by genetic and environmental factors. Environmental factors can alter epigenetic marks, which regulate gene expression and cause an array of systemic changes. Several studies have demonstrated the association of epigenetic modulations in schizophrenia, which can influence clinical course, symptoms, and even treatment. Based on this, we have examined the global DNA methylation patterns, namely the 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC); and the global RNA modification N6-methyladenosine (m6A) RNA methylation status in peripheral blood cells. First-Episode Psychosis (FEP) patients who were diagnosed with Schizophrenia (SCZ) and undergoing treatment were stratified as Treatment-Responsive (TR) and Treatment-Non-Responsive (TNR). Age- and sex-matched healthy subjects served as controls.

Results

The methylation pattern of 5mC and 5hmC showed significant increases in patients in comparison to controls. Further, when patients were classified based on their response to treatment, there was a statistically significant increase in methylation patterns in the treatment non-responder group. 5fC and m6A levels did not show any statistical significance across the groups. Further, gender-based stratification did not yield any significant difference for the markers.

Conclusion

The study highlights the increased global methylation pattern in SCZ patients and a significant difference between the TR versus TNR groups. Global 5mC and 5hmC epigenetic marks suggest their potential roles in schizophrenia pathology, and also in the treatment response to antipsychotics. Since not many studies were available on the treatment response, further validation and the use of more sensitive techniques to study methylation status could unravel the potential of these epigenetic modifications as biomarkers for SCZ as well as distinguishing the antipsychotic treatment response in patients.

Revisiting Epigenetics Fundamentals and Its Biomedical Implications

In light of the post-genomic era, epigenetics brings about an opportunity to better understand how the molecular machinery works and is led by a complex dynamic set of mechanisms, often intricate and complementary in many aspects. In particular, epigenetics links developmental biology and genetics, as well as many other areas of knowledge. The present work highlights substantial scopes and relevant discoveries related to the development of the term from its first notions. To our understanding, the concept of epigenetics needs to be revisited, as it is one of the most relevant and multifaceted terms in human knowledge. To redirect future novel experimental or theoretical efforts, it is crucial to compile all significant issues that could impact human and ecological benefit in the most precise and accurate manner. In this paper, the reader can find one of the widest compilations of the landmarks and epistemic considerations of the knowledge of epigenetics across the history of biology from the earliest epigenetic formulation to genetic determinism until the present. In the present work, we link the current body of knowledge and earlier pre-genomic concepts in order to propose a new definition of epigenetics that is faithful to its regulatory nature.

A role for a Trypanosoma brucei cytosine RNA methyltransferase homolog in ribosomal RNA processing

In Trypanosoma brucei, gene expression is primarily regulated posttranscriptionally making RNA metabolism critical. T. brucei has an epitranscriptome containing modified RNA bases. Yet, the identity of the enzymes catalyzing modified RNA base addition and the functions of the enzymes and modifications remain unclear. Homology searches indicate the presence of numerous T. brucei cytosine RNA methyltransferase homologs. One such homolog, TbNop2 was studied in detail. TbNop2 contains the six highly conserved motifs found in cytosine RNA methyltransferases and is evolutionarily related to the Nop2 protein family required for rRNA modification and processing. RNAi experiments targeting TbNop2 resulted in reduced levels of TbNop2 RNA and protein, and a cessation of parasite growth. Next generation sequencing of bisulfite-treated RNA (BS-seq) detected the presence of two methylation sites in the large rRNA; yet TbNop2 RNAi did not result in a significant reduction of methylation. However, TbNop2 RNAi resulted in the retention of 28S internal transcribed spacer RNAs, indicating a role for TbNop2 in rRNA processing.

Anti-resorption role of low-intensity pulsed ultrasound (LIPUS) during large-scale bone reconstruction using porous titanium alloy scaffolds through inhibiting osteoclast differentiation

BACKGROUND

Ti6Al4V biomaterials combine with low-intensity pulsed ultrasound (LIPUS) has been reported with great bone regeneration capacity. It is important to better understand how LIPUS benefits bone microenvironment to seek for target of therapeutic medicine. Osteoclast differentiation plays a crucial role in bone resorption. Recent advances in molecular biology have revealed that N6-methyladenosine (m6A) RNA modifications can modulate biological processes, but their role in bone biology, particularly in osteoclast differentiation, remains unclear. We aim to understand how LIPUS regulates bone microenvironment especially osteoclast formation during bone regeneration to provide new therapeutic options for preventing and delaying bone resorption, thus with better bone regeneration efficiency.

RESULTS

1. LIPUS promoted bone ingrowth and bone maturity while inhibiting osteoclast formation within Ti6Al4V scaffolds in large-scale bone defect model. 2. LIPUS was found to inhibit osteoclast differentiation by decreasing the overall expression of osteoclast markers in vitro. 3. LIPUS decreases RNA m6A-modification level through upregulating FTO expression during osteoclast differentiation during. 4. Inhibiting FTO expression and function leads to less inhibition during osteoclast differentiation.

CONCLUSION

LIPUS suppresses osteoclast differentiation during bone regeneration through reducing m6A modification of osteoclastic RNAs by up regulating FTO expression.

Development of a sensitive microplate assay for characterizing RNA methyltransferase activity: Implications for epitranscriptomics and drug development

RNA methylation is a ubiquitous post-transcriptional modification found in diverse RNA classes and is a critical regulator of gene expression. In this study, we used Zika virus RNA methyltransferase (MTase) to develop a highly sensitive microplate assay that uses a biotinylated RNA substrate and radiolabeled AdoMet coenzyme. The assay is fast, highly reproducible, exhibits linear progress-curve kinetics under multiple turnover conditions, has high sensitivity in competitive inhibition assays, and significantly lower background levels compared with the currently used method. Using our newly developed microplate assay, we observed no significant difference in the catalytic constants of the full-length nonstructural protein 5 enzyme and the truncated MTase domain. These data suggest that, unlike the Zika virus RNA-dependent RNA polymerase activity, the MTase activity is unaffected by RNA-dependent RNA polymerase-MTase interdomain interaction. Given its quantitative nature and accuracy, this method can be used to characterize various RNA MTases, and, therefore, significantly contribute to the field of epitranscriptomics and drug development against infectious diseases.

Modifications of noncoding RNAs in cancer and their therapeutic implications

In the last 50 years, over 150 various chemical modifications on RNA molecules, including mRNAs, rRNAs, tRNAs, and other noncoding RNAs (ncRNAs), have been identified and characterized. These RNA modifications regulate RNA biogenesis and biological functions and are widely involved in various physiological processes and diseases, including cancer. In recent decades, broad interest has arisen in the epigenetic modification of ncRNAs due to the increased knowledge of the critical roles of ncRNAs in cancer. In this review, we summarize the various modifications of ncRNAs and highlight their roles in cancer initiation and progression. In particular, we discuss the potential of RNA modifications as novel biomarkers and therapeutic targets in cancer.

Emerging role of mRNA methylation in regulating the hallmarks of cancer

The dynamic chemical modifications of DNA, RNA, and proteins can transform normal cells into malignant ones. While the DNA and protein modifications in cancer have been described extensively in the literature, there are fewer reports about the role of RNA modifications in cancer. There are over 100 forms of RNA modifications and one of these, mRNA methylation, plays a critical role in the malignant properties of the cells. mRNA methylation is a reversible modification responsible for regulating protein expression at the post-transcriptional level. Despite being discovered in the 1970s, a complete understanding of the different proteins involved and the mechanism behind mRNA methylation remains largely unknown. However, these mRNA methylations have been shown to foster cancer hallmarks via specific cellular targets inside the cell. In this review, we provide a brief overview of mRNA methylation and its emerging role in regulating the various hallmarks of cancer.

Synthesis of 2'-modified N6-methyladenosine phosphoramidites and their incorporation into siRNA

A synthesis of 2'-fluoro and 2'-methoxy N6-methyladenosine phosphoramidites and their successful incorporation into oligonucleotides is reported. 2'-fluoro and 2́-methoxy modifications of sugars in siRNAs are known to aid stability and N6-methylation modifies the potency of therapeutic silencing RNAs (siRNA). We demonstrate that a combination of those modifications incorporated into the antisense strand of siRNA leads to efficient knockdown of a target gene in cells. This work broadens the available pool of chemical modifications of therapeutic siRNAs and provides tools for their efficient synthesis.

N6-methyladenosine (m6A) RNA modification as a metabolic switch between plant cell survival and death in leaf senescence

Crop losses caused by climate change and various (a)biotic stressors negatively affect agriculture and crop production. Therefore, it is vital to develop a proper understanding of the complex response(s) to (a)biotic stresses and delineate them for each crop plant as a means to enable translational research. In plants, the improvement of crop quality by m⁶A editing is believed to be a promising strategy. As a reaction to environmental changes, m⁶A modification showed a high degree of sensitivity and complexity. We investigated differences in gene medleys between dark-induced leaf senescence (DILS) and developmental leaf senescence in barley, including inter alia RNA modifications active in DILS. The identified upregulated genes in DILS include RNA methyltransferases of different RNA types, embracing enzymes modifying mRNA, tRNA, and rRNA. We have defined a decisive moment in the DILS model which determines the point of no return, but the mechanism of its control is yet to be uncovered. This indicates the possibility of an unknown additional switch between cell survival and cell death. Discoveries of m⁶A RNA modification changes in certain RNA species in different stages of leaf senescence may uncover the role of such modifications in metabolic reprogramming. Nonetheless, there is no such data about the process of leaf senescence in plants. In this scope, the prospect of finding connections between the process of senescence and m⁶A modification of RNA in plants seems to be compelling.

Mitochondrial Genetic and Epigenetic Regulations in Cancer: Therapeutic Potential

Mitochondria are dynamic organelles managing crucial processes of cellular metabolism and bioenergetics. Enabling rapid cellular adaptation to altered endogenous and exogenous environments, mitochondria play an important role in many pathophysiological states, including cancer. Being under the control of mitochondrial and nuclear DNA (mtDNA and nDNA), mitochondria adjust their activity and biogenesis to cell demands. In cancer, numerous mutations in mtDNA have been detected, which do not inactivate mitochondrial functions but rather alter energy metabolism to support cancer cell growth. Increasing evidence suggests that mtDNA mutations, mtDNA epigenetics and miRNA regulations dynamically modify signalling pathways in an altered microenvironment, resulting in cancer initiation and progression and aberrant therapy response. In this review, we discuss mitochondria as organelles importantly involved in tumorigenesis and anti-cancer therapy response. Tumour treatment unresponsiveness still represents a serious drawback in current drug therapies. Therefore, studying aspects related to genetic and epigenetic control of mitochondria can open a new field for understanding cancer therapy response. The urgency of finding new therapeutic regimens with better treatment outcomes underlines the targeting of mitochondria as a suitable candidate with new therapeutic potential. Understanding the role of mitochondria and their regulation in cancer development, progression and treatment is essential for the development of new safe and effective mitochondria-based therapeutic regimens.

Obesity II: Establishing causal links between chemical exposures and obesity

Obesity is a multifactorial disease with both genetic and environmental components. The prevailing view is that obesity results from an imbalance between energy intake and expenditure caused by overeating and insufficient exercise. We describe another environmental element that can alter the balance between energy intake and energy expenditure: obesogens. Obesogens are a subset of environmental chemicals that act as endocrine disruptors affecting metabolic endpoints. The obesogen hypothesis posits that exposure to endocrine disruptors and other chemicals can alter the development and function of the adipose tissue, liver, pancreas, gastrointestinal tract, and brain, thus changing the set point for control of metabolism. Obesogens can determine how much food is needed to maintain homeostasis and thereby increase the susceptibility to obesity. The most sensitive time for obesogen action is in utero and early childhood, in part via epigenetic programming that can be transmitted to future generations. This review explores the evidence supporting the obesogen hypothesis and highlights knowledge gaps that have prevented widespread acceptance as a contributor to the obesity pandemic. Critically, the obesogen hypothesis changes the narrative from curing obesity to preventing obesity.

Emerging role of m6A modification in osteogenesis of stem cells

The differentiation of stem cells into osteoblasts is a key link in the treatment of bone defects and other orthopedic diseases. N6-methyladenosine (m6A) modification, an important post-transcriptional modification, is a methylation that occurs at the N6 site of RNA adenylate. The modification plays a regulatory role in the growth and development of biological individuals, the directional differentiation of stem cells and the occurrence of diseases. It is involved in various processes of the fate decision of stem cells. And it regulates the development and constant renewal of bone and keeps bone homeostasis by controlling and maintaining the balance between osteogenesis and adipogenesis. Meanwhile, it also affects the progress of orthopedic-associated diseases such as degenerative osteoporosis and bone tumor. In this review, we mainly summarize the new findings of three key molecules including Writers, Erasers and Readers which regulate m6A modification, and the emerging role of m6A modification in determining the fate and directed differentiation potential of stem cells, especially highlight the regulatory mechanism of osteogenic differentiation, the balance between osteogenesis and adipogenesis and the occurrence and development of bone-related diseases. It may provide some important ideas about finding new strategies to recover from bone defect and degenerative bone disease.

Modulation of DNA/RNA Methylation by Small-Molecule Modulators and Their Implications in Cancer

Chromatin is an organized complex of DNA, histone proteins, and RNA. Chromatin modifications include DNA methylation, RNA methylation, and histone acetylation and methylation. The methylation of chromatin complexes predominantly alters the regulation of gene expression, and its deregulation is associated with several human diseases including cancer. Cancer is a disease characterized by dynamic changes in the genetic and epigenetic architecture of a cell. Altered DNA methylation by DNA methyltransferases (DNMTs) and m6A RNA methylation facilitate tumor initiation and progression and thus serve as critical targets for cancer therapy. Small-molecule modulators of these epigenetic targets are at the hotspots of current cancer drug discovery research. Indeed, recent studies have led to the discovery of several chemical modulators against these targets, some of which have already gained approval for cancer therapy while others are undergoing clinical trials. In this chapter, we will focus on the role of small-molecule modulators in regulating DNA/RNA methylation and their implications in cancer.

Extracellular Vesicles in Lung Cancer Metastasis and Their Clinical Applications

Extracellular vesicles (EVs) are heterogenous membrane-encapsulated vesicles secreted by every cell into the extracellular environment. EVs carry bioactive molecules, including proteins, lipids, DNA, and different RNA forms, which can be internalized by recipient cells, thus altering their biological characteristics. Given that EVs are commonly found in most body fluids, they have been widely described as mediators of communication in several physiological and pathological processes, including cancer. Moreover, their easy detection in biofluids makes them potentially useful candidates as tumor biomarkers. In this manuscript, we review the current knowledge regarding EVs and non-coding RNAs and their role as drivers of the metastatic process in lung cancer. Furthermore, we present the most recent applications for EVs and non-coding RNAs as cancer therapeutics and their relevance as clinical biomarkers.

Post-transcriptional diversity in riboproteins and RNAs in aging and cancer

Post-transcriptional (PtscM) and post-translational (PtrnM) modifications of nucleotides and amino acids are covalent modifications able to change physio-chemical properties of RNAs and proteins. In the ribosome, the adequate assembly of rRNAs and ribosomal protein subunits in the nucleolus ensures suitable translational activity, with protein synthesis tuned according to intracellular demands of energy production, replication, proliferation, and growth. Disruption in the regulatory control of PtscM and PtrnM can impair ribosome biogenesis and ribosome function. Ribosomal impairment may, in turn, impact the synthesis of proteins engaged in functions as varied as telomere maintenance, apoptosis, and DNA repair, as well as intersect with mitochondria and telomerase activity. These cellular processes often malfunction in carcinogenesis and senescence. Here we discuss regulatory mechanisms of PtscMs and PtrnMs on ribosomal function. We also address chemical modification in rRNAs and their impacts on cellular metabolism, replication control, and senescence. Further, we highlight similarities and differences of PtscMs and PtrnMs in ribosomal intermediates during aging and carcinogenesis. Understanding these regulatory mechanisms may uncover critical steps for the development of more efficient oncologic and anti-aging therapies.

Synthesis of N4 -Methylcytidine (m4 C) and N4 ,N4 -Dimethylcytidine (m4 2 C) Modified RNA

This article summarizes the protocols for phosphoramidite chemistry and solid phase synthesis of RNA oligonucleotides containing N⁴ -methylcytidine (m⁴ C) and N⁴ ,N⁴ -dimethylcytidine (m⁴ ₂ C) residues for base-pairing, structural, and enzymatic activity studies. The two key m⁴ C and m⁴ ₂ C phosphoramidite building blocks can be synthesized starting from the partially protected cytidine nucleosides, followed by solid-phase synthesis and HPLC purification of the modified target RNA oligonucleotides. These modified RNA strands are then prepared for base pairing stability, specificity, and structural studies using UV-melting temperature (T_m ) measurements and X-ray crystallography. Functional studies are performed by reverse transcription assays in primer extension reactions employing different enzymes. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Chemical synthesis of m⁴ C phosphoramidite Basic Protocol 2: Synthesis of m⁴ ₂ C phosphoramidite Basic Protocol 3: Synthesis and purification of m⁴ C and m⁴ ₂ C containing RNA oligonucleotides.

Identification of Abundant and Functional dodecaRNAs (doRNAs) Derived from Ribosomal RNA

Using a modified RNA-sequencing (RNA-seq) approach, we discovered a new family of unusually short RNAs mapping to ribosomal RNA 5.8S, which we named dodecaRNAs (doRNAs), according to the number of core nucleotides (12 nt) their members contain. Using a new quantitative detection method that we developed, we confirmed our RNA-seq data and determined that the minimal core doRNA sequence and its 13-nt variant C-doRNA (doRNA with a 5' Cytosine) are the two most abundant doRNAs, which, together, may outnumber microRNAs. The C-doRNA/doRNA ratio is stable within species but differed between species. doRNA and C-doRNA are mainly cytoplasmic and interact with heterogeneous nuclear ribonucleoproteins (hnRNP) A0, A1 and A2B1, but not Argonaute 2. Reporter gene activity assays suggest that C-doRNA may function as a regulator of Annexin II receptor (AXIIR) expression. doRNAs are differentially expressed in prostate cancer cells/tissues and may control cell migration. These findings suggest that unusually short RNAs may be more abundant and important than previously thought.

Long non-coding RNAs and their involvement in bipolar disorders

Non-coding RNAs (nc-RNAs) can be defined as RNA molecules that are not translated into proteins. Although the functional meaning of many nc-RNAs remains still to be verified, several of these molecules have a clear biological importance, which goes from translation of mRNAs to DNA replication. Indeed, regulatory nc-RNAs can be classified into two groups: short non-coding RNAs (sncRNAs) and long-non coding RNAs (lncRNAs). In the last years, lncRNAs have gained increasing importance in the study of gene regulation, helping authors understand the molecular mechanisms underlying cellular physiology and pathology. LncRNAs are greater than 200 bp and accumulate in nucleus, cytoplasm and exosomes with high tissue specificity, acting in cis or in trans in order to exert enhancer or silencer modulation on gene expression. Such regulatory features, which are widespread in human cells and tissues, can be disrupted in several morbid states. Recent evidences may suggest a disruption of lncRNAs in bipolar disorders, a cluster of severe, chronic and disabling psychiatric diseases, which are characterized by major depressive states cyclically alternating with manic episodes. Here, the authors reviewed genes, classification, biogenesis, structures, functions and databases regarding lncRNAs, and also focused on bipolar disorders, in which some lncRNAs, especially those involved in inflammation and neuronal development, has reported to be dysregulated.

Current understanding of epigenetics mechanism as a novel target in reducing cancer stem cells resistance

At present, after extensive studies in the field of cancer, cancer stem cells (CSCs) have been proposed as a major factor in tumor initiation, progression, metastasis, and recurrence. CSCs are a subpopulation of bulk tumors, with stem cell-like properties and tumorigenic capabilities, having the abilities of self-renewal and differentiation, thereby being able to generate heterogeneous lineages of cancer cells and lead to resistance toward anti-tumor treatments. Highly resistant to conventional chemo- and radiotherapy, CSCs have heterogeneity and can migrate to different organs and metastasize. Recent studies have demonstrated that the population of CSCs and the progression of cancer are increased by the deregulation of different epigenetic pathways having effects on gene expression patterns and key pathways connected with cell proliferation and survival. Further, epigenetic modifications (DNA methylation, histone modifications, and RNA methylations) have been revealed to be key drivers in the formation and maintenance of CSCs. Hence, identifying CSCs and targeting epigenetic pathways therein can offer new insights into the treatment of cancer. In the present review, recent studies are addressed in terms of the characteristics of CSCs, the resistance thereof, and the factors influencing the development thereof, with an emphasis on different types of epigenetic changes in genes and main signaling pathways involved therein. Finally, targeted therapy for CSCs by epigenetic drugs is referred to, which is a new approach in overcoming resistance and recurrence of cancer.

Multiple Functions of RNA Methylation in T Cells: A Review

RNA modification represents one of the most ubiquitous mechanisms of epigenetic regulation and plays an essential role in modulating cell proliferation, differentiation, fate determination, and other biological activities. At present, over 170 types of RNA modification have been discovered in messenger RNA (mRNA) and noncoding RNA (ncRNA). RNA methylation, as an abundant and widely studied epigenetic modification, is crucial for regulating various physiological or pathological states, especially immune responses. Considering the biological significance of T cells as a defense against viral infection and tumor challenge, in this review, we will summarize recent findings of how RNA methylation regulates T cell homeostasis and function, discuss the open questions in this rapidly expanding field of RNA modification, and provide the theoretical basis and potential therapeutic strategies involving targeting of RNA methylation to orchestrate beneficial T cell immune responses.

Non-Coding RNAs in Cancer Diagnosis and Therapy: Focus on Lung Cancer

Over the last several decades, clinical evaluation and treatment of lung cancers have largely improved with the classification of genetic drivers of the disease, such as EGFR, ALK, and ROS1. There are numerous regulatory factors that exert cellular control over key oncogenic pathways involved in lung cancers. In particular, non-coding RNAs (ncRNAs) have a diversity of regulatory roles in lung cancers such that they have been shown to be involved in inducing proliferation, suppressing apoptotic pathways, increasing metastatic potential of cancer cells, and acquiring drug resistance. The dysregulation of various ncRNAs in human cancers has prompted preclinical studies examining the therapeutic potential of restoring and/or inhibiting these ncRNAs. Furthermore, ncRNAs demonstrate tissue-specific expression in addition to high stability within biological fluids. This makes them excellent candidates as cancer biomarkers. This review aims to discuss the relevance of ncRNAs in cancer pathology, diagnosis, and therapy, with a focus on lung cancer.

Hypermethylation of Mitochondrial Cytochrome b and Cytochrome c Oxidase II Genes with Decreased Mitochondrial DNA Copy Numbers in the APP/PS1 Transgenic Mouse Model of Alzheimer's Disease

Alzheimer's disease (AD) is the most common cause of dementia. Increasing evidence shows that mitochondrial DNA (mtDNA) methylation plays an essential role in many diseases related to mitochondrial dysfunction. Since mitochondrial impairment is a key feature of AD, mtDNA methylation may also contribute to AD, but few studies have addressed this issue. Methylation changes of the mitochondrial cytochrome b (CYTB) and cytochrome c oxidase II (COX II) genes in AD have not been reported. We analyzed mtDNA methylation changes of the CYTB and COX II genes in an APP/PS1 transgenic mouse model of AD using pyrosequencing. We examined mtDNA copy numbers and the levels of expression by quantitative real-time PCR. Average methylation levels of different CpG sites were ≤ 4.0%. Methylated mtDNA accounted for only a small part of the total mtDNA. We also observed hypermethylation of mitochondrial CYTB and COX II genes with decreased mtDNA copy numbers and expression in the hippocampi of APP/PS1 transgenic mice. mtDNA methylation may play an important role in AD pathology, which may open a new window for AD therapy.

Context-Dependent Roles of RNA Modifications in Stress Responses and Diseases

RNA modifications are diverse post-transcriptional modifications that regulate RNA metabolism and gene expression. RNA modifications, and the writers, erasers, and readers that catalyze these modifications, serve as important signaling machineries in cellular stress responses and disease pathogenesis. In response to stress, RNA modifications are mobilized to activate or inhibit the signaling pathways that combat stresses, including oxidative stress, hypoxia, therapeutic stress, metabolic stress, heat shock, DNA damage, and ER stress. The role of RNA modifications in response to these cellular stressors is context- and cell-type-dependent. Due to their pervasive roles in cell biology, RNA modifications have been implicated in the pathogenesis of different diseases, including cancer, neurologic and developmental disorders and diseases, and metabolic diseases. In this review, we aim to summarize the roles of RNA modifications in molecular and cellular stress responses and diseases.

Potential regulatory role of epigenetic RNA methylation in cardiovascular diseases

Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality worldwide, especially in developing countries. To date, several approaches have been proposed for the prevention and treatment of CVDs. However, the increased risk of developing cardiovascular events that result in hospitalization has become a growing public health concern. The pathogenesis of CVDs has been analyzed from various perspectives. Recent data suggest that regulatory RNAs play a multidimensional role in the development of CVDs. Studies have identified several mRNA modifications that have contributed to the functional characterization of various cardiac diseases. RNA methylation, such as N6-methyladenosine, N1-methyladenosine, 5-methylcytosine, N7-methylguanosine, N4-acetylcytidine, and 2'-O-methylation are novel epigenetic modifications that affect the regulation of cell growth, immunity, DNA damage, calcium signaling, apoptosis, and aging in cardiomyocytes. In this review, we summarize the role of RNA methylation in the pathophysiology of CVDs and the potential of using epigenetics to treat such disorders.

Long non-coding RNA levels can be modulated by 5-azacytidine in Schistosoma mansoni

Schistosoma mansoni is a flatworm that causes schistosomiasis, a neglected tropical disease that affects more than 200 million people worldwide. There is only one drug indicated for treatment, praziquantel, which may lead to parasite resistance emergence. The ribonucleoside analogue 5-azacytidine (5-AzaC) is an epigenetic drug that inhibits S. mansoni oviposition and ovarian development through interference with parasite transcription, translation and stem cell activities. Therefore, studying the downstream pathways affected by 5-AzaC in S. mansoni may contribute to the discovery of new drug targets. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein coding potential that have been involved in reproduction, stem cell maintenance and drug resistance. We have recently published a catalog of lncRNAs expressed in S. mansoni life-cycle stages, tissues and single cells. However, it remains largely unknown if lncRNAs are responsive to epigenetic drugs in parasites. Here, we show by RNA-Seq re-analyses that hundreds of lncRNAs are differentially expressed after in vitro 5-AzaC treatment of S. mansoni females, including intergenic, antisense and sense lncRNAs. Many of these lncRNAs belong to co-expression network modules related to male metabolism and are also differentially expressed in unpaired compared with paired females and ovaries. Half of these lncRNAs possess histone marks at their genomic loci, indicating regulation by histone modification. Among a selected set of 8 lncRNAs, half of them were validated by RT-qPCR as differentially expressed in females, and some of them also in males. Interestingly, these lncRNAs are also expressed in other life-cycle stages. This study demonstrates that many lncRNAs potentially involved with S. mansoni reproductive biology are modulated by 5-AzaC and sheds light on the relevance of exploring lncRNAs in response to drug treatments in parasites.

Epigenetic Modification 6-Methyladenosine Can Impact the Potency and Specificity of siRNA

The introduction of N6-methyladenosine (m6 A) into siRNA targeting Factor VII impacts its potency in cells and has a significant influence on the selectivity of siRNA, including reduced off-targeting. These effects are dependent on the position of m6 A in the siRNA duplex, with some of the sequences identified as more potent and/or selective than their non-methylated counterpart. These findings broaden the repertoire of available chemical modifications for siRNA therapeutics and imply potential regulatory role of N6-methyladenosine in the RNAi pathways.

The Role of Circulating MicroRNA in Glioblastoma Liquid Biopsy

Glioblastoma multiforme (GBM) is the most common and aggressive primary malignancy of the central nervous system. The standard used to monitor disease progression and therapeutic response has been magnetic resonance imaging, which is usually obtained preoperatively and postoperatively. Patients with GBM are monitored every 2-3 months and scans are repeated until progression is detected. Sometimes there is an inability to detect tumor progression or difficulty in differentiating tumor progression from pseudoprogression. With the difficulty of distinguishing disease progression, as well as the cost of imaging, there may be a need for the existence of a noninvasive liquid biopsy. There is no reliable biomarker for GBM that can be used for liquid biopsy, but if one could be detected in serum or cerebrospinal fluid and vary with tumor burden, then, it could be developed into one. MicroRNAs (miRNAs) are short, single-stranded, noncoding RNAs that posttranscriptionally control gene expression. They play vital roles in tumor progression, migration, invasion, and stemness. Because miRNAs are secreted in stable forms in bodily fluid, either via extracellular vesicles or in cell-free form, they have great potential as biomarkers that can be used for liquid biopsy. Various miRNAs that are dysregulated in GBM have been identified in tissue, cerebrospinal fluid, and serum samples. There needs to be standardization of sample collection and quantification for both cell-free and exosomal-derived samples. Further studies need to be performed on larger cohorts to evaluate the sensitivity and specificity of not just miRNAs but most potential biomarkers.

Mitoepigenetics and Its Emerging Roles in Cancer

In human beings, there is a ∼16,569 bp circular mitochondrial DNA (mtDNA) encoding 22 tRNAs, 12S and 16S rRNAs, 13 polypeptides that constitute the central core of ETC/OxPhos complexes, and some non-coding RNAs. Recently, mtDNA has been shown to have some covalent modifications such as methylation or hydroxylmethylation, which play pivotal epigenetic roles in mtDNA replication and transcription. Post-translational modifications of proteins in mitochondrial nucleoids such as mitochondrial transcription factor A (TFAM) also emerge as essential epigenetic modulations in mtDNA replication and transcription. Post-transcriptional modifications of mitochondrial RNAs (mtRNAs) including mt-rRNAs, mt-tRNAs and mt-mRNAs are important epigenetic modulations. Besides, mtDNA or nuclear DNA (n-DNA)-derived non-coding RNAs also play important roles in the regulation of translation and function of mitochondrial genes. These evidences introduce a novel concept of mitoepigenetics that refers to the study of modulations in the mitochondria that alter heritable phenotype in mitochondria itself without changing the mtDNA sequence. Since mitochondrial dysfunction contributes to carcinogenesis and tumor development, mitoepigenetics is also essential for cancer. Understanding the mode of actions of mitoepigenetics in cancers may shade light on the clinical diagnosis and prevention of these diseases. In this review, we summarize the present study about modifications in mtDNA, mtRNA and nucleoids and modulations of mtDNA/nDNA-derived non-coding RNAs that affect mtDNA translation/function, and overview recent studies of mitoepigenetic alterations in cancer.

Molecular Mechanisms Driving mRNA Degradation by m6A Modification

N⁶-Methyladenosine (m⁶A), the most prevalent internal modification associated with eukaryotic mRNAs, influences many steps of mRNA metabolism, including splicing, export, and translation, as well as stability. Recent studies have revealed that m⁶A-containing mRNAs undergo one of two distinct pathways of rapid degradation: deadenylation via the YT521-B homology (YTH) domain-containing family protein 2 (YTHDF2; an m⁶A reader protein)-CCR4/NOT (deadenylase) complex or endoribonucleolytic cleavage by the YTHDF2-HRSP12-ribonuclease (RNase) P/mitochondrial RNA-processing (MRP) (endoribonuclease) complex. Some m⁶A-containing circular RNAs (circRNAs) are also subject to endoribonucleolytic cleavage by YTHDF2-HRSP12-RNase P/MRP. Here, we highlight recent progress on the molecular mechanisms underlying rapid mRNA degradation via m⁶A and describe our current understanding of the dynamic regulation of m⁶A-mediated mRNA decay through the crosstalk between m⁶A (or YTHDF2) and other cellular factors.

Guide RNA modification as a way to improve CRISPR/Cas9-based genome-editing systems

Genome-editing technologies, in particular, CRISPR systems, are widely used for targeted regulation of gene expression and obtaining modified human and animal cell lines, plants, fungi, and animals with preassigned features. Despite being well described and easy to perform, the most common methods for construction and delivery of CRISPR/Cas9-containing plasmid systems possess significant disadvantages, mostly associated with effects of the presence of exogenous DNA within the cell. Transfection with active ribonucleoprotein complexes of Cas9 with single-guide RNAs (sgRNAs) represents one of the most promising options because of faster production of sgRNAs, the ability of a researcher to control the amount of sgRNA delivered into the cell, and consequently, fewer off-target mutations. Artificial-RNA synthesis strategies allow for the introduction of various modified components, such as backbone alterations, native structural motifs, and labels for visualization. Modifications of RNA can increase its resistance to hydrolysis, alter the thermodynamic stability of RNA-protein and RNA-DNA complexes, and reduce the immunogenic and cytotoxic effects. This review describes various approaches to improving synthetic guide RNA function through nucleotide modification.

HIV-1 Replication Benefits from the RNA Epitranscriptomic Code

The effects of RNA methylation on HIV-1 replication remain largely unknown. Recent studies have discovered new insights into the effect of 2'-O-methylation and 5-methylcytidine marks on the HIV-1 RNA genome. As so far, HIV-1 benefits from diverse RNA methylations through distinct mechanisms. In this review, we summarize the recent advances in this emerging field and discuss the role of RNA methylation writers and readers in HIV-1 infection, which may help to find alternative strategies to control HIV-1 infection.

Detection and analysis of RNA methylation

Our understanding of the expanded genetic alphabet has been growing rapidly over the last two decades, and many of these developments came more than 80 years after the original discovery of a modified guanine in tuberculosis DNA. These new understandings, leading to the field of epigenetics, have led to exciting new fundamental and applied knowledge and to the development of novel classes of drugs exploiting this new biology. The number of methyl modifications to RNA is about seven times greater than those found on DNA, and our ability to interrogate these enigmatic nucleobases has lagged significantly until recent years as an explosion in technologies and understanding has revealed the roles and regulation of RNA methylation in several fundamental and disease-associated biological processes. Here, we outline how the technology has evolved and which strategies are commonly used in the modern epitranscriptomics revolution and give a foundation in the understanding and application of the rich variety of these methods to novel biological questions.

Making Sense of the Epigenome Using Data Integration Approaches

Epigenetic research involves examining the mitotically heritable processes that regulate gene expression, independent of changes in the DNA sequence. Recent technical advances such as whole-genome bisulfite sequencing and affordable epigenomic array-based technologies, allow researchers to measure epigenetic profiles of large cohorts at a genome-wide level, generating comprehensive high-dimensional datasets that may contain important information for disease development and treatment opportunities. The epigenomic profile for a certain disease is often a result of the complex interplay between multiple genetic and environmental factors, which poses an enormous challenge to visualize and interpret these data. Furthermore, due to the dynamic nature of the epigenome, it is critical to determine causal relationships from the many correlated associations. In this review we provide an overview of recent data analysis approaches to integrate various omics layers to understand epigenetic mechanisms of complex diseases, such as obesity and cancer. We discuss the following topics: (i) advantages and limitations of major epigenetic profiling techniques, (ii) resources for standardization, annotation and harmonization of epigenetic data, and (iii) statistical methods and machine learning methods for establishing data-driven hypotheses of key regulatory mechanisms. Finally, we discuss the future directions for data integration that shall facilitate the discovery of epigenetic-based biomarkers and therapies.

Emerging impacts of biological methylation on genetic information

The central dogma of molecular biology explains the fundamental flow of genetic information for life. Although genome sequence (DNA) itself is a static chemical signature, it includes multiple layers of information composed of mRNA, tRNA, rRNA and small RNAs, all of which are involved in protein synthesis and is passing from parents to offspring via DNA. Methylation is a biologically important modification, because DNA, RNAs and proteins, components of the central dogma, are methylated by a set of methyltransferases. Recent works focused on understanding a variety of biological methylation have shed light on new regulation of cellular functions. In this review, we briefly discuss some of those recent findings of methylation, including DNA, RNAs and proteins.

Regulatory Role of RNA N6-Methyladenosine Modification in Bone Biology and Osteoporosis

Osteoporosis is a metabolic skeletal disorder in which bone mass is depleted and bone structure is destroyed to the degree that bone becomes fragile and prone to fractures. Emerging evidence suggests that N⁶-methyladenosine (m⁶A) modification, a novel epitranscriptomic marker, has a significant role in bone development and metabolism. M⁶A modification not only participates in bone development, but also plays important roles as writers and erasers in the osteoporosis. M⁶A methyltransferase METTL3 and demethyltransferase FTO involves in the delicate process between adipogenesis differentiation and osteogenic differentiation, which is important for the pathological development of osteoporosis. Conditional knockdown of the METTL3 in bone marrow stem cells (BMSCs) could suppress PI3K-Akt signaling, limit the expression of bone formation-related genes (such as Runx2 and Osterix), restrain the expression of vascular endothelial growth factor (VEGF) and down-regulate the decreased translation efficiency of parathyroid hormone receptor-1 mRNA. Meanwhile, knockdown of the METTL3 significantly promoted the adipogenesis process and janus kinase 1 (JAK1) protein expression via an m⁶A-dependent way. Specifically, there was a negative correlation between METTL3 expression and porcine BMSCs adipogenesis. The evidence above suggested that the relationship between METTL3 expression and adipogenesis was inverse, and osteogenesis was positive, respectively. Similarly, FTO regulated for BMSCs fate determination during osteoporosis through the GDF11-FTO-PPARγ axis, prompting the shift of MSC lineage commitment to adipocyte and inhibiting bone formation during osteoporosis. In this systematic review, we summarize the most up-to-date evidence of m⁶A RNA modification in osteoporosis and highlight the potential role of m⁶A in prevention, treatment, and management of osteoporosis.