Transcriptome-wide Mapping of Internal N7-Methylguanosine Methylome in Mammalian mRNA

tRNA modifications: greasing the wheels of translation and beyond

Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.

RNA methylation: A new promising biomaker in cancer liquid biopsy

RNA methylation is a vital epigenetic modification that regulates gene expression by influencing RNA processes such as transcription, degradation, translation, and transport. Aberrant methylation, including modifications like m6A, m5C, m1A, m7G, and m3C, is closely linked to tumorigenesis and progression. Liquid biopsy, a non-invasive technique analyzing tumor markers in body fluids, offers significant potential for early diagnosis and dynamic monitoring. In this context, RNA methylation, due to its tumor-specific properties, is emerging as a valuable marker. However, significant challenges remain in its clinical application. This review explores the roles of RNA methylation in cancer, recent advances in detection technologies, and its potential as a liquid biopsy marker in tumor management. It highlights its promising applications in cancer diagnosis, prognosis, and personalized treatment in the era of precision oncology.

METTL13 is essential for the survival of acute myeloid leukemia cells by regulating MYC

Recently, some methyltransferase-like (METTL) proteins have been found to play crucial roles in the development of acute myeloid leukemia (AML) through mediating RNA modifications, such as METTL3/14/16 mediated N6-methyladenosine (m6A) and METTL1 mediated N7-methylguanosine (m7G). However, the roles of other METTL proteins in AML progression remain unknown. Here, we examined the expression levels of all METTL members in AML samples and showed that METTL13 was increased in AML and positively correlated with poor prognosis. Moreover, METTL13 deficiency impaired AML cell proliferation capability in vitro, improved the survival of AML cell line xenograft immune-deficient mice, and reduced tumor infiltration in vivo. Mechanistically, MYC was downregulated after METTL13 knockdown and forced expression of MYC rescued the cell proliferation defect in METTL13-deficient AML cells. Our findings uncover the critical role of METTL13 in the survival of AML cells and identify MYC as a potential downstream target of METTL13. This work highlights METTL13 as a promising candidate target for AML therapy.

Immunomodulatory role of RNA modifications in sex hormone-dependent cancers

Recent studies have identified that RNA epigenetic modifications, including m6A, m1A, m5C, etc, play pivotal roles in tumor progression. These modifications influence mRNA stability, RNA processing, translational efficiency, and decoding precision. However, comprehensive reviews detailing the connection between m6A RNA modifications and hormone-dependent cancers in both male and female populations remain scarce(breast cancer, ovarian cancer, and endometrial cancer, prostate cancer). In this article, we explore the cellular and molecular roles of various RNA modifications alongside the key elements of the tumor microenvironment. We examine how these RNA modifications influence the development of hormone-dependent cancers through their impact on immune mechanisms. By enhancing our understanding of the function of RNA modifications within the immune systems of four specific tumors, we offer fresh insights for their potential applications in diagnosis and treatment.

Role of m7G modification regulators as biomarkers in gastric cancer subtyping and precision immunotherapy

This study investigated the role of N7-methylguanosine (m7G) modification regulators as biomarkers in subtyping and precision immunotherapy of gastric cancer (GC). Through multi-omics analyses, including RNA sequencing, proteomics, and single-cell measurement, the study revealed heterogeneity in the m7G regulatory landscape among GC patients. Three m7G subtypes were identified, each with distinct pathways and phenotypes. Patients with low m7Gscores, based on an established scoring system, showed better survival outcomes and increased antitumor immune cell infiltration, as well as higher tumor mutation loads and lower PD-L1 expression. The predictive value of m7Gscore was confirmed in two immunotherapy cohorts. These findings highlight the potential of m7G modification in shaping the tumor microenvironment and provide new insights for immunotherapeutic strategies in GC patients.

Mechanistic insights into stem cell fate regulation via RNA methylation

Stem cells possess an extraordinary ability for self-renewal and differentiation, making them essential for tissue repair, regeneration, and anti-aging. RNA methylation is crucial in regulating stem cell fate by modulating gene expression. This review synthesizes current research on RNA methylation modifications, such as m6A, m7G, m5C, and m1A, and their impact on adult stem cell fate. It provides a comprehensive overview of the molecular machinery involved in RNA methylation, emphasizes the critical roles of these modifications in stem cell biology, reviews the latest advancements in sequencing technologies, and discusses potential crosstalk between RNA methylation and epigenetic mechanisms.

The m7G methylation modification: An emerging player of cardiovascular diseases

Cardiovascular diseases severely endanger human health and are closely associated with epigenetic dysregulation. N7-methylguanosine (m7G), one of the common epigenetic modifications, is present in many different types of RNA molecules and has attracted significant attention due to its impact on various physiological and pathological processes. Recent studies have demonstrated that m7G methylation plays an important role in the occurrence and development of multiple cardiovascular diseases. Application of small molecule inhibitors to target m7G modification mediated by methyltransferase-like protein 1 (METTL1) has shown potentiality in the treatment of cardiovascular diseases. In this review, we summarize the basic knowledge about m7G modification and discuss its role and therapeutic potential in diverse cardiovascular diseases, aiming to provide a theoretical foundation for future research and therapeutic intervention.

Advancements in chemically inducible modified tRNA sequencing techniques: Elucidating novel insights into tRNA epitranscriptomics

In this review, we examine and expound upon the most recent and groundbreaking advancements in the sequencing of tRNA modifications, focusing specifically on the innovative chemical treatment approaches that have revolutionized this field. By delving into the intricate details of these cutting-edge methodologies, we aim to provide an overview of the current state of the art in tRNA modification sequencing, highlighting their unique strengths, limitations, and potential applications.

The importance of physiological and disease contexts in capturing mRNA modifications

The variety of modifications decorating various RNA species has prompted researchers to study messenger RNA (mRNA) modifications that are likely to have, like N6-methyladenosine (m6A), important biological functions. Yet tackling these modifications has proved more complicated than anticipated. In this Perspective, we discuss two major obstacles to progress in epitranscriptomic research: the low abundance of most mRNA modification and the nonspecificity of many mRNA modifiers. We then shift our focus to the removal of mRNA modifications and their upstream regulation, emphasizing the context-dependent nature of epitranscriptomic regulation. We illustrate how specific modifications, such as N1-methyladenosine (m1A) and pseudouridine, are enriched in distinct environments, most notably within mitochondria and in certain physiopathological conditions. By focusing on biological settings in which non-m6A modifications are more abundant, we could deepen our understanding of their precise roles in gene regulation.

METTL1-mediated m7G modification promotes colorectal cancer metastasis via stabilization of ICAM-1

Colorectal cancer (CRC) is one of the most common tumors worldwide, and metastatic CRC is likely to have a poor prognosis. N7-methylguanosine (m7G) is a common methylation modification that is catalyzed primarily by methyltransferase 1 (METTL1). However, the role of m7G in metastatic CRC remains unclear. The role of METTL1 in progressive CRC was initially explored using bioinformatics analysis. Subsequently, its relationship with CRC was further validated through in vitro and in vivo experiments. Potential downstream targets were identified through RNA-seq and quantitative real-time PCR (RT‒qPCR), and the underlying mechanisms were investigated using methylated RNA immunoprecipitation (MeRIP) and RNA degradation assays. Our results revealed that METTL1 is differentially expressed and significantly upregulated in metastatic CRC. This correlation was further confirmed by in vivo and in vitro experiments. RNA sequencing of CRC cells with METTL1 knockdown revealed that intercellular adhesion molecule-1 (ICAM-1) was a significant downstream target and could be stabilized by m7G modification. We revealed that METTL1 is significantly upregulated in metastatic CRC and plays a critical role in CRC progression by stabilizing ICAM-1 through m7G modification.

RNA m7G methylation regulators and targets significantly contribute to chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is one of the most common lung injury diseases, closely associated with aging, air pollution and smoking exposure. The novel epigenetic modification 7-methylguanosine (m7G) RNA methylation affects the pathogenesis and progression of COPD. In this study, the combined roles of m7G methylation regulators were explored in COPD for the first time by integrated bioinformatic methods. The machine algorithms screened 7 disease signature genes relevant to clinical indicators, including CYFIP2, EIF3D, EIF4G3, GEMIN5, METTL1, SNUPN and NCBP2, and METTL1 was related to the progression in COPD. COPD patients could be well divided into two m7G subtypes by consensus clustering, and the two groups had differential immune profiles, visualized by single-cell sequencing and immune infiltration landscapes. More importantly, CAT was found to be a meaningful key target gene in METTL1-CAT axis for m7G methylation in COPD. We also used the cell premature senescence model for the preliminary validation of the above biosignature analysis results. The qRT-PCR and GSEA results revealed the important regulatory roles of the seven disease signature genes in COPD and aging-related diseases. Taken together, METTL1 and its target CAT have played an important role in COPD, as excellent candidates for its prevention and intervention.

Modifications of RNA in cancer: a comprehensive review

RNA modifications play essential roles in post-transcriptional gene regulation and have emerged as significant contributors to cancer biology. Major chemical modifications of RNA include N6-methyladenosine (m6A), 5-methylcytosine (m5C), N1-methyladenosine (m1A), pseudouridine (ψ), and N7-methylguanosine (m7G). Their dynamic regulation highlights their roles in gene expression modulation, RNA stability, and translation. Advanced high-throughput detection methods, ranging from liquid chromatography-mass spectrometry and high-performance liquid chromatography to next-generation sequencing (NGS) and nanopore direct RNA sequencing, have enabled detailed studies of RNA modifications in cancer cells. Aberrant RNA modifications are associated with the dysregulation of tumor suppressor genes and oncogenes, influencing cancer progression, therapy resistance, and immune evasion. Emerging research suggests the therapeutic potential of targeting RNA-modifying enzymes and their inhibitors in cancer treatment. This review compiles and analyzes the latest findings on RNA modifications, presenting an in-depth discussion of the diverse chemical alterations that occur in RNA and their profound implications in cancer biology. It integrates fundamental principles with cutting-edge research, offering a holistic perspective on how RNA modifications influence gene expression, tumor progression, and therapeutic resistance. It emphasizes the need for further studies to elucidate the complex roles of RNA modifications in cancer, as well as the potential for multimodality therapeutic strategies that exploit the dynamic and reversible nature of these epitranscriptomic marks. It also attempts to highlight the challenges, gaps, and limitations of RNA modifications in cancer that should be tackled before their functional implications. Understanding the interplay between RNA modifications, cancer pathways, and their inhibitors will be crucial for developing promising RNA-based therapeutic approaches to cancer and personalized medicine strategies.

Construction of a diagnostic model utilizing m7G regulatory factors for the characterization of diabetic nephropathy and the immune microenvironment

Diabetic nephropathy (DN), a prevalent and severe complication of diabetes, is associated with poor prognosis and limited treatment options. N7-Methylguanosine (m7G) modification plays a crucial role in regulating RNA structure and function, linking it closely to metabolic disorders. However, despite its biological significance, the interplay between m7G methylation and immune status in DN remains largely unexplored. Leveraging data from the GEO database, we conducted consensus clustering of m7G regulators in DN patients to identify distinct molecular subtypes. To construct and validate m7G-related prognostic features and risk scores, we integrated multiple machine learning approaches, including Support Vector Machine-Recursive Feature Elimination, Random Forest, LASSO, Cox regression, and ROC curves analysis. In addition, we employed GSVA, ssGSEA, CIBERSORT, and Gene Set Enrichment Analysis to investigate the associated biological pathways and the immune landscape, providing deeper insights into the role of m7G methylation in DN. Based on the expression levels of 18 m7G-related regulatory factors, we identified nine key regulators. Through machine learning techniques, we identified four significant regulators (METTL1, CYFIP2, EIF3D, and NUDT4). Consensus clustering classified these genes into two distinct m7G-related clusters. To characterize these subtypes, we conducted immune infiltration analysis, differential expression analysis, and enrichment analysis, uncovering significant biological differences between the clusters. Additionally, we developed an m7G-related risk scoring model using the PCA algorithm. The differential expression of the four key regulators was further validated through in vivo experiments, reinforcing their potential role in disease progression. The m7G-related genes METTL1, CYFIP2, EIF3D, and NUDT4 may serve as potential diagnostic biomarkers for DN, providing new insights into its molecular mechanisms and immune landscape.

Dysregulated ribosome quality control in human diseases

Precise regulation of mRNA translation is of fundamental importance for maintaining homeostasis. Conversely, dysregulated general or transcript-specific translation, as well as abnormal translation events, have been linked to a multitude of diseases. However, driven by the misconception that the transient nature of mRNAs renders their abnormalities inconsequential, the importance of mechanisms that monitor the quality and fidelity of the translation process has been largely overlooked. In recent years, there has been a dramatic shift in this paradigm, evidenced by several seminal discoveries on the role of a key mechanism in monitoring the quality of mRNA translation - namely, Ribosome Quality Control (RQC) - in the maintenance of homeostasis and the prevention of diseases. Here, we will review recent advances in the field and emphasize the biological significance of the RQC mechanism, particularly its implications in human diseases.

Mettl1 knockdown alleviates cardiac I/R injury in mice by inactivating the Mettl1-CYLD-P53 positive feedback loop

The N7-methylguanosine (m7G) methyltransferase Mettl1 has been recently implicated in cardiac repair and fibrosis. In this study we investigated the role of Mettl1 in mouse cardiomyocytes injury and the underlying mechanisms. Cardiac ischemia/reperfusion (I/R) I/R model was established in mice by ligation of the left anterior descending coronary artery (LAD) for 45 min followed by reperfusion for 24 h. We showed the mRNA and protein levels of Mettl1 were significantly upregulated in mouse I/R hearts and H2O2-treated neonatal mouse cardiomyocytes (NMCMs). Mettl1 knockdown markedly ameliorated cardiac I/R injury, evidenced by decreased infarct size, apoptosis, and improved cardiac function. Overexpression of Mettl1 triggered cardiomyocytes apoptosis in vivo and in vitro. By performing RNA sequencing combined with m7G methylated RNA sequencing in Mettl1-overexpressing mouse hearts, we revealed that Mettl1 catalyzed m7G modification of the deubiquitinase cylindromatosis (CYLD) mRNA to increase the expression of CYLD, which enhanced the stability of P53 via abrogating its ubiquitination degradation. Vice versa, P53 served as a transcriptional factor to positively regulate Mettl1 expression during I/R injury. Knockdown of CYLD mitigated cardiomyocytes apoptosis induced by Mettl1 overexpression or oxidative stress. From the available drug-targets databases and literature, we identified 4 small molecule inhibitors of m7G modification. Sinefungin, one of the Mettl1 inhibitors exerted profound protection against cardiac I/R injury in vivo and in vitro. Collectively, this study has identified Mettl1 as a key regulator of cardiomyocyte apoptosis, and targeting the Mettl1-CYLD-P53 positive feedback circuit may represent a novel therapeutic avenue for alleviating cardiac I/R injury.

m7G-modified mt-tRF3b-LeuTAA regulates mitophagy and metabolic reprogramming via SUMOylation of SIRT3 in chondrocytes

N7-methylguanosine (m7G) modification is one of the most prevalent RNA modifications, and methyltransferase-like protein-1 (METTL1) is a key component of the m7G methyltransferase complex. METTL1-catalyzed m7G as a new RNA modification pathway that regulates RNA structure, biogenesis, and cell migration. Increasing evidence indicates that m7G modification has been implicated in the pathophysiological process of osteoarthritis (OA). However, the underlying molecular mechanisms of m7G modification remains incompletely elucidated during the progression of OA. Here we found that METTL1 and m7G levels were markedly increased in OA chondrocytes. In addition, METTL1-mediated m7G modification upregulated mt-tRF3b-LeuTAA expression to exacerbate chondrocyte degeneration. Mechanistically, mt-tRF3b-LeuTAA decreased the SUMO-specific protease 1 (SENP1) protein expression and upregulated the level of sirtuin 3 (SIRT3) SUMOylation to inhibit PTEN induced kinase 1 (PINK1)/Parkin-mediated mitochondrial mitophagy. Intra-articular injection of PMC-tRF3b-LeuTAA inhibitor (Polyamidoamine-polyethylene glycol surface-modified with Minimal self-peptides and Chondrocyte-affinity peptides, PMC) attenuated destabilization of the medial meniscus (DMM) mouse cartilage degeneration in vivo. Our study demonstrates that METTL1/m7G/mt-tRF3b-LeuTAA axis accelerate cartilage degradation by inhibiting mitophagy and promoting mitochondrial dysfunction through SIRT3 SUMOylation, and suggest that targeting METTL1 and its downstream signaling axis could be a promising therapeutic target for OA treatment.

RNA methylation homeostasis in ocular diseases: All eyes on Me

RNA methylation is a pivotal epigenetic modification that adjusts various aspects of RNA biology, including nuclear transport, stability, and the efficiency of translation for specific RNA candidates. The methylation of RNA involves the addition of methyl groups to specific bases and can occur at different sites, resulting in distinct forms, such as N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), and 7-methylguanosine (m7G). Maintaining an optimal equilibrium of RNA methylation is crucial for fundamental cellular activities such as cell survival, proliferation, and migration. The balance of RNA methylation is linked to various pathophysiological conditions, including senescence, cancer development, stress responses, and blood vessel formation, all of which are pivotal for comprehending a spectrum of eye diseases. Recent findings have highlighted the significant role of diverse RNA methylation patterns in ophthalmological conditions such as age-related macular degeneration, diabetic retinopathy, cataracts, glaucoma, uveitis, retinoblastoma, uveal melanoma, thyroid eye disease, and myopia, which are critical for vision health. This thorough review endeavors to dissect the influence of RNA methylation on common and vision-impairing ocular disorders. It explores the nuanced roles that RNA methylation plays in key pathophysiological mechanisms, such as oxidative stress and angiogenesis, which are integral to the onset and progression of these diseases. By synthesizing the latest research, this review offers valuable insights into how RNA methylation could be harnessed for therapeutic interventions in the field of ophthalmology.

CAP-m7G: A capsule network-based framework for specific RNA N7-methylguanosine site identification using image encoding and reconstruction layers

N7-methylguanosine (m7G) modifications play a pivotal role in RNA stability, mRNA export, and protein translation. They are closely associated with ribosome function and the regulation of gene expression. Dysregulation of m7G has been implicated in various diseases, including cancers and neurodegenerative disorders, where the loss of m7G can lead to genomic instability and uncontrolled cell proliferation. Accurate identification of m7G sites is thus essential for elucidating these mechanisms. Due to the high cost of experimentally validating m7G sites, several artificial intelligence models have been developed to predict these sites. However, the performance of these models is not yet optimal, and a user-friendly web server is still needed. To address these issues, we developed CAP-m7G, an innovative model that integrates Chaos Game Representation, Capsule Networks, and reconstruction layers. CAP-m7G achieved an accuracy of 96.63%, a specificity of 95.07%, and a Matthews correlation coefficient (MCC) of 0.933 on independent test data. Our results demonstrate that the integration of Chaos Game Representation with Capsule Network can effectively capture the crucial sequence information associated with m7G sites. The web server can be accessed at https://awi.cuhk.edu.cn/~biosequence/CAP-m7G/index.php.

Structural Features of 5' Untranslated Region in Translational Control of Eukaryotes

Gene expression is a complex process regulated at multiple levels in eukaryotic cells. Translation frequently represents a pivotal step in the control of gene expression. Among the stages of translation, initiation is particularly important, as it governs ribosome recruitment and the efficiency of protein synthesis. The 5' untranslated region (5' UTR) of mRNA plays a key role in this process, often exhibiting a complicated and structured landscape. Numerous eukaryotic mRNAs possess long 5' UTRs that contain diverse regulatory elements, including RNA secondary structures, specific nucleotide motifs, and chemical modifications. These structural features can independently modulate translation through their intrinsic properties or by serving as platforms for trans-acting factors such as RNA-binding proteins. The dynamic nature of 5' UTR elements allows cells to fine-tune translation in response to environmental and cellular signals. Understanding these mechanisms is not only fundamental to molecular biology but also holds significant biomedical potential. Insights into 5' UTR-mediated regulation could drive advancements in synthetic biology and mRNA-based targeted therapies. This review outlines the current knowledge of the structural elements of the 5' UTR, the interplay between them, and their combined functional impact on translation.

RNA modifications in plant biotic interactions

The chemical modifications of DNA and proteins are powerful mechanisms for regulating molecular and biological functions, influencing a wide array of signaling pathways in eukaryotes. Recent advancements in epitranscriptomics have shown that RNA modifications play crucial roles in diverse biological processes. Since their discovery in the 1970s, scientists have sought to decipher, identify, and elucidate the functions of these modifications across biological systems. Over the past decade, mounting evidence has demonstrated the importance of RNA modification pathways in plants, prompting significant efforts to decipher their physiological relevance. With the advent of high-resolution mapping techniques for RNA modifications and the gradual uncovering of their biological roles, our understanding of this additional layer of regulation is beginning to take shape. In this review, we summarize recent findings on the major RNA modifications identified in plants, with an emphasis on N6-methyladenosine (m6A), the most extensively studied modification. We discuss the functional significance of the effector components involved in m6A modification and its diverse roles in plant biotic interactions, including plant-virus, plant-bacterium, plant-fungus, and plant-insect relationships. Furthermore, we highlight new technological developments driving research progress in this field and outline key challenges that remain to be addressed.

Advanced reactivity-based sequencing methods for mRNA epitranscriptome profiling

Currently, over 170 chemical modifications identified in RNA introduce an additional regulatory attribute to gene expression, known as the epitranscriptome. The development of detection methods to pinpoint the location and quantify these dynamic and reversible modifications has significantly expanded our understanding of their roles. This review goes deep into the latest progress in enzyme- and chemical-assisted sequencing methods, highlighting the opportunities presented by these reactivity-based techniques for detailed characterization of RNA modifications. Our survey provides a deeper understanding of the function and biological roles of RNA modification.

Deciphering the secret codes in N7-methylguanosine modification: Context-dependent function of methyltransferase-like 1 in human diseases

N7-methylguanosine (m7G) is one of the most prevalent post-transcriptional modifications of RNA and plays a critical role in RNA translation and stability. As a pivotal m7G regulator, methyltransferase-like 1 (METTL1) is responsible for methyl group transfer during the progression of m7G modification and contributes to the structure and functional regulation of RNA. Accumulating evidence in recent years has revealed that METTL1 plays key roles in various diseases depending on its m7G RNA methyltransferase activity. Elevated levels of METTL1 are typically associated with disease development and adverse consequences. In contrast, METTL1 may act as a disease suppressor in several disorders. While the roles of m7G modifications in disease have been extensively reviewed, the critical functions of METTL1 in various types of disease and the potential targeting of METTL1 for disease treatment have not yet been highlighted. This review describes the various biological functions of METTL1, summarises recent advances in understanding its pathogenic and disease-suppressive functions and discusses the underlying molecular mechanisms. Given that METTL1 can promote or inhibit disease processes, the possibility of applying METTL1 inhibitors and agonists is further discussed, with the goal of providing novel insights for future disease diagnosis and potential intervention targets. KEY POINTS: METTL1-mediated m7G modification is crucial for various biological processes, including RNA stability, maturation and translation. METTL1 has emerged as a critical epigenetic modulator in human illnesses, with its dysregulated expression correlating with multiple diseases progression and presenting opportunities for both diagnostic biomarker development and molecular-targeted therapy. Enormous knowledge gaps persist regarding context-dependent regulatory networks of METTL1 and dynamic m7G modification patterns, necessitating mechanistic interrogation to bridge basic research with clinical translation in precision medicine.

N7-methylguanosine modification in cancers: from mechanisms to therapeutic potential

N7-methylguanosine (m7G) is an important RNA modification involved in epigenetic regulation that is commonly observed in both prokaryotic and eukaryotic organisms. Their influence on the synthesis and processing of messenger RNA, ribosomal RNA, and transfer RNA allows m7G modifications to affect diverse cellular, physiological, and pathological processes. m7G modifications are pivotal in human diseases, particularly cancer progression. On one hand, m7G modification-associated modulate tumour progression and affect malignant biological characteristics, including sustained proliferation signalling, resistance to cell death, activation of invasion and metastasis, reprogramming of energy metabolism, genome instability, and immune evasion. This suggests that they may be novel therapeutic targets for cancer treatment. On the other hand, the aberrant expression of m7G modification-associated molecules is linked to clinicopathological characteristics, including tumour staging, lymph node metastasis, and unfavourable prognoses in patients with cancer, indicating their potential as tumour biomarkers. This review consolidates the discovery, identification, detection methodologies, and functional roles of m7G modification, analysing the mechanisms by which m7G modification-associated molecules contribute to tumour development, and exploring their potential clinical applications in cancer diagnostics and therapy, thereby providing innovative strategies for tumour identification and targeted treatment.

METTL1 coordinates cutaneous squamous cell carcinoma progression via the m7G modification of the ATF4 mRNA

Methyltransferase-like 1 (METTL1)-mediated m7G modification is a common occurrence in various RNA species, including mRNAs, tRNAs, rRNAs, and miRNAs. Recent evidence suggests that this modification is linked to the development of several cancers, making it a promising target for cancer therapy. However, the specific role of m7G modification in cutaneous squamous cell carcinoma (cSCC) is not well understood. In this study, we observed conspicuously elevated levels of METTL1 in cSCC tumors and cell lines. Inhibiting METTL1 led to reduced survival, migration, invasion, and xenograft tumor growth in cSCC cells. Mechanistically, through a combination of RNA sequencing, m7G methylated immunoprecipitation (MeRIP)-qPCR, and mRNA stability assays, we discovered that METTL1 is responsible for the m7G modification of ATF4 mRNA, leading to increased expression of ATF4. Importantly, we demonstrated that this modification is dependent on the methyltransferase activity of METTL1. Additionally, we observed a positive association between ATF4 expression and METTL1 levels in cSCC tumors. Intriguingly, restoring ATF4 expression in cSCC cells not only promoted glycolysis but also reversed the anti-tumor effects of METTL1 knockdown. In conclusion, our results underscore the critical role of METTL1 and m7G modification in cSCC tumorigenesis, suggesting a promising target for future cSCC therapies.

snoRNA-facilitated protein secretion revealed by transcriptome-wide snoRNA target identification

Small nucleolar RNAs (snoRNAs) are non-coding RNAs known for guiding RNA modifications, including 2'-O-methylation (Nm) and pseudouridine (Ψ). While snoRNAs may also interact with other RNAs, such as mRNA, the full repertoire of RNAs targeted by snoRNA remains elusive due to the lack of effective technologies that identify snoRNA targets transcriptome wide. Here, we develop a chemical crosslinking-based approach that comprehensively detects cellular RNA targets of snoRNAs, yielding thousands of previously unrecognized snoRNA-mRNA interactions in human cells and mouse brain tissues. Many interactions occur outside of snoRNA-guided RNA modification sites, hinting at non-canonical functions beyond RNA modification. We find that one of these snoRNAs, SNORA73, targets mRNAs that encode secretory proteins and membrane proteins. SNORA73 also interacts with 7SL RNA, part of the signal recognition particle (SRP) required for protein secretion. The mRNA-SNORA73-7SL RNA interactions enhance the association of the SNORA73-target mRNAs with SRP, thereby facilitating the secretion of encoded proteins.

m1A-regulated DIAPH3 promotes the invasiveness of colorectal cancer via stabilization of KRT19

BACKGROUND

In recent years, the emphasis has shifted to understanding the role of N1-methyladenosine (m1A) in tumor progression as little is known about its regulatory effect on mRNA and its role in the metastasis of colorectal cancer (CRC).

METHODS

We performed methylated RNA immunoprecipitation sequencing of tumor tissues and tumor-adjacent normal tissues from three patients with CRC to determine the m1A profile of mRNA in CRC. The expression of diaphanous-related formin 3 (DIAPH3) and its correlation with clinicopathological characteristics of CRC were evaluated using immunohistochemistry and online datasets. The role of DIAPH3 in the migration and invasion of CRC cells was evaluated using wound healing assay, Transwell assay and xenograft metastatic model. The downstream targets of DIAPH3 were screened using mass spectrometry. By co-transfecting DIAPH3 siRNA and a keratin 19 (KRT19) ectopic plasmid into CRC cells, the role of DIAPH3-KRT19 signaling axis was confirmed.

RESULTS

The mRNA level of DIAPH3 and its m1A modifications increased simultaneously in the CRC tissues. In addition, high DIAPH3 expression in CRC tissues is significantly associated with metastasis and progression to an advanced stage. After the knockdown of DIAPH3, the migration and invasion capabilities of CRC cells suffered a notable decline, which could be rescued by overexpressing KRT19. In addition, the proteasome inhibitor MG132 could block the degradation of KRT19 induced by DIAPH3 silencing.

CONCLUSIONS

Our study reveals that DIAPH3 mRNA was modified in CRC cells by m1A methylation. Silencing DIAPH3 suppresses the migration and invasion of CRC cells, potentially through the proteasome-dependent degradation of downstream KRT19.

The Role of mRNA Modifications in Bone Diseases

As a type of epigenetic modifications, mRNA modifications regulate the metabolism of mRNAs, thereby influencing gene expression. Previous studies have indicated that dysregulation of mRNA modifications is closely associated with the occurrence and progression of bone diseases (BDs). In this study, we first introduced the dynamic regulatory processes of five major mRNA modifications and their effects on the nucleus export, stability, and translation of mRNAs. We then summarized the mechanisms of mRNA modifications involved in the development of osteoporosis, osteoarthritis, rheumatoid arthritis, ankylosing spondylitis, fractures, osteomyelitis, and osteosarcoma. Finally, we reviewed therapeutic strategies for BDs based on the above mechanisms, focusing on regulating osteoblast and osteoclast differentiation, inhibiting cellular senescence and injury, and alleviating inflammation. This review identified mRNA modifications as potential targets for treating BDs and proposes perspectives on the diversity, targetability, and safety of mRNA-modifying therapies.

Functions of METTL1/WDR4 and QKI as m7G modification - related enzymes in digestive diseases

N7-methylguanosine (m7G) modification is one of the most prevalent forms of chemical modification in RNA molecules, which plays an important role in biological processes such as RNA stability, translation regulation and ribosome recognition. Methyl-transferation of m7G modification is catalyzed by the enzyme complex of methyltransferase-like 1 (METTL1) and WD repeat domain 4 (WDR4), and Quaking (QKI) recognizes internal m7G methylated mRNA and regulates mRNA translation and stabilization. Recent studies have found that m7G modification - related enzymes are associated with the onset and progression of digestive cancer, such as colorectal cancer, liver cancer, and other digestive diseases such as ulcerative colitis. This review will focus on the latest research progress on the roles of m7G methyltransferase METTL1/WDR4 and recognized enzyme QKI in digestive diseases.

Sci-ModoM: a quantitative database of transcriptome-wide high-throughput RNA modification sites

We present Sci-ModoM, the first next-generation RNome database offering a holistic view of the epitranscriptomic landscape. Sci-ModoM has a simple yet powerful interface, underpinned by FAIR data principles, a standardized nomenclature, and interoperable formats, fostering the use of common standards within the epitranscriptomics community. Sci-ModoM provides quantitative measurements per site and dataset, enabling users to assess confidence levels based on score, coverage, and stoichiometry. Data in Sci-ModoM is directly traceable to its sources. Users can Search and Compare over six million modifications across 156 datasets, Browse or download datasets, and retrieve metadata. A comparison tool offers a novel and unique opportunity to compare modifications site-wise across datasets, with the ability to securely upload and compare user data against latest published research. Sci-ModoM empowers researchers, including non-experts, to access a broad spectrum of recent quantitative RNA modification data, thereby enhancing the utility and impact of latest discoveries, and opening new avenues in biological and medical research.

RNA methylation modifications in neurodegenerative diseases: Focus on their enzyme system

BACKGROUND

Neurodegenerative diseases (NDs) constitute a significant public health challenge, as they are increasingly contributing to global mortality and morbidity, particularly among the elderly population. Pathogenesis of NDs is intricate and multifactorial. Recently, post-transcriptional modifications (PTMs) of RNA, with a particular focus on mRNA methylation, have been gaining increasing attention. At present, several regulatory genes associated with mRNA methylation have been identified and closely associated with neurodegenerative disorders.

AIM OF REVIEW

This review aimed to summarize the RNA methylation enzymes system, including the writer, reader, and eraser proteins and delve into their functions in the central nervous system (CNS), hoping to open new avenues for exploring the mechanisms and therapeutic strategies for NDs.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Recently, studies have highlighted the critical role of RNA methylation in the development and function of the CNS, and abnormalities in this process may contribute to brain damage and NDs, aberrant expression of enzymes involved in RNA methylation has been implicated in the onset and development of NDs.

Recent advances in methylation modifications of microRNA

microRNAs (miRNAs) are short single-stranded non-coding RNAs between 21 and 25 nt in length in eukaryotic organisms, which control post-transcriptional gene expression. Through complementary base pairing, miRNAs generally bind to their target messenger RNAs and repress protein production by destabilizing the messenger RNA and translational silencing. They regulate almost all life activities, such as cell proliferation, differentiation, apoptosis, tumorigenesis, and host-pathogen interactions. Methylation modification is the most common RNA modification in eukaryotes. miRNA methylation exists in different types, mainly N6-methyladenosine, 5-methylcytosine, and 7-methylguanine, which can change the expression level and biological mode of action of miRNAs and improve the activity of regulating gene expression in a very fine-tuned way with flexibility. In this review, we will summarize the recent findings concerning methylation modifications of miRNA, focusing on their biogenesis and the potential role of miRNA fate and functions.

Dynamic Profiles of Internal m7G Methylation on mRNAs in the Progression from HBV Infection to Hepatocellular Carcinoma

BACKGROUND

Emerging evidence indicates a robust association between internal RNA N7-methylguanosine (m7G) modification and hepatocarcinogenesis. However, the precise implications of altered internal m7G modifications within mRNA on the progression of Hepatitis B Virus (HBV)-induced Hepatocellular Carcinoma (HCC) remain inadequately elucidated.

METHODS

This study utilized a previously published dataset from the Gene Expression Omnibus (GEO) that includes samples of normal liver tissue, HBV positive (HP) liver tissue, and HP HCC tissue to investigate the profiling of mRNA internal m7G methylation. The STRING database and in vitro experiments were employed for the screening and validation of key m7G-related genes. The Cancer Genome Atlas cohorts were utilized to analyze the association of these key genes with the prognosis of HCC patients.

RESULTS

Comparative analyses revealed internal m7G modification alterations in 1546 mRNAs between HP liver and normal liver tissues, and in 3424 mRNAs between HP HCC and HP liver tissues. Following Protein-Protein Interaction (PPI) network analyses, validation experiments confirmed sustained high levels of internal m7G methylation modifications in EZH2, SMARCA4, and YY1. Furthermore, these genes were found to exhibit m7G modification-dependent expression changes during the transition from HBV infection to HCC, and were closely associated with the prognosis of HCC patients.

CONCLUSIONS

This study provides validation of substantial dynamic alternations in mRNA internal methylation profiles during the HBV infection to HCC. EZH2, SMARCA4, and YY1 emerge as promising molecular targets within this intricate regulatory landscape, offering avenues for further research and potential therapeutic exploration.

High-throughput detection of RNA modifications at single base resolution

RNA is modified by > 170 chemical modifications that affect its structure and function. Accordingly, RNA modifications have been implicated in regulation of gene expression and cellular outcomes in a variety of species spanning the phylogenetic tree. The study of RNA modifications is accelerated by generation of high-throughput methods for detecting RNA modifications at single base resolution. Here, we review recent advancement in next generation sequencing based approaches for detection of 14 distinct RNA modifications present in rRNA, tRNA and mRNA. We further outline the molecular and computational principles underlying currently available methods.

METTL1 mediates PKM m7G modification to regulate CD155 expression and promote immune evasion in colorectal cancer

BACKGROUND

Colorectal cancer (CRC) is characterized by poor responsiveness to immune evasion and immunotherapy. RNA 7-methylguanine (m7G) modification plays a key role in tumorigenesis. However, the mechanisms by which m7G-modified RNA metabolism affects tumor progression are not fully understood, nor is the contribution of m7G-modified RNA to the CRC immune microenvironment.

METHODS

The expression levels of Methyltransferase-like 1 (METTL1) and m7G in human tissues were determined. In this study, the effect of METTL1 on RNA m7G levels was evaluated, the effect of METTL1 on PKM mRNA modification was confirmed, the expression level of the PKM2 protein was detected, and the mechanism involved RT‒qPCR, Western blot, RNA stability analysis and RIP analysis. Lactate and H3K9 lactylation (H3K9la) induced by METTL1/PKM2 were analyzed via the extracellular acidification rate (ECAR) and lactic acid assays. Cut&Run was used to detect METTL1/PKM2-induced CD155 (PVR) transcription. In addition, METTL1 knockout mice were studied in vivo with CD155 blockers.

RESULTS

We demonstrated that m7G RNA METTL1 enhances PKM2 expression by acting on PKM mRNA, leading to tumor progression and increased glycolysis. Specifically, METTL1 mediates m7G methylation of PKM mRNA and enhances the expression of its encoded PKM2, which in turn enhances glycolysis, promotes H3K9la, and activates METTL1 transcription, creating a positive feedback loop. Moreover, increased PKM2 dimer expression and nuclear translocation activated CD155 expression and induced CRC immune evasion.

CONCLUSIONS

Our findings reveal a general mechanism by which METTL1/PKM2/H3K9la signaling regulates RNA metabolism and highlight METTL1 targeting as a potential strategy for CRC immunotherapy.

Bioinformatics analysis and validation of RNA methylation-related genes in osteogenic and adipogenic differentiation of rat bone marrow mesenchymal stem cells

BACKGROUND

The regulatory mechanisms of RNA methylation during the processes of osteogenic and adipogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) have yet to be fully understood. The objective of our study was to analyze and validate the contribution of RNA methylation regulators to the mechanisms underlying the osteogenic and adipogenic differentiation of rat BMSCs.

METHODS

We downloaded the GSE186026 from the Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were screened using the DESeq2 package in R software (version 3.6.3). A total of 50 RNA methylation genes obtained from literature review and summary were intersected with the previous DEGs to obtain RNA methylation genes, which have different expressions (RM-DEGs). Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were utilized to reveal the functional enrichment. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to validate RM-DEGs. Protein-protein interaction network (PPI) analysis and visual analysis were performed using STRING and Cytoscape. RM-DEGs regulatory network was constructed to analyze the top 10 hub genes. The relationship between RM-DEGs, some enriched GO and pathways was also been analyzed. The miRNAs and RM-DEGs regulatory networks were established by using miRWalk and TargetScan.

RESULTS

As part of our research, we detected varying levels of expression for m6A regulators Mettl3 and Rbm15, as well as m7G regulators Mettl1 and Wdr4, in relation to osteogenic differentiation, along with m6A regulator Fmr1 in adipogenic differentiation. The protein-protein interaction (PPI) networks were constructed for 49 differentially expressed genes (DEGs) related to RNA methylation during the process of osteogenic differentiation, and 13 DEGs for adipogenic differentiation. Moreover, top10 hub genes were calculated. In osteogenic differentiation, Mettl3 regulated the Wnt pathway and Hippo pathway by regulating Smad3, Rbm15 regulated the Notch pathway by Notch1, Mettl1 regulated the PI3K-Akt pathway by Gnb4. In adipogenic differentiation, Fmr1 regulated the PI3K-Akt pathway by Egfr. M6A methylation sites of Smad3, Notch1 and Gnb4 were predicted, and the results showed that all three genes were possibly methylated by m6A, and more than 9 sites per gene were possibly methylated. Finally, we constructed the regulatory networks of Mettl3, Rbm15, Mettl1, and Wdr4 and 109 miRNAs in osteogenic differentiation, Fmr1 and 118 miRNAs in adipogenic differentiation.

CONCLUSIONS

Mettl3(m6A), Rbm15(m6A), Wdr4 and Mettl1(m7G) were differentially expressed in osteogenic differentiation, while Fmr1(m6A) was differentially expressed in adipogenic differentiation. These findings offered potential candidates for further research on the involvement of RNA methylation in the osteogenic and adipogenic differentiation of BMSCs.

The role of RNA modifications in disease-associated macrophages

In recent years, the field of epitranscriptomics has witnessed significant breakthroughs with the identification of more than 150 different chemical modifications in different RNA species. It has become increasingly clear that these chemical modifications play an important role in the regulation of fundamental processes linked to cell fate and development. Further interest was sparked by the ability of the epitranscriptome to regulate pathogenesis. However, despite the involvement of macrophages in a multitude of diseases, a clear knowledge gap exists in the understanding of how RNA modifications regulate the phenotype of these cells. Here, we provide a comprehensive overview of the known roles of macrophage RNA modifications in the context of different diseases.

RNA tertiary structure and conformational dynamics revealed by BASH MaP

The functional effects of an RNA can arise from complex three-dimensional folds known as tertiary structures. However, predicting the tertiary structure of an RNA and whether an RNA adopts distinct tertiary conformations remains challenging. To address this, we developed BASH MaP, a single-molecule dimethyl sulfate (DMS) footprinting method and DAGGER, a computational pipeline, to identify alternative tertiary structures adopted by different molecules of RNA. BASH MaP utilizes potassium borohydride to reveal the chemical accessibility of the N7 position of guanosine, a key mediator of tertiary structures. We used BASH MaP to identify diverse conformational states and dynamics of RNA G-quadruplexes, an important RNA tertiary motif, in vitro and in cells. BASH MaP and DAGGER analysis of the fluorogenic aptamer Spinach reveals that it adopts alternative tertiary conformations which determine its fluorescence states. BASH MaP thus provides an approach for structural analysis of RNA by revealing previously undetectable tertiary structures.

Therapeutic mRNAs for cancer immunotherapy: From structure to delivery

mRNA carries genetic information and is used for the synthesis of proteins, fragments of proteins, and peptides in the scope of biotechnology and medicine. Once introduced into cells, this mRNA gets translated into a corresponding protein with cellular machinery. All kinds of mRNA encoding any protein, peptide, and fragment of proteins have been designed to be used for various therapeutic goals, including cancerous diseases, immunotherapy, vaccine preparation, tissue engineering, and genetic disorders, among others. These vaccines encode tumor-specific antigens that stimulate the immune system to recognize and attack cancer cells. Additionally, mRNA can be designed to produce proteins that modulate immune checkpoints, thereby enhancing the immune system's ability to target cancer cells. Synthetic mRNA can also engineer immune cells, such as T cells, to improve their cancer-fighting capabilities. For instance, mRNA can be engineered to generate CAR T cells targeting specific antigens that are expressed in the cancer. Designed mRNA can encode functional proteins in patients suffering from genetic disorders characterized by an absence or defect in a particular protein. However, mRNA is intrinsically unstable and may require special mechanisms to protect it from degradation. mRNA delivery to target cells remains a challenge. Engineered nanocarriers containing mRNA can improve the efficiency and enable the delivery to specific sites, that can provide a stimulant or substance for therapeutic purposes. This combination may improve their stability and efficacy in multiple applications of therapies. The following chapter throws light on basic advances in mRNA-based cancer therapy and provides insights into the nanotherapeutics using mRNA in key preclinical developments and the evolving clinical landscape.

Transfer RNAs and transfer RNA-derived small RNAs in cerebrovascular diseases

This article explores the important functions of transfer RNA and - transfer RNA derived small RNAs (tsRNAs) in cellular processes and disease pathogenesis, with a particular emphasis on their involvement in cerebrovascular disorders. It discusses the biogenesis and structure of tsRNAs, including types such as tRNA halves and tRNA-derived fragments, and their functional significance in gene regulation, stress response, and cell signaling pathways. The importance of tsRNAs in neurodegenerative diseases, cancer, and cardiovascular diseases has already been highlighted, while their role in cerebrovascular diseases is in early phase of exploration. This paper presents the latest advancements in the field of tsRNAs in cerebrovascular conditions, such as ischemic stroke, intracerebral hemorrhage, and moyamoya disease. Furthermore, revealing the aptitude of tsRNAs as biomarkers for the prediction of cerebrovascular diseases and as targets for therapeutic intervention. It provides insights into the role of tsRNAs in these conditions and proposes directions for future research.

Transcriptome-wide mapping of internal mRNA N7-methylguanosine in sporulated and unsporulated oocysts of Eimeria tenella reveals stage-specific signatures

BACKGROUND

Growing evidence indicates that N7-methylguanosine (m7G) modification plays critical roles in epigenetic regulation. However, no data regarding m7G modification are currently available in Eimeria tenella, a highly virulent species causing coccidiosis in chickens.

METHODS

In the present study, we explore the distribution of internal messenger RNA (mRNA) m7G modification in sporulated and unsporulated oocysts of E. tenella as well as its potential biological functions during oocyst development using methylated RNA immunoprecipitation sequencing (MeRIP-seq) and mRNA sequencing (mRNA-seq), and the mRNA-seq and MeRIP-seq data were verified by the quantitative reverse transcription polymerase chain reaction (RT-qPCR) and MeRIP-qPCR, respectively.

RESULTS

Our data showed that m7G peaks were detected throughout the whole mRNA body, and the coding DNA sequence (CDS) region displayed the most methylation modification. Compared with unsporulated oocysts, 7799 hypermethylated peaks and 1945 hypomethylated peaks were identified in sporulated oocysts. Further combined analysis of differentially methylated genes (DMGs) and differentially expressed genes (DEGs) showed that there was a generally positive correlation between m7G modification levels and gene transcript abundance. Unsurprisingly, the mRNA-seq and MeRIP-seq data showed good consistency with the results of the RT-qPCR and MeRIP-qPCR, respectively. Gene Ontology (GO) and pathway enrichment analysis of DEGs with altered m7G-methylated peaks were involved in diverse biological functions and pathways, including DNA replication, RNA transport, spliceosome, autophagy-yeast, and cAMP signaling pathway.

CONCLUSIONS

Altogether, our findings revealed the potential significance of internal m7G modification in E. tenella oocysts, providing some directions and clues for later in-depth research.

RNA modifications: emerging players in the regulation of reproduction and development

The intricate world of RNA modifications, collectively termed the epitranscriptome, covers over 170 identified modifications and impacts RNA metabolism and, consequently, almost all biological processes. In this review, we focus on the regulatory roles and biological functions of a panel of dominant RNA modifications (including m 6A, m 5C, Ψ, ac 4C, m 1A, and m 7G) on three RNA types-mRNA, tRNA, and rRNA-in mammalian development, particularly in the context of reproduction as well as embryonic development. We discuss in detail how those modifications, along with their regulatory proteins, affect RNA processing, structure, localization, stability, and translation efficiency. We also highlight the associations among dysfunctions in RNA modification-related proteins, abnormal modification deposition and various diseases, emphasizing the roles of RNA modifications in critical developmental processes such as stem cell self-renewal and cell fate transition. Elucidating the molecular mechanisms by which RNA modifications influence diverse developmental processes holds promise for developing innovative strategies to manage developmental disorders. Finally, we outline several unexplored areas in the field of RNA modification that warrant further investigation.

RNA modifications in long non-coding RNAs and their implications in cancer biology

Long non-coding RNAs (lncRNAs) represent the most diverse class of RNAs in cells and play crucial roles in maintaining cellular functions. RNA modifications, being a significant factor in regulating RNA biology, have been found to be extensively present in lncRNAs and exert regulatory effects on their behavior and biological functions. Most common types of RNA modifications in lncRNAs include N6-methyladenosine (m6A), 5-methylcytosine (m5C), and N1-methyladenosine (m1A). In this review, we summarize the major RNA modification types associated with lncRNAs, the regulatory roles of each modification, and the implications of modified lncRNAs in tumorigenesis and development. By examining these aspects, we aim to provide insights into the role of RNA modifications in lncRNAs and their potential impact on cancer biology.

GenoM7GNet: An Efficient N7-Methylguanosine Site Prediction Approach Based on a Nucleotide Language Model

N-methylguanosine (m7G), one of the mainstream post-transcriptional RNA modifications, occupies an exceedingly significant place in medical treatments. However, classic approaches for identifying m7G sites are costly both in time and equipment. Meanwhile, the existing machine learning methods extract limited hidden information from RNA sequences, thus making it difficult to improve the accuracy. Therefore, we put forward to a deep learning network, called "GenoM7GNet," for m7G site identification. This model utilizes a Bidirectional Encoder Representation from Transformers (BERT) and is pretrained on nucleotide sequences data to capture hidden patterns from RNA sequences for m7G site prediction. Moreover, through detailed comparative experiments with various deep learning models, we discovered that the one-dimensional convolutional neural network (CNN) exhibits outstanding performance in sequence feature learning and classification. The proposed GenoM7GNet model achieved 0.953in accuracy, 0.932in sensitivity, 0.976in specificity, 0.907in Matthews Correlation Coefficient and 0.984in Area Under the receiver operating characteristic Curve on performance evaluation. Extensive experimental results further prove that our GenoM7GNet model markedly surpasses other state-of-the-art models in predicting m7G sites, exhibiting high computing performance.

Breaking the barrier: Epigenetic strategies to combat platinum resistance in colorectal cancer

Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide. Platinum-based drugs, such as cisplatin and oxaliplatin, are frontline chemotherapy for CRC, effective in both monotherapy and combination regimens. However, the clinical efficacy of these treatments is often undermined by the development of drug resistance, a significant obstacle in cancer therapy. In recent years, epigenetic alterations have been recognized as key players in the acquisition of resistance to platinum drugs. Targeting these dysregulated epigenetic mechanisms with small molecules represents a promising therapeutic strategy. This review explores the complex relationship between epigenetic changes and platinum resistance in CRC, highlighting current epigenetic therapies and their effectiveness in countering resistance mechanisms. By elucidating the epigenetic underpinnings of platinum resistance, this review aims to contribute to ongoing efforts to improve treatment outcomes for CRC patients.

Recent insights into RNA m5C methylation modification in hepatocellular carcinoma

RNA 5-methylcytosine (m5C) methylation involves the addition of a methyl (-CH3) group to the cytosine (C) base within an RNA molecule, forming the m5C modification. m5C plays a role in numerous essential biological processes, including the regulation of RNA stability, nuclear export, and protein translation. Recent studies have highlighted the importance of m5C in the pathogenesis of various diseases, particularly tumors. Emerging evidence indicates that RNA m5C methylation is intricately implicated in the mechanisms underlying hepatocellular carcinoma (HCC). Dysregulation of m5C-associated regulatory factors is common in HCC and shows significant associations with prognosis, treatment response, and clinicopathological features. This review provides an in-depth analysis of the components and functions of m5C regulators, particularly emphasizing their research advancements in the context of HCC.

RNA modification in normal hematopoiesis and hematologic malignancies

N6-methyladenosine (m6A) is the most abundant RNA modification in eukaryotic cells. Previous studies have shown that m6A plays a critical role under both normal physiological and pathological conditions. Hematopoiesis and differentiation are highly regulated processes, and recent studies on m6A mRNA methylation have revealed how this modification controls cell fate in both normal and malignant hematopoietic states. However, despite these insights, a comprehensive understanding of its complex roles between normal hematopoietic development and malignant hematopoietic diseases remains elusive. This review first provides an overview of the components and biological functions of m6A modification regulators. Additionally, it highlights the origin, differentiation process, biological characteristics, and regulatory mechanisms of hematopoietic stem cells, as well as the features, immune properties, and self-renewal pathways of leukemia stem cells. Last, the article systematically reviews the latest research advancements on the roles and mechanisms of m6A regulatory factors in normal hematopoiesis and related malignant diseases. More importantly, this review explores how targeting m6A regulators and various signaling pathways could effectively intervene in the development of leukemia, providing new insights and potential therapeutic targets. Targeting m6A modification may hold promise for achieving more precise and effective leukemia treatments.

Identification and validation of novel genes related to immune microenvironment in polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is one of the most complicated chronic inflammatory diseases in women of reproductive age and is one of the primary factors responsible for infertility. There is substantial dispute relating to the pathophysiology of PCOS. Consequently, there is a critical need for further research to identify the factors underlying the pathophysiology of PCOS. Three transcriptome profiles of granulosa cells from patients with PCOS and normal controls were obtained from the gene expression integration database. We also obtained relevant microarrays of granulocytes prepared from PCOS patients and normal controls from the gene expression integration database. Then, we used the R package to perform correlations and identify differences between PCOS and normal controls with regard to immune infiltrating cells and functionality. Subsequently, intersecting genes were identified and risk models were constructed. Finally, the results were validated by enzyme linked immunosorbent assay and real-time PCR. We identified 8 genes related to cuproptosis (SLC31A1, PDHB, PDHA1, DLST, DLD, DLAT, DBT, and ATP7A) and 5 genes related to m7G (SNUPN, NUDT16, GEMIN5, DCPS, and EIF4E3) that were associated with immune infiltration. Furthermore, the expression levels of DLAT (P = .049) and NUDT16 (P = .024) differed significantly between the PCOS patients and normal controls, as revealed by multifactorial analysis. Both DLAT and NUDT16 were negatively correlated with immune cell expression and function and expression levels were significantly lower in the PCOS group. Finally, real-time PCR and enzyme linked immunosorbent assay demonstrated that the expression levels of DLAT and NUDT16 were significantly reduced in the granulosa cells of PCOS patients. In conclusion, our findings shed fresh light on the roles of immune infiltration, cuproptosis, and m7G alternations in PCOS. We also provide a reliable biomarker for the pathological classification of PCOS patients.

Microbiome-induced reprogramming in post-transcriptional landscape using nanopore direct RNA sequencing

It has been widely recognized that the microbiota has the capacity to shape host gene expression and physiological functions. However, there remains a paucity of comprehensive study revealing the host transcriptional landscape regulated by the microbiota. Here, we comprehensively examined mRNA landscapes in mouse tissues (brain and cecum) from specific-pathogen-free and germ-free mice using nanopore direct RNA sequencing. Our results show that the microbiome has global influence on a host's RNA modifications (m6A, m5C, Ψ), isoform generation, poly(A) tail length, and transcript abundance in both brain and cecum tissues. Moreover, the microbiome exerts tissue-specific effects on various post-transcriptional regulatory processes. In addition, the microbiome impacts the coordination of multiple RNA modifications in host brain and cecum tissues. In conclusion, we establish the relationship between microbial regulation and gene expression. Our results help the understanding of the mechanisms by which the microbiome reprograms host gene expression.

Identification and validation of an m7G-related lncRNAs signature for predicting prognosis, immune response and therapy landscapes in ovarian cancer

Background

Ovarian cancer is the most mortality malignancy in gynecology. N7-methylguanosine (m7G) is one of the most prevalent RNA modifications in the development and progression of cancer. The aim of this study is to investigate the effect of m7G-related lncRNA on ovarian cancer in terms of instruction prognosis and immunotherapy.

Methods

After integrating and processing the RNA expression profiles with the clinical sample information in the TCGA database, we initially screened to the m7G-related lncRNAs by Spearman correlation analysis, and subsequently obtained a prognostic model constructed by five m7G-related lncRNAs with Univariate Cox analysis, LASSO regression analysis, and Multivariate Cox regression analysis, after which we further evaluated and validated the prognostic value of the model using Kaplan-Meier survival analysis, Principal component analysis, Nomogram, and ROC curve. In addition, based on this risk model, we explored the differentially enriched pathways and functions of the high and low risk groups, and characterized the immune cells, immune functions, gene mutations, and drug sensitivity between the two groups.

Results

After a series of rigorous filtering, we finally attained a prognostic risk model consisting of KRT7-AS, USP30-AS1, ZFHX4-AS1, ACAP2-IT1, and TWSG1-DT which is excellent in predicting the prognostic survival of ovarian cancer patients as well as existing as an independent prognostic factor. Moreover, the model has certain relevance in the immune cells and functions between high and low risk groups, and simultaneously, the signature has the role of guiding the option of immunotherapy and chemotherapeutic drugs.

Conclusion

Altogether, our study established a tight connection between m7G-associated lncRNAs and ovarian cancer, with potential that the prognostic patterns contribute to steering the prognosis of ovarian cancer patients, measuring the efficacy of immunotherapeutic approaches, and detecting effective chemotherapeutic agents.

Cofactor binding triggers rapid conformational remodelling of the active site of a methyltransferase ribozyme

The methyltransferase ribozyme SMRZ-1 utilizes S-adenosyl-methionine (SAM) and Cu (II) ions to methylate RNA. A comparison of the SAM-bound and unbound RNA structures has shown a conformational change in the RNA. However, the contribution of specific interactions and the role of a pseudo-triplex motif in the catalytic center on the methylation reaction is not completely understood. In this study, we have used atomic substitutions and mutational analysis to investigate the reaction specificity and the key interactions required for catalysis. Substitution of the fluorescent nucleotide 2-aminopurine within the active ribozyme enabled the conformational dynamics of the RNA upon co-factor binding to be explored using fluorescence spectroscopy. We show that fast co-factor binding (t1/2 ∼ 0.7 s) drives a conformational change in the RNA to facilitate methyl group transfer. The importance of stacking interactions at the pseudo-triplex motif and chelation of the Cu (II) ion were shown to be essential for SAM binding.