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Epitranscriptomic mechanisms, which constitute an important layer in post-transcriptional gene regulation, are involved in numerous cellular processes under health and disease such as stem cell development or cancer. Among various such mechanisms, RNA methylation is considered to have vital roles in eukaryotes primarily due to its dynamic and reversible nature. There are numerous RNA methylations that include, but are not limited to, 2’-O-dimethyladenosine (m6Am), N7-methylguanosine (m7G), N6-methyladenosine (m6A) and N1-methyladenosine (m1A). These biochemical modifications modulate the fate of RNA by affecting the processes such as translation, target site determination, RNA processing, polyadenylation, splicing, structure, editing and stability. Thus, it is highly important to quantitatively measure the changes in RNA methylation marks to gain insight into cellular processes under health and disease. Although there are complicating challenges in identifying certain methylation marks genome wide, various methods have been developed recently to facilitate the quantitative measurement of methylated RNAs. To this end, the detection methods for RNA methylation can be classified in five categories such as antibody-based, digestion-based, ligation-based, hybridization-based or direct RNA-based methods. In this review, we have aimed to summarize our current understanding of the detection methods for RNA methylation, highlighting their advantages and disadvantages, along with the current challenges in the field.

Among over 170 different types of chemical modifications on RNA nucleobases identified so far, RNA methylation is the major type of epitranscriptomic modifications existing on almost all types of RNAs, and has been demonstrated to participate in the entire process of RNA metabolism, including transcription, pre-mRNA alternative splicing and maturation, mRNA nucleus export, mRNA degradation and stabilization, mRNA translation. Attributing to the development of high-throughput detection technologies and the identification of both dynamic regulators and recognition proteins, mechanisms of RNA methylation modification in regulating the normal development of the organism as well as various disease occurrence and developmental abnormalities upon RNA methylation dysregulation have become increasingly clear. Here, we particularly focus on three types of RNA methylations: N 6 -methylcytosine (m 6 A), 5-methylcytosine (m 5 C), and N 7 -methyladenosine (m 7 G). We summarize the elements related to their dynamic installment and removal, specific binding proteins, and the development of high-throughput detection technologies. Then, for a comprehensive understanding of their biological significance, we also overview the latest knowledge on the underlying mechanisms and key roles of these three mRNA methylation modifications in gametogenesis, embryonic development, immune system development, as well as disease and tumor progression.

N6-methyladenosine (m6A) is one of the most prevalent internal reversible chemical modification of RNAs in eukaryotes, which has attracted widespread attention recently owing to its regulatory roles in a plethora of normal developmental processes and human diseases like cancer. Deposition of the m6A mark on RNAs is mediated by the dynamic interplay between m6A regulatory proteins such as m6A RNA methyltransferases (m6A writers), m6A RNA demethylases (m6A erasers) and m6A RNA binding proteins (m6A readers). m6A regulators are ectopically expressed in various cancer types, often leading to aberrant expression of tumor-suppressor and oncogenic mRNAs either directly or indirectly via regulating the biogenesis of non-coding RNAs like miRNAs. miRNAs are tiny regulators of gene expression, which often impact various hallmarks of cancer and thus influence tumorigenesis. It is becoming increasingly clear that m6A RNA modification impacts biogenesis and function of miRNAs, and recent studies have interestingly, uncovered many miRNAs whose biogenesis and function are regulated by m6A writers, erasers and readers. In this review, we discuss various mechanisms by which m6A RNA methylation regulates miRNA biogenesis, the functional crosstalk between m6A RNA methylation and miRNAs and how it modulates various aspects of tumorigenesis. The potential of m6A RNA methylation regulated miRNAs as biomarkers and novel therapeutic targets to treat various cancers is also addressed.

The AlkB homologs ( ALKBH ) gene family regulates N 6 -methyladenosine (m 6 A) RNA methylation and is involved in plant growth and the abiotic stress response. Poplar is an important model plant for studying perennial woody plants. Poplars typically have a long juvenile period of 7–10 years, requiring long periods of time for studies of flowering or mature wood properties. Consequently, functional studies of the ALKBH genes in Populus species have been limited. Based on AtALKBHs sequence similarity with Arabidopsis thaliana , 23 PagALKBHs were identified in the genome of the poplar 84K hybrid genotype ( P. alba   ×   P. tremula var. glandulosa ), and gene structures and conserved domains were confirmed between homologs. The PagALKBH proteins were classified into six groups based on conserved sequence compared with human, Arabidopsis, maize, rice, wheat, tomato, barley, and grape. All homologs of PagALKBHs were tissue-specific; most were highly expressed in leaves. ALKBH9B and ALKBH10B are m 6 A demethylases and overexpression of their homologs PagALKBH9B and PagALKBH10B reduced m 6 A RNA methylation in transgenic lines. The number of adventitious roots and the biomass accumulation of transgenic lines decreased compared with WT. Therefore, PagALKBH9B and PagALKBH10B mediate m 6 A RNA demethylation and play a regulatory role in poplar growth and development. Overexpression of PagALKBH9B and PagALKBH10B can reduce the accumulation of H 2 O 2 and oxidative damage by increasing the activities of SOD, POD, and CAT, and enhancing protection for Chl a/b, thereby increasing the salt tolerance of transgenic lines. However, overexpression lines were more sensitive to drought stress due to reduced proline content. This research revealed comprehensive information about the PagALKBH gene family and their roles in growth and development and responsing to salt stress of poplar.

RNA methylation modification has always been a research hotspot. RNA methylation modification can regulate processes such as transcription, translation, splicing, stability, and degradation of RNA, in which effector proteins play an important role, including ‘writers’, ‘erasers’, and ‘readers’. There are various types of proteins involved in cancer progression, and in recent years, research on their mechanisms of action has been increasing, providing new ideas for targeted cancer therapy. By regulating the expression of related genes and affecting signaling pathways, protein writing plays a role in promoting or inhibiting cancer in the proliferation, invasion, migration, and metastasis of different tumors, providing direction for the treatment of malignant tumors. This article reviews the mechanisms of common RNA methylation modified writers and their prospects in targeted cancer therapy.

The C‐REPEAT‐BINDING FACTOR (CBF) pathway has important roles in plant responses to cold stress. How the CBF genes themselves are activated after cold acclimation remains poorly understood. In this study, we characterized cold tolerance of null mutant of RNA‐DIRECTED DNA METHYLATION 4 (RDM4), which encodes a protein that associates with RNA polymerases Pol V and Pol II, and is required for RNA‐directed DNA methylation (RdDM) in Arabidopsis. The results showed that dysfunction of RDM4 reduced cold tolerance, as evidenced by decreased survival and increased electrolyte leakage. Mutation of RDM4 resulted in extensive transcriptomic reprogramming. CBFs and CBF regulon genes were down‐regulated in rdm4 but not nrpe1 (the largest subunit of PolV) mutants, suggesting that the role of RDM4 in cold stress responses is independent of the RdDM pathway. Overexpression of RDM4 constitutively increased the expression of CBFs and regulon genes and decreased cold‐induced membrane injury. A great proportion of genes affected by rdm4 overlapped with those affected by CBFs. Chromatin immunoprecipitation results suggested that RDM4 is important for Pol II occupancy at the promoters of CBF2 and CBF3. We present evidence of a considerable role for RDM4 in regulating gene expression at low temperature, including the CBF pathway in Arabidopsis.

A healthy reproductive system is fundamental to human fertility. N6-adenosine methylation (m6A), the most prevalent RNA modification in eukaryotes, plays a critical role in regulating RNA metabolism, including splicing, degradation, and translation. Emerging evidence demonstrates that m6A RNA methylation is a key modulator of various reproductive processes, such as spermatogenesis, testicular function, oogenesis, ovarian homeostasis, embryo implantation, and parturition. Dysregulation of m6A RNA methylation has been closely linked to a spectrum of reproductive disorders in both males and females, including asthenozoospermia, premature ovarian insufficiency, polycystic ovary syndrome, spontaneous abortion, and endometriosis. This review summarizes the mechanisms underlying m6A RNA methylation and highlights recent advances in understanding its role in human reproduction related diseases. By elucidating these molecular pathways, we aim to provide novel insights into the prevention, diagnosis, and therapeutic strategies for reproductive health disorders.

Purpose Thyroid cancer (TC) is one of the most common endocrine malignancies, and its morbidity continues to rise. N 6 -methyladenosine (m 6 A) RNA methylation, an epigenetic modification, is an important regulator of gene expression in TC. Therefore, it’s worth finding the characteristics and predictive value of the m 6 A RNA methylation regulators in thyroid cancer (TC). Method RNA-seq data of TC was downloaded from the Cancer Genome Atlas (TCGA) database to screen out the differential expressed regulators. The absolute contraction selection operator (Lasso) Cox regression was used to construct the risk model of m 6 A methylation regulators. The predictive value of the risk scoring model was evaluated by Kaplan Meier (K-M) analysis and receiver operating characteristic (ROC) curves. The underlying mechanism of m 6 A methylation regulators in TC was predicted by gene set enrichment analysis (GSEA). Further validation was performed by using immunohistochemistry (IHC) and q-PCR. The correlation between risk-related gene and immune infiltration was evaluated by Tumour Immune Estimation Resource (TIMER). Results IGF2BP2, YTHDF1 and YTHDF3 were screened out as strong independent prognostic factors of TC. Then a risk score model was established to further screen the predictors. Finally, according to the results of overall survival (OS) and clinical characteristics of TC, YTHDF3 was screened out as a potential predictor. Meanwhile, IHC and qPCR confirmed that YTHDF3 was expressed differential in TC. The expression of YTHDF3 was positively associated with the infiltration level of CD4 + T cells and macrophages. It was strongly correlated with a variety of immune markers in TC. Conclusion We confirmed that YTHDF3 can be used as a potential prognostic biomarker of TC. It not only plays a decisive role in the initiation and development of TC, but also provides a new perspective for understanding the modification of m 6 A RNA in TC.

Background Global climate change has significantly increased environmental stress in marine ecosystems, with rising sea surface temperatures and declining dissolved oxygen (DO) levels. These stressors pose critical challenges to aquaculture, particularly for Apostichopus japonicus , an economically significant species in China. A. japonicus is highly sensitive to combined high-temperature and hypoxia stress, which disrupts physiological processes, suppresses immune responses, and increases mortality. While epigenetic mechanisms such as N6-methyladenosine (m6A) RNA modifications are known to regulate stress adaptation, their role under dual stressors in A. japonicus remains poorly understood. Results This study integrates m6A methylation sequencing (MeRIP-seq) and transcriptomic analysis (RNA-seq) to investigate molecular responses in A. japonicus under combined high-temperature (32 °C) and hypoxia (DO = 2 mg/L). Results show that approximately 90% of genes had 1–3 m6A peaks, with single peaks being the most frequent (∼ 60%). Genes with m6A modifications exhibited varying expression levels, with some showing significantly higher expression, suggesting a complex relationship between m6A methylation and stress-responsive gene expression. GO and KEGG enrichment analyses revealed that m6A-modified genes regulate pathways associated with oxidative stress, protein homeostasis, and energy metabolism, such as the PI3K-Akt and MAPK signaling pathways. Key stress-responsive genes, including HSP70 , NOX5 , and SLC7A11 , exhibited dynamic m6A methylation changes, highlighting their roles in redox homeostasis and cellular resilience. Comparative analysis across experimental groups revealed distinct molecular responses to hypoxia, high-temperature stress, and their combination, with combined stress inducing more pronounced changes in m6A methylation and gene expression. Conclusion In this study, we explored the central regulatory role of m6A RNA methylation in the response of A. japonicus to the dual environmental stress of high-temperature and hypoxia. The findings show that m6A modification regulates the expression of key genes, allowing A. japonicus to effectively adapt to harsh environmental conditions. This study not only provides an important new perspective on the molecular stress recovery mechanism of marine invertebrates in the face of complex environmental stress, but it also provides theoretical support for aquaculture practice, assisting in the development of more stress-resistant aquaculture systems to deal with the severe challenges posed by global climate change.

Myelodysplastic syndromes (MDS) are myeloid malignancies with heterogeneous genotypes and phenotypes, characterized by ineffective haematopoiesis and a high risk of progression towards acute myeloid leukaemia (AML). Prognosis for patients treated with hypomethylating agents (HMAs), as is azacytidine, the main drug used as frontline therapy for MDS is mostly based on cytogenetics and next generation sequencing (NGS) of the initial myeloid clone. Although the critical influence of the epigenetic landscape upon cancer cells survival and development as well on tumour environment establishment is currently recognized and approached within current clinical practice in MDS, the heterogenous response of the patients to epigenetic therapy is suggesting a more complex mechanism of action, as is the case of RNA methylation. In this sense, the newly emerging field of epitranscriptomics could provide a more comprehensive perspective upon the modulation of gene expression in malignancies, as is the proof‐of‐concept of MDS. We initially did RNA methylation sequencing on MDS patients (n = 6) treated with azacytidine and compared responders with non‐responders. Afterwards, the genes identified were assessed in vitro and afterwards validated on a larger cohort of MDS patients treated with azacytidine (n = 58). Our data show that a more accurate prognosis could be based on analysing the methylome and thus we used methylation sequencing to differentially split high‐grade MDS patients with identical demographical and cytogenetic features, between azacytidine responders and non‐responders.