Advances in RNA cytosine-5 methylation: detection, regulatory mechanisms, biological functions and links to cancer

Xue, Chen; Zhao, Yalei; Li, Lanjuan

doi:10.1186/s40364-020-00225-0

Cited by 98 publications

(100 citation statements)

References 85 publications

(173 reference statements)

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“…DNA methylation modification is an important regulator of cell activity, and abnormal regulation due to alterations in methylation can lead to tumorigenesis 15 . DNMTs are involved in initiation of mammalian chromatin remodeling and gene expression regulation in diverse physiological and pathophysiological processes 23 , 24 . m5C functions as an important epigenetic modifier in DNA and RNA with transcriptional expression 25 .…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics analysis of DNMT1 expression and its role in head and neck squamous cell carcinoma prognosis

Cui

Zheng

Zhang

et al. 2021

Sci Rep

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Head and neck squamous cell carcinoma (HNSCC) is the sixth most common type of malignancy in the world. DNA cytosine-5-methyltransferase 1 (DNMT1) play key roles in carcinogenesis and regulation of the immune micro-environment, but the gene expression and the role of DNMT1 in HNSCC is unknown. In this study, we utilized online tools and databases for pan-cancer and HNSCC analysis of DNMT1 expression and its association with clinical cancer characteristics. We also identified genes that positively and negatively correlated with DNMT1 expression and identified eight hub genes based on protein–protein interaction (PPI) network analysis. Enrichment analyses were performed to explore the biological functions related with of DNMT1. The Tumor Immune Estimation Resource (TIMER) database was performed to explore the relationship between DNMT1 expression and immune-cell infiltration. We demonstrated that DNMT1 gene expression was upregulated in HNSCC and associated with poor prognosis. Based on analysis of the eight hub genes, we determined that DNMT1 may be involved in cell cycle, proliferation and metabolic related pathways. We also found that significant difference of B cells infiltration based on TP 53 mutation. These findings suggest that DNMT1 related epigenetic alterations have close relationship with HNSCC progression, and DNMT1 could be a novel diagnostic biomarker and a promising therapeutic target for HNSCC.

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Section: Discussionmentioning

confidence: 99%

Bioinformatics analysis of DNMT1 expression and its role in head and neck squamous cell carcinoma prognosis

Cui

Zheng

Zhang

et al. 2021

Sci Rep

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“…Like DNA, the methylation of RNA also requires writer, reader, eraser, and related enzymes have been found in some plants ( Xue et al, 2020 ). In the process of long-distance transportation to specific target tissues to function, mRNA molecules undergo at least one state switch: transportation and translation.…”

Section: Discussionmentioning

confidence: 99%

“…A methyltransferase TRM4, selectively methylated specific nucleotides on certain tRNAs in yeast, can significantly enhance the stability of tRNAs and avoid tRNA degradation caused by environmental changes ( Müller et al, 2019 ; Xue et al, 2020 ). As mentioned before, TLS was found be significantly enriched in mobile mRNA datasets of Arabidopsis .…”

Section: Rna Methylation Is Involved In Promoting Mrna Transport In Pmentioning

confidence: 99%

RNA Motifs and Modification Involve in RNA Long-Distance Transport in Plants

Wang

Zhang

et al. 2021

Front. Cell Dev. Biol.

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A large number of RNA molecules have been found in the phloem of higher plants, and they can be transported to distant organelles through the phloem. RNA signals are important cues to be evolving in fortification strategies by long-distance transportation when suffering from various physiological challenges. So far, the mechanism of RNA selectively transportation through phloem cells is still in progress. Up to now, evidence have shown that several RNA motifs including Polypyrimidine (poly-CU) sequence, transfer RNA (tRNA)-related sequence, Single Nucleotide Mutation bound with specific RNA binding proteins to form Ribonucleotide protein (RNP) complexes could facilitate RNA mobility in plants. Furthermore, some RNA secondary structure such as tRNA-like structure (TLS), untranslation region (UTR) of mRNA, stem-loop structure of pre-miRNA also contributed to the mobility of RNAs. Latest researchs found that RNA methylation such as methylated 5′ cytosine (m5C) played an important role in RNA transport and function. These studies lay a theoretical foundation to uncover the mechanism of RNA transport. We aim to provide ideas and clues to inspire future research on the function of RNA motifs in RNA long-distance transport, furthermore to explore the underlying mechanism of RNA systematic signaling.

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“…The differentiational stage-dependent effects of 5-azaC on chondrogenic cells suggest the need of careful design for therapeutic application of this compound during the intended treatment of joint diseases. Moreover, 5-azaC can also inhibit RNA methylation, which might provide another regulatory layer for chondrogenic differentiation [55]. Therefore, it is reasonable to consider that option when the effect of 5-azaC treatment is evaluated.…”

Section: Resultsmentioning

confidence: 99%

Modulation of DNA Methylation Influences Cartilage Formation in Murine Chondrogenic Models

Vágó¹,

Kiss²,

Karanyicz³

et al. 2021

Preprint

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The aim of this study was to investigate the role of DNA methylation in the regulation of in vitro and in vivo cartilage formation. Based on the data of an RNA chip-assay performed on chondrifying BMP2-overexpressing C3H10T1/2 cells, the relative expression of Tet1 (tet methylcytosine dioxygenase 1), Dnmt3a (DNA methyltransferase 3) and Ogt (O-linked N-acetylglucosamine transferase) genes was examined with RT-qPCR in mouse cell-line based and primary micromass cultures. RNA probes for in situ hybridization were used on frozen sections of 15-day-old mouse embryos. DNA methylation was inhibited with 5-azacytidine during culturing. We found very strong but gradually decreasing expression of Tet1 throughout the entire course of in vitro cartilage differentiation along with strong signals in the cartilaginous embryonic skeleton. Dnmt3a and Ogt expressions did not show significant changes with RT-qPCR and gave weak in situ hybridization signals. Inhibition of DNA methylation applied during early stages of differentiation reduced cartilage-specific gene expression and cartilage formation. In contrast, it had stimulatory effect when added to differentiated chondrocytes. Our results indicate that the DNA demethylation-inducing Tet1 is a significant epigenetic factor of chondrogenesis, and inhibition of DNA methylation exerts distinct effects in different phases of in vitro cartilage formation.

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Advances in RNA cytosine-5 methylation: detection, regulatory mechanisms, biological functions and links to cancer

Cited by 98 publications

References 85 publications

Bioinformatics analysis of DNMT1 expression and its role in head and neck squamous cell carcinoma prognosis

Bioinformatics analysis of DNMT1 expression and its role in head and neck squamous cell carcinoma prognosis

RNA Motifs and Modification Involve in RNA Long-Distance Transport in Plants

Modulation of DNA Methylation Influences Cartilage Formation in Murine Chondrogenic Models

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