bims-rimeca Biomed News
on RNA methylation in cancer
Issue of 2020‒12‒13
twenty papers selected by
Sk Ramiz Islam
Saha Institute of Nuclear Physics


  1. Cancer Biol Med. 2020 Nov 15. 17(4): 937-952
    Shen X, Hu B, Xu J, Qin W, Fu Y, Wang S, Dong Q, Qin L.
      Objective: Epigenetic aberration plays an important role in the development and progression of hepatocellular carcinoma (HCC). However, the alteration of RNA N6-methyladenosine (m6A) modifications and its role in HCC progression remain unclear. We therefore aimed to provide evidence using bioinformatics analysis.Methods: We comprehensively analyzed the m6A regulator modification patterns of 605 HCC samples and correlated them with metabolic alteration characteristics. We elucidated 390 gene-based m6A-related signatures and defined an m6Ascore to quantify m6A modifications. We then assessed their values for predicting prognoses and therapeutic responses in HCC patients.
    Results: We identified 3 distinct m6A modification patterns in HCC, and each pattern had distinct metabolic characteristics. The evaluation of m6A modification patterns using m6Ascores could predict the prognoses, tumor stages, and responses to sorafenib treatments of HCC patients. A nomogram based on m6Ascores showed high accuracy in predicting the overall survival of patients. The area under the receiver operating characteristic curve of predictions of 1, 3, and 5-year overall survivals were 0.71, 0.69, and 0.70 in the training cohort, and in the test cohort it was 0.74, 0.75, and 0.71, respectively. M6Acluster C1, which corresponded to hypoactive mRNA methylation, lower expression of m6A regulators, and a lower m6Ascore, was characterized by metabolic hyperactivity, lower tumor stage, better prognosis, and lower response to sorafenib treatment. In contrast, m6Acluster C3 was distinct in its hyperactive mRNA methylations, higher expression of m6A regulators, and higher m6Ascores, and was characterized by hypoactive metabolism, advanced tumor stage, poorer prognosis, and a better response to sorafenib. The m6Acluster, C2, was intermediate between C1 and C3.
    Conclusions: HCCs harbored distinct m6A regulator modification patterns that contributed to the metabolic heterogeneity and diversity of HCC. Development of m6A gene signatures and the m6Ascore provides a more comprehensive understanding of m6A modifications in HCC, and helps predict the prognosis and treatment response.
    Keywords:  Hepatocellular carcinoma; RNA N6-methyladenosine, metabolism, bioinformatics, prognosis
    DOI:  https://doi.org/10.20892/j.issn.2095-3941.2020.0402
  2. RNA Biol. 2020 Dec 09. 1-10
    Wang S, Zhang J, Wu X, Lin X, Liu XM, Zhou J.
      N6-methyladenosine (m6A) has emerged as a crucial epitranscriptomic mark which regulates a broad spectrum of physiological processes including stem cell differentiation. m6A-binding YTHDF proteins have recently been proposed to mediate differentiation of leukemia cell in a redundant manner. However, whether these proteins play semblable roles in pluripotent stem cell remain largely unknown. Here, we showed the differential functions of YTHDF1 and YTHDF3 in controlling the differentiation of embryonic stem cells (ESCs). Depletion of YTHDF3 in ESCs resulted in loss of pluripotency with accelerated expressions of marker genes involved in formation of three germ layers. Phenotypic and transcriptomic analyses revealed that loss of YTHDF1 led to dramatic impairment of cardiomyocytes (CMs) differentiation, accompanied by downregulated CM-specific genes. While, knockdown of YTHDF3 accelerated differentiation through facilitating the expressions of CM-specific gene. Notably, YTHDF3 appears to modulate cellular differentiation partially through suppression of YTHDF1, supporting the distinguishable but interrelated roles of YTHDF1 and YTHDF3 in cell fate determination.
    Keywords:  N6-methyladenosine; YTHDF; cardiomyocyte; differentiation; embryonic stem cell
    DOI:  https://doi.org/10.1080/15476286.2020.1850628
  3. Eye Vis (Lond). 2020 Dec 01. 7(1): 55
    Zhu L, Li S, He S, Tong Q, Wang L, Li X, Wu X, Meng Q, Jin E, Zhang C, Li T, Xu N, Huang L, Wang Y, Zhao M.
      PURPOSE: To investigate the role of N6-methyladenosine (m6A) RNA modification in the pathogenesis of Graves' ophthalmopathy (GO).METHODS: Surgically excised extraocular muscles from 7 patients with GO and 5 subjects without GO were used. The global m6A levels in the specimens were determined using an m6A RNA methylation quantification kit. RNA sequencing (RNA-seq) was used to analyze the molecules involved in the regulation of m6A RNA methylation and the differential expression of mRNAs between the two groups (4 eyes, respectively). The expression of m6A RNA modification genes was evaluated by real-time PCR. The functional implications of the gene alterations between the GO and control specimens were determined by Gene Ontology analysis.
    RESULTS: The m6A level was significantly increased in the specimens of GO patients compared to the control specimens (P < 0.05). The expression of m6A methylation regulators, such as WT1 associated protein (WTAP), alkylation repair homolog protein 5 (ALKBH5), E74 like ETS transcription factor 3 (ELF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTHDF3 and YTH domain containing 2 (YTHDC2), was significantly upregulated (P < 0.05). Gene Ontology enrichment analysis showed that the most highly upregulated genes and biological pathways were related to the immune response and inflammatory processes such as lymphocyte activation, leukocyte differentiation, cytokine production and cytokine-mediated signaling pathways.
    CONCLUSIONS: Our results suggest that m6A methylation may play a critical role in the pathogenesis of GO and that targeting genes that regulate m6A methylation may provide a new therapeutic approach for GO.
    Keywords:  Graves' ophthalmopathy; Pathogenesis; RNA-seq; m6A methylation
    DOI:  https://doi.org/10.1186/s40662-020-00221-3
  4. J Cell Physiol. 2020 Dec 11.
    Yang N, Wang T, Li Q, Han F, Wang Z, Zhu R, Zhou J.
      Cancer cells sustain high levels of glycolysis and glutaminolysis via reprogramming of intracellular metabolism, which represents a driver of hepatocellular carcinoma (HCC) progression. Understanding the mechanisms of cell metabolic reprogramming may present a new basis for liver cancer treatment. Herein, we collected HCC tissues and noncancerous liver tissues and found hepatitis B virus X-interacting protein (HBXIP) was found to be upregulated in HCC tissues and associated with poor prognosis. The N6-methyladenosine (m6A) level of hypoxia-inducible factor-1α (HIF-1α) in HCC cells was evaluated after the intervention of METTL3. The possible m6A site of HIF-1α was queried and the binding relationship between METTL3 and HIF-1α was verified. The interference of HBXIP suppressed HCC malignant behaviors and inhibited the Warburg effect in HCC cells. METTL3 was upregulated in HCC tissues and positively regulated by HBXIP. Overexpression of METTL3 restored cell metabolic reprogramming in HCC cells with partial loss of HBXIP. HBXIP mediated METTL3 to promote the metabolic reprogramming and malignant biological behaviors of HCC cells. The levels of total m6A in HCC cells and m6A in HIF-1α were increased. METTL3 had a binding relationship with HIF-1α and mediated the m6A modification of HIF-1α. In conclusion, HBXIP drives metabolic reprogramming in HCC cells via METTL3-mediated m6A modification of HIF-1α.
    Keywords:  HBXIP; HIF-1α; METTL3; N6-methyladenosine methylation; hepatocellular carcinoma
    DOI:  https://doi.org/10.1002/jcp.30128
  5. Anticancer Res. 2020 Dec;40(12): 6665-6676
    Nakagawa N, Tanaka K, Sonohara F, Kandimalla R, Sunagawa Y, Inokawa Y, Takami H, Hayashi M, Yamada S, Kanda M, Tanaka C, Nakayama G, Koike M, Kodera Y.
      BACKGROUND/AIM: N6-Methyladenosine (m6A), the most abundant internal modification of RNA, plays a critical role in cancer development. However, the clinical implications of m6A in hepatocellular carcinoma (HCC) remain unclear.MATERIALS AND METHODS: We analyzed 177 HCC and paired noncancerous liver tissues from patients who underwent hepatectomy according to global m6A quantification and expression of m6A demethylases fat mass and obesity-associated protein (FTO) and alpha-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5).
    RESULTS: The global m6A quantification revealed no significant difference between HCC and non-cancerous tissue. The expression of m6A demethylases FTO and ALKBH5, was significantly lower in HCC than in non-cancerous tissues (both p<0.001). Furthermore, low ALKBH5 expression in non-cancerous tissues was significantly correlated with worse recurrence-free survival (median of 16.3 vs. 38.9 months, p=0.001).
    CONCLUSION: m6A in HCC and its demethylase in surrounding non-cancerous liver tissues might be involved in inherent mechanisms for HCC development and affect malignant potential after HCC resection.
    Keywords:  Hepatocellular carcinoma; RNA demethylase; methylation of N6 adenosine; prognosis
    DOI:  https://doi.org/10.21873/anticanres.14690
  6. J Mol Cell Cardiol. 2020 Dec 03. pii: S0022-2828(20)30334-5. [Epub ahead of print]
    Rajan KS, Ramasamy S, Garikipati VNS, Suvekbala V.
      Post-transcriptional RNA modification has been observed in all kingdoms of life and more than a hundred different types of RNA modifications decorate the chemical and topological properties of these ribose nucleotides. These RNA modifications can potentially alter the RNA structure and also affect the binding affinity of proteins, thus regulating the mRNA stability as well as translation. Emerging evidence suggest that these modifications are not static, but are dynamic; vary upon different cues and are cell-type or tissue-specific. The cardiac transcriptome is not exceptional to such RNA modifications and is enriched with the abundant base methylation such as N6-methyladenosine (m6A) and also 2'-O-Methylation (Nm). In this review we will focus on the technologies available to map these modifications and as well as the contribution of these post-transcriptional modifications during various pathological conditions of the heart.
    DOI:  https://doi.org/10.1016/j.yjmcc.2020.11.011
  7. Small. 2020 Dec 07. e2005086
    Zheng Y, Ling Y, Zhang DY, Tan CP, Zhang H, Yang GG, Wang H, Ji LN, Mao ZW.
      The epigenetic dysregulation and hypoxia are two important factors that drive tumor malignancy, and N6 -methyladenosine (m6 A) in mRNA is involved in the regulation of gene expression. Herein, a nanocatalyst OsSx -PEG (PEG = poly(ethylene glycol)) nanoparticles (NPs) as O2 modulator is developed to improve tumor hypoxia. OsSx -PEG NPs can significantly downregulate genes involved in hypoxia pathway. Interestingly, OsSx -PEG NPs elevate RNA m6 A methylation levels to cause the m6 A-dependent mRNA degradation of the hypoxia-related genes. Moreover, OsSx -PEG NPs can regulate the expression of RNA m6 A methyltransferases and demethylases. Finally, DOX@OsSx -PEG (DOX = doxorubicin; utilized as a model drug) NPs modulate tumor hypoxia and regulate mRNA m6 A methylation of hypoxia-related genes in vivo. As the first report about relationship between catalytic nanomaterials and RNA modifications, the research opens a new avenue for unveiling the underlying action mechanisms of hypoxia-modulating nanomaterials and shows potential of regulating RNA modification to overcome chemoresistance.
    Keywords:  RNA methylation; hypoxia; mRNA degradation; nanocatalysts; osmium
    DOI:  https://doi.org/10.1002/smll.202005086
  8. Cell Biosci. 2020 Nov 25. 10(1): 136
    Wang Y, Zhang Y, Du Y, Zhou M, Hu Y, Zhang S.
      N6-Methyladenosine (m6A) is the most abundant, dynamic, and reversible epigenetic RNA modification that is found in coding and non-coding RNAs. Emerging studies have shown that m6A and its regulators affect multiple steps in RNA metabolism and play broad roles in various cancers. Worldwide, breast cancer is the most prevalent cancer in female. It is a very heterogeneous disease characterized by genetic and epigenetic variations in tumor cells. Increasing evidence has shown that the dysregulation of m6A-related effectors, as methyltransferases, demethylases, and m6A binding proteins, is pivotal in breast cancer pathogenesis. In this review, we have summarized the most up-to-date research on the biological functions of m6A modification in breast cancer and have discussed the potential clinical applications and future directions of m6A modification as a biomarker as well as a therapeutic target of breast cancer.
    Keywords:  Breast cancer; Clinical applications; Epigenetics; Molecular mechanism; m6A
    DOI:  https://doi.org/10.1186/s13578-020-00502-3
  9. Essays Biochem. 2020 Dec 07. 64(6): 967-979
    Wang Y, Jia G.
      Research on N6-methyladenosine (m6A) in recent years has revealed the complex but elegant regulatory role of this RNA modification in multiple physiological processes. The advent of m6A detection technologies is the basis for studying the function of this RNA modification. These technologies enable the detection of m6A sites across transcriptome or at specific gene, thereby revealing the alternation and dynamic of RNA modification. However, non-specific signals that arise from the antibody-based methods and the low-resolution landscape have become the major drawback of classic m6A detection methods. In this review, we summarize the current available methods and categorized them into three groups according to the utilization purpose, including measurement of total m6A levels, detection m6A locus in single gene, and m6A sequencing. We hope this review helps researchers in epitranscriptomic field find an appropriate m6A detection tool that suites their experimental design.
    Keywords:  RNA; biochemical techniques and resources; biotechnology
    DOI:  https://doi.org/10.1042/EBC20200039
  10. PeerJ. 2020 ;8 e10385
    Li Y, Zheng JN, Wang EH, Gong CJ, Lan KF, Ding X.
      Background: Increasing evidence has shown that N6-methyladenosine (m6A) RNA methylation regulators have important biological functions in human cancers. However, there are few studies on the value of m6A reader protein YTHDC2 in the diagnosis and tumor-infiltrating of head and neck squamous cell carcinoma (HNSCC). Therefore, it is important to understand the potential clinical value of YTHDC2 in the prognosis and immune infiltration of HNSCC.Methods: In this study, gene expression profiles and the corresponding clinical information of 270 HNSCC patients were downloaded from the Gene Expression Omnibus (GEO) database. The gene co-expression network was established to verify whether YTHDC2 was related to the prognosis of HNSCC and verified again in the public database. The correlations between YTHDC2 and immune infiltration was investigated via Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA).
    Results: The results showed that YTHDC2 appeared in the blue module related to survival time and survival state and had a close correlation with the prognosis and immune infiltration level of HNSCC in public database. Patients with low expression of YTHDC2 had poor overall survival (OS) and recurrence-free survival (RFS) than those with high expression. In addition, the expression of YTHDC2 was positively correlated with the level of CD4+ T cell subpopulations infiltration in HNSCC.
    Conclusions: Through this study, we found that YTHDC2 is a tumor suppressor gene with high expression in normal tissues and low expression in tumor tissues. In addition, YTHDC2 is correlated with the immune infiltrating levels of B cells, CD8+ T cells, CD4+ T cells, neutrophils, and dendritic cells in HNSCC, which may become a potential marker for prognosis and immune infiltration of HNSCC.
    Keywords:  Head and neck squamous cell carcinoma (HNSCC); N6-methyladenosine (m6A); Survival analysis; Tumor-infiltrating; Weighted gene co-expression network analysis; YTHDC2
    DOI:  https://doi.org/10.7717/peerj.10385
  11. Cancer Res. 2020 Dec 08. pii: canres.1619.2020. [Epub ahead of print]
    Gao S, Gu Y, Niu S, Wang Y, Duan L, Pan Y, Tong Z, Zhang X, Yang Z, Peng B, Wang X, Han X, Li Y, Cheng T, Liu Y, Shang L, Liu T, Yang X, Sun M, Jiang S, Zhang C, Zhang N, Ye Q.
      Aberrant N6-methyladenosine (m6A) modification has emerged as a driver of tumor initiation and progression, yet how lncRNA are involved in the regulation of m6A remains unknown. Here we utilize data from 12 cancer types from The Cancer Genome Atlas to comprehensively map lncRNA that are potentially deregulated by DNA methylation. A novel DNA methylation-deregulated and RNA m6A reader-cooperating lncRNA (DMDRMR) facilitated tumor growth and metastasis in clear cell renal cell carcinoma (ccRCC). Mechanistically, DMDRMR bound insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) to stabilize target genes, including the cell cycle kinase CDK4 and three extracellular matrix components (COL6A1, LAMA5, and FN1), by specifically enhancing IGF2BP3 activity on them in an m6A-dependent manner. Consequently, DMDRMR and IGF2BP3 enhanced the G1/S transition, thus promoting cell proliferation in ccRCC. In ccRCC patients, high coexpression of DMDRMR and IGF2BP3 was associated with poor outcomes. Our findings reveal that DMDRMR cooperates with IGF2BP3 to regulate target genes in an m6A-dependent manner and may represent a potential diagnostic, prognostic, and therapeutic target in ccRCC.
    DOI:  https://doi.org/10.1158/0008-5472.CAN-20-1619
  12. Biomark Res. 2020 Nov 10. 8(1): 61
    Yang X, Hu X, Liu J, Wang R, Zhang C, Han F, Chen Y, Ma D.
      Non-coding RNAs are the main component of the extensive transcription results of the mammalian genome. They are not transcribed into proteins but play critical roles in regulating multiple biological processes and affecting cancer progression. m6A modification is one of the most abundant internal RNA modification of mammalian cells, and it involves almost all aspects of RNA metabolism. Recent research revealed tight correlations between m6A modification and ncRNAs and indicated the interaction between m6A and ncRNAs act a pivotal part in the development of cancer. The correlation between m6A modification and ncRNAs provides a new perspective for exploring the potential regulatory mechanism of tumor gene expression, and suggest that m6A modification and ncRNAs may be important prognostic markers and therapeutic targets for multiple cancers. In this review, we summarize the potential regulatory mechanisms between m6A methylation and ncRNAs, highlighting how their relationship affects biological functions in cancer.
    Keywords:  Cancer; Noncoding RNAs; m6A modification
    DOI:  https://doi.org/10.1186/s40364-020-00244-x
  13. J Am Chem Soc. 2020 Dec 11.
    Nappi M, Hofer A, Balasubramanian S, Gaunt MJ.
      Selective chemistry that modifies the structure of DNA and RNA is essential to understanding the role of epigenetic modifications. We report a visible-light-activated photocatalytic process that introduces a covalent modification at a C(sp3)-H bond in the methyl group of N6-methyl deoxyadenosine and N6-methyl adenosine, epigenetic modifications of emerging importance. A carefully orchestrated reaction combines reduction of a nitropyridine to form a nitrosopyridine spin-trapping reagent and an exquisitely selective tertiary amine-mediated hydrogen-atom abstraction at the N6-methyl group to form an α-amino radical. Cross-coupling of the putative α-amino radical with nitrosopyridine leads to a stable conjugate, installing a label at N6-methyl-adenosine. We show that N6-methyl deoxyadenosine-containing oligonucleotides can be enriched from complex mixtures, paving the way for applications to identify this modification in genomic DNA and RNA.
    DOI:  https://doi.org/10.1021/jacs.0c10616
  14. BMB Rep. 2020 Dec 11. pii: 5186. [Epub ahead of print]
    Han SH, Choe J.
      Post-transcriptional regulation is an indispensable cellular mechanism of gene expression control that dictates various cellular functions and cell fate decisions. Recently, various chemical RNA modifications, termed the "epitranscriptome," have been proposed to play crucial roles in the regulation of post-transcriptional gene expression. To date, more than 170 RNA modifications have been identified in almost all types of RNA. As with DNA modification-mediated control of gene expression, regulation of gene expression via RNA modification is also accomplished by three groups of proteins: writers, readers, and erasers. Several emerging studies have revealed that dysregulation in RNA modification is closely associated with tumorigenesis. Notably, the molecular outcomes of specific RNA modifications often have opposite cellular consequences. In this review, we highlight the current progress in the elucidation of the mechanisms of cancer development due to chemical modifications of various RNA species.
  15. Front Oncol. 2020 ;10 580018
    Feng C, Huang X, Li X, Mao J.
      Epigenetic modifications including histone modifications and DNA and RNA modifications are involved in multiple biological processes and human diseases. One disease, kidney cancer, includes a common type of tumor, accounts for about 2% of all cancers, and usually has poor prognosis. The molecular mechanisms and therapeutic strategy of kidney cancer are still under intensive study. Understanding the roles of epigenetic modifications and underlying mechanisms in kidney cancer is critical to its diagnosis and clinical therapy. Recently, the function of DNA and RNA modifications has been uncovered in kidney tumor. In the present review, we summarize recent findings about the roles of epigenetic modifications (particularly DNA and RNA modifications) in the incidence, progression, and metastasis of kidney cancer, especially the renal cell carcinomas.
    Keywords:  DNA hydroxymethylation; DNA methylation; RNA methylation; ten-eleven translocases; tumor
    DOI:  https://doi.org/10.3389/fonc.2020.580018
  16. Technol Cancer Res Treat. 2020 Jan-Dec;19:19 1533033820977525
    Zhou J, Xiao D, Qiu T, Li J, Liu Z.
      OBJECTIVE: Extracellular vesicles (Evs) secreted from cells have been revealed to mediate signal transduction between cells. Nevertheless, the mechanisms through which molecules transported by EVs function remain to be elucidated. In the present study, the functional relevance of endothelial cells (ECs)-secreted Evs carrying microRNA-376c (miR-376c) in the biological activities of non-small cell lung cancer (NSCLC) cells was investigated, including the related mechanisms.METHODS: Two cell lines with the highest YTH N6-methyladenosine (m6A) RNA binding protein 1 (YTHDF1) expression were selected for subsequent experiments. Cellular proliferation, migration, invasion and apoptosis were measured by EdU, wound healing, Transwell assays and flow cytometry, respectively. The binding relationship between miR-376c and YTHDF1 was analyzed by dual-luciferase reporter assays. The miR-376c, YTHDF1 and β-catenin expression was evaluated by qPCR assays and western blot assays.
    RESULTS: The expression patterns of YTHDF1 were higher in NSCLC cells, whereas miR-376c was reduced versus the normal bronchial epithelial cells. Silencing of YTHDF1 repressed NSCLC cell proliferation, invasion and migration abilities, whereas enhanced apoptosis. miR-376c negatively modulated YTHDF1 expression. Under co-culture conditions, ECs transmitted miR-376c into NSCLC cells through Evs, and inhibited the intracellular YTHDF1 expression and the Wnt/β-catenin pathway activation. Rescue experiments revealed that YTHDF1 overexpression reversed the inhibitory role of miR-376c released by EC-Evs in NSCLC cells.
    CONCLUSION: EC-delivered Evs inhibit YTHDF1 expression and the Wnt/β-catenin pathway induction via miR-376c overexpression, thus inhibiting the malignant phenotypes of NSCLC cells.
    Keywords:  YTHDF1; extracellular vesicles; microRNA-376c; non-small cell lung cancer; the Wnt/β-catenin pathway
    DOI:  https://doi.org/10.1177/1533033820977525
  17. Front Genet. 2020 ;11 559138
    Lan N, Lu Y, Zhang Y, Pu S, Xi H, Nie X, Liu J, Yuan W.
      In recent years, the prevalence of obesity and cancer have been rising. Since this poses a serious threat to human health, the relationship between the two has attracted much attention. This study examined whether fat mass and obesity-associated (FTO) genes are linked, taking into account a Genome-wide Association Study (GWAS) that revealed multiple single nucleotide polymorphism sites (SNPs) of the FTO gene, indicating an association between obesity and cancer in different populations. FTO proteins have been proved to participate in adipogenesis and tumorigenesis with post-transcriptional regulation of downstream molecular expression or through the target of the mammalian target protein rapamycin (mTOR). FTO inhibitors have also been found to share anti-obesity and anti-cancer effects in vivo. In this review, we comprehensively discuss the correlation between obesity and cancer by measuring FTO gene polymorphism, as well as the molecular mechanism involved in these diseases, emphasizing FTO as the common genetic basis of obesity and cancer.
    Keywords:  FTO; FTO inhibitors; M6A modification; SNP; cancer; mTOR; obesity
    DOI:  https://doi.org/10.3389/fgene.2020.559138
  18. Brief Funct Genomics. 2020 Dec 07. pii: elaa022. [Epub ahead of print]
    Lee SY, Kim JJ, Miller KM.
      Post-translational modifications of proteins are well-established participants in DNA damage response (DDR) pathways, which function in the maintenance of genome integrity. Emerging evidence is starting to reveal the involvement of modifications on RNA in the DDR. RNA modifications are known regulators of gene expression but how and if they participate in DNA repair and genome maintenance has been poorly understood. Here, we review several studies that have now established RNA modifications as key components of DNA damage responses. RNA modifying enzymes and the binding proteins that recognize these modifications localize to and participate in the repair of UV-induced and DNA double-strand break lesions. RNA modifications have a profound effect on DNA-RNA hybrids (R-loops) at DNA damage sites, a structure known to be involved in DNA repair and genome stability. Given the importance of the DDR in suppressing mutations and human diseases such as neurodegeneration, immunodeficiencies, cancer and aging, RNA modification pathways may be involved in human diseases not solely through their roles in gene expression but also by their ability to impact DNA repair and genome stability.
    Keywords:  DNA damage; DNA repair; R-loops; RNA modification; genome integrity; transcription
    DOI:  https://doi.org/10.1093/bfgp/elaa022
  19. EMBO J. 2020 Dec 07. e105496
    Navarro IC, Tuorto F, Jordan D, Legrand C, Price J, Braukmann F, Hendrick AG, Akay A, Kotter A, Helm M, Lyko F, Miska EA.
      Methylation of carbon-5 of cytosines (m5 C) is a post-transcriptional nucleotide modification of RNA found in all kingdoms of life. While individual m5 C-methyltransferases have been studied, the impact of the global cytosine-5 methylome on development, homeostasis and stress remains unknown. Here, using Caenorhabditis elegans, we generated the first organism devoid of m5 C in RNA, demonstrating that this modification is non-essential. Using this genetic tool, we determine the localisation and enzymatic specificity of m5 C sites in the RNome in vivo. We find that NSUN-4 acts as a dual rRNA and tRNA methyltransferase in C. elegans mitochondria. In agreement with leucine and proline being the most frequently methylated tRNA isoacceptors, loss of m5 C impacts the decoding of some triplets of these two amino acids, leading to reduced translation efficiency. Upon heat stress, m5 C loss leads to ribosome stalling at UUG triplets, the only codon translated by an m5 C34-modified tRNA. This leads to reduced translation efficiency of UUG-rich transcripts and impaired fertility, suggesting a role of m5 C tRNA wobble methylation in the adaptation to higher temperatures.
    Keywords:   Caenorhabditis elegans ; 5-methylcytosine; NSUN; RNA modifications; translation efficiency
    DOI:  https://doi.org/10.15252/embj.2020105496
  20. Nucleic Acids Res. 2020 Dec 10. pii: gkaa1178. [Epub ahead of print]
    Levi O, Arava YS.
      Modification of nucleotides within an mRNA emerges as a key path for gene expression regulation. Pseudouridine is one of the most common RNA modifications; however, only a few mRNA modifiers have been identified to date, and no one mRNA pseudouridine reader is known. Here, we applied a novel genome-wide approach to identify mRNA regions that are bound by yeast methionine aminoacyl tRNAMet synthetase (MetRS). We found a clear enrichment to regions that were previously described to contain pseudouridine (Ψ). Follow-up in vitro and in vivo analyses on a prime target (position 1074 within YEF3 mRNA) demonstrated the importance of pseudouridine for MetRS binding. Furthermore, polysomal and protein analyses revealed that Ψ1074 mediates translation. Modification of this site occurs presumably by Pus6, a pseudouridine synthetase known to modify MetRS cognate tRNA. Consistently, the deletion of Pus6 leads to a decrease in MetRS association with both tRNAMet and YEF3 mRNA. Furthermore, while global protein synthesis decreases in pus6Δ, translation of YEF3 increases. Together, our data imply that Pus6 'writes' modifications on tRNA and mRNA, and both types of RNAs are 'read' by MetRS for translation regulation purposes. This represents a novel integrated path for writing and reading modifications on both tRNA and mRNA, which may lead to coordination between global and gene-specific translational responses.
    DOI:  https://doi.org/10.1093/nar/gkaa1178