N6-methyladenosine links RNA metabolism to cancer progression

Dai, Dongjun; Wang, Hanying; Zhu, Liyuan; Jin, Hongchuan; Wang, Xian

doi:10.1038/s41419-017-0129-x

Cited by 370 publications

(359 citation statements)

References 103 publications

(126 reference statements)

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“…Nucleotide modifications can affect RNA shape, local charge and base-pairing potential, thus altering protein-binding affinity 42 . N6-methyladenine (m6A) is the most common internal modification on mRNA 43 , and has been implicated in many facets of RNA metabolism 44 . m6A dysregulation has been linked to deleterious effects on cell differentiation and stress tolerance, and to a number of human diseases, including obesity and cancer 45 .…”

Section: Modification Detectionmentioning

confidence: 99%

Nanopore native RNA sequencing of a human poly(A) transcriptome

Workman

Tang

et al. 2018

Preprint

186

349

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High throughput cDNA sequencing technologies have dramatically advanced our understanding of transcriptome complexity and regulation. However, these methods lose information contained in biological RNA because the copied reads are often short and because modifications are not carried forward in cDNA. We address these limitations using a native poly(A) RNA sequencing strategy developed by Oxford Nanopore Technologies (ONT). Our study focused on poly(A) RNA from the human cell line GM12878, generating 9.9 million aligned sequence reads. These native RNA reads had an aligned N50 length of 1294 bases, and a maximum aligned length of over 21,000 bases. A total of 78,199 high-confidence isoforms were identified by combining long nanopore reads with short higher accuracy Illumina reads. We describe strategies for assessing 3′ poly(A) tail length, base modifications and transcript haplotypes from nanopore RNA data. Together, these nanopore-based techniques are poised to deliver new insights into RNA biology.

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Section: Modification Detectionmentioning

confidence: 99%

Nanopore native RNA sequencing of a human poly(A) transcriptome

Workman

Tang

et al. 2018

Preprint

186

349

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“…m 6 A abundance was significantly reduced in PASMCs and PAECs when exposed to hypoxia (0.107% ± 0.007 vs. 0.054% ± 0.118, p = 0.023 in PASMCs; 0.114% ± 0.011 vs. 0.059% ± 0.008, p = 0.031 in PAECs, Fig 6A). m 6 A abundance in circRNAs was lower than it in mRNAs (0.1–0.4%) (17, 18). Next, we confirmed the back-splicing of circXpo6 and circTmtc3 by CIRI software.…”

Section: Resultsmentioning

confidence: 99%

“…m 6 A plays important roles in various biological processes. m 6 A is associated with cancer progression, promoting the proliferation of cancer cells and contributing to the cancer stem cell self-renewal (18, 21). Lipid accumulation was reduced in hepatic cells when m 6 A abundance in peroxisome proliferator-activator ( PPaR) was decreased (34).…”

Section: Discussionmentioning

confidence: 99%

“…The methyltransferase complex is known as writers, including methyltransferase-like-3, −14 and −16 (METTL3/METTL14/METTL16), Wilms tumour 1-associated protein (WTAP), RNA binding motif protein 15 (RBM15), vir like m 6 A methyltransferase associated (KIAA1429) and zinc finger CCCH-type containing 13 (ZC3H13), appending m 6 A on DRACH (17, 20, 21). METTL3 is regarded as the core catalytically active subunit, while METTL14 and WTAP play a structural role in METTL3’s catalytic activity (18, 22). The “erasers”, fat mass and obesity related protein (FTO) and alkylation repair homolog 5 (ALKBH5), catalyze the N-alkylated nucleic acid bases oxidatively demethylated (22).…”

Section: Introductionmentioning

confidence: 99%

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Transcriptome-wide map of m⁶A circRNAs identified in hypoxic pulmonary hypertension rat model

Zhou

et al. 2019

Preprint

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32Hypoxic pulmonary hypertension (HPH) is a lethal disease. CircRNAs and m 6 A 33 circRNAs have been reported to be associated with cancer progression, but the 34 expression profiling of m 6 A circRNAs has not been identified in HPH. This study was 35 to investigate the transcriptome-wide map of m 6 A circRNAs in HPH. In this study, 36 hypoxia-induced PH rat model was established. Total RNA was extracted and purified 37 from lungs of rats, then circRNAs were detected and annotated by RNA-seq analysis. 38 m 6 A RNA Immunoprecipitation (MeRIP) was performed following rRNA depletion, 39 and RNA-seq library was constructed. CircRNA-miRNA-mRNA co-expression 40 network was also constructed. In vitro, total m 6 A was measured. m 6 A circXpo6 and 41 m 6 A circTmtc3 were detected in pulmonary artery smooth muscle cells (PASMCs) and 42 pulmonary artery endothelial cells (PAECs) exposed to 21% O 2 and 1% O 2 for 48 h, 43 respectively. m 6 A abundance in 166 circRNAs was significantly upregulated and m 6 A 44 abundance in 191 circRNAs was significantly downregulated in lungs of HPH rats. 45 m 6 A abundance in circRNAs was significantly reduced in hypoxia in vitro. m 6 A 46 circRNAs were mainly derived from single exons of protein-coding genes. m 6 A 47 influenced the circRNA-miRNA-mRNA co-expression network in hypoxia. m 6 A 48 circXpo6 and m 6 A circTmtc3 were downregulated in hypoxia. In general, our study 49 firstly identified the transcriptome-wide map of m 6 A circRNAs in HPH. m 6 A level in 50 circRNAs was decreased in lungs of HPH rats and in PASMCs and PAECs exposed to 51 hypoxia. Downregulated or upregulated m 6 A level influenced circRNA-miRNA-52 mRNA co-expression network in HPH. Moreover, we firstly identified two 53 downregulated m 6 A circRNAs in HPH: circXpo6 and circTmtc3. We suggested that 54 m 6 A circRNAs may be used as a potential diagnostic marker or therapy target in the 55 future.56 57 58 59 60 3 61 62 Author summary 63 HPH is a disease with great morbidity and mortality. It is often caused by chronic 64 hypoxic lung diseases, such as chronic obstructive pulmonary disease and interstitial 65 lung diseases. It lacks effective therapy methods so far. CircRNAs are a type of non-66 coding RNAs and can be used as biomarkers because they are differentially enriched in 67 specific cell types or tissues and not easily degraded. m 6 A is identified as the most 68 universal modification on non-coding RNAs in eukaryotes. CircRNAs can be modified 69 by m 6 A. m 6 A circRNAs in HPH is not well understood yet. Here we identify the 70 transcriptome-wide map of m 6 A circRNAs in HPH. We elucidate that m 6 A level in 71circRNAs is decreased in lungs of HPH rats and in PASMCs and PAECs exposed to 72 hypoxia. We find that downregulated or upregulated m 6 A level influences circRNA-73 miRNA-mRNA co-expression network in HPH. Moreover, we are the first to identify 74 two downregulated m 6 A circRNAs in HPH: circXpo6 and circTmtc3. We suggest that 75 m 6 A circRNAs may be used as a potential diagnostic marker or thera...

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“…The malfunctions of the cellular machinery regulating the m 6 A modification have in turn been linked to pathologies like obesity (Ben-Haim, Moshitch-Moshkovitz, & Rechavi, 2015), cancer (Peng, Yuan, Jiang, Tang, & Li, 2016), and neurodegeneration (Satterlee et al, 2014). Therefore, the m 6 A field has recently attracted broad attention of drug discovery community (Boriack-Sjodin, Ribich, & Copeland, 2018;Dai, Wang, Zhu, Jin, & Wang, 2018;Delaunay & Frye, 2019;.…”

Section: Introductionmentioning

confidence: 99%

Flexible binding of m⁶A reader protein YTHDC1 to its preferred RNA motif

Bedi

Wiedmer

et al. 2019

Preprint

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N6-methyladenosine (m 6 A) is the most prevalent chemical modification in human mRNAs. Its recognition by reader proteins enables many cellular functions, including splicing and translation of mRNAs. However, the binding mechanisms of m 6 A-containing RNAs to their readers are still elusive due to the unclear roles of m 6 A-flanking ribonucleotides. Here, we use a model system, YTHDC1 with its RNA motif 5'-G-2G-1(m 6 A)C+1U+2-3', to investigate the binding mechanisms by atomistic simulations, X-ray crystallography, and isothermal titration calorimetry. The experimental data and simulation results show that m 6 A is captured by an aromatic cage of YTHDC1 and the 3' terminus nucleotides are stabilized by cation-π-π interactions, while the 5' terminus remains flexible. Moreover, simulations of unbound RNA motifs reveal that the methyl group of m 6 A and the 5' terminus shift the conformational preferences of the oligoribonucleotides to the bound-like conformation, thereby facilitating the association process. The proposed binding mechanisms may help in the discovery of chemical probes against m 6 A reader proteins.

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N6-methyladenosine links RNA metabolism to cancer progression

Cited by 370 publications

References 103 publications

Nanopore native RNA sequencing of a human poly(A) transcriptome

Nanopore native RNA sequencing of a human poly(A) transcriptome

Transcriptome-wide map of m⁶A circRNAs identified in hypoxic pulmonary hypertension rat model

Flexible binding of m⁶A reader protein YTHDC1 to its preferred RNA motif

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N6-methyladenosine links RNA metabolism to cancer progression

Cited by 370 publications

References 103 publications

Nanopore native RNA sequencing of a human poly(A) transcriptome

Nanopore native RNA sequencing of a human poly(A) transcriptome

Transcriptome-wide map of m6A circRNAs identified in hypoxic pulmonary hypertension rat model

Flexible binding of m6A reader protein YTHDC1 to its preferred RNA motif

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Resources

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Transcriptome-wide map of m⁶A circRNAs identified in hypoxic pulmonary hypertension rat model

Flexible binding of m⁶A reader protein YTHDC1 to its preferred RNA motif