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Research Paper

Crosstalk between m6A mRNAs and m6A circRNAs and the time-specific biogenesis of m6A circRNAs after OGD/R in primary neurons

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Article: 2181575 | Received 28 Apr 2022, Accepted 07 Feb 2023, Published online: 01 Mar 2023

References

  • Zhao Z, Lu C, Li T, et al. The protective effect of melatonin on brain ischemia and reperfusion in rats and humans: in vivo assessment and a randomized controlled trial. J Pineal Res. 2018;65(4):e12521.
  • Wiberg S, Hassager C, Schmidt H, et al. Neuroprotective effects of the glucagon-like peptide-1 analog exenatide after out-of-hospital cardiac arrest: a randomized controlled trial. Circulation. 2016;134(25):2115–21.
  • Sun L, Li M, Ma X, et al. Inhibition of HMGB1 reduces rat spinal cord astrocytic swelling and AQP4 expression after oxygen-glucose deprivation and reoxygenation via TLR4 and NF-κB signaling in an IL-6-dependent manner. J Neuroinflammation. 2017;14(1):231.
  • Sasaki T, Takemori H, Yagita Y, et al. SIK2 is a key regulator for neuronal survival after ischemia via TORC1-CREB. Neuron. 2011;69(1):106–119.
  • Song Y, Li Z, He T, et al. M2 microglia-derived exosomes protect the mouse brain from ischemia-reperfusion injury via exosomal miR-124. Theranostics. 2019;9(10):2910–2923.
  • Wang P, Xu TY, Wei K, et al. ARRB1/beta-arrestin-1 mediates neuroprotection through coordination of BECN1-dependent autophagy in cerebral ischemia. Autophagy. 2014;10(9):1535–1548.
  • Fu Y, Dominissini D, Rechavi G, et al. Gene expression regulation mediated through reversible m(6)A RNA methylation. Nat Rev Genet. 2014;15(5):293–306.
  • Meyer KD, Jaffrey SR. The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nat Rev Mol Cell Biol. 2014;15(5):313–326.
  • Boccaletto P, Machnicka MA, Purta E, et al. MODOMICS: a database of RNA modification pathways. 2017 update. Nucleic Acids Res. 2018;46(D1):D303–D307.
  • Gilbert WV, Bell TA, Schaening C. Messenger RNA modifications: form, distribution, and function. Science. 2016;352(6292):1408–1412.
  • Han D, Liu J, Chen C, et al. Anti-tumour immunity controlled through mRNA m(6)A methylation and YTHDF1 in dendritic cells. Nature. 2019;566(7743):270–274.
  • Xu K, Yang Y, Feng GH, et al. Mettl3-mediated m(6)A regulates spermatogonial differentiation and meiosis initiation. Cell Res. 2017;27(9):1100–1114.
  • Cheng Y, Luo H, Izzo F, et al. m(6)A RNA methylation maintains hematopoietic stem cell identity and symmetric commitment. Cell Rep. 2019;28(7):1703–1716.e6.
  • Yu J, Chen M, Huang H, et al. Dynamic m6A modification regulates local translation of mRNA in axons. Nucleic Acids Res. 2018;46(3):1412–1423.
  • Weng YL, Wang X, An R, et al. Epitranscriptomic m(6)A regulation of axon regeneration in the adult mammalian nervous system. Neuron. 2018;97(2):313–325.e6.
  • Shi H, Zhang X, Weng YL, et al. m(6)A facilitates hippocampus-dependent learning and memory through YTHDF1. Nature. 2018;563(7730):249–253.
  • Hansen TB, Jensen TI, Clausen BH, et al. Natural RNA circles function as efficient microRNA sponges. Nature. 2013;495(7441):384–388.
  • Memczak S, Jens M, Elefsinioti A, et al. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature. 2013;495(7441):333–338.
  • Guo JU, Agarwal V, Guo H, et al. Expanded identification and characterization of mammalian circular RNAs. Genome Biol. 2014;15(7):409.
  • Rybak-Wolf A, Stottmeister C, Glazar P, et al. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Mol Cell. 2015;58(5):870–885.
  • You X, Vlatkovic I, Babic A, et al. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nat Neurosci. 2015;18(4):603–610.
  • Han B, Zhang Y, Zhang Y, et al. Novel insight into circular RNA HECTD1 in astrocyte activation via autophagy by targeting MIR142-TIPARP: implications for cerebral ischemic stroke. Autophagy. 2018;14(7):1164–1184.
  • Nan A, Chen L, Zhang N, et al. A novel regulatory network among LncRpa, CircRar1, MiR-671 and apoptotic genes promotes lead-induced neuronal cell apoptosis. Arch Toxicol. 2017;91(4):1671–1684.
  • Yang Y, Fan X, Mao M, et al. Extensive translation of circular RNAs driven by N(6)-methyladenosine. Cell Res. 2017;27(5):626–641.
  • Zhou C, Molinie B, Daneshvar K, et al. Genome-wide maps of m6A circRNAs identify widespread and cell-type-specific methylation patterns that are distinct from mRNAs. Cell Rep. 2017;20(9):2262–2276.
  • Chen RX, Chen X, Xia LP, et al. N(6)-methyladenosine modification of circNSUN2 facilitates cytoplasmic export and stabilizes HMGA2 to promote colorectal liver metastasis. Nat Commun. 2019;10(1):4695.
  • Park OH, Ha H, Lee Y, et al. Endoribonucleolytic cleavage of m(6) A-containingRNAs by RNase P/MRP complex. Mol Cell. 2019;74(3):494–507.e8.
  • Tang C, Xie Y, Yu T, et al. m(6)A-dependent biogenesis of circular RNAs in male germ cells. Cell Res. 2020;30(3):211–228.
  • Chen C, Yuan W, Zhou Q, et al. N6-methyladenosine-induced circ1662 promotes metastasis of colorectal cancer by accelerating YAP1 nuclear localization. Theranostics. 2021;11(9):4298–4315.
  • Fan HN, Chen ZY, Chen XY, et al. METTL14-mediated m(6)A modification of circORC5 suppresses gastric cancer progression by regulating miR-30c-2-3p/AKT1S1 axis. Mol Cancer. 2022;21(1):51.
  • Liu Z, Wang T, She Y, et al. N(6)-methyladenosine-modified circIGF2BP3 inhibits CD8(+) T-cell responses to facilitate tumor immune evasion by promoting the deubiquitination of PD-L1 in non-small cell lung cancer. Mol Cancer. 2021;20(1):105.
  • Hilgenberg LG, Smith MA. Preparation of dissociated mouse cortical neuron cultures. J Vis Exp. 2007;10. DOI:10.3791/562
  • Tasca CI, Dal-Cim T, Cimarosti H. In vitro oxygen-glucose deprivation to study ischemic cell death. Methods Mol Biol. 2015;1254:197–210.
  • Ryou MG, Mallet RT. An in vitro oxygen-glucose deprivation model for studying ischemia-reperfusion injury of neuronal cells. Methods Mol Biol. 2018;1717:229–235.
  • Meyer KD, Saletore Y, Zumbo P, et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3’ UTRs and near stop codons. Cell. 2012;149(7):1635–1646.
  • Huang W, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009;37(1):1–13.
  • Huang W, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44–57.
  • Yu G, Wang LG, Han Y, et al. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16(5):284–287.
  • Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnetjournal. 2011;17(1):10.
  • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12(4):357–360.
  • Cheng J, Metge F, Dieterich C. Specific identification and quantification of circular RNAs from sequencing data. Bioinformatics. 2016;32(7):1094–1096.
  • Feng J, Liu T, Qin B, et al. Identifying ChIP-seq enrichment using MACS. Nat Protoc. 2012;7(9):1728–1740.
  • Shen L, Shao NY, Liu X, et al. diffReps: detecting differential chromatin modification sites from ChIP-seq data with biological replicates. PLoS One. 2013;8(6):e65598.
  • Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature. 2012;485(7397):201–206.
  • Csepany T, Lin A, Baldick CJ, et al. Sequence specificity of mRNA N6-adenosine methyltransferase. J Biol Chem. 1990;265(33):20117–20122.
  • Harper JE, Miceli SM, Roberts RJ, et al. Sequence specificity of the human mRNA N6-adenosine methylase in vitro. Nucleic Acids Res. 1990;18(19):5735–5741.
  • Chen LL. The biogenesis and emerging roles of circular RNAs. Nat Rev Mol Cell Biol. 2016;17(4):205–211.
  • Xiao W, Adhikari S, Dahal U, et al. Nuclear m(6)A reader YTHDC1 regulates mRNA splicing. Mol Cell. 2016;61(4):507–519.
  • Kumazoe M, Sugihara K, Tsukamoto S, et al. 67-kDa laminin receptor increases cGMP to induce cancer-selective apoptosis. J Clin Invest. 2013;123(2):787–799.
  • Zhang Y, Alexander PB, Wang XF. TGF-beta family signaling in the control of cell proliferation and survival. Cold Spring Harb Perspect Biol. 2017;9(4):a022145.
  • Lee YJ, Choi SY, Yang JH. AMP-activated protein kinase is involved in perfluorohexanesulfonate-induced apoptosis of neuronal cells. Chemosphere. 2016;149:1–7.
  • Wei CM, Gershowitz A, Moss B. Methylated nucleotides block 5’ terminus of HeLa cell messenger RNA. Cell. 1975;4(4):379–386.
  • Li S, Mason CE. The pivotal regulatory landscape of RNA modifications. Annu Rev Genomics Hum Genet. 2014;15:127–150.
  • Adams JM, Cory S. Modified nucleosides and bizarre 5’-termini in mouse myeloma mRNA. Nature. 1975;255(5503):28–33.
  • Canaani D, Kahana C, Lavi S, et al. Identification and mapping of N6-methyladenosine containing sequences in simian virus 40 RNA. Nucleic Acids Res. 1979;6(8):2879–2899.
  • Bodi Z, Button JD, Grierson D, et al. Yeast targets for mRNA methylation. Nucleic Acids Res. 2010;38(16):5327–5335.
  • Lee M, Kim B, Kim VN. Emerging roles of RNA modification: m(6)A and U-tail. Cell. 2014;158(5):980–987.
  • Wang X, Zhao BS, Roundtree IA, et al. N(6)-methyladenosine modulates messenger RNA translation efficiency. Cell. 2015;161(6):1388–1399.
  • Caboche M, Bachellerie JP. RNA methylation and control of eukaryotic RNA biosynthesis. Effects of cycloleucine, a specific inhibitor of methylation, on ribosomal RNA maturation. Eur J Biochem. 1977;74(1):19–29.
  • Cui Q, Shi H, Ye P, et al. m(6)A RNA methylation regulates the self-renewal and tumorigenesis of glioblastoma stem cells. Cell Rep. 2017;18(11):2622–2634.
  • Li Z, Weng H, Su R, et al. FTO plays an oncogenic role in acute myeloid leukemia as a N(6)-methyladenosine RNA demethylase. Cancer Cell. 2017;31(1):127–141.
  • Ma JZ, Yang F, Zhou CC, et al. METTL14 suppresses the metastatic potential of hepatocellular carcinoma by modulating N(6) -methyladenosine-dependent primary MicroRNA processing. Hepatology. 2017;65(2):529–543.
  • Chen YG, Chen R, Ahmad S, et al. N6-methyladenosine modification controls circular RNA immunity. Mol Cell. 2019;76(1):96–109.e9.
  • Yang Y, Gao X, Zhang M, et al. Novel role of FBXW7 circular RNA in repressing glioma tumorigenesis. J Natl Cancer Inst. 2018;110(3):304–315.
  • Brühl J, Trautwein J, Schäfer A, et al. The DNA repair protein SHPRH is a nucleosome-stimulated ATPase and a nucleosome-E3 ubiquitin ligase. Epigenetics Chromatin. 2019;12(1):52.
  • Lee D, An J, Park YU, et al. SHPRH regulates rRNA transcription by recognizing the histone code in an mTOR-dependent manner. Proc Natl Acad Sci U S A. 2017;114(17):E3424–e3433.
  • Caudron-Herger M, Pankert T, Rippe K. Regulation of nucleolus assembly by non-coding RNA polymerase II transcripts. Nucleus. 2016;7(3):308–318.
  • Marzahn MR, Marada S, Lee J, et al. Higher-order oligomerization promotes localization of SPOP to liquid nuclear speckles. EMBO J. 2016;35(12):1254–1275.
  • Guo L, Shorter J. It’s raining liquids: RNA tunes viscoelasticity and dynamics of membraneless organelles. Mol Cell. 2015;60(2):189–192.
  • Zhang H, Elbaum-Garfinkle S, Langdon EM, et al. RNA controls PolyQ protein phase transitions. Mol Cell. 2015;60(2):220–230.
  • Chen T, Hao YJ, Zhang Y, et al. m(6)A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. Cell Stem Cell. 2015;16(3):289–301.
  • Shi H, Wei J, He C. Where, when, and how: context-dependent functions of RNA methylation writers, readers, and erasers. Mol Cell. 2019;74(4):640–650.
  • Mapperley C, van de Lagemaat LN, Lawson H, et al. The mRNA m6A reader YTHDF2 suppresses proinflammatory pathways and sustains hematopoietic stem cell function. J Exp Med. 2021;218(3). DOI:10.1084/jem.20200829.
  • Ma C, Chang M, Lv H, et al. RNA m(6)A methylation participates in regulation of postnatal development of the mouse cerebellum. Genome Biol. 2018;19(1):68.
  • Lence T, Akhtar J, Bayer M, et al. m(6)A modulates neuronal functions and sex determination in Drosophila. Nature. 2016;540(7632):242–247.
  • Shafik AM, Zhang F, Guo Z, et al. N6-methyladenosine dynamics in neurodevelopment and aging, and its potential role in Alzheimer’s disease. Genome Biol. 2021;22(1):17.
  • Mathiyalagan P, Adamiak M, Mayourian J, et al. FTO-dependent N(6)-methyladenosine regulates cardiac function during remodeling and repair. Circulation. 2019;139(4):518–532.