The RNA G-quadruplex (rG4) is a kind of non-canonical high-order secondary structure with important biological functions and is enriched in untranslated regions (UTRs) of protein-coding genes. However, how rG4 structures evolve is largely unknown. Here, we systematically investigated the evolution of RNA sequences around UTR rG4 structures in 5 eukaryotic organisms. We found universal selection on UTR sequences, which facilitated rG4 formation in all the organisms that we analyzed. While G-rich sequences were preferred in the rG4 structural region, C-rich sequences were selectively not preferred. The selective pressure acting on rG4 structures in the UTRs of genes with higher G content was significantly smaller. Furthermore, we found that rG4 structures experienced smaller evolutionary selection near the translation initiation region in the 5′ UTR, near the polyadenylation signals in the 3′ UTR, and in regions flanking the miRNA targets in the 3′ UTR. These results suggest universal selection for rG4 formation in the UTRs of eukaryotic genomes and the selection may be related to the biological functions of rG4s.
MillevoiSMoineHVagnerS.G-quadruplexes in RNA biology. WIRES RNA. 2012;3:495-507.
16.
LaneANChairesJBGrayRDTrentJO.Stability and kinetics of G-quadruplex structures. Nucleic Acids Res. 2008;36:5482-5515.
17.
WongAWuG.Selective binding of monovalent cations to the stacking G-quartet structure formed by guanosine 5′-monophosphate: a solid-state NMR study. J Am Chem Soc. 2003;125:13895-13905.
18.
FayMMLyonsSMIvanovP.RNA G-quadruplexes in biology: principles and molecular mechanisms. J Mol Biol. 2017;429:2127-2147.
19.
KamuraTKatsudaYKitamuraYIharaT.G-quadruplexes in mRNA: a key structure for biological function. Biochem Biophy Res Commun. 2020;526:261-266.
20.
SundquistWIHeaphyS.Evidence for interstrand quadruplex formation in the dimerization of human immunodeficiency virus-1 genomic RNA. Proc Natl Acad Sci U.S.A. 1993;90:3393-3397.
21.
BurgeSParkinsonGNHazelPToddAKNeidleS.Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 2006;34:5402-5415.
22.
SinghVAzarkhMExnerTEHartigJSDrescherM.Human telomeric quadruplex conformations studied by pulsed EPR. Angew Chem Int Ed. 2009;48:9728-9730.
23.
LippsHJGruissemWPrescottDM.Higher-order DNA-structure in macronuclear chromatin of the hypotrichous ciliate oxytricha nova. Proc Natl Acad Sci U.S.A. 1982;79:2495-2499.
24.
SundquistWIKlugA.Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 1989;342:825-829.
25.
KharelPBalaratnamSBealsNBasuS.The role of RNA G-quadruplexes in human diseases and therapeutic strategies. WIRES RNA. 2020;11:e1568.
26.
ZhangDHFujimotoTSaxenaSYuHQMiyoshiDSugimotoN.Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors. Biochemistry. 2010;49:4554-4563.
27.
BedratALacroixLMergnyJ-L.Re-evaluation of G-quadruplex propensity with G4Hunter. Nucleic Acids Res. 2016;44:1746-1759.
28.
KwokCKMarsicoGBalasubramanianS.Detecting RNA G-quadruplexes (rG4s) in the transcriptome. Cold Spring Harbor Perspect Biol. 2018;10:a032284.
29.
KwokCKMarsicoGSahakyanABChambersVSBalasubramanianS.rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome. Nat Methods. 2016;13:841-844.
30.
YangXCheemaJZhangY, et al. RNA G-quadruplex structures exist and function in vivo in plants. Genome Biol. 2020;21:226.
31.
GuoJUBartelDP.RNA G-quadruplexes are globally unfolded in eukaryotic cells and depleted in bacteria. Science. 2016;353:aaf5371.
32.
HuangHZhangJHarveySEHuXChengC.RNA G-quadruplex secondary structure promotes alternative splicing via the RNA-binding protein hnRNPF. Genes Dev. 2017;31:2296-2309.
33.
BeaudoinJDPerreaultJP.Exploring mRNA 3′-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening. Nucleic Acids Res. 2013;41:5898-5911.
34.
SubramanianMRageFTabetRFlatterEMandelJ-LMoineH.G-quadruplex RNA structure as a signal for neurite mRNA targeting. EMBO Rep. 2011;12:697-704.
35.
KanaiYDohmaeNHirokawaN.Kinesin transports RNA: isolation and characterization of an RNA-transporting granule. Neuron. 2004;43:513-525.
36.
PandeySAgarwalaPJayarajGGGargalloRMaitiS.The RNA stem-loop to G-quadruplex equilibrium controls mature microRNA production inside the cell. Biochemistry. 2015;54:7067-7078.
37.
StefanovicSBassellGJMihailescuMR.G quadruplex RNA structures in PSD-95 mRNA: potential regulators of miR-125a seed binding site accessibility. RNA. 2015;21:48-60.
KumariSBugautAHuppertJLBalasubramanianS.An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nat Chem Biol. 2007;3:218-221.
40.
MuratPMarsicoGHerdyBGhanbarianATPortellaGBalasubramanianS.RNA G-quadruplexes at upstream open reading frames cause DHX36- and DHX9-dependent translation of human mRNAs. Genome Biol. 2018;19:229.
41.
SimoneRFrattaPNeidleSParkinsonGNIsaacsAM.G-quadruplexes: emerging roles in neurodegenerative diseases and the non-coding transcriptome. FEBS Lett. 2015;589:1653-1668.
42.
LeeDSMGhanemLRBarashY. Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations. Nat. Commun. 2020;11:527.
BrazdaVKolomaznikJLysekJ, et al. G4Hunter web application: a web server for G-quadruplex prediction. Bioinformatics. 2019;35:3493-3495.
45.
KharelPTsvetkovV.Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back. Nucleic Acids Res. 2020;48:12534-12555.
46.
PrabhuV.Symmetry observed in long nucleotide sequences. Nucleic Acids Res. 1993;21:2797-2800.
47.
KozakM.Influences of mRNA secondary structure on initiation by eukaryotic ribosomes. Proc Natl Acad Sci U.S.A. 1986;83:2850-2854.
48.
KozakM.Circumstances and mechanisms of inhibition of translation by secondary structure in eucaryotic mRNAs. Mol Cell Biol. 1989;9:5134-5142.
49.
KoromilasAELazaris-KaratzasASonenbergN.mRNAs containing extensive secondary structure in their 5′ non-coding region translate efficiently in cells overexpressing initiation factor eIF-4E. EMBO J. 1992;11:4153-4158.
50.
KumariSBugautABalasubramanianS.Position and stability are determining factors for translation repression by an RNA G-quadruplex-forming sequence within the 5′ UTR of the NRAS proto-oncogene. Biochemistry. 2008;47:12664-12669.
51.
MorrisMJBasuS.An unusually stable G-quadruplex within the 5′-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells. Biochemistry. 2009;48:5313-5319.
52.
BalkwillGDDereckaKGarnerTPHodgmanCFlintAPFSearleMS.Repression of translation of human estrogen receptor alpha by G-quadruplex formation. Biochemistry. 2009;48:11487-11495.
53.
ShahidRBugautABalasubramanianS.The BCL-2 5′ untranslated region contains an RNA G-quadruplex-forming motif that modulates protein expression. Biochemistry. 2010;49:8300-8306.
54.
GomezDGuedinAMergnyJL, et al. A G-quadruplex structure within the 5′-UTR of TRF2 mRNA represses translation in human cells. Nucleic Acids Res. 2010;38:7187-7198.
55.
LammichSKampFWagnerJ, et al. Translational repression of the disintegrin and metalloprotease ADAM10 by a stable G-quadruplex secondary structure in Its 5′-untranslated region. J Biol Chem. 2011;286:45063-45072.
56.
DaiJLiuZQWangXQ, et al. Discovery of small molecules for up-regulating the translation of antiamyloidogenic secretase, a disintegrin and metalloproteinase 10 (ADAM10), by binding to the G-quadruplex-forming sequence in the 5′ untranslated region (UTR) of its mRNA. J Med Chem. 2015;58:3875-3891.
57.
AgarwalaPPandeySMapaKMaitiS.The G-quadruplex augments translation in the 5′ untranslated region of transforming growth factor beta 2. Biochemistry. 2013;52:1528-1538.
58.
KudlaGMurrayAWTollerveyDPlotkinJB.Coding-sequence determinants of gene expression in Escherichia coli. Science. 2009;324:255.
59.
GuWZhouTWilkeCO.A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol. 2010;6:e1000664.
60.
KellerTEMisSDJiaKEWilkeCO.Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol Evol. 2012;4:80-88.
61.
ZarudnayaMIKolomietsIMPotyahayloALHovorunDM.Downstream elements of mammalian pre-mRNA polyadenylation signals: primary, secondary and higher-order structures. Nucleic Acids Res. 2003;31:1375-1386.
62.
HuppertJLBugautAKumariSBalasubramanianS.G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res. 2008;36:6260-6268.
63.
ChenFWiluszJ.Auxiliary downstream elements are required for efficient polyadenylation of mammalian pre-mRNAs. Nucleic Acids Res. 1998;26:2891-2898.
64.
WooH-HBakerTLaszloCChambersS.Nucleolin mediates microRNA-directed CSF-1 mRNA deadenylation but increases translation of CSF-1 mRNA. Mol Cell Proteomics. 2013;12:1661-1677.
65.
BooyEPHowardRMarushchakO, et al. The RNA helicase RHAU (DHX36) suppresses expression of the transcription factor PITX1. Nucleic Acids Res. 2014;42:3346-3361.
66.
KinsellaRJKähäriAHaiderS, et al. Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database. 2011;2011:bar030.
67.
ChenYWangX.miRDB: an online database for prediction of functional microRNA targets. Nucleic Acids Res. 2020;48:D127-D131.
68.
FrankishADiekhansMJungreisI, et al. GENCODE 2021. Nucleic Acids Res. 2021;49:D916-D923.
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