ReviewRevealinglncRNAStructuresandInteractionsbySequencing-BasedApproachesXingyangQian,1,3JieyuZhao,2,3PuiYanYeung,2,3QiangfengCliffZhang,1,*andChunKitKwok,2,*LongnoncodingRNAs(lncRNAs)haveemergedassignificantplayersinalmosteverylevelofgenefunctionandregulation.Thus,characterizingthestructuresandinteractionsoflncRNAsisessentialforunderstandingtheirmechanisticrolesincells.Throughacombinationof(bio)chemicalapproachesandautomatedcapillaryandhigh-throughputsequencing(HTS),thecomplexityanddiversityofRNAstructuresandinteractionshasbeenrevealedinthetranscriptomesofmultiplespecies.ThesemethodshaveuncoveredimportantbiologicalinsightsintothemechanisticandfunctionalrolesoflncRNAingeneexpressionandRNAmetabolism,aswellasindevelopmentanddisease.Inthisreview,wesummarizethelatestsequencingstrategiestorevealRNAstructure,RNA–RNA,RNA–DNA,andRNA–proteininteractions,andhighlighttherecentapplicationsoftheseapproachestomapfunctionallncRNAs.Wediscusstheadvantagesandlimitationsofthesestrategies,andproviderecommendationstofurtheradvancemethodologiescapableofmappingRNAstructureandinteractionsinordertodiscovernewbiologyoflncRNAsanddeciphertheirmolecularmechanismsandimplicationindiseases.BiologicalSignificanceoflncRNAsandRNAStructureInthehumangenome,approximately93%ofDNAcanbetranscribedasRNA,only2%ofwhichisprotein-encodingmRNAs,whiletheremaining98%isknownasnoncodingRNAs[1,2].AmongthesenoncodingRNA‘darkmatters’,RNAslongerthan200basesareclassifiedaslncRNAs.Sincetheadventofthegenomicerainthe2000s,significantprogresshasbeenmadetowardtheunderstandingoftheprevalence,abundance,biogenesis,andfunctionsoflncRNAsacrossdifferentcelltypesandspecies[3,4].Inparticular,lncRNAshavebeendemonstratedtoplayimportantrolesinepigeneticcontrolandtheregulationoftranscription,translation,RNAmetabo-lism(Table1),aswellasstemcellmaintenanceanddifferentiation,cellautophagyandapoptosis,andembryonicdevelopment[5–7].Inaddition,lncRNAshavebeenimplicatedinmajordiseasesincludingdifferenttypesofcancer,andneurologicalandcar...
