根据《中国科学院学部“十二五”工作规划纲要》中关于组织开展学科发展战略研究的要求,2012年12月8日,中国科学院生物学与医学学部常务委员会会议批准开展关于RNA研究的战略研究项目,并于2013年1月启动。2013年6月,中国科学院学部与国家自然科学基金委员会联合开展的“RNA研究中的若干重大科学问题”项目启动。
项目启动后,按照国家自然科学基金委员会与中国科学院学科发展战略研究项目的要求,项目组由施蕴渝、陈润生、王恩多和屈良鹄领导,召开两次小范围、高层次的RNA研究战略研讨会,规模45~50人。会上,文献情报专家提供RNA研究情报资料,还两次发放美国加利福尼亚大学圣迭戈分校付向东教授撰写的关于RNA研究的评述文章。项目组汇聚了国内RNA 研究领域的一批优秀科学家,特别是一批年轻的科学家,瞄准国际学术前沿,凝聚科学问题,交流新的学术思想、学术成果、新技术和新方法。通过研讨会,项目组凝聚了国内最优秀的 RNA研究领域的学术研究队伍,召开的“RNA研究的战略研讨会”和“学术讨论会”已形成品牌。
在此基础上,屈良鹄主要负责并开始撰写《中国学科发展战略 RNA研究中的重大科学问题》,内容包括:RNA研究的科学意义与战略价值;RNA研究的发展规律与研究特点;RNA研究的发展现状与发展态势。在学术研讨的基础上,项目组凝练学科发展的前沿方向,分别由在RNA研究前沿研究领域从事一线工作的优秀科学家撰写了RNA研究的发展思路与发展方向,内容包括RNA信息学,RNA生成、加工和降解,RNA生理与遗传,RNA结构生物学,非编码RNA与医学,非编码RNA与农学,非编码RNA研究中的新方法和新技术等七个方向。每个方向按照概述、关键科学问题、发展思路、前沿方向及研究内容、发展目标和我国在该领域的优势加以撰写。具体编写分工如下
以姓氏拼音为序。*标注的为该部分主要执笔人。:①RNA信息学:陈润生、鲁志、屈良鹄、杨建华*、郑凌伶;②RNA生成、加工和降解:陈玲玲、程红、刘默芳、倪挺、戚益军、吴立刚*、徐永镇、杨运桂;③RNA生理与遗传:曹晓风、陈玲玲、 光寿红、刘默芳*、单革、汪阳明、王恩多;④RNA结构生物学:麻锦彪、王艳丽、叶克穷*;⑤非编码RNA与医学:宋尔卫、吴缅、庄诗美*;⑥非编码RNA与农学:曹晓风、陈月琴、陈晓亚、何新建、戚益军*、王佳伟;⑦非编码RNA研究中的新方法和新技术:陈匡时、方显杨、刘晓*、王宏伟、王江云、伊成器、张强锋、郑晓飞。此外,文献情报专家熊燕和阮梅花为本书提供了文献情报支撑服务。
人类基因组中编码蛋白质的序列只占2%,而占基因组98%的是不编码蛋白质的序列(即非编码区域),但人类基因组中大约80%的序列是可以被转录的。同时,大量疾病相关的突变发生在非编码区域上,并构成了由蛋白质、RNA、DNA和小分子组成的复杂的调控网络。此外,物种间最主要的差别也存在于这些非编码区域上。因此,我们认为非编码RNA是生命科学新的研究前沿,蕴含着生命活动的基本规律。对非编码RNA的研究充分体现了科学研究的前瞻性、基础性和重要性的特点,其研究水平将影响未来生命科学,包括医学和农学的发展。我国的非编码RNA研究起步时间与国际同行差距不大,近十年来已取得一批具有重要国际影响的原始创新成果,是生命科学有望取得国际领先地位的重要领域,是一个有可能取得原创突破的战略方向。因此,在本书资助机制与政策建议部分中,项目组提出:鉴于《国家中长期科学和技术发展规划纲要(2006—2020年)》中“非编码核糖核酸的表达调控与功能”已作为科学前沿被列入主要研究方向,建议中国科学院学部与国家自然科学基金委员会在编制国家“十三五”科学发展规划时,能充分考虑非编码RNA研究的重要意义;同时建议科技部在“国家重点研发计划”中予以考虑。
《中国学科发展战略 RNA研究中的重大科学问题》初稿于2013年秋完成。2014年秋学术会议传达了中国科学院学部工作局对“中国学科发展战略”项目研究成果的出版要求,要求各专题组在以往工作报告的基础上做出修订。2015年3月完成第二稿。 2016年2月完成第三稿 。2016年2月20~21日在广州召开的会议上进行了认真讨论,按照国家自然科学基金委员会中国科学院“学科发展战略研究”工作联合领导小组的要求进一步修改了第三稿,形成第四稿。2016年5月,书稿由中国科学院学部与国家自然科学基金委员会组织通讯评审通过,进入正式出版流程。
由于认识局限,书中难免存在缺陷和不足,敬请读者批评指正。
施蕴渝
2016年9月
总序 …………………………………………………………………………… i
前言 …………………………………………………………………………… v
摘要 …………………………………………………………………………… i x
犃犫狊狋狉犪犮狋 …………………………………………………………………… xxiii
第一章 犚犖犃研究的科学意义与战略价值 ………………………… 1
第二章 犚犖犃研究的发展规律与研究特点 ………………………… 5
第三章 犚犖犃研究的发展现状与发展态势 ………………………… 11
第一节 国际非编码RNA研究的规划和布局……………………… 11
第二节 我国非编码RNA研究的规划和布局……………………… 12
第三节 国内外研究成果计量分析 ………………………………… 15
一、成果所属国家分析 ………………………………………… 16
二、成果所属机构分析 ………………………………………… 18
三、资助机构分析 ……………………………………………… 19
四、高被引论文分析 …………………………………………… 20
第四节 我国论文发表情况 ………………………………………… 23
第五节 总结 ………………………………………………………… 27
第四章 犚犖犃研究的发展思路与发展方向 ………………………… 28
第一节 RNA信息学 ………………………………………………… 29
一、概述 ………………………………………………………… 29
二、关键科学问题 ……………………………………………… 32
三、发展思路 …………………………………………………… 32
四、前沿方向及研究内容 ……………………………………… 32
五、发展目标 …………………………………………………… 35
六、我们的优势 ………………………………………………… 35
第二节 RNA生成、加工和降解 …………………………………… 38
一、概述 ………………………………………………………… 38
二、关键科学问题 ……………………………………………… 42
三、发展思路 …………………………………………………… 43
四、前沿方向及研究内容 ……………………………………… 43
五、发展目标 …………………………………………………… 55
六、我们的优势 ………………………………………………… 55
第三节 RNA生理与遗传 …………………………………………… 58
一、概述 ………………………………………………………… 58
二、关键科学问题 ……………………………………………… 65
三、发展思路 …………………………………………………… 65
四、前沿方向及研究内容 ……………………………………… 66
五、发展目标 …………………………………………………… 67
六、我们的优势 ………………………………………………… 67
第四节 RNA结构生物学 …………………………………………… 69
一、概述 ………………………………………………………… 69
二、该领域的关键科学问题 …………………………………… 73
三、发展思路 …………………………………………………… 74
四、前沿方向及研究内容 ……………………………………… 75
五、发展目标 …………………………………………………… 77
六、我们的优势 ………………………………………………… 77
第五节 非编码RNA与医学………………………………………… 78
一、概述 ………………………………………………………… 78
二、关键科学问题 ……………………………………………… 81
三、发展思路 …………………………………………………… 81
四、前沿方向及研究内容 ……………………………………… 82
五、发展目标 …………………………………………………… 84
六、我们的优势 ………………………………………………… 84
第六节 非编码RNA与农学………………………………………… 87
一、研究背景 …………………………………………………… 87
二、关键科学问题 ……………………………………………… 90
三、发展思路 …………………………………………………… 91
四、前沿方向及研究内容 ……………………………………… 91
五、发展目标 …………………………………………………… 93
六、我们的优势 ………………………………………………… 93
第七节 非编码RNA研究中的新方法和新技术…………………… 95
一、概述 ………………………………………………………… 95
二、关键科学问题 ……………………………………………… 103
三、发展思路 …………………………………………………… 104
四、前沿方向及研究内容 ……………………………………… 105
五、发展目标 …………………………………………………… 108
六、我们的优势 ………………………………………………… 108
第五章 资助机制与政策建议 ……………………………………… 110
参考文献…………………………………………………………………… 111
附录 缩略词 …………………………………………………………… 141
关键词索引………………………………………………………………… 143
金由辛.1999.109次香山学术讨论会——— “面向21世纪的RNA研究”简况. 生物化学与
生物物理学报,31:119123.
屈良鹄.2009.RNA组学:后基因组时代的科学前沿. 中国科学:生命科学,39:12.
郑凌伶,屈良鹄.2010. 计算RNA 组学:非编码RNA 结构识别与功能分析. 中国科学:
生命科学,40:294310.
AdachiT,NakanishiM,OtsukaY,etal.2010.PlasmamicroRNA499asabiomarkerof
acutemyocardialinfarction.ClinicalChemistry,56:11831185.
AdamsPL,StahleyMR,KosekAB,etal.2004.Crystalstructureofaselfsplicinggroup
Iintronwithbothexons.Nature,430:4550.
AlakonyaA,KumarR,KoenigD,etal.2012.InterspecificRNAinterferenceofSHOOT
MERISTEMLESSlikedisruptsCuscutapentagonaplantparasitism.ThePlantCell,24:
31533166.
AltmanS.2007.AnoverviewoftheRNAworld:fornow.BiolChem,388:663664.
AltmanS.2013.TheRNAProteinWorld.Rna,19:589590.
AmaralPP,DingerME,MercerTR,etal.2008.TheeukaryoticgenomeasanRNAma
chine.Science,319:17871789.
AmbrosoneA,CostaA,LeoneA,etal.2012.Beyondtranscription:RNAbindingpro
teinsasemergingregulatorsofplantresponsetoenvironmentalconstraints.PlantSci,
182:1218.
AnderssonP,GidlofO,BraunOO,etal.2012.PlasmalevelsofliverspecificmiR122ismas
sivelyincreasedinaporcinecardiogenicshockmodelandattenuatedbyhypothermia.Shock,37:
234238.
AnkoM L,NeugebauerK M.2012.RNAproteininteractionsinvivo:globalgetsspecif
ic.TrendsBiochemSci,37:255262.
ArielF,JeguT,LatrasseD,etal.2014.NoncodingtranscriptionbyalternativeRNApoly
merases dynamically regulates an auxindriven chromatin loop.Molecular Cell,55:
383396.
Arkov A L,Ramos A.2010.Building RNAprotein granules:insightfrom the germ
line.TrendsCellBiol,20:482490.
AshwalFlussR,Meyer M,PamudurtiN R,etal.2014.circRNA biogenesiscompetes
withpremRNAsplicing.MolCell,56:5566.
BahnJH,AhnJ,LinX,etal.2015.GenomicanalysisofADAR1bindinganditsinvolve
mentinmultipleRNAprocessingpathways.NatCommun,6:6355.
BamfordS,DawsonE,ForbesS,etal.2004.TheCOSMIC (CatalogueofSomaticMuta
tionsinCancer)databaseandwebsite.BrJCancer,91:355358.
BaraniskinA,NopelDunnebackeS,AhrensM,etal.2013.CirculatingU2smallnuclear
RNAfragmentsasanoveldiagnosticbiomarkerforpancreaticandcolorectaladenocarcino
ma.IntJCancer,132:E48E57.
BaumJA,BogaertT,ClintonW,etal.2007.Controlofcoleopteraninsectpeststhrough
RNAinterference.NatureBiotechnology,25:13221326.
BeaulieuYB,KleinmanCL,LandryVoyerA M,etal.2012.Polyadenylationdependent
controloflongnoncoding RNA expressionbythepoly (A)bindingproteinnuclear
1.PLoSGenet,8:e1003078.
BekrisL M,LutzF,MontineTJ,etal.2013.MicroRNAinAlzheimersdisease:anex
ploratorystudyinbrain,cerebrospinalfluidandplasma.Biomarkers,18:455466.
BenAmorB,WirthS,MerchanF,etal.2009.NovellongnonproteincodingRNAsin
volvedinArabidopsisdifferentiationandstressresponses.GenomeRes,19:5769.
BenneR,vandenBurgJ,BrakenhoffJP,etal.1986.Majortranscriptoftheframeshifted
coxIIgenefromtrypanosomemitochondriacontainsfournucleotidesthatarenotencoded
intheDNA.Cell,46:819826.
BergM G,SinghLN,YounisI,etal.2012.U1snRNPdeterminesmRNAlengthandreg
ulatesisoformexpression.Cell,150:5364.
BergetSM,MooreC,SharpPA.1977.Splicedsegmentsatthe5′terminusofadenovirus2
latemRNA.ProcNatlAcadSciUSA,74:31713175.
BlackDL.2003.MechanismsofalternativepremessengerRNAsplicing.Anualreviewof
biochemistry,72:291336.
BoettcherM,McManusM T.2015.Choosingtherighttoolforthejob:RNAi,TALEN,
orCRISPR.MolCell,58:575585.
BonfilsG,JaquenoudM,BontronS,etal.2012.LeucyltRNAsynthetasecontrolsTORC1
viatheEGOcomplex.MolCell,46:105110.
BrannanCI,DeesEC,IngramRS,etal.1990.TheproductoftheH19genemayfunction
asanRNA.MolCellBiol,10:2836.
BraunIC,RohrbachE,SchmittC,etal.1999.TAPbindstotheconstitutivetransportel
ement (CTE)throughanovelRNAbindingmotifthatissufficienttopromoteCTEde
pendentRNAexportfromthenucleus.EMBOJ,18:19531965.
BreakerRR.2011.Prospectsforriboswitchdiscoveryandanalysis.MolCell,43:867879.
BrenneckeJ,Aravin A A,Stark A,etal.2007.DiscretesmallRNAgeneratinglocias
masterregulatorsoftransposonactivityinDrosophila.Cell,128:10891103.
BrownCJ,BallabioA,RupertJL,etal.1991.AgenefromtheregionofthehumanXin
activationcentreisexpressedexclusivelyfromtheinactiveXchromosome.Nature,349:
3844.
BuD,YuK,SunS,etal.2012.NONCODEv3.0:integrativeannotationoflongnoncod
ingRNAs.NucleicAcidsRes,40:D210D215.
BuckanovichRJ,DarnellRB.1997.TheneuronalRNAbindingproteinNova1recognizes
specificRNAtargetsinvitroandinvivo.MolCellBiol,17:31943201.
BurroughsA M,AndoY,deHoonMJ,etal.2010.Acomprehensivesurveyof3′animal
miRNAmodificationeventsandapossiblerolefor3′adenylationinmodulatingmiRNA
targetingeffectiveness.GenomeRes,20:13981410.
Calin G A,Croce C M.2006.MicroRNAcancerconnection:the beginning ofa new
tale.CancerRes,66:73907394.
CalinGA,DumitruCD,ShimizuM,etal.2002.Frequentdeletionsanddownregulation
ofmicroRNAgenesmiR15andmiR16at13q14inchroniclymphocyticleukemia.Proc
NatlAcadSciUSA,99:1552415529.
CampoSM,ZulloA,ScandaviniC M,etal.2013.Pseudoachalasia:apeculiarcasereport
andreviewoftheliterature.WorldJGastrointestEndosc,5:450454.
CancerGenomeAtlasResearch.2008.Comprehensivegenomiccharacterizationdefineshuman
glioblastomagenesandcorepathways.Nature,455:10611068.
CaoM,DuP,WangX,etal.2014.Virusinfectiontriggerswidespreadsilencingofhost
genesbyadistinctclassofendogenoussiRNAsinArabidopsis.ProceedingsoftheNational
AcademyofSciences,111:1461314618.
CastanottoD,RossiJJ.2009.ThepromisesandpitfallsofRNAinterferencebasedthera
peutics.Nature,457:426433.
CastelSE,MartienssenRA.2013.RNAinterferenceinthenucleus:rolesforsmallRNAs
intranscription,epigeneticsandbeyond.NatureReviewsGenetics,14:100112.
CastelloA,FischerB,HentzeM W,etal.2013.RNAbindingproteinsinMendeliandis
ease.TrendsGenet,29:318327.
CechT,SteeleF.2013.The (noncoding)RNAworld.NucleicAcidTher,23:1.
CechTR.1989.RNAasanenzyme.BiochemInt,18:714.
CechTR.2012.TheRNAworldsincontext.ColdSpringHarbPerspectBiol,4:a006742.
ChavezA,ScheimanJ,VoraS,etal.2015.HighlyefficientCas9mediatedtranscriptional
programming.NatureMethods,12:326328.
CheRH,TongH N,ShiBH,etal.2015.ControlofgrainsizeandriceyieldbyGL2me
diatedbrassinosteroidresponses.NatPlants.
ChenA K,BehlkeM A,TsourkasA.2007.Avoidingfalsepositivesignalswithnuclease
vulnerable molecular beacons in single living cells.Nucleic Acids Research,35:
e105e105.
ChenAK,BehlkeM A,TsourkasA.2008c.Efficientcytosolicdeliveryofmolecularbeacon
conjugatesandflowcytometricanalysisoftargetRNA.NucleicAcidsResearch,36:e69
e69.
ChenB,HuangB.2014.ImaginggenomicelementsinlivingcellsusingCRISPR/Cas9.Methods
Enzymol,546:337354.
ChenG,WangZ,WangD,etal.2013.LncRNADisease:adatabaseforlongnoncoding
RNAassociateddiseases.NucleicAcidsRes,41:D983D986.
ChenLL,CarmichaelG G.2009.AlterednuclearretentionofmRNAscontaininginverted
repeatsinhumanembryonicstemcells:functionalroleofanuclearnoncodingRNA.Mol
Cell,35:467478.
ChenLL,CarmichaelGG.2010.LongnoncodingRNAsinmammaliancells:what,where,
andwhy?WileyInterdiscipRevRNA,1:221.
ChenL L,DeCerbo J N,Carmichael G G.2008b.Alu elementmediated gene silen
cing.EMBOJ,27:16941705.
ChenQ,YanM,CaoZ,etal.2016.SpermtsRNAscontributetointergenerationalinherit
anceofanacquiredmetabolicdisorder.Science,351:397400.
ChenX,BaY,MaL,etal.2008a.CharacterizationofmicroRNAsinserum:anovelclass
ofbiomarkersfordiagnosisofcancerandotherdiseases.CellRes,18:9971006.
ChengG.2015.CirculatingmiRNAs:rolesincancerdiagnosis,prognosisandtherapy.Adv
DrugDelivRev,81:7593.
ChengH,DufuK,LeeCS,etal.2006.HumanmRNAexportmachineryrecruitedtothe
5′endofmRNA.Cell,127:13891400.
ChiB,WangK,DuY,etal.2014.AsubelementinPREenhancesnuclearexportofin
tronlessmRNAsbyrecruitingtheTREXcomplexviaZC3H18.NucleicAcidsRes,42:
73057318.
ChiB,WangQ,WuG,etal.2013.AlyandTHOarerequiredforassemblyofthehuman
TREXcomplexandassociationofTREXcomponentswiththespliced mRNA.Nucleic
AcidsRes,41:12941306.
ChiS W,ZangJB,MeleA,etal.2009.ArgonauteHITSCLIPdecodesmicroRNAmR
NAinteractionmaps.Nature,460:479486.
ChuC,QuK,ZhongFL,etal.2011.GenomicmapsoflongnoncodingRNAoccupancy
revealprinciplesofRNAchromatininteractions.MolCell,44:667678.
ChuC,ZhangQC,daRochaST,etal.2015.SystematicdiscoveryofXistRNAbinding
proteins.Cell,161:404416.
ClemsonC M,HutchinsonJN,SaraSA,etal.2009.Anarchitecturalroleforanuclear
noncodingRNA:NEAT1RNAisessentialforthestructureofparaspeckles.MolCell,
33:717726.
CongL,RanFA,CoxD,etal.2013.MultiplexGenomeEngineeringUsingCRISPR/Cas
Systems.Science,339:819823.
Consortium T E P.2012.Anintegrated encyclopedia of DNA elementsinthe human
genome.Nature,489:5774.
CorcoranDL,GeorgievS,MukherjeeN,etal.2011.PARalyzer:definitionofRNAbind
ingsitesfromPARCLIPshortreadsequencedata.GenomeBiol,12:R79.
DaiX,YuJ,MaJ,etal.2007.OverexpressionofZm401,anmRNAlikeRNA,hasdis
tincteffectsonpollendevelopmentinmaize.PlantGrowthRegulation,52:229239.
DarnellJE,Jr.2013.ReflectionsonthehistoryofpremRNAprocessingandhighlightsof
currentknowledge:aunifiedpicture.RNA,19:443460.
DavidCJ,ManleyJL.2011.TheRNApolymeraseCterminaldomain:anewroleinspli
ceosomeassembly.Transcription,2:221225.
DengX,GuL,LiuC,etal.2010.ArgininemethylationmediatedbytheArabidopsishom
ologofPRMT5isessentialforproperpremRNAsplicing.ProcNatlAcadSciUSA,107:
1911419119.
DiC,YuanJ,WuY,etal.2014.CharacterizationofstressresponsivelncRNAsinArabi
dopsisthalianabyintegratingexpression,epigeneticandstructuralfeatures.PlantJ,80:
848861.
DiGiammartinoDC,NishidaK,ManleyJL.2011.Mechanismsandconsequencesofalter
nativepolyadenylation.MolCell,43:853866.
DingJ,HuangS,WuS,etal.2010.GainofmiR151onchromosome8q24.3facilitates
tumourcellmigrationandspreadingthroughdownregulating RhoGDIA.NatCellBiol,
12:390399.
DingJ,LuQ,OuyangY,etal.2012.AlongnoncodingRNAregulatesphotoperiodsensi
tivemalesterility,anessentialcomponentofhybridrice.Proceedingsofthe National
AcademyofSciences,109:26542659.
Ding SW,Voinnet O.2007.Antiviralimmunity directed by small RNAs.Cell,130:
413426.
DominguezC,SchubertM,DussO,etal.2011.Structuredeterminationanddynamicsof
proteinRNAcomplexesbyNMRspectroscopy.ProgNuclMagnResonSpectrosc,58:1
61.
DominissiniD,MoshitchMoshkovitzS,SchwartzS,etal.2012.Topologyofthehuman
andmousem6ARNAmethylomesrevealedbym6Aseq.Nature,485:201206.
DouK,HuangCF,MaZY,etal.2013.ThePRP6likesplicingfactorSTA1isinvolved
inRNAdirectedDNAmethylationbyfacilitatingtheproductionofPolVdependentscaf
foldRNAs.NucleicAcidsResearch,41:84898502.
DuH,ZhaoY,HeJ,etal.2016.YTHDF2destabilizesm (6)AcontainingRNAthrough
directrecruitment ofthe CCR4NOT deadenglase complex.Nature Communication,
T:12626.
DuP,WuJ,ZhangJ,etal.2011.ViralinfectioninducesexpressionofnovelphasedmicroRNAs
fromconservedcellularmicroRNAprecursors.PlosPathogens,7:e1002176e1002176.
DuX,WangED.2003.TertiarystructurebasepairsbetweenDandTpsiCloopsofEsche
richiacolitRNA (Leu)playimportantrolesinbothaminoacylationandediting.Nucleic
AcidsRes,31:28652872.
DuanC G,GuoH S.2012.SuppressionofArabidopsisARGONAUTE1mediatedslicing,
transgeneinducedRNAsilencing,andDNA methylationbydistinctdomainsofthecu
cumbermosaicvirus2bprotein.PlantCell,24:259274.
DuanJ,LiL,LuJ,etal.2009.StructuralmechanismofsubstrateRNArecruitmentinH/
ACARNAguidedpseudouridinesynthase.MolCell,34:427439.
DuanPG,NiS,WangJ,etal.2015.RegulationofOsGRF4byOsmiR396controlsgrain
sizeandyieldinrice.NatPlants.
DunhamI,KundajeA,AldredSF,etal.2012.AnintegratedencyclopediaofDNAele
mentsinthehumangenome.Nature,489:5774.
DuranR V,HallM N.2012.LeucyltRNAsynthetase:doubledutyinaminoacidsens
ing.CellRes,22:12071209.
ElkonR,UgaldeA P,AgamiR.2013.Alternativecleavageandpolyadenylation:extent,
regulationandfunction.NatRevGenet,14:496506.
ElmenJ,Lindow M,SchutzS,etal.2008.LNAmediatedmicroRNAsilencinginnonhu
manprimates.Nature,452:896899.
EmermanM,VazeuxR,PedenK.1989.Therevgeneproductofthehumanimmunodefi
ciencyvirusaffectsenvelopespecificRNAlocalization.Cell,57:11551165.
EngreitzJM,PandyaJonesA,McDonelP,etal.2013.TheXistlncRNAexploitsthreedimen
sionalgenomearchitecturetospreadacrosstheXchromosome.Science,341:1237973.
EngreitzJM,SirokmanK,McDonelP,etal.2014.RNARNAinteractionsenablespecific
targetingofnoncodingRNAstonascentPremRNAsandchromatinsites.Cell,159:188
199.
EnrightAJ,JohnB,GaulU,etal.2003.MicroRNAtargetsinDrosophila.GenomeBiol,
5:R1.
EsauC,DavisS,MurraySF,etal.2006.miR122regulationoflipidmetabolismrevealed
byinvivoantisensetargeting.CellMetab,3:8798.
FangX,CuiY,LiY,etal.2015a.TranscriptionandprocessingofprimarymicroRNAsare
coupledbyElongatorcomplexinArabidopsis.NaturePlants,1.
FangX,QiY.2016.RNAiinplants:anargonautecenteredview.ThePlantCell.
FangYY,SmithNA,ZhaoJH,etal.2015b.CloningandprofilingofsmallRNAsfrom
cucumbermosaicvirussatelliteRNA.PlantVirologyProtocols:New ApproachestoDe
tectVirusesandHostResponses,99109.
FejesTothK K P,FoissacSK,SotirovaV,etal.2009.Posttranscriptionalprocessing
generatesadiversityof5′modifiedlongandshortRNAs.Nature,457:10281032.
FelberBK,HadzopoulouCladarasM,CladarasC,etal.1989.revproteinofhumanimmu
nodeficiencyvirustype1affectsthestabilityandtransportoftheviralmRNA.ProcNatl
AcadSciUSA,86:14951499.
FengB,MandavaCS,GuoQ,etal.2014.Structuralandfunctionalinsightsintothemode
ofactionofauniversallyconservedobgGTPase.PLoSBiol,12:e1001866.
FengS,JacobsenSE,ReikW.2010.Epigeneticreprogramminginplantandanimaldevel
opment.Science,330:622627.
FerreDAmareAR,ScottW G.2010.Smallselfcleavingribozymes.ColdSpringHarbPer
spectBiol,2:a003574.
FireA,XuS,Montgomery M K,etal.1998.Potentandspecificgeneticinterferenceby
doublestrandedRNAinCaenorhabditiselegans.Nature,391:806811.
FrancoZorrillaJ M,ValliA,Todesco M,etal.2007.Target mimicryprovidesanew
mechanismforregulationofmicroRNAactivity.NatGenet,39:10331037.
FriedlanderM R,ChenW,AdamidiC,etal.2008.DiscoveringmicroRNAsfromdeepse
quencingdatausingmiRDeep.NatureBiotechnology,26:407415.
FuH,TieY,XuC,etal.2005.IdentificationofhumanfetallivermiRNAsbyanovel
method.FEBSLett,579:38493854.
FuY,DominissiniD,RechaviG,etal.2014.Geneexpressionregulationmediatedthrough
reversiblem6ARNAmethylation.NatRevGenet,15:293306.
FuY,SunY,LiY,etal.2011.Differentialgenomewideprofilingoftandem3′UTRsa
monghumanbreastcancerandnormalcellsbyhighthroughputsequencing.GenomeRes,
21:741747.
FuscoD,AccorneroN,LavoieB,etal.2003.SinglemRNAmoleculesdemonstrateproba
bilisticmovementinlivingmammaliancells.CurrentBiology,13:161167.
GaoF,WangK,LiuY,etal.2015.BlockingmiR396increasesriceyieldbyshapinginflo
rescencearchitecture.NatPlants.
GaoM,WeiW,LiM M,etal.2014.Ago2facilitatesRad51recruitmentandDNAdouble
strandbreakrepairbyhomologousrecombination.CellRes,24:532541.
GappK,JawaidA,SarkiesP,etal.2014.ImplicationofspermRNAsintransgenerational
inheritanceoftheeffectsofearlytraumainmice.NatNeurosci,17:667669.
GersteinM B,RozowskyJ,YanK K,etal.2014.Comparativeanalysisofthetranscrip
tomeacrossdistantspecies.Nature,512:445448.
GilbertW.1986.TheRNAworld.Nature,319:618.
GoodarziH,LiuX,NguyenH C,etal.2015.EndogenoustRNADerivedfragmentssup
pressbreastcancerprogressionviaYBX1displacement.Cell,161:790802.
GouJY,FelippesFF,LiuCJ,etal.2011.Negativeregulationofanthocyaninbiosynthe
sisin Arabidopsis by a miR156targeted SPL transcription factor.Plant Cell,23:
15121522.
GouLT,DaiP,YangJH,etal.2014.PachytenepiRNAsinstructmassivemRNAelimi
nationduringlatespermiogenesis.CellRes,24:680700.
GrimesJM,FullerSD,StuartDI.1999.Complementingcrystallography:theroleofcryo
electron microscopy in structural biology.Acta Crystallographica Section D,55:
17421749.
GrosjeanH.2015.RNAmodification:theGoldenPeriod19952015.RNA,21:625626.
GroteP,WittlerL,HendrixD,etal.2013.ThetissuespecificlncRNAFendrrisanessen
tialregulatorofheartandbodywalldevelopmentinthemouse.DevCell,24:206214.
GuSG,PakJ,GuangS,etal.2012.AmplificationofsiRNAinCaenorhabditiselegans
generatesatransgenerationalsequencetargetedhistone H3lysine9 methylationfoot
print.NatGenet,44:157164.
GuZ,HuangC,LiF,etal.2014.Aversatilesystemforfunctionalanalysisofgenesand
microRNAsincotton.PlantBiotechnologyJournal,12:638649.
GuanDG,LiaoJY,QuZ H,etal.2011.mirExplorer:detectingmicroRNAsfromge
nomeandnextgenerationsequencingdatausingthe AdaBoostmethod withtransition
probabilitymatrixandcombinedfeatures.RNABiol,8:922934.
GuangS,BochnerA F,BurkhartK B,etal.2010.SmallregulatoryRNAsinhibitRNA
polymeraseIIduringtheelongationphaseoftranscription.Nature,465:10971101.
GuangS,BochnerAF,PavelecD M,etal.2008.AnArgonautetransportssiRNAsfrom
thecytoplasmtothenucleus.Science,321:537541.
GuoQ,YuanY,XuY,etal.2011.StructuralbasisforthefunctionofasmallGTPaseRs
gAonthe30Sribosomalsubunitmaturationrevealedbycryoelectron microscopy.Proc
NatlAcadSciUSA,108:1310013105.
GuoW T,WangX W,WangY.2014.Micromanagementofpluripotentstemcells.Protein
Cell,5:3647.
GuoX,GaoL,LiaoQ,etal.2013.LongnoncodingRNAsfunctionannotation:aglobal
predictionmethodbasedonbicolorednetworks.NucleicAcidsRes,41:e35.
GuttmanM,AmitI,GarberM,etal.2009.Chromatinsignaturerevealsoverathousand
highlyconservedlargenoncodingRNAsinmammals.Nature,458:223227.
GuttmanM,DonagheyJ,CareyBW,etal.2011.lincRNAsactinthecircuitrycontrolling
pluripotencyanddifferentiation.Nature,477:295300.
GuttmanM,RinnJL.2012.ModularregulatoryprinciplesoflargenoncodingRNAs.Nature,
482:339346.
HaagJR,Ream TS,MarascoM,etal.2012.InvitrotranscriptionactivitiesofPolIV,
PolV,andRDR2revealcouplingofPolIVandRDR2fordsRNAsynthesisinplantRNA
silencing.MolCell,48:811818.
HacisuleymanE,GoffLA,TrapnellC,etal.2014.Topologicalorganizationofmultichro
mosomalregionsbythelongintergenicnoncodingRNAFirre.NatStructMolBiol,21:
198206.
Hafner M,Landthaler M,Burger L,etal.2010.Transcriptomewideidentification of
RNAbindingproteinandmicroRNAtargetsitesbyPARCLIP.Cell,141:129141.
HameraS,Song X,LeiS,etal.2012.Cucumber mosaicvirussuppressor2bbindsto
AGO4relatedsmallRNAsandimpairsAGO4activities.PlantJournalforCell& Molecu
larBiology,69:104115.
HanBW,Wang W,LiC,etal.2015.NoncodingRNA.piRNAguidedtransposoncleav
ageinitiatesZucchinidependent,phasedpiRNAproduction.Science,348:817821.
HanJM,JeongSJ,ParkMC,etal.2012.LeucyltRNAsynthetaseisanintracellularleu
cinesensorforthemTORC1signalingpathway.Cell,149:410424.
HandwergerKE,GallJG.2006.Subnuclearorganelles:newinsightsintoformandfunc
tion.TrendsCellBiol,16:1926.
HangJ,WanR,YanC,etal.2015.StructuralbasisofpremRNAsplicing.Science,349:
11911198.
HansenTB,JensenTI,ClausenB H,etal.2013.NaturalRNAcirclesfunctionaseffi
cientmicroRNAsponges.Nature,495:384388.
Heard E, Martienssen R A.2014.Transgenerationalepigeneticinheritance:mythsand
mechanisms.Cell,157:95109.
HeoJB,SungS.2011.Vernalizationmediatedepigeneticsilencingbyalongintronicnon
codingRNA.Science,331:7679.
HerrAJ,JensenMB,DalmayT,etal.2005.RNApolymeraseIVdirectssilencingofen
dogenousDNA.Science,308:118120.
HolbrookJA,NeuYilikG,HentzeM W,etal.2004.Nonsensemediateddecayapproa
chestheclinic.NatGenet,36:801808.
HolcikM,LiebhaberSA.1997.FourhighlystableeukaryoticmRNAsassemble3′untrans
latedregionRNAproteincomplexessharingcisandtranscomponents.Proceedingsofthe
NationalAcademyofSciencesoftheUnitedStatesofAmerica,94:24102414.
HollickJB.2012.Paramutation:atranshomologinteractionaffectingheritablegeneregula
tion.CurrentOpinioninPlantBiology,15:536543.
HoqueM,JiZ,ZhengD,etal.2013.Analysisofalternativecleavageandpolyadenylation
by3′regionextractionanddeepsequencing.NatMethods,10:133139.
HoskinsA A,Moore M J.2012.Thespliceosome:aflexible,reversiblemacromolecular
machine.TrendsBiochemSci,37:179188.
HouJ,LinL,ZhouW,etal.2011.IdentificationofmiRNomesinhumanliverandhepato
cellularcarcinomarevealsmiR199a/b3pastherapeutictargetforhepatocellularcarcino
ma.CancerCell,19:232243.
HsuSD,ChuCH,TsouAP,etal.2008.miRNAMap2.0:genomicmapsofmicroRNAs
inmetazoangenomes.NucleicAcidsRes,36:D165D169.
HsuSD,LinFM,WuW Y,etal.2011.miRTarBase:adatabasecuratesexperimentally
validatedmicroRNAtargetinteractions.NucleicAcidsRes,39:D163D169.
HuJ,WangY,FangY,etal.2015a.ArarealleleofGS2enhancesgrainsizeandgrain
yieldinrice.MolPlant,8:14551465.
HuL,DiC,KaiM,etal.2015a.Acommonsetofdistinctfeaturesthatcharacterizenon
codingRNAsacrossmultiplespecies.NucleicAcidsRes,43:104114.
HuX,FengY,ZhangD,etal.2014.AfunctionalgenomicapproachidentifiesFAL1asan
oncogeniclongnoncodingRNAthatassociateswithBMI1andrepressesp21expressionin
cancer.CancerCell,26:344357.
HuangH,QiaoR,ZhaoD,etal.2009a.ProfilingofmismatchdiscriminationinRNAiena
bledrationaldesignofallelespecificsiRNAs.NucleicAcidsRes,37:75607569.
HuangJ,BrownAF,WuJ,etal.2014.StructuralbasisforproteinRNArecognitionin
telomerase.NatStructMolBiol,21:507512.
HuangQ,YaoP,ErianiG,etal.2012.InvivoidentificationofessentialnucleotidesintR
NALeutoitsfunctionsbyusingaconstructedyeasttRNALeuknockoutstrain.Nucleic
AcidsRes,40:1046310477.
HuangS,SpectorDL.1992.U1andU2smallnuclearRNAsarepresentinnuclearspeck
les.ProcNatlAcadSciUSA,89:305308.
HuangY,JiL,HuangQ,etal.2009b.Structuralinsightsintomechanismsofthesmall
RNAmethyltransferaseHEN1.Nature,461:823827.
HuarteM,GuttmanM,FeldserD,etal.2010.AlargeintergenicnoncodingRNAinduced
byp53mediatesglobalgenerepressioninthep53response.Cell,142:409419.
HwangH W,WentzelEA,MendellJT.2007.AhexanucleotideelementdirectsmicroR
NAnuclearimport.Science,315:97100.
ItoH,GaubertH,BucherE,etal.2011.AnsiRNApathwaypreventstransgenerational
retrotranspositioninplantssubjectedtostress.Nature,472:115119.
JacksonR N,GoldenS M,vanErpPB,etal.2014.CrystalstructureoftheCRISPR
RNAguidedsurveillancecomplexfrom犈狊犮犺犲狉犻犮犺犻犪犮狅犾犻.Science,345:14731479.
JalaliS,BhartiyaD,LalwaniM K,etal.2013.Systematictranscriptomewideanalysisof
lncRNAmiRNAinteractions.PLoSOne,8:e53823.
JeckW R,SorrentinoJA,WangK,etal.2013.CircularRNAsareabundant,conserved,
andassociatedwithALUrepeats.RNA,19:141157.
JenalM,ElkonR,LoayzaPuchF,etal.2012.Thepoly (A)bindingproteinnuclear1
suppressesalternativecleavageandpolyadenylationsites.Cell,149:538553.
JiJ,ShiJ,BudhuA,etal.2009a.MicroRNAexpression,survival,andresponsetointer
feroninlivercancer.NEnglJMed,361:14371447.
JiL,ChenX.2012.RegulationofsmallRNAstability:methylationandbeyond.CellRes,
22:624636.
JiX,TakahashiR,HiuraY,etal.2009b.PlasmamiR208asabiomarkerofmyocardial
injury.ClinChem,55:19441949.
JiZ,LuoW,LiW,etal.2011.Transcriptionalactivityregulatesalternativecleavageand
polyadenylation.MolSystBiol,7:534.
JiangL,LinC,SongL,etal.2012a.MicroRNA30e promoteshumangliomacellinva
sivenessinanorthotopicxenotransplantationmodelbydisruptingtheNFkappaB/Ikappa
Balphanegativefeedbackloop.JClinInvest,122:3347.
JiangL,QianD,ZhengH,etal.2012b.RNAdependentRNApolymerase6ofrice (Ory
zasativa)playsroleinhostdefenseagainstnegativestrandRNAvirus,Ricestripevi
rus.VirusResearch,163:512519.
JiangQ,WangY,HaoY,etal.2009.miR2Disease:amanuallycurateddatabaseformi
croRNAderegulationinhumandisease.NucleicAcidsRes,37:D98D104.
JiaoY,WangY,XueD,etal.2010.RegulationofOsSPL14byOsmiR156definesideal
plantarchitectureinrice.NatGenet,42:541544.
JinekM,DoudnaJA.2009.AthreedimensionalviewofthemolecularmachineryofRNA
interference.Nature,457:405412.
JinekM,JiangF,TaylorD W,etal.2014.StructuresofCas9endonucleasesrevealRNA
mediatedconformationalactivation.Science,343:1247997.
JonesRhoadesM W,BartelDP,BartelB.2006.MicroRNASandtheirregulatoryrolesin
plants.AnnuRevPlantBiol,57:1953.
KamikawaR,InagakiY,RogerAJ,etal.2011.SplintronsinGiardiaintestinalis:Spliceo
somalintronsinasplitform.CommunIntegrBiol,4:454456.
KarijolichJ,Yu Y T.2011.Convertingnonsensecodonsintosensecodonsbytargeted
pseudouridylation.Nature,474:395398.
KataokaM,WangDZ.2014.NoncodingRNAsincludingmiRNAsandlncRNAsincardio
vascularbiologyanddisease.Cells,3:883898.
KeA,DoudnaJA.2004.CrystallizationofRNAand RNAproteincomplexes.Methods,
34:408414.
KeJ,ChenRZ,BanT,etal.2013.StructuralbasisforRNArecognitionbyadimeric
PPRproteincomplex.NatStructMolBiol,20:13771382.
KellisM,WoldB,SnyderM P,etal.2014.DefiningfunctionalDNAelementsinthehu
mangenome.ProcNatlAcadSciUSA,111:61316138.
KerteszM,IovinoN,UnnerstallU,etal.2007.TheroleofsiteaccessibilityinmicroRNA
targetrecognition.NatureGenetics,39:12781284.
KerteszM,WanY,MazorE,etal.2010.GenomewidemeasurementofRNAsecondary
structureinyeast.Nature,467:103107.
KimE,GorenA,AstG.2008.Alternativesplicinganddisease.RNABiol,5:1719.
KimSH,SuddathFL,QuigleyGJ,etal.1974.Threedimensionaltertiarystructureof
yeastphenylalaninetransferRNA.Science,185:435440.
KinoT,HurtD E,IchijoT,etal.2010.NoncodingRNAgas5isagrowtharrestand
starvationassociatedrepressoroftheglucocorticoidreceptor.SciSignal,3:ra8.
KissT.2002.SmallnucleolarRNAs:anabundantgroupofnoncodingRNAswithdiverse
cellularfunctions.Cell,109:145148.
KongL,ZhangY,YeZQ,etal.2007.CPC:assesstheproteincodingpotentialoftran
scriptsusingsequencefeaturesandsupportvector machine.Nucleic Acids Res,35:
W345W349.
KonigJ,ZarnackK,RotG,etal.2011.iCLIPtranscriptomewidemappingofprotein
RNAinteractionswithindividualnucleotideresolution.JournalofVisualizedExperiments,
2638.
KosakaN,YoshiokaY,HagiwaraK,etal.2013.Trashortreasure:extracellularmicroR
NAsandcelltocellcommunication.FrontGenet,4:173.
KrekA,GrunD,Poy M N,etal.2005.CombinatorialmicroRNAtargetpredictions.Nat
Genet,37:495500.
KretzM,SiprashviliZ,ChuC,etal.2013.Controlofsomatictissuedifferentiationbythe
longnoncodingRNATINCR.Nature,493:231235.
KrugerK,GrabowskiPJ,ZaugAJ,etal.1982.SelfsplicingRNA:autoexcisionandau
tocyclizationoftheribosomal RNA intervening sequence of Tetrahymena.Cell,31:
147157.
KrutzfeldtJ,RajewskyN,BraichR,etal.2005.SilencingofmicroRNAsinvivowith‘an
tagomirs’.Nature,438:685689.
KuT H,ZhangT,LuoH,etal.2015.Nucleicacidaptamers:anemergingtoolforbio
technologyandbiomedicalsensing.Sensors (Basel,Switzerland),15:1628116313.
KumarswamyR,BautersC,VolkmannI,etal.2014.CirculatinglongnoncodingRNA,
LIPCAR,predictssurvivalinpatientswithheartfailure.CircRes,114:15691575.
LagosQuintanaM,RauhutR,LendeckelW,etal.2001.Identificationofnovelgenescod
ingforsmallexpressedRNAs.Science,294:853858.
LaiF,GardiniA,Zhang A,etal.2015.Integratormediatesthebiogenesisofenhancer
RNAs.Nature,525:399403.
LambertN,RobertsonA,JangiM,etal.2014.RNABindnSeq:quantitativeassessment
ofthesequenceandstructuralbindingspecificityofRNAbindingproteins.MolCell,54:
887900.
LanderES,LintonLM,BirrenB,etal.2001.Initialsequencingandanalysisofthehuman
genome.Nature,409:860921.
Lasda E,Parker R.2014.Circular RNAs:diversity ofform andfunction.RNA,20:
18291842.
LauNC,LimLP,WeinsteinEG,etal.2001.AnabundantclassoftinyRNAswithprob
ableregulatoryrolesinCaenorhabditiselegans.Science,294:858862.
LeeM,KimB,KimVN.2014.EmergingrolesofRNAmodification:m (6)AandUtail
.Cell,158:980987.
Lee R C, Ambros V.2001.An extensive class of small RNAs in Caenorhabditis
elegans.Science,294:862864.
LeeRC,FeinbaumRL,AmbrosV.1993.TheC.elegansheterochronicgenelin4encodes
smallRNAswithantisensecomplementaritytolin14.Cell,75:843854.
LewisBP,BurgeCB,BartelDP.2005.Conservedseedpairing,oftenflankedbyadeno
sines,indicatesthatthousandsofhumangenesaremicroRNAtargets.Cell,120:1520.
LewisBP,ShihIH,JonesRhoadesM W,etal.2003.PredictionofmammalianmicroR
NAtargets.Cell,115:787798.
LiCF,PontesO,ElShamiM,etal.2006.AnARGONAUTE4containingnuclearpro
cessingcentercolocalizedwithCajalbodiesinArabidopsisthaliana.Cell,126:93106.
LiF,DongJ,HuX,etal.2015a.AcovalentapproachforsitespecificRNAlabelingin
Mammaliancells.AngewChemIntEdEngl,54:45974602.
LiF,HuangC,LiZ,etal.2014a.SuppressionofRNAsilencingbyaplantDNAvirussat
elliterequiresahostcalmodulinlikeproteintorepressRDR6expression.PLoSPathog,
10:e1003921.
LiF,WangW,ZhaoN,etal.2015b.Regulationofnicotinebiosynthesisbyanendogenous
targetmimicryofmicroRNAintobacco.PlantPhysiology,169 (2):10621071.
LiH,XieH,LiuW,etal.2009a.AnovelmicroRNAtargetingHDAC5regulatesosteo
blastdifferentiationinmiceandcontributestoprimaryosteoporosisinhumans.JClinIn
vest,119:36663677.
LiJ,GongLY,SongLB,etal.2010a.OncoproteinBmi1rendersapoptoticresistanceto
gliomacellsthroughactivationoftheIKKnuclearfactorkappaBPathway.AmJPathol,
176:699709.
LiJ,GuanH Y,GongLY,etal.2008b.Clinicalsignificanceofsphingosinekinase1ex
pressioninhumanastrocytomasprogressionandoverallpatientsurvival.ClinCancerRes,
14:69967003.
LiJ,ZhangH,WuJ,etal.2010b.Prognosticsignificanceofintegrinlinkedkinase1over
expressioninastrocytoma.IntJCancer,126:14361444.
LiJH,LiuS,ZhouH,etal.2014a.starBasev2.0:decodingmiRNAceRNA,miRNA
ncRNAandproteinRNAinteractionnetworksfromlargescaleCLIPSeqdata.Nucleic
AcidsRes,42:D92D97.
LiJJ,FangX,SchusterSM,etal.2000.Molecularbeacons:anovelapproachtodetect
proteinDNAinteractions.AngewandteChemieInternationalEdition,39:10491052.
LiL,EichtenSR,ShimizuR,etal.2014c.Genomewidediscoveryandcharacterizationof
maizelongnoncodingRNAs.GenomeBiol,15:R40.
LiL,FengT,LianY,etal.2009b.RoleofhumannoncodingRNAsinthecontroloftu
morigenesis.ProcNatlAcadSciUSA,106:1295612961.
LiL,YeK.2006.Crystalstructureofan H/ACAboxribonucleoproteinparticle.Nature,
443:302307.
LiN,ChenY,GuoQ,etal.2013a.CryoEMstructuresofthelatestageassemblyinter
mediatesofthebacterial50Sribosomalsubunit.NucleicAcidsRes,41:70737083.
LiX,ZhuP,MaS,etal.2015b.Chemicalpulldownrevealsdynamicpseudouridylationof
themammaliantranscriptome.NatChemBiol,11:592597.
LiXJ,LuoXQ,HanB W,etal.2013b.MicroRNA100/99a,deregulatedinacutelym
phoblasticleukaemia,suppressproliferationandpromoteapoptosisbyregulatingtheFK
BP51andIGF1R/mTORsignallingpathways.BrJCancer,109:21892198.
LiY,LuoJ,ZhouH,etal.2008a.StressinducedtRNAderivedRNAs:anovelclassof
smallRNAsintheprimitiveeukaryote Giardialamblia.Nucleic Acids Research,36:
60486055.
LiY,ZhangQ,ZhangJ,etal.2010c.IdentificationofmicroRNAsinvolvedinpathogen
associated molecularpatterntriggered plantinnateimmunity.Plant Physiology,152:
22222231.
LiZ,HuangC,BaoC,etal.2015a.ExonintroncircularRNAsregulatetranscriptionin
thenucleus.NatStructMolBiol,22:256264.
LiaoM,CaoE,JuliusD,etal.2013.StructureoftheTRPV1ionchanneldeterminedby
electroncryomicroscopy.Nature,504:107112.
LiaoQ,LiuC,YuanX,etal.2011a.LargescalepredictionoflongnoncodingRNAfunc
tionsin a codingnoncoding gene coexpression network.Nucleic Acids Res,39:
38643878.
LiaoQ,Xiao H,BuD,etal.2011a.ncFANs:awebserverforfunctionalannotationof
longnoncodingRNAs.NucleicAcidsRes,39:W118W124.
LicatalosiDD,MeleA,FakJJ,etal.2008.HITSCLIPyieldsgenomewideinsightsinto
brainalternativeRNAprocessing.Nature,456:464469.
LimLP,GlasnerME,YektaS,etal.2003a.VertebrateMicroRNAgenes.Science,299:
15401540.
LimLP,LauN C,WeinsteinEG,etal.2003b.ThemicroRNAsofCaenorhabditisele
gans.Genes& Development,17:9911008.
LinH.2007.piRNAsinthegermline.Science,316:397.
LinJ,LaiS,JiaR,etal.2011.Structuralbasisforsitespecificribosemethylationbybox
C/DRNAproteincomplexes.Nature,469:559563.
LinPC,XuR M.2012.StructureandassemblyoftheSF3asplicingfactorcomplexofU2
snRNP.EMBOJ,31:15791590.
LinXJ,ChongY,GuoZW,etal.2015.Aserum microRNAclassifierforearlydetection
ofhepatocellularcarcinoma:amulticentre,retrospective,longitudinalbiomarkeridentifi
cationstudywithanestedcasecontrolstudy.LancetOncol,16:804815.
LippaG M,LibermanJA,JenkinsJL,etal.2012.Crystallographicanalysisofsmallri
bozymesandriboswitches.MethodsMolBiol,848:159184.
LiuB,ChenZ,SongX,etal.2007.Oryzasativadicerlike4revealsakeyroleforsmallin
terferingRNAsilencinginplantdevelopment.PlantCell,19:27052718.
LiuB,LiPC,LiX,etal.2005b.LossoffunctionofOsDCL1affectsmicroRNAaccumu
lationandcausesdevelopmentaldefectsinrice.PlantPhysiology,139:296305.
LiuB,SunL,LiuQ,etal.2015a.AcytoplasmicNFkappaBinteractinglongnoncoding
RNAblocksIkappaB phosphorylationandsuppressesbreastcancer metastasis.Cancer
Cell,27:370381.
LiuC,BaiB,SkogerboG,etal.2005a.NONCODE:anintegratedknowledgedatabaseof
noncodingRNAs.NucleicAcidsRes,33:D112D115.
LiuH,WangX,WangHD,etal.2012a.EscherichiacolinoncodingRNAscanaffectgene
expressionandphysiologyofCaenorhabditiselegans.NatCommun,3:1073.
LiuJ,JungC,XuJ,etal.2012b.Genomewideanalysisuncoversregulationoflonginter
genicnoncodingRNAsinArabidopsis.PlantCell,24:43334345.
LiuJF,GoughJ,RostB.2006.Distinguishingproteincodingfrom noncoding RNAs
throughsupportvectormachines.PlosGenetics,2:529536.
LiuJJ,BratkowskiM A,LiuX,etal.2014a.Visualizationofdistinctsubstraterecruit
mentpathwaysintheyeastexosomebyEM.NatStructMolBiol,21:95102.
LiuL,WuJ,YingZ,etal.2010.Astrocyteelevatedgene1upregulatesmatrixmetallopro
teinase9andinduceshumangliomainvasion.CancerRes,70:37503759.
LiuN,ChenNY,CuiRX,etal.2012c.PrognosticvalueofamicroRNAsignatureinna
sopharyngealcarcinoma:amicroRNAexpressionanalysis.LancetOncol,13:633641.
LiuS,LiJH,WuJ,etal.2015a.StarScan:awebserverforscanningsmallRNAtargets
fromdegradomesequencingdata.NucleicAcidsRes,43:W480W486.
LiuZW,ShaoCR,ZhangCJ,etal.2014b.TheSETdomainproteinsSUVH2andSU
VH9arerequiredforPolVoccupancyatRNAdirectedDNAmethylationloci.PLoSGen
et,10:e1003948.
LoY M,CorbettaN,ChamberlainPF,etal.1997.PresenceoffetalDNAin maternal
plasmaandserum.Lancet,350:485487.
LoewerS,CabiliM N,Guttman M,etal.2010.LargeintergenicnoncodingRNARoR
modulatesreprogrammingofhumaninducedpluripotentstemcells.NatGenet,42:1113
1117.
LongJC,CaceresJF.2009.TheSRproteinfamilyofsplicingfactors:masterregulatorsof
geneexpression.BiochemJ,417:1527.
LorenzenJM,SchauerteC,KielsteinJT,etal.2015.CirculatinglongnoncodingRNATa
pSakiisapredictorofmortalityincriticallyillpatientswithacutekidneyinjury.Clin
Chem,61:191201.
LoweT M,EddySR.1997.tRNAscanSE:aprogramforimproveddetectionoftransfer
RNAgenesingenomicsequence.NucleicAcidsRes,25:955964.
LoweT M,EddyS R.1999.AcomputationalscreenformethylationguidesnoRNAsin
yeast.Science,283:11681171.
LuM,ZhangQ,DengM,etal.2008.AnanalysisofhumanmicroRNAanddiseaseassoci
ations.PLoSOne,3:e3420.
LuT,ZhuC,LuG,etal.2012.StrandspecificRNAseqrevealswidespreadoccurrenceof
novelcisnaturalantisensetranscriptsinrice.BMCGenomics,13:721.
LuZ,ZhangQC,LeeB,etal.2016.RNAduplexmapinlivingcellsrevealshigherorder
transcriptomestructure.Cell,165:12671279.
MaherB.2012.ENCODE:Thehumanencyclopaedia.Nature,489:4648.
MakarovaK S,HaftD H,BarrangouR,etal.2011.Evolutionandclassificationofthe
CRISPRCassystems.NatRevMicrobiol,9:467477.
MaliP,EsveltK M,Church G M.2013.Cas9asaversatiletoolforengineeringbiolo
gy.NatureMethods,10:957963.
MaloneCD,HannonGJ.2009.MolecularevolutionofpiRNAandtransposoncontrolpath
waysinDrosophila.ColdSpringHarbSympQuantBiol,74:225234.
ManiatisT,ReedR.2002.Anextensivenetworkofcouplingamonggeneexpression ma
chines.Nature,416:499506.
MaoYB,CaiWJ,WangJW,etal.2007.SilencingacottonbollwormP450monooxygen
asegenebyplantmediatedRNAiimpairslarvaltoleranceofgossypol.NatBiotechnol,25:
13071313.
MaquatLE.2004.NonsensemediatedmRNAdecay:splicing,translationandmRNPdy
namics.NatRevMolCellBiol,5:8999.
MarquesAC,PontingCP.2009.CataloguesofmammalianlongnoncodingRNAs:modest
conservationandincompleteness.GenomeBiol,10:R124.
MartinA,TroadecC,Boualem A,etal.2009.Atransposoninducedepigeneticchange
leadstosexdeterminationinmelon.Nature,461:11351138.
MasudaS,DasR,ChengH,etal.2005.RecruitmentofthehumanTREXcomplextomR
NAduringsplicing.GenesDev,19:15121517.
MattickJS.2004.Thehiddengeneticprogramofcomplexorganisms.SciAm,291:6067.
MayrC,BartelDP.2009.Widespreadshorteningof3′UTRsbyalternativecleavageand
polyadenylationactivatesoncogenesincancercells.Cell,138:673684.
McHughCA,RussellP,GuttmanM.2014.Methodsforcomprehensiveexperimentaliden
tificationofRNAproteininteractions.GenomeBiol,15:203.
MeloSA,MoutinhoC,RoperoS,etal.2010.Ageneticdefectinexportin5trapsprecur
sormicroRNAsinthenucleusofcancercells.CancerCell,18:303315.
MeloSA,RoperoS,MoutinhoC,etal.2009.A TARBP2mutationinhumancancerim
pairsmicroRNAprocessingandDICER1function.NatGenet,41:365370.
MemczakS,JensM,ElefsiniotiA,etal.2013.CircularRNAsarealargeclassofanimal
RNAswithregulatorypotency.Nature,495:333338.
MengJ,LiP,ZhangQ,etal.2014.AfourlongnoncodingRNAsignatureinpredicting
breastcancersurvival.JExpClinCancerRes,33:84.
MeyerKD,PatilDP,ZhouJ,etal.2015.5′UTR m (6)Apromotescapindependent
translation.Cell,163:9991010.
MeyerKD,SaletoreY,ZumboP,etal.2012.ComprehensiveanalysisofmRNAmethyla
tionrevealsenrichmentin3′UTRsandnearstopcodons.Cell,149:16351646.
MiS,CaiT,HuY,etal.2008.SortingofsmallRNAsintoArabidopsisargonautecomple
xesisdirectedbythe5′terminalnucleotide.Cell,133:116127.
MirandaKC,HuynhT,TayY,etal.2006.Apatternbasedmethodfortheidentification
of MicroRNA binding sites and their corresponding heteroduplexes.Cell,126:
12031217.
MohnF,HandlerD,BrenneckeJ.2015.NoncodingRNA.piRNAguidedslicingspecifies
transcriptsforZucchinidependent,phasedpiRNAbiogenesis.Science,348:812817.
MooreMJ,ProudfootNJ.2009.PremRNAprocessingreachesbacktotranscriptionand
aheadtotranslation.Cell,136:688700.
MulepatiS,HerouxA,BaileyS.2014.CrystalstructureofaCRISPRRNAguidedsurveil
lancecomplexboundtoassDNAtarget.Science,345:14791484.
MullenTE,MarzluffW F.2008.DegradationofhistonemRNArequiresoligouridylation
followedbydecappingandsimultaneousdegradationofthemRNAboth5′to3′and3′to
5′.GenesDev,22:5065.
NaganoT,MitchellJA,SanzLA,etal.2008.TheairnoncodingRNAepigeneticallysi
lencestranscriptionbytargetingG9atochromatin.Science,322:17171720.
NaganumaT,NakagawaS,TanigawaA,etal.2012.Alternative3′endprocessingoflong
noncodingRNAinitiatesconstructionofnuclearparaspeckles.EMBOJ,31:40204034.
NavarroL,DunoyerP,JayF,etal.2006.AplantmiRNAcontributestoantibacterialre
sistancebyrepressingauxinsignaling.Science,312:436439.
NellesDA,FangM Y,OConnellM R,etal.2016.ProgrammableRNAtrackinginlive
cellswithCRISPR/Cas9.Cell,165:488496.
NguyenTC,CaoX,YuP,etal.2016a.MappingRNARNAinteractomeandRNAstruc
tureinvivobyMARIO.NatCommun,7:12023.
NguyenT H,Galej W P,BaiX C,etal.2016b.CryoEM structureoftheyeastU4/
U6.U5trisnRNPat3.7?resolution.Nature,530:298302.
NguyenT H,GalejW P,BaiXC,etal.2015.ThearchitectureofthespliceosomalU4/
U6.U5trisnRNP.Nature,523:4752.
NishikuraK.2010.FunctionsandregulationofRNAeditingby ADARdeaminases.Annu
RevBiochem,79:321349.
NishimasuH,RanFA,HsuPD,etal.2014.Crystalstructureofcas9incomplexwith
guideRNAandtargetDNA.Cell,156:935949.
NiuY,ZhaoX,WuYS,etal.2013.N6methyladenosine (m6A)inRNA:anoldmodi
ficationwithanovelepigeneticfunction.GenomicsProteomicsBioinformatics,11:817.
Orom U A,DerrienT,GuigoR,etal.2010.LongnoncodingRNAsasenhancersofgene
expression.ColdSpringHarbSympQuantBiol,75:325331.
Orom U A,ShiekhattarR.2013.LongnoncodingRNAsusherinanewerainthebiologyof
enhancers.Cell,154:11901193.
PaigeJS,WuK Y,JaffreySR.2011.RNA mimicsofgreenfluorescentprotein.Science,
333:642646.
PanQ,ShaiO,LeeLJ,etal.2008.Deepsurveyingofalternativesplicingcomplexityin
thehumantranscriptomebyhighthroughputsequencing.NatGenet,40:14131415.
PanZ,SunX,Shan H,etal.2012.MicroRNA101inhibitedpostinfarctcardiacfibrosis
andimprovedleftventricularcomplianceviatheFBJosteosarcomaoncogene/transforming
growthfactorbeta1pathway.Circulation,126:840850.
PandeyG K,MitraS,SubhashS,etal.2014.TheriskassociatedlongnoncodingRNA
NBAT1controlsneuroblastomaprogressionbyregulatingcellproliferationandneuronal
differentiation.CancerCell,26:722737.
PanwarV,McCallumB,BakkerenG.2013.Hostinducedgenesilencingofwheatleafrust
fungusPucciniatriticinapathogenicitygenes mediatedbytheBarleystripe mosaicvi
rus.PlantMolecularBiology,81:595608.
ParkJK,KogureT,NuovoGJ,etal.2011.miR221silencingblockshepatocellularcarci
nomaandpromotessurvival.CancerRes,71:76087616.
ParkerR,SongH.2004.TheenzymesandcontrolofeukaryoticmRNAturnover.NatStruct
MolBiol,11:121127.
PeselisA,Serganov A.2014.Themesand variationsinriboswitchstructureandfunc
tion.BiochimBiophysActa,1839:908918.
PitinoM,ColemanAD,MaffeiME,etal.2011.SilencingofaphidgenesbydsRNAfeed
ingfromplants.PloSOne,6:e25709.
PontesO,LiCF,CostaNunesP,etal.2006.TheArabidopsischromatinmodifyingnucle
arsiRNApathwayinvolvesanucleolarRNAprocessingcenter.Cell,126:7992.
PrasanthK V,PrasanthS G,XuanZ,etal.2005.Regulatinggeneexpressionthrough
RNAnuclearretention.Cell,123:249263.
PrescottD M.1994.TheDNAofciliatedprotozoa.MicrobiologicalReviews,58:233267.
QuL.2013.NoncodingRNAannotation:decipheringthesecondgeneticcode.SciChinaLife
Sci,56:865866.
RamakrishnanV.2014.Theribosomeemergesfromablackbox.Cell,159:979984.
RaynerKJ,EsauCC,HussainFN,etal.2011.InhibitionofmiR33a/binnonhuman
primatesraisesplasmaHDLandlowersVLDLtriglycerides.Nature,478:404407.
RechaviO,HouriZeeviL,AnavaS,etal.2014.Starvationinducedtransgenerationalin
heritanceofsmallRNAsinC.elegans.Cell,158:277287.
RehmsmeierM,SteffenP,HochsmannM,etal.2004.Fastandeffectivepredictionofmi
croRNA/targetduplexes.Rna,10:15071517.
ReinhartBJ,SlackFJ,BassonM,etal.2000.The21nucleotidelet7RNAregulatesde
velopmentaltiminginCaenorhabditiselegans.Nature,403:901906.
RinnJL,KerteszM,WangJK,etal.2007.Functionaldemarcationofactiveandsilent
chromatindomainsinhumanHOXlocibynoncodingRNAs.Cell,129:13111323.
RivasE,Klein RJ,Jones T A,etal.2001.Computationalidentificationofnoncoding
RNAsinEcolibycomparativegenomics.CurrentBiology,11:13691373.
RobertsT C.2014.The microRNA biologyofthe mammaliannucleus.MolTherNucleic
Acids,3:e188.
RoemerI,ReikW,DeanW,etal.1997.Epigeneticinheritanceinthemouse.CurrBiol,7:
277280.
RubioSomozaI,ZhouCM,ConfrariaA,etal.2014.Temporalcontrolofleafcomplexity
bymiRNAregulatedlicensingofproteincomplexes.CurrentBiology,24:27142719.
SalmenaL,PolisenoL,TayY,etal.2011.AceRNAhypothesis:theRosettaStoneofa
hiddenRNAlanguage?Cell,146:353358.
SalzmanJ,GawadC,WangPL,etal.2012.CircularRNAsarethepredominanttranscript
isoformfromhundredsofhumangenesindiversecelltypes.PLoSOne,7:e30733.
SandbergR,NeilsonJR,SarmaA,etal.2008.ProliferatingcellsexpressmRNAswith
shortened 3 untranslated regions and fewer microRNA target sites.Science,320:
16431647.
SauvageauM,GoffLA,LodatoS,etal.2013.Multipleknockoutmousemodelsreveallin
cRNAsarerequiredforlifeandbraindevelopment.Elife,2:e01749.
SchierAF.2007.Thematernalzygotictransition:deathandbirthofRNAs.Science,316:
406407.
SchirleNT,SheuGruttadauriaJ,MacRaeIJ.2014.StructuralbasisformicroRNAtarge
ting.Science,346:608613.
Schmeing T M,Ramakrishnan V.2009.Whatrecentribosomestructureshaverevealed
aboutthemechanismoftranslation.Nature,461:12341242.
SchoenbergDR,MaquatLE.2012.RegulationofcytoplasmicmRNAdecay.NatRevGen
et,13:246259.
SchottJ,Stoecklin G.2010.Networks controlling mRNA decayin theimmune sys
tem.WileyInterdiscipRevRNA,1:432456.
SchwartzS,AgarwalaSD,MumbachM R,etal.2013.Highresolutionmappingrevealsa
conserved,widespread,dynamic mRNA methylation program in yeast meiosis.Cell,
155:14091421.
SchwartzS,BernsteinDA,Mumbach M R,etal.2014.Transcriptomewidemappingre
vealswidespreaddynamicregulatedpseudouridylationofncRNAandmRNA.Cell,159:
148162.
Schwarzenbach,H.2015.Thepotentialofcirculatingnucleicacidsascomponentsofcom
paniondiagnosticsforpredictingandmonitoringchemotherapyresponse.ExpertRevMol
Diagn,15:267275.
SegevN,HayN.2012.HijackingleucyltRNAsynthetaseforaminoaciddependentregula
tionofTORC1.MolCell,46:46.
SeoJK,WuJ,LiiY,etal.2013.ContributionofsmallRNApathwaycomponentsinplant
immunity.MolecularPlantMicrobeInteractions,26:617625.
ShangR,ZhangF,XuB,etal.2015.RibozymeenhancedsinglestrandedAgo2processed
interferingRNAtriggersefficientgenesilencingwithfewerofftargeteffects.NatCom
mun,6:8430.
ShaoW,ZhaoQY,WangXY,etal.2012.Alternativesplicingandtranssplicingevents
revealedbyanalysisoftheBombyxmoritranscriptome.RNA,18:13951407.
SharmaE,SterneWeilerT,OHanlonD,etal.2016.Globalmappingofhuman RNA
RNAinteractions.MolCell,62:618626.
ShengG,ZhaoH,WangJ,etal.2014.StructurebasedcleavagemechanismofThermus
thermophilusArgonauteDNAguidestrandmediatedDNAtargetcleavage.ProcNatlAcad
SciUSA,111:652657.
ShuaiP,LiangD,TangS,etal.2014.Genomewideidentificationandfunctionalprediction
ofnoveland droughtresponsivelincRNAsin Populustrichocarpa.J Exp Bot,65:
49754983.
SimonM,PlattnerH.2014.Unicellulareukaryotesasmodelsincellandmolecularbiology:
criticalappraisaloftheirpastandfuturevalue.IntRevCellMolBiol,309:141198.
SimonM D,WangCI,KharchenkoPV,etal.2011.Thegenomicbindingsitesofanon
codingRNA.ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesof
America,108:2049720502.
SinghDP,SaudemontB,GuglielmiG,etal.2014.GenomedefencesmallRNAsexapted
forepigeneticmatingtypeinheritance.Nature,509:447452.
SmythiesJ,EdelsteinL,RamachandranV.2014.Molecularmechanismsfortheinheritance
ofacquiredcharacteristicsexosomes,microRNAshuttling,fearandstress:Lamarckres
urrected?FrontGenet,5:133.
SongCX,YiC,HeC.2012a.Mappingnewnucleotidevariantsinthegenomeandtran
scriptome.NatureBiotechnology,30:11071116.
SongL,LiuL,WuZ,etal.2012b.TGFbetainducesmiR182tosustainNFkappaBacti
vationingliomasubsets.JClinInvest,122:35633578.
SongX,LiP,ZhaiJ,etal.2012c.RolesofDCL4andDCL3binricephasedsmallRNAbi
ogenesis.PlantJournal,69:462474.
SongX,WangD,MaL,etal.2012d.RiceRNAdependentRNA polymerase6actsin
smallRNAbiogenesisandspikeletdevelopment.PlantJournal,71:378389.
SpiesN,BurgeCB,BartelDP.2013.3UTRisoformchoicehaslimitedinfluenceonthe
stabilityandtranslationalefficiencyofmostmRNAsinmousefibroblasts.GenomeRes,
23:20782090.
SpilmanM,CocozakiA,HaleC,etal.2013.StructureofanRNAsilencingcomplexofthe
CRISPRCasimmunesystem.MolCell,52:146152.
SpitaleRC,FlynnRA,ZhangQC,etal.2015.StructuralimprintsinvivodecodeRNA
regulatorymechanisms.Nature,519:486490.
SquiresJE,PatelHR,NouschM,etal.2012.Widespreadoccurrenceof5methylcytosine
inhumancodingandnoncodingRNA.NucleicAcidsResearch,40:50235033.
StaalsRH,AgariY,MakiYonekuraS,etal.2013.StructureandactivityoftheRNAtar
getingtypeIIIBCRISPRCascomplexofThermusthermophilus.MolCell,52:135145.
StaalsR H,ZhuY,TaylorD W,etal.2014.RNAtargetingbythetypeIIIACRISPR
CasCsmcomplexofThermusthermophilus.MolCell,56:518530.
StaleyJ P,Guthrie C.1998.Mechanicaldevices ofthespliceosome:motors,clocks,
springs,andthings.Cell,92:315326.
Stark H,LuhrmannR.2006.Cryoelectron microscopyofspliceosomalcomponents.Annu
RevBiophysBiomolStruct,35:435457.
Stein L D.2010.The casefor cloud computingin genomeinformatics.Genome Biol,
11:207.
StrasserK,BasslerJ,HurtE.2000.BindingoftheMex67p/Mtr2pheterodimertoFXFG,
GLFG,andFGrepeatnucleoporinsisessentialfornuclearmRNAexport.JCellBiol,
150:695706.
StrasserK,MasudaS,MasonP,etal.2002.TREXisaconservedcomplexcouplingtran
scriptionwithmessengerRNAexport.Nature,417:304308.
SugimotoY,KnigJ,HussainS,etal.2012.AnalysisofCLIPandiCLIPmethodsfornu
cleotideresolutionstudiesofproteinRNAinteractions.GenomeBiology,13:R67R67.
SunK,ChenX,JiangP,etal.2013.iSeeRNA:identificationoflongintergenicnoncoding
RNAtranscriptsfromtranscriptomesequencingdata.BMCGenomics,14(Suppl2):S7.
SwiezewskiS,LiuF,Magusin A,etal.2009.Coldinducedsilencingbylongantisense
transcriptsofanArabidopsisPolycombtarget.Nature,462:799802.
SzafranskiP,DharmadhikariA V,BrosensE,etal.2013.Smallnoncodingdifferentially
methylatedcopynumbervariants,includinglncRNAgenes,causealethallungdevelop
mentaldisorder.GenomeRes,23:2333.
Tam O H,AravinA A,SteinP,etal.2008.PseudogenederivedsmallinterferingRNAs
regulategeneexpressioninmouseoocytes.Nature,453:534538.
TayY,RinnJ,PandolfiPP.2014.ThemultilayeredcomplexityofceRNAcrosstalkand
competition.Nature,505:344352.
TianB,HuJ,Zhang H,etal.2005.AlargescaleanalysisofmRNApolyadenylationof
humanandmousegenes.NucleicAcidsRes,33:201212.
TianN,YangY,SachsenmaierN,etal.2011.AstructuraldeterminantrequiredforRNA
editing.NucleicAcidsRes,39:56695681.
TongYS,WangX W,ZhouXL,etal.2015.IdentificationofthelongnoncodingRNA
POU3F3inplasmaasanovelbiomarkerfordiagnosisofesophagealsquamouscellcarcino
ma.MolCancer,14:3.
ToorN,KeatingKS,TaylorSD,etal.2008.CrystalstructureofaselfsplicedgroupII
intron.Science,320:7782.
TorresLariosA,SwingerKK,PanT,etal.2006.StructureofribonucleasePauniversal
ribozyme.CurrOpinStructBiol,16:327335.
TorresAG,BatlleE,RibasdePouplanaL.2014.RoleoftRNA modificationsinhuman
diseases.TrendsMolMed,20:306314.
TryndyakVP,LatendresseJR,MontgomeryB,etal.2012.PlasmamicroRNAsaresensi
tiveindicatorsofinterstraindifferencesintheseverityofliverinjuryinducedinmicebya
cholineandfolatedeficientdiet.ToxicolApplPharmacol,262:5259.
TsaiMC,ManorO,WanY,etal.2010.LongnoncodingRNAasmodularscaffoldofhis
tonemodificationcomplexes.Science,329:689693.
TyagiS,KramerF R.1996.Molecularbeacons:probesthatfluoresceupon hybridiza
tion.NatBiotech,14:303308.
UleJ,JensenKB,RuggiuM,etal.2003.CLIPidentifiesNovaregulatedRNAnetworks
inthebrain.Science,302:12121215.
UlitskyI,BartelDP.2013.lincRNAs:genomics,evolution,andmechanisms.Cell,154:
2646.
UpadhyaySK,ChandrashekarK,ThakurN,etal.2011.RNAinterferenceforthecontrol
ofwhiteflies (Bemisiatabaci)byoralroute.JournalofBiosciences,36:153161.
VargasDY,RajA,MarrasSAE,etal.2005.MechanismofmRNAtransportinthenu
cleus.ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica,
102:1700817013.
VenterJC,AdamsMD,MyersEW,etal.2001.Thesequenceofthehumangenome.Science,
291:13041351.
VoinnetO.2009.Origin,biogenesis,andactivityofplantmicroRNAs.Cell,136:669687.
WanB,TangT,UptonH,etal.2015.TheTetrahymenatelomerasep75p45p19subcom
plexisauniqueCSTcomplex.NatStructMolBiol,22:10231026.
WanR,YanC,BaiR,etal.2016.The3.8AstructureoftheU4/U6.U5trisnRNP:in
sightsintospliceosomeassemblyandcatalysis.Science,351:466475.
WanY,QuK,ZhangQC,etal.2014.LandscapeandvariationofRNAsecondarystruc
tureacrossthehumantranscriptome.Nature,505:706709.
WangB,WangL,ChenF,etal.2016a.MicroRNAprofilingofthewhiteflyBemisiatabaci
MiddleEastAisaMinorIfollowingtheacquisitionofTomatoyellowleafcurlChinavi
rus.VirologyJournal,13:1.
WangD,GarciaBassetsI,BennerC,etal.2011a.Reprogrammingtranscriptionbydistinct
classesofenhancersfunctionallydefinedbyeRNA.Nature,474:390394.
WangG,CuiY,ZhangGF,etal.2009a.Regulationofprotooncogenetranscription,cell
proliferation,and tumorigenesis in mice by PSF protein and a VL30 noncoding
RNA.ProceedingsoftheNationalAcademyofSciencesoftheUnitedStatesofAmerica,
106:1679416798.
WangJF,ZhouH,ChenYQ,etal.2004.Identificationof20microRNAsfromOryzasa
tiva.NucleicAcidsResearch,32:16881695.
WangJ,LiJ,Zhao H,etal.2015.Structuraland mechanisticbasisofPAMdependent
spaceracquisitioninCRISPRCassystems.Cell,163:840853.
WangJ,LiuT,ZhaoB,etal.2016a.sRNATarBase3.0:anupdateddatabaseforsRNA
targetinteractionsinbacteria.NucleicAcidsRes,44:D248D253.
WangJ,Lu M,QiuC,etal.2010a.TransmiR:atranscriptionfactormicroRNAregula
tiondatabase.NucleicAcidsRes,38:D119D122.
WangJW,ParkMY,WangLJ,etal.2011.miRNAcontrolofvegetativephasechangein
trees.PLoSGenet,7:e1002012.
WangL,FengZ,WangX,etal.2010a.DEGseq:anRpackageforidentifyingdifferential
lyexpressedgenesfromRNAseqdata.Bioinformatics,26:136138.
WangL,SongX,GuL,etal.2013b.NOT2proteinspromotepolymeraseIIdependent
transcriptionandinteractwithmultipleMicroRNAbiogenesisfactorsinArabidopsis.Plant
Cell,25:715727.
WangL,ZhangLF,WuJ,etal.2014b.IL1betamediatedrepressionofmicroRNA101is
crucialforinflammationpromotedlungtumorigenesis.CancerRes,74:47204730.
WangP,XueYQ,HanY M,etal.2014a.TheSTAT3bindinglongnoncodingRNAlnc
DCcontrolshumandendriticcelldifferentiation.Science,344:310313.
WangW,WangL,ZouY,etal.2011c.CooperationofEscherichiacoliHfqhexamersin
DsrAbinding.GenesDev,25:21062117.
WangX,LuZ,GomezA,etal.2014.N6methyladenosinedependentreglationofmessen
gerRNAstability.Nature,505:117120.
WangX,HeC.2014.ReadingRNAmethylationcodesthroughmethylspecificbindingpro
teins.RNABiol,11:669672.
WangX W,ZhangJ,GuJ,etal.2005.MicroRNAidentificationbasedonsequenceand
structurealignment.Bioinformatics,21:36103614.
WangY,DangM,HouH,etal.2014c.IdentificationofanRNAsilencingsuppressoren
codedbyamastrevirus.JournalofGeneralVirology,95:20822088.
WangY,FanX,LinF,etal.2014d.ArabidopsisnoncodingRNAmediatescontrolofpho
tomorphogenesisbyredlight.Proceedingsofthe NationalAcademyofSciences,111:
1035910364.
WangY,JuranekS,LiH,etal.2009b.Nucleation,propagationandcleavageoftarget
RNAsinAgosilencingcomplexes.Nature,461:754761.
WangY,WangX,DengW,etal.2014e.Genomicfeaturesandregulatoryrolesofinterme
diatesizednoncodingRNAsinArabidopsis.MolPlant,7:514527.
WangY,XuZY,JiangJF,etal.2013a.EndogenousmiRNAspongelincRNARoRregu
latesOct4,Nanog,andSox2inhumanembryonicstemcellselfrenewal.Developmental
Cell,25:6980.
WangY,ZhangD,WuK,etal.2014f.LongnoncodingRNA MRULpromotesABCB1ex
pressioninmultidrugresistantgastriccancercellsublines.MolCellBiol,34:31823193.
WangY,ZhouXL,RuanZR,etal.2016b.Ahumandiseasecausingpointmutationin
mitochondrialthreonyltRNAsynthetaseinducesbothstructuralandfunctionaldefects.J
BiolChem,291:65076520.
WashietlS,HofackerIL,LukasserM,etal.2005.MappingofconservedRNAsecondary
structurespredictsthousandsoffunctionalnoncodingRNAsinthehumangenome.Nat
Biotechnol,23:13831390.
WatanabeT,LinH.2014.PosttranscriptionalregulationofgeneexpressionbyPiwiproteins
andpiRNAs.MolCell,56:1827.
WatsonJD,CrickFH.1953.Molecularstructureofnucleicacids:astructurefordeoxyri
bosenucleicacid.Nature,171:737738.
WeiL,GuL,SongX,etal.2014.Dicerlike3producestransposableelementassociated
24ntsiRNAsthatcontrolagriculturaltraitsinrice.ProcNatlAcadSciUSA,111:3877
3882.
WeiW,BaZ,GaoM,etal.2012.AroleforsmallRNAsinDNAdoublestrandbreakre
pair.Cell,149:101112.
WeickE M,MiskaE A.2014.piRNAs:from biogenesistofunction.Development,141:
34583471.
WenJ,ParkerBJ,WeillerGF.2007.InSilicoidentificationandcharacterizationofmRNA
likenoncodingtranscriptsinMedicagotruncatula.InSilicoBiol,7:485505.
WernerA,SayerJA.2009.NaturallyoccurringantisenseRNA:functionandmechanisms
ofaction.CurrOpinNephrolHypertens,18:343349.
WestraER,SwartsD C,StaalsR H,etal.2012.TheCRISPRs,theyareachangin′:
howprokaryotesgenerateadaptiveimmunity.AnnuRevGenet,46:311339.
WierzbickiAT,HaagJR,PikaardCS.2008.NoncodingtranscriptionbyRNApolymerase
PolIVb/PolV mediatestranscriptionalsilencingofoverlappingandadjacentgenes.Cell,
135:635648.
WierzbickiAT,ReamTS,HaagJR,etal.2009.RNApolymeraseVtranscriptionguides
ARGONAUTE4tochromatin.NatureGenetics,41:630634.
WuJ,YangZ,WangY,etal.2015.ViralinducibleArgonaute18confersbroadspectrum
virusresistanceinricebysequesteringahostmicroRNA.Elife,4.
WuL,ZhouH,ZhangQ,etal.2010.DNA methylationmediatedbyamicroRNApath
way.MolCell,38:465475.
XiangJF,YinQF,ChenT,etal.2014.HumancolorectalcancerspecificCCAT1Lln
cRNA regulateslongrangechromatininteractionsatthe MYClocus.Cell Res,24:
513531.
XiaoW,AdhikariS,DahalU,etal.2016.Nuclearm (6)AreaderYTHDC1regulates
mRNAsplicing.MolCell,61:507519.
XiaoZD,DiaoLT,YangJH,etal.2013.Decipheringthetranscriptionalregulationof
microRNAgenesinhumanswithACTLocater.NucleicAcidsRes,41:e5.
XieZ,JohansenLK,GustafsonA M,etal.2004.Geneticandfunctionaldiversificationof
smallRNApathwaysinplants.PlosBiology,2:642652.
XinM,WangY,YaoY,etal.2011.Identificationandcharacterizationofwheatlongnon
proteincodingRNAsresponsivetopowderymildewinfectionandheatstressbyusingmi
croarrayanalysisandSBSsequencing.BMCPlantBiol,11:61.
XingZ,LinA,LiC,etal.2014.lncRNAdirectscooperativeepigeneticregulationdown
streamofchemokinesignals.Cell,159:11101125.
XuJ,LiCX,LiYS,etal.2011.MiRNAmiRNAsynergisticnetwork:constructionvia
coregulatingfunctionalmodulesanddiseasemiRNAtopologicalfeatures.NucleicAcids
Res,39:825836.
XueCH,LiF,HeT,etal.2005.ClassificationofrealandpseudomicroRNAprecursorsusing
localstructuresequencefeaturesandsupportvectormachine.BmcBioinformatics,6.
XueY,OuyangK,HuangJ,etal.2013.Directconversionoffibroblaststoneuronsbyre
programmingPTBregulatedmicroRNAcircuits.Cell,152:8296.
YanC,HangJ,WanR,etal.2015.Structureofayeastspliceosomeat3.6angstromreso
lution.Science,349:11821191.
YanL,YangM,GuoH,etal.2013.SinglecellRNASeqprofilingofhumanpreimplanta
tionembryosandembryonicstemcells.NatStructMolBiol,20:11311139.
YangB,LinH,XiaoJ,etal.2007.ThemusclespecificmicroRNAmiR1regulatescardiac
arrhythmogenicpotentialbytargetingGJA1andKCNJ2.NatMed,13:486491.
YangF,WangX Y,ZhangZ M,etal.2013b.Splicingproofreadingat5′splicesitesby
ATPasePrp28p.NucleicAcidsRes,41:46604670.
YangF,ZhangH,MeiY,etal.2014.ReciprocalregulationofHIF1alphaandlincRNA
p21modulatestheWarburgeffect.MolCell,53:88100.
YangJH,LiJH,JiangS,etal.2013a.ChIPBase:adatabasefordecodingthetranscrip
tionalregulationoflong noncoding RNA and microRNA genesfrom ChIPSeqda
ta.NucleicAcidsRes,41:D177D187.
YangJH,LiJH,ShaoP,etal.2011a.starBase:adatabaseforexploringmicroRNAmR
NAinteractionmapsfrom ArgonauteCLIPSeqandDegradomeSeqdata.NucleicAcids
Res,39:D202D209.
YangJH,ShaoP,ZhouH,etal.2010.deepBase:adatabasefordeeplyannotatingand
miningdeepsequencingdata.NucleicAcidsRes,38:D123D130.
YangJ H,ZhangX C,HuangZP,etal.2006.snoSeeker:anadvancedcomputational
packageforscreeningofguideandorphansnoRNAgenesinthehumangenome.Nucleic
AcidsResearch,34:51125123.
YangL.2015.SplicingnoncodingRNAsfromtheinsideout.WileyInterdiscipRevRNA,6:
651660.
YangL,DuffM O,GraveleyBR,etal.2011a.Genomewidecharacterizationofnonpolya
denylatedRNAs.GenomeBiol,12:R16.
YangX,YanX,RajaP,etal.2011c.Suppressionofmethylationmediatedtranscriptional
genesilencingby?2C1SAHH proteininteractionduringgeminivirusbetasatelliteinfec
tion.PlosPathogens,7:e1002329.
YangY,ZhanL,Zhang W,etal.2011b.RNAsecondarystructureinmutuallyexclusive
splicing.NatStructMolBiol,18:159168.
YangY G,QiY.2015.RNAdirectedrepairofDNA doublestrandbreaks.DNA Repair
(Amst),32:8285.
YaoYD,SunT M,HuangSY,etal.2012.TargeteddeliveryofPLK1siRNAbyScFv
suppressesHer2+ breastcancergrowthandmetastasis.SciTranslMed,4:130ra148.
YeR,ChenZ,LianB,etal.2016.AdicerindependentrouteforbiogenesisofsiRNAsthat
directDNAmethylationinArabidopsis.MolecularCell,61:222235.
YeR,WangW,IkiT,etal.2012.Cytoplasmicassemblyandselectivenuclearimportof
ArabidopsisArgonaute4/siRNAcomplexes.MolCell,46:859870.
YeW,LvQ,WongCK,etal.2008.TheeffectofcentralloopsinmiRNA:MREduple
xesontheefficiencyofmiRNAmediatedgeneregulation.PLoSOne,3:e1719.
YinP,LiQ,YanC,etal.2013.Structuralbasisforthemodularrecognitionofsingle
strandedRNAbyPPRproteins.Nature,504:168171.
YinQF,YangL,ZhangY,etal.2012.LongnoncodingRNAswithsnoRNAends.Mol
Cell,48:219230.
YingXB,LiD,Zhu H,etal.2010.RNAdependentRNApolymerase1fromnicotiana
tabacumsuppressesRNAsilencingandenhancesviralinfectioninnicotianabenthami
ana.PlantCell,22:13581372.
YouL,WuJ,FengY,etal.2015.APASdb:adatabasedescribingalternativepoly (A)
sitesand selection of heterogeneous cleavage sites downstream of poly (A)sig
nals.NucleicAcidsRes,43:D59D67.
YuB,CassaniM,Wang M,etal.2015.StructuralinsightsintoRhinomediatedgermline
piRNAclusterformation.CellRes,25:525528.
YuF,YaoH,ZhuP,etal.2007.let7regulatesselfrenewalandtumorigenicityofbreast
cancercells.Cell,131:11091123.
YuS,CaoL,ZhouCM,etal.2013.Sugarisanendogenouscueforjuveniletoadultphase
transitioninplants.ElifeSciences,2:e00269e00269.
YuS,Galvao V C,Zhang Y C,etal.2012.Gibberellinregulatesthearabidopsisfloral
transitionthrough miR156targetedSQUAMOSA PROMOTER BINDINGLIKEtran
scriptionfactors.PlantCell,24:33203332.
YuanJH,YangF,WangF,etal.2014.AlongnoncodingRNAactivatedbyTGFbeta
promotestheinvasionmetastasiscascadeinhepatocellularcarcinoma.CancerCell,25:
666681.
ZahidK,ZhaoJH,SmithNA,etal.2015.NicotianasmallRNAsequencessupportahost
genomeoriginofcucumbermosaicvirussatelliteRNA.PLoSGenet,11:e1004906.
ZappullaDC,CechTR.2006.RNAasaflexiblescaffoldforproteins:Yeasttelomeraseand
beyond.ColdSpringHarborSymposiaonQuantitativeBiology,71:217224.
ZenK,ZhangCY.2012.CirculatingmicroRNAs:anovelclassofbiomarkerstodiagnose
andmonitorhumancancers.MedResRev,32:326348.
ZengC W,ChenZH,ZhangXJ,etal.2014.MIR125B1repressesthedegradationofthe
PMLRARAoncoproteinbyanautophagylysosomalpathwayinacutepromyelocyticleu
kemia.Autophagy,10:17261737.
ZhangCJ,NingYQ,ZhangSW,etal.2012b.IDN2anditsparalogsformacomplexre
quiredforRNAdirectedDNAmethylation.PlosGenetics,8:e1002693e1002693.
ZhangCJ,ZhouJX,LiuJ,etal.2013a.ThesplicingmachinerypromotesRNAdirected
DNA methylation and transcriptional silencing in Arabidopsis.Embo Journal,32:
11281140.
ZhangC,DarnellRB.2011.MappinginvivoproteinRNAinteractionsatsinglenucleotide
resolutionfrom HITSCLIPdata.NatBiotechnol,29:607614.
ZhangJ,BaranJ,CrosA,etal.2011.Internationalcancergenomeconsortiumdatapor
tal—aonestopshopforcancergenomicsdata.Database (Oxford),2011:bar026.
ZhangJX,SongW,ChenZH,etal.2013b.PrognosticandpredictivevalueofamicroR
NAsignatureinstageIIcoloncancer:amicroRNAexpressionanalysis.LancetOncol,
14:12951306.
ZhangL,Hou D,Chen X,etal.2012a.Exogenousplant MIR168aspecificallytargets
mammalianLDLRAP1:evidenceofcrosskingdom regulationby microRNA.CellRes,
22:107126.
ZhangL,ZhangS,YaoJ,etal.2015b.MicroenvironmentinducedPTENlossbyexosomal
microRNAprimesbrainmetastasisoutgrowth.Nature,527:100104.
ZhangP,KangJY,GouLT,etal.2015a.MIWIandpiRNAmediatedcleavageofmes
sengerRNAsinmousetestes.CellRes,25:193207.
ZhangX,SongY,ShahAY,etal.2013c.Quantitativeassessmentofratiometricbimolec
ularbeaconsasatoolforimagingsingleengineeredRNAtranscriptsandmeasuringgene
expressioninlivingcells.NucleicAcidsResearch,41:e152e152.
ZhangX,ZuoX,YangB,etal.2014b.MicroRNAdirectlyenhancesmitochondrialtransla
tionduringmuscledifferentiation.Cell,158:607619.
ZhangX O,Wang H B,ZhangY,etal.2014a.Complementarysequencemediatedexon
circularization.Cell,159:134147.
ZhangY,GuanDG,YangJH,etal.2010a.ncRNAimprint:acomprehensivedatabaseof
mammalianimprintednoncodingRNAs.RNA,16:18891901.
ZhangY,JiaY,ZhengR,etal.2010b.PlasmamicroRNA122asabiomarkerforviral,
alcohol,andchemicalrelatedhepaticdiseases.ClinChem,56:18301838.
ZhangY,LiuD,ChenX,etal.2010c.SecretedmonocyticmiR150enhancestargeteden
dothelialcellmigration.MolCell,39:133144.
ZhangY,YangL,ChenLL.2014c.LifewithoutAtail:newformatsoflongnoncoding
RNAs.IntJBiochemCellBiol,54:338349.
ZhangY,ZhangXO,ChenT,etal.2013b.CircularintroniclongnoncodingRNAs.Mol
Cell,51:792806.
ZhangYC,LiaoJY,LiZY,etal.2014d.Genomewidescreeningandfunctionalanalysis
identifyalargenumberoflongnoncodingRNAsinvolvedinthesexualreproductionof
rice.GenomeBiol,15:512.
ZhangYC,YuY,WangCY,etal.2013a.OverexpressionofmicroRNA OsmiR397im
provesriceyieldbyincreasinggrainsizeandpromotingpaniclebranching.NatBiotechnol.
ZhangY E,VibranovskiM D,KrinskyB H,etal.2010d.Agedependentchromosomal
distributionofmalebiasedgenesinDrosophila.GenomeRes,20:15261533.
ZhangY E,VibranovskiM D,LandbackP,etal.2010e.Chromosomalredistributionof
malebiasedgenesinmammalianevolutionwithtwoburstsofgenegainontheXchromo
some.PLoSBiol,8.
ZhaoH,ShengG,WangJ,etal.2014a.CrystalstructureoftheRNAguidedimmunesur
veillanceCascadecomplexinEscherichiacoli.Nature,515:147150.
ZhaoJ,SunB K,ErwinJA,etal.2008.Polycombproteinstargetedbyashortrepeat
RNAtothemouseXchromosome.Science,322:750756.
ZhaoS,GouLT,ZhangM,etal.2013.piRNAtriggeredMIWIubiquitinationandremov
albyAPC/Cinlatespermatogenesis.DevCell,24:1325.
ZhaoT,LiG,MiS,etal.2007.AcomplexsystemofsmallRNAsintheunicellulargreen
algaChlamydomonasreinhardtii.GenesDev,21:11901203.
ZhaoY,LinJ,XuB,etal.2014a.MicroRNAmediatedrepressionofnonsensemRNAs.Elife,
3:e03032.
ZhaoY,YuanJ,ChenR.2016.NONCODEv4:annotationofnoncodingRNAswithempha
sisonlongnoncodingRNAs.MethodsMolBiol,1402:243254.
ZhengG,DahlJA,NiuY,etal.2013.ALKBH5isamammalianRNAdemethylasethat
impactsRNAmetabolismandmousefertility.MolCell,49:1829.
ZhengLL,LiJH,WuJ,etal.2016.deepBasev2.0:identification,expression,evolu
tionandfunctionofsmallRNAs,LncRNAsandcircularRNAsfromdeepsequencingda
ta.NucleicAcidsRes,44:D196D202.
ZhengY,LiYF,SunkarR,etal.2012.SeqTar:aneffectivemethodforidentifyingmicroRNA
guidedcleavagesitesfromdegradomeofpolyadenylatedtranscriptsinplants.NucleicAcidsRes,
40:e28.
ZhouC M,ZhangT Q,WangX,etal.2013.Molecularbasisofagedependentvernaliza
tionincardamineflexuosa.Science,340:10971100.
ZhouH,LiuQ,LiJ,etal.2012.Photoperiodandthermosensitivegenicmalesterilityin
ricearecausedbyapointmutationinanovelnoncoding RNAthatproducesasmall
RNA.CellResearch,22:649660.
ZhouJ,WanJ,GaoX,etal.2015a.Dynamicm (6)AmRNAmethylationdirectstransla
tionalcontrolofheatshockresponse.Nature,526:591594.
ZhouJ,YuL,GaoX,etal.2011.PlasmamicroRNApaneltodiagnosehepatitisBvirus
relatedhepatocellularcarcinoma.JClinOncol,29:47814788.
ZhouL,HangJ,ZhouY,etal.2014a.CrystalstructuresoftheLsmcomplexboundtothe
3′endsequenceofU6smallnuclearRNA.Nature,506:116120.
ZhouM,LuoH.2013.MicroRNAmediatedgeneregulation:potentialapplicationsforplant
geneticengineering.PlantMolBiol,83:5975.
ZhouX,LiX,ChengY,etal.2014a.BCLAF1anditssplicingregulatorSRSF10regulate
thetumorigenicpotentialofcoloncancercells.NatCommun,5:4581.
ZhouX,WangE.2013.TransferRNA:adancerbetweenchargingand mischargingfor
proteinbiosynthesis.SciChinaLifeSci,56:921932.
ZhouX,XuF,MaoH,etal.2014b.NuclearRNAicontributestothesilencingofofftar
getgenesandrepetitivesequencesinCaenorhabditiselegans.Genetics,197:121132.
ZhouX,YinC,DangY,etal.2015b.IdentificationofthelongnoncodingRNA H19in
plasmaasanovelbiomarkerfordiagnosisofgastriccancer.SciRep,5:11516.
ZhuEL,ZhaoFQ,XuG,etal.2010.mirTools:microRNAprofilinganddiscoverybased
onhighthroughputsequencing.NucleicAcidsResearch,38:W392W397.
ZongFY,FuX,WeiWJ,etal.2014.TheRNAbindingproteinQKIsuppressescancer
associatedaberrantsplicing.PLoSGenet,10:e1004289.