Plant Epigenetics PDF
Preview Plant Epigenetics
RNA Technologies Nikolaus Rajewsky Stefan Jurga Jan Barciszewski E ditors Plant Epigenetics RNA Technologies Moreinformationaboutthisseriesathttp://www.springer.com/series/8619 Nikolaus Rajewsky (cid:129) Stefan Jurga (cid:129) Jan Barciszewski Editors Plant Epigenetics Editors NikolausRajewsky StefanJurga MaxDelbrückCenterfor NanobiomedicalCenter MolecularMedicine AdamMickiewiczUniversity BerlinInstituteforMedical Poznan´,Poland SystemsBiology Berlin-Buch,Berlin Germany JanBarciszewski PolishAcademyofSciences InstituteofBioorganicChemistry Poznan´,Poland ISSN2197-9731 ISSN2197-9758 (electronic) RNATechnologies ISBN978-3-319-55519-5 ISBN978-3-319-55520-1 (eBook) DOI10.1007/978-3-319-55520-1 LibraryofCongressControlNumber:2017937907 ©SpringerInternationalPublishingAG2017 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpartof the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilarmethodologynowknownorhereafterdeveloped. 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Printedonacid-freepaper ThisSpringerimprintispublishedbySpringerNature TheregisteredcompanyisSpringerInternationalPublishingAG Theregisteredcompanyaddressis:Gewerbestrasse11,6330Cham,Switzerland Preface Plant Epigenetics: From Genotype to Phenotype The Last Unicellular Common Ancestor (LUCA) has existed more than 1 billion yearsago.Duringthattime,theplantandanimalkingdomshaveevolvedseparately and adopted a multicellular system, with sophisticated pathways of development and capability for perfect adaptation to the environment. Today, in the era of genomics it is known that many developmental processes of plants and animals aresimilar,althoughtheyhaveevolvedindependently.Thecarriersofthelogicin thesetwomajorlineagesaredifferentandshowacomplicatednetworkofancient proteinandnucleicaciddomains,butatthesametimeaveryhighconservationand similarity of chromatin proteins and regulatory mechanisms is observed. This, however, does not exclude differences of structure and functions of chromatin thatexistbetweenplantsandanimals.Theyhaveevolvedveryefficientandflexible but different adaptation mechanisms to the local environment in order to ensure survival and reproduction. The specific differences connected to lineage-specific featuresmayprovidestronginformationonthegeneralmechanismsunderlyingthe complexity and regulatory and integratory role of chromatin in all eukaryotes. During a movement towards their final differentiated states, various changes occurincellsduetogeneticandenvironmentalfactors.Resultedalteredproperties ofthecellshavebeenmemorizedaftereachcelldivision. Recenttechnologicaladvancesallowgenome-wideanalysisofDNAandhistone modifications, which affect their structures, and have the potential to reveal the regulation mechanisms in plants on the level above nucleotide sequence. Those chemical changes allow the manifestation of multiple phenotypes encoded in the same DNAsequence. Inthisway,chromatinmodificationscontributetovariation atmultiplelevels,rangingfromtheexpressionofindividualgenes,tothedifferen- tiationofcelltypes,topopulation-levelphenotypicdiversity.Inotherwords,thatis epigenetics. v vi Preface Formally, the term epigenetics is a combination of two words ‘epigenesis’ and ‘genetics’andhasbeencoined75yearsago(BrilliantJubilee)in1942byConrad H.Waddington.Heproposedepigeneticsasthebranchofbiologythatstudiesthe causalinteractiongenesandtheirproducts,whichbringsthephenotypeintobeing, and proposed the concept of the epigenetic landscape as a metaphor for cell differentiation. Currently, epigenetics is interpreted as the study of mitotically and/or meiotically heritable changes in patterns of gene expression that occur without alterations in DNA sequence. Generally, epigenetic studies are focused onchemicalmodificationsofchromatinandtheirrolesintranscriptionalsilencing. Epigeneticmodificationscontributetophenotypicvariationatmultiplelevels,from gene regulation to development, stress response, and population level phenotypic diversity and evolution. A lot of epigenomic features have been comprehensively profiledinhealthanddiseaseacrosscelltypes,tissuesandindividuals. Plant development particularly depends on epigenetics. They integrate various environmentalsignalsintodifferentphenotypicorgrowthresponses.Therefore,an understandingofmechanismsofhowepigeneticmodificationsaffecttheexpression ofgenotypeintophenotypeinplantsisofprimeinterest. Thereareanumberofepigeneticphenomenadiscoveredinplants:(i)paramutation whichdescribestheheritablechangeinexpressionstatusofanalleleuponitsexposure to an allele with the same sequence but displays a different expression status, (ii) nucleolar dominance that is a selective silencing of the ribosomal RNA genes inheritedfromoneprogenitorofagenetichybrid,(iii)imprintingwhichischaracter- izedbyselectiveexpressionofgenesinheritedfromonlythematernalorthepaternal parent, (iv) vernalization which induces flowering in plants in response to cold, (v) RNA-mediated homology-dependent technologies that have important contribu- tionsforplantgeneticengineering,(vi)RNA-mediatedDNAmethylationthatleadsto genedownregulationand(vii)RNA-mediatedmRNAdegradationorinactivation. Nowadays, genome sequences for Arabidopsis, rice, poplar, maize and many otherplantsareknownandthusfacilitategenome-wide analysesofDNAmethyl- ation and histone modifications and their relationships to coding as well as short (miRNAs, siRNAs) and long noncoding RNAs, which can function as epigenetic marks of transcriptional gene silencing and also a defence against transposable elementsandviruses.Thus,plantsaregoodmodelsystemsandstayasfirstlineof discoveriesinthefieldsofepigenetics. To deeply discuss and present the frontiers of plant epigenetics, we brought together a diverse group of experts from academia, who working both from the bottom(mechanism)upandtop(phenotype)down.Webelievethatthesecomple- mentaryapproachesenablehigh-impactscience. Inthebook,thereare26chapters,whichpresentthecurrentstateofepigenomic profiling, and how functional information can be indirectly inferred is discussed. New approaches that promise functional answers, collectively referred to as epigenome editing, are also described. The book highlights the latest important advances in our understanding of the functions of plant epigenomics or new technologiesforthestudyofepigenomicmarksandmechanismsinplants.Topics includethedepositionorremovalofchromatinmodificationsandhistonevariants, Preface vii the role of epigenetics in development and response to environmental signals, natural variation and ecology, and applications for epigenetics in crop improve- ment. The chapters in this book are variable in nature, ranging from the complex regulation of stress and heterosis to the precise mechanisms of DNA and histone modifications, providing breakthroughs in the explanation of complex phenotypic phenomena.Wehopethatthechaptersinthisbookpresentoutstandingsignificance andwillcapturebroadinterest. Berlin NikolausRajewsky Poznan´ StefanJurga Poznan´ JanBarciszewski January2017 Contents Conservation,Divergence,andAbundanceofMiRNAsandTheirEffect inPlants.. . . . . .. . . . . . .. . . . . .. . . . . .. . . . . .. . . . . . .. . . . . .. . . . 1 FlordeFa´timaRosas-Ca´rdenasandStefandeFolter TheRoleofMiRNAsinAuxinSignalingandRegulationDuringPlant Development. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 CleliaDe-la-Pe~na,GeovannyI.Nic-Can,JohnyAvilez-Montalvo, Jose´ E.Cetz-Chel,andV´ıctorM.Loyola-Vargas GrowingDiversityofPlantMicroRNAsandMIR-Derived SmallRNAs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49 MariyanaGozmanova,VesselinBaev,ElenaApostolova,GauravSablok, andGalinaYahubyan AnEvolutionaryViewoftheBiogenesisandFunctionofRice SmallRNAs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69 TianTang,MingWen,PeiLin,andYushuaiWang SmallRNAs:MasterRegulatorsofEpigeneticSilencinginPlants. . . . 89 SarmaRajeevKumar,Safia,andRamalingamSathishkumar SmallRNABiogenesisandDegradationinPlants. . . . . . . . . . . . . . . . . 107 QimingYu,YalingLiu,MuLi,andBinYu PlantEpigenetics:Non-codingRNAsasEmergingRegulators. . . . . . . 129 JuanSebastianRamirez-Prado,FedericoAriel,MoussaBenhamed, andMartinCrespi Genome-WideFunctionAnalysisoflincRNAsasmiRNATargets orDecoysinPlant. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149 GuanglinLi,ZhiqiangHao,ChunyanFan,andXianmiaoWu ix x Contents PlantNon-codingRNAsandtheNewParadigms. . . . . . . . . . . . . . . . . 163 RodrigoSiqueiraReisandJulesDeforges EpigeneticRegulationbyNoncodingRNAsinPlantDevelopment. . . . 183 Yu-ChanZhangandYue-QinChen RNAiSuppressors:BiologyandMechanisms. . . . . . . . . . . . . . . . . . . . 199 NeetiSanan-Mishra,SupriyaChakraborty,DineshGupta, andSunilKumarMukherjee AnalysisofNucleicAcidsMethylationinPlants. . . . . . . . . . . . . . . . . . 231 Bi-FengYuan DNAMethylationinPlantsbymicroRNAs. . . . . . . . . . . . . . . . . . . . . . 247 SachinTeotia,DeepaliSingh,andGuiliangTang DNAMethylationinPlantsandItsImplicationsinDevelopment, HybridVigour,andEvolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 263 AnnalisaVarriale DynamicDNAMethylationPatternsinStressResponse. . . . . . . . . . . . 281 LuigiViggianoandMariaConcettadePinto Locus-SpecificDNAMethylationAnalysisandApplications toPlants.. . . . . .. . . . . . .. . . . . .. . . . . .. . . . . .. . . . . . .. . . . . .. . . . 303 AlexandreHow-Kit,EmelineTeyssier,Jean-Franc¸oisDeleuze, andPhilippeGallusci EpigeneticsinPlantReproductiveDevelopment:AnOverview fromFlowerstoSeeds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329 AntoineL.F.Gady,CristianeS.Alves,andFabioT.S.Nogueira EpigeneticRegulationofPhaseTransitionsinArabidopsisthaliana. . . . 359 IneˆsTrindade,DanielSchubert,andVale´rieGaudin EpigeneticsinPlant–PathogenInteractions. . . . . . . . . . . . . . . . . . . . . . 385 GiorgioGambinoandVitantonioPantaleo EpigeneticReprogrammingDuringPlantReproduction. . . . . . . . . . . . 405 Jer-YoungLinandTzung-FuHsieh RiceEpigenomics:HowDoesEpigeneticManipulationofCrops ContributetoAgriculture?. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 427 YoshikiHabu EpigeneticCharacterizationofSatelliteDNAinSugarBeet (Betavulgaris). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 445 FalkZakrzewskiandThomasSchmidt UniversalandLineage-SpecificPropertiesofLinkerHistones andSWI/SNF-ChromatinRemodelingComplexesinPlants. . . . . . . . . 463 AndrzejJerzmanowskiandRafalArchacki
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