Table Of ContentRNA 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
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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
