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Epigenetic regulation in plants (Ch.

9)
Marjori Matzke & Ortrun Mittelsen Scheid
1.All known epigenetic pathways represented (histone, D A, ! A" #.$olyploid (endosper%& do%esticated plants, e.g., wheat, cotton, peanut" '.Meriste% (ste% cells"( plasticity ).!dDM (! A $ol *+,dependent" -.*%printing 6.Arabidopsis thaliana Ani%als and plants (.a/le *" Similar 1.Se0ual propagation 1ia %eiosis and 2ertilization #.3o%para/le geno%e sizes and co%ple0ity, 3453 '.D A cytosine %ethylation ).*%printing (endosper%4placenta" Dissimilar 1.6ene sizes (ani%als, '-,)- k/& plants, # k/" #.7 protein coding se8uence (ani%als, )7& plants, 19,'97" '.$lants do not ha1e epigenetic erasure during ga%etogenesis ).6er% line de2ined late -.So%atic e%/ryogenesis :.;asy to esta/lish ho%ozygous genotypes (sel2 pollination& recessi1es"

Sexual (right) and somatic (left) propagation

Diploid embryo; triploid endosperm

Table II: components of epigenetic regulation in Arabidopsis


DNA methylation M;.14DDM# 3M.'4D!M14DM; (D A glycosylase" Histone modification 5DA1 (histone acetylase"& 5DA: (5DA3"& S<+5# (5A." Chromatin remodeling DDM1 (S=*#, S ># A.$ase" RNAi-mediated silencing D3?1,' (Dicer like, ! ase ***" Argonaute ($*=* do%ain protein" !D!1,: (!d!$" !$D1a4/ (! A $ol *+ su/unit, !dDM"

Epigenetic discoveries made with plants


1.$arental i%printing #..ransposa/le ele%ents and epigenetic regulation '.5o%ology,dependent gene silencing ($.6S, .6S" ).!dDM (! A induces changes in D A %ethylation"

D ! c"tosine C# meth"lation
;sta/lish%ent, %aintenance, reading & erasure D A M.ases De novo and %aintenance (he%i%ethylated inter%ediate" 3p6, 3p p6 & 3p p (plants"& 3p6 (ani%als@although ;S di22erentiation" .riggers largely unknownA candidates include@. ! A, other proteins, topology, transcriptional inter2erence M;.1 (Dn%t1 BlikeC" Dn%t# BlikeC D!M (Dn%t' BlikeC", !dDM pathway 3M.' (chro%o%ethylase, 3p p6" Met ! cmt" and drm %utants are 1ia/le and 2ertile

D ! demeth"lation
$assi1e (D A replication" and acti1e (non,di1iding cells" De%eter (DM;" & !OS1 (repressor o2 silencing" 1.6lycosylase enzy%es #. icking on %ethylated D A '.DM; e0pressed in 2e%ale ga%etophyte (Medea, M;A control" Methyl,D A /inding proteins (readers" 1.MDD, transduce %ethylation in2or%ation to transcriptional acti1ity #.!ecruit other acti1ities (e.g., 5DA3" '.$lants (1#"& 11, %a%%als& - Drosophila& #, C.elegans ).5u%an diseases associated with MDD %utations

5istone %odi2ying enzy%es


5A.s (1#" and 5DA3S (1E" Silent genes (hypoacetylation & 3p6 %ethylation" 5istone M.ases 1.?ysine (5FM.s& S;. do%ains (S<(+A!""" ('# " #.Mono,, di, and tri,%ethylated '.5'FG%e' (53, ani%als & 2ungi"& euchro%atin in Arabidopsis ).5'FG%1 & 5'FG%# (53, Arabidopsis& euchro%atin in %a%%als" De%ethylation 5'FG%1 and 5'FG%# (not 5'FG%'" in (?SD1, %a%%als, see 3hs. 19, 1'"

$arental i%printing
1.Di22erential allelic e0pression (parent o2 origin" #.>lowering plants & %a%%als '.$arent,o22spring con2lict (5aig" (3hapter 1G" ).Maternal tissue4nutrient source (triploid endosper% or placenta" ArabidopsisA M#A and $%A 1.Maternal copy acti1ated (de%ethylation /y DM; in 2e%ale ga%etophyte" #.$aternal copy re%ains %ethylated and silent

Chromatin$remodeling proteins
Switch#4Sucrose non,2er%enta/le1 (S=*#4S >#" 2actors (disco1ered in yeast" swi (s&itch"& sn2 (sucrose nonfer%enting" 1.!esult in the BslidingC o2 nucleoso%es #.Direct link to D A %ethylation '.Decreased D A %ethylation (DDM1"Hloss o2 geno%ic D A %ethylation ).Ortholog in %a%%alsA ?y%phoid,speci2ic helicase (?S5" -.6lo/al %ethylation control, e%/ryogenesis

1. ;ssential 2or creating accessi/le chro%atin & geno%e %aintenance (weaken tight wrapping o2 D A around histone octa%ers" #. ?arge %ultisu/unit co%ple0es (#,1# su/units" '. O2ten in1ol1ed in D A repair ). All contain a core A.$ase (D A dependent"

% !i$mediated gene silencing pathwa"s


ds! A ! ase ***,like Dicer $.6S, .6S Argonaute, $AI do%ain, s%all ! A /inding si! A (#1 nt ! As" #1,#) nt, %icro (%i" ! As $.6S

mi% !s
1.;ndogenous ds! A, %! A (clea1age or translational repression" '.ArabidopsisA G# loci& #J distinct %i! As& de1elop%entally regulated '.;1olutionarily conser1ed ).$lant %i! AsA nearly per2ect co%ple%entarity to coding regions& not so 2or ani%als

T&': %dD(
1.D!M #.5DA: (5DA3" & S=*#4S ># are also essential '.5FM. (FK$4S<+5)" 3p p6 %ethylation ).$lant,speci2ic ! A poly%erase B$ol *+C re8uired& $ol *,*** 2ound in all eukaryotes -.$ol *+a needed 2or si! A generation :.!D!# synthesizes ds ! A& D3?' J.$ol *+/ needed to signal D A %ethylationA create chro%atin to allow de no1o D A %ethylation 3on2licting in2or%ation on !dDM in %a%%als

.argeting o2 chro%atin re%odeling co%ple0es (%achines, 3!Ms"


D ! binding factors

(eth"lated D !

uclear scaffold

!cet"lated histones

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