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8na i or9ani:ation o; 9eneti in;or ation 5

ª 2011 The &uthor7The Plant Journal ª 2011 la @>ell PuCli7hin9 %td, The Plant Journal, (2011), 66, 4–17

nu lei. in e o t o; the in;or ation on eu@ar8ote hroo o e i 9enerated in a alian ell 8 te >e >ill

al o in lude re ent data ;ro hu an and ani al hro oo e or9ani ation.

# *&T-' T T $

%o> le?el hro atin ;oldin9 odel

The eu@ar8ote hro o o e on i t o; a lon9 hro atin;iCer that i ;olded and o =a ted in u h a >a8 that the9eno i eGuen e i e;;i ientl8 tored Cut an Ceretrie?ed

ondition the trin9 o; nu leo o e an in tantl8 ;or a30 n tru ture (+an #olde, 1ABBD ednar et al., 1AAB).The30 n ;iCer under9oe o =le" ;oldin9 te= 9eneratin9hi9her le?el o; hro atin o =a tion u= to the e"tre el8

onden ed eta=ha e hro o o e. e =ite 8ear o;

e"ten i?e hro o o e tudie >e are till i9norant o; the internal hro atin or9ani ation aCo?e the 30 n le?el.$?en the or9ani ation o; the 30 n ;iCer re ain a atter o; deCate (*ae hi a et al., 2010). The urrent ?ie> o; the30 n ;iCer i a heli al arran9e ent >ith a o =a tion

) 1

u=on reGue t ;or tran ri=tion, re=li ation or other 9eno i de9ree o; 70–160 @Cl ( oCin on et al., 2006), ;or >hi h

a ti?itie . The 9eneral =i ture o; the hro atin ;iCer i a=ol8 er o; nu leo o e , ea h o; >hi h i ;or ed C8 ano ta er o; the anoni al hi tone #2&, #2 , #3 and#4, around >hi h a 147 C= '& heli" ( i9ure 1a) i>ra==ed1.7 ti e (%u9er et al., 1AA7). The lo>e t le?el o;

hro atin or9ani ation i the KCead on the trin9Lon;i9uration, >hi h ha Ceen oC er?ed under non

=h8 iolo9i al ondi tion . #o>e?er, it i not li@el8 thatthi on;i9uration o; nu leo o e e"i t in a li?in9 ell,

in e under =h8 iolo9i al

t>o Ca i odel ha?e Ceen =ro=o ed ( u et al., 2007). Theone tart heli" ( olenoid) i linearl8 arran9ed, >herea thet>o tart heli" ( i9 a9) ;or t>o nu leo o al ro> in

u h a >a8 that the ;ollo>in9 nu leo o e alternate ;roone to the other ro> ( i9ure 1C–d) and e ond neare tnei9hCor nu leo o e Ce o e intera tin9 =artner .

e ent e"=eri ental data, in ludin9 r8 tal tru tureanal8 i , re?eal t>o ta @ o; nu leo o e , >hi h ;a?orthe i9 a9 odel ( ori9o et al., 2004D hal h et al., 2005D

ri9or8e? et al.,200A). ithin the t>o tart i9 a9 odel t>o uC odelare

& di tin9ui hed, the Kheli al riCConL and the K ro ed lin@erLt8=e, ea h e"=lainin9 di;;erent hara teri ti o; the 30 n;iCer, de=endin9 on the len9th o; the lin@er '&, >hi h ithe tret h o; '& onne tin9 t>o adja ent nu leo o e( ori9o et al., 2004D u et al., 2007).

hro atin tru ture de=end on '& lin@er len9th

i9ure 1. tru ture and arran9e ent o; nu leo o e .(a) To= ?ie> o; nu leo o e ho>in9 the '& heli" (9re8) >ra==ed aroundan o ta er o; hi tone ( olored).(C) To= ?ie> o; the one tart heli al olenoid odel. 'u leo o e ;or a

=iral arran9e ent.

( , d) ide ?ie> o; the t>o tart heli" on;i9uration. #i tone tail (9ra8 line )=rotrude ;ro the nu leo o e ( ) and ;ollo>in9 nu leo o e di =la8 a

i9 a9 tru ture (d).*odi;ied a;ter ori9o et al. (2004) and Pollard and $arn ha> (2002).


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6 Paul ran and #an de Jon9

ª 2011 The &uthor7The Plant Journal ª 2011 la @>ell PuCli7hin9 %td, The Plant Journal, (2011), 66, 4–17

The a?era9e len9th o; '& a o iated >ith onenu leo o e i the nu leo o e re=eat len9th (' %), o; >hi h the lin@er '& i the ?ariaCle o =onent. '&lin@er len9th are u uall8 in te= o; 10 C=, u h a 20, 30u= to A0 C= ( on9 et al., 2007), orre =ondin9 to thenu Cer o; Ca e =air >ithin one rotational turn o; the

'& heli" ( ido , 1AA2). To9ether >ith the nu leo o al'& (147 C=) the8 9i?e ri e to ' % o; 167, 177 u= to 237

C=, re =e ti?el8, >hi h or re =ond to the re=eat unitlen9th o; an8 atellite '& re=eat la e . The a?era9e

'& lin@er len9th ho> ti ue and =e ie =e i;i it8:20 C= in 8ea t (%ee et al., 2007),30 C= in ro o=hila (*a?ri h et al., 200B), 40 C= in

a al ( hone et al., 200B) and 30 C= in &raCido= i

( hoda?a ra=u et al., 2010). The Cindin9 o; lin@er hi tone(#1, #5) to lin@er '& in the interior o; the ;iCer indu e a ;urther o =a tion and taCili ation o; the 30 n;iCer, in =arti ular a;ter dea et8lation o; ore hi tone andin u==ort o; &TP de=endent nu leo o e re odelin9

o =le"e ( oCin on et al., 200BD %i et al., 2010).#o>e?er, a o =arati?e tud8 Cet>een hro atin arra8>ith di;;erent ' % , 167 and 1A7, re?ealed that thede=enden 8 on lin@er hi tone ;or o =a tion idi;;erent Cet>een hort and lon9er '& lin@er ( outh etal., 200B). %on9er lin@er '& tret he reGuire lin@er hi tone ;or ore o =a tion and re9ular nu leo o earran9e ent. -n ontra t, hro atin tret he >ith hort

'& lin@er are le a;;e ted C8 lin@er hi tone and


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9i?e ri e to a le o =a t hro atin ;iCer ( outh et al.,200BD ri9or8e? et al., 200A). $?identl8, lon9 lin@er

hro a tin i a o iated >ith a re=re ed hro atin tate,>herea hro atin >ith hort lin@er orre =ond to atran ri= tionall8 a ti?e tate. The hi9hl8 a ti?e 8ea t

hro o o e ha?e hort lin@er '& tret he , >hilelon9 '& lin@er ha?e Ceen ;ound in ina ti?e hro atinu h a in =er atid nu lei (&the8 et al., 1AA0). '& lin@er

len9th i there;ore an i =ortant ;a tor in hro atintru ture and a ti?it8.

'u leo o e =o itionin9 i dire tl8 related to hro atina ti?it8

The a?era9e '& lin@er len9th i re;le ted in the nu leoo e =o itionin9, de;ined a the =roCaCilit8 that a

nu leo o e tart at a 9i?en Ca e =air >ithin the9eno e ( e9al and ido , 200A). in e nu leo o e9enerall8 o lude '& eGuen e ;ro intera tion >ith

'& Cindin9 =rotein , u h a a ti?ator and re=re or ,nu leo o e =o itionin9 =la8 an i =ortant role in thea ti?ation and re=re ion o; hro atin re9ion ( 8ri @ etal., 1AAA). on eGuentl8, ;a tor that re9ulate nu leo o e=o itionin9 ontrol hro atin a ti?it8. & nu Cer o; ;a torha?e Ceen =ro=o ed to dire t nu leo o e =o itionin9. &ne"=eri ental and o =uta tional tud8 de on tratedthat 9eno e en ode an intrin i nu leo o eor9ani ation, =ointin9 at a nu leo o e =o i tionin9 odein the '& eGuen e ( e9al et al., 2006D Ha=lan et al.,200A). #o>e?er, the 9eno i eGuen e a8 not Ce the=ri ar8 deter inant ;or nu leo o e =o itionin9 (Mhan9 et

al., 200A). There i e?iden e that '& eth8lation ?ia=rotein intera tion in the ajor 9roo?e a;;e t '& ;le"iCilit8 and hen e nu leo o e =o itionin9 (Pennin9 et al.,2005). &l o hi tone odi;i ation are li@el8 to a;;e t the lo al=o ition o; nu leo o e . *odelin9 tudie o; oli9onu leo

o e tru ture re?ealed that hi tone tail , in =arti ular o; hi tone #4, =la8 an i =ortant role in the hi9her order

o =a tion o; hro atin (&r8a and hli @, 2006, 200A).-ndeed, h8=era et8lation o; hi tone in rea e thea e iCilit8 o; nu leo o al '& (&nder on et al., 2001D*anohar et al.,200A). $?en a in9le a et8lation e?ent at #4H16 an =re?ent;or ation o; o =a t hro atin ;iCer in ?itro ( ho9ren

Hnaa@ et al., 2006). olle ti?el8, the hi tone odi;i ationto9ether >ith '& eth8lation, tran ri=tion ;a tor ,

hro atin re odeler and the '& eGuen e dire t the=o ition o; nu leo o e alon9 the ;iCer and re9ulate thea ti?it8 o; hro atin re9ion .

ntil ;e> 8ear a9o onl8 li ited 9ene re9ion ouldCe e"a ined ;or nu leo o e =o itionin9 in relation to

eGuen e and their e;;e t on tran ri=tion. -t a==eared that=ro oter ho> a =e i;i arran9e ent o; nu leo o e .The tran ri=tion tart ite (T ) i =re eded C8 a nu leo

o e ;ree re9ion (' ), >hi h i ;lan@ed C8 on er?ed

=o itionin9 o; relati?el8 taCle nu leo o e that ontainthe hi tone ?ariant #2&.M (%ee et al., 2004D ai ner et al.,2005D uan et al., 2005). ue to the ra=id de?elo= ent o;


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hi9h throu9h=ut =ro e in9 te hnolo9ie , lar9e nu Cer o; hro atin =ro;ilin9 data ha?e Ceen 9enerated, in ludin9 the

9loCal nu leo o e =o itionin9. #i9h re olution 9eno e>ide a= o; nu leo o e di triCution in 8ea t (%ee et al.,2007) and hu an ( hone et al., 200B) ho>ed on a9eno e >ide ale that =e i;i and o?erall =attern o; nu leo o e o u=an 8 orrelate >ith tran ri=taCundan e and tran ri=tion rate. The re=ort on;ir theo urren e o; the ' in =ro oter , >herea the 9eneCodie , e =e iall8 e"on , ho> a hi9h den it8 o; nu leo o e (&nder on et al., 200A). The ' ha Ceen;ound e =e iall8 in on tit uti?e 9ene , ;or e"a =le9ene en odin9 9l8 ol8 i =ro tein , and i ;lan@ed C8

taCle nu leo o e at the E1 and ) 1 =o ition. The E1nu leo o e lie at or near the T . %e a ti?e=ro oter u h a tho e ;ro tre 9ene , e.9. the P#9ene in 8ea t, ha?e a di ini hed ' or are o =letel8

o?ered >ith nu leo o e ( hi?a >a 8 et al., 200B). The8reGuire hro atin re odeler and a ti?ator to in rea e

a e iCilit8 o; the =ro oter. & re ent =a=er ha de ontrated that the ' o; a ti?e =ro oter i li@el8 to Ce

o u=ied to a on ideraCle e"tent C8 un taCle #3.3/#2&.Montainin9 nu leo o e (Jin et al., 200A). Their

=uri;i ation =roto ol enaCled the i olation o; hro atin;ra9 ent >ith un taCle nu leo o e , >hi h a==eared toCe enri hed ;or #3.3 and #2&.M. -n thi onte"t the terKun taCle nu leo o e re9ion L i =erha= orea==ro=riate.

Plant ho> i ilar hara teri ti and =attern >ithre =e t to nu leo o e =o itionin9. eno e >ide nu leo

o e =o itionin9 in relation to '& eth8lation >are entl8 tudied in &raCido= i ( hoda?ara=u et al., 2010).

in9 hi9h throu9h=ut eGuen in9 o; nu leo o e a o iated ;ra9 ent in o Cination >ith their Ci ul;ate eGuen in9 data at in9le nu leotide re olution the authordi o?ered a 10 C= =eriodi it8 o?er nu leo o e Cound

'& in the eth8lated 8to ine =ro;ile , irre =e ti?e o; the eGuen e onte"t o; the 8to ine ( , # , ##). Thi

ean that eth8lation =roCaCl8 ta@e =la e to nu leo oal '& rather than to lin@er '&. -ndeed, 9ene Cod8

re9ion , in =arti ular e"on , are hi9her '& eth8lated andontain ore nu leo o e than ;lan@in9 re9ion (&nderon et al., 200AD hoda?ara=u et al., 2010). $?identl8, '&eth8ltran ;era e =re;erentiall8 tar9et nu leo o e Cound'&, >hi h u99e t that nu leo o e =o itionin9 ontrol'& eth8lation. i ilar =attern >ere oC er?ed in hu an

nu leo o al '&, indi atin9 that nu leo o e ontrolled

'& eth8lation i on er?ed Cet>een =lant andhu an . -n ;a t, 9ene Cod8 eth8lation ha Ceende on trated to Ce a hi9hl8 on er?ed ;eature in =lantand hu an ( en9 et al., 2010D Me a h et al., 2010).

#i tone ?ariant #2&.M ountera t '& eth8lation

& =ro inent ar@ o; =ro oter in eu hro atin i the hitone ?ariant #2&.M, >hi h ha Ceen ;ound in the =ro oter re9ion o; nearl8 all 9ene , a ti?e and ina ti?e ( ai ner


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et al., 2005). The hi tone ?ariant i 9enerall8 lo ated in thenu leo o e that ;lan@ the ' . -t ha Ceen =ro=o ed that#2&.M er?e a an anti ilen in9 ;a tor to anta9oni e the

>it h ;ro a ti?e eu hro atin to ina ti?e hetero hro atin(*ene9hini et al., 2003). #o>e?er, #2&.M a8 al o Ce

in?ol?ed in hetero hro atin ilen in9, ;or e"a =le in oCination >ith the hetero hro atin =rotein #P1 a ( an et al.,2004). Thi u99e t that #2&.M ha o==o ite ;un tion in9ene re9ulation. in9 a hi9h re olution (300 C=) hi=–

hi= a==roa h, uille ette et al. (2005) de on trated that#2&.M =re;erentiall8 a o iate >ith =ro oter o; ina ti?e 8ea t 9ene and on lude that the #2&.Min or=oration indu e the hro atin to =oi e 9ene ;or tran ri=tional a ti?ation.

Plant are no di;;erent ;ro 8ea t and hu an >ithre =e t to #2&.M ;un tion. &raCido= i #2&.M i de=o ited,li@e in other or9ani , in the E1 nu leo o e (MilCer anet al., 200B), under orin9 the idea o; a on er?ed nu leo

o e at or near the T . The in or=oration i arried outC8 the &TPa e hro atin re odeler 1 and =ro otetran ri=tional o =eten e o; the 9ene. e ar@aCl8, #2&.M>a aC ent ;ro eth8lated 9ene Codie and eth8latedtran =o on . tri@in9l8, there i an o==o ite =attern o; '&

eth8lation alon9 the 9eno e o =ared >ith #2&.M di triCution. &==arentl8, the t>o hro atin ar@ are utuall8e" lu i?e e=i9eneti trait . 8 anal8 in9 =attern o; #2&.M in or=oration and eth8lated '& in =e i;i

utant , in?ol?ed in either hro atin ;eature, the authoron lude that '& eth8lation e" lude #2&.M

in or=oration, >hile #2&.M in turn =rote t '& ;ro

eth8lation and hen e ;ro 9ene ilen in9. Thion;ir the oC er?ation that #2&.M i ;ound in a ti?e=ro oter , or =ro oter that are =oi ed to a ti?it8, >hilethe 9ene Cod8 ontain eth8lated '& ( o@u et al.,200BD en9 et al., 2010D *auna@ea et al.,2010D Me a h et al., 2010).

# * *$ &'-M&T- ' -' T#$ -'T$ P#& $' %$

Po ition and orientation o; the hro o o e territor8de=end on an8 ;a tor

The e;;i ient =a @in9 o; lon9 '& ;iCer into a all

nu lear =a e and the a urate retrie?al o; 9enetiin;or ation ?ia lo al un;oldin9 o; hro atin i ru ial ;or an or9ani to ana9e the 9eno e. 'u leo o e den it8a;;e t the ti;; ne o; the hro atin ;iCer and

on eGuentl8 han9e the ;oldin9 =ro=ertie o; thehro o o e. ro a na@ed '& ;iCer to the 30 n ;iCer ean a==ro"i atel8 40 ;old o =a tion and a three

;old de rea e in ti;;ne ( ta he? @8,2002). oldin9 and Cendin9 o; the hro atin ;iCer >ill Ce

ore li ited to>ard hi9her order le?el o; or9ani ation o; the hro o o e, >ith the eta=ha e hro o o e athe ulti ate tate o; hro o o e o =a tion. The Ciolo9

i al =rin i=le underl8in9 nu leo o e =o itionin9 are li@el8to 9o?ern the hi9her order or9ani ation o; hro atin


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;iCer and the ;oldin9 =attern o; entire hro o o e .#o> hro o o e are =atiall8 or9ani ed in the ellnu leu de=end on a ultitude o; ;a tor , u h a

hro o o e i e, di triCution o; hetero hro atin alon9the linear hro o o e, nu lear =a e, '& eGuen eand 9ene a ti?it8, Cut al o 9eneti Ca @9round ande"ternal (a)Cioti ;a tor ( ee Celo>).

hro o o e o u=8 di tin t nu lear uCdo ain ,@no>n a hro o o e territorie ( T ). The ;ir t on e=t o; a T >a =ro=o ed aCout 100 8ear a9o C8 o?eri (1A0A), Cut>a e taCli hed onl8 t>o de ade a9o in hu an ell(%i hter et al. , 1ABBD *anuelidi and orden, 1ABB) u in9;luore en e in itu h8Cridi ation ( - #) >ith hro o o e

=e i;i '& =roCe . -n =lant the hro o o e =e i;ido ain >ere ;ir t oC er?ed in ono o i addition lineu in9 9eno i in itu h8Cridi ation (re?ie>ed in

huCert et al., 2001). -ndi?idual =lant hro o o e>ere initiall8 ?i uali ed in &raCido= i u in9

hro o o e =e i;i Ca terial arti;i ial hro o o e

( & ) '& =roCe (%8 a@ et al., 2001D Pe in@a et al., 2004)and later in related ru i;er =e ie ( err et al.,

2006D %8 a@et al., 2006). -n e Cer o; other =lant;a ilie , u h a *edi a9o, ri e ( r8 a ati?a) and to ato( olanu l8 o=er i u ), hro o o e =e i;i & - #>a u e ;ull8 a==lied to dete t all hro o o aluCre9ion (Huli@o?a et al., 2001D 'a9a@i et al., 2004D ina8

et al., 2010). -n ide the hro o o e territor8 theentro ere and telo ere re9ion o u=8 =e i;i

=o ition . hile entro ere re9ion are 9enerall8 lo atednear the nu lear =eri=h er8, the =o ition o; the telo ere

?arie not onl8 Cet>een di;;erent =e ie Cut al oCet>een the ta9e o; the ell 8 le. or e"a =le, in

hu an ell (3000 *C) the entro ere are either atta hed to the nu lear e Crane or are ore internal inthe nu leu , de=endin9 on the ell 8 le =ha e ( olo?eiet al., 2004), >hile telo ere are d8na i in the interior

o; the nu leu (*olenaar et al., 2003). Plant =e ie >ith alar9e 9eno e di =la8 a aCl on;i9uration o; their

hro o o e >ith entro ere and telo ere =o itioned ;a in9 o==o ite =ole o; the nu leu a a reli ;rothe late ana=ha e o; the =re edin9 ito i ( i9ure 2Da>lin et al., 1AA1D &ra9on &l aide et al., 1AA7). #o>e?er,o =arati?e tudie >ith e?eral =lant =e ie u99e t that

a ini u hro o o e i e rather than the 9eno e i ea ount ;or the aCl orientation ( on9 and Jian9, 1AAB).

or e"a =le, in re=i a=illari (1 N 2000 *C, n N 3) thehro o o e ha?e a aCl on;i9uration, >herea hro o

o e in ai e (Mea a8 D 1 N 2540 *C, n N 10) do not,de =ite the lar9er i e o; it 9eno e. The o t =lau iClee"=lanation ;or thi di re=an 8 i that re=i hro o o e(a==ro"i atel8 670 *C) are i9ni;i antl8 lar9er than thea?era9e i e o; a ai e hro o o e (a==ro"i atel8

250 *C). o =arin9 hro o o e i e and 9eno e i e indi;;erent =lant =e ie no> u99e t that the riti al hro

o o e i e ;or a aCl on;i9uration i around 500 *C.hro o o e i e, ho>e?er, i not the onl8 ;a tor that


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Hordeum vulgareSolanum lycopersicum

Arabidopsis thaliana Oryza sativa

i9ure 2. ia9ra ati re=re entation o; hetero hro atin di triCution alon9 the linear hro o o e, hro o o e territor8 ( T) or9ani ation and 4¢,6dia idino2 =hen8lindole ( &P-) tained nu lei in =lant >ith di;;erent hro o o e i e .

&ll =lant ha?e their entro ere (red) to>ard the nu lear =eri=her8, urrounded C8 =eri entri hetero hro atin (dar@ 9ra8), >hile telo ere (9reen) o u=8di;;erent =o ition . The hro o o al a"e (>a?8 line ) run ;ro entro ere to telo ere. Plant >ith lar9e hro o o e , u h a #ordeu ?ul9are, ho> a t8=i al

aCl orientation >ith entro ere and telo ere at o==o ite =ole o; the nu leu . The ajor =art o; the T i o u=ied C8 hetero hro atin. Plant >ith ato ato t8=e arran9e ent ( olanu l8 o=er i u ) ha?e their telo ere at the ed9e o; the hetero hro ati i land . The &raCido= i t8=e ha the telo ere

lo e to the nu leolu . The ri e t8=e ( r8 a ati?a) ha ore di;;u e hetero hro atin e9 ent alon9 the ar and telo ere are to>ard the nu lear =eri=her8.

ontrol the orientation and =o ition o; hro o o e . -n=e ie >ith relati?el8 all hro o o e ?ariou telo ere

di =o ition ha?e Ceen re=orted ( i9ure 2). -n &raCido= i (150 *C) the telo ere are around thenu leolu , >hile entro ere lo ali e in on =i uouhetero hro atin do ain , @no>n a hro o enter ,that are lo ated at the nu lear =eri=her8 ( ran et al.,2002). The telo ere in to ato (A50 *C), ho>e?er, are atthe ed9e o; =eri=heral hetero hro ati i land thata o odate the entro ere ( ran , 2004), >herea inri e (4A0 *C) the telo ere and entro ere aredi =er ed around the nu lear =eri=her8 (Prieto et al.,2004). -n Ca@erL 8ea t ( a haro 8 e ere ?i iaeD 16*C) entro ere are al o at the =eri=her8 o==o ite tothe nu leolu , >hile telo ere are at the =eri=her8 near the nu lear =ore (Jin et al., 2000D ae +a Gue and

adal, 2010). o e =e ie >ith all hro o o e e?enho>ed aCl oriented hro o o e . The hro o o e in

. ere?i iae di =la8 a aCl li@eorientation >ith a t8=i al+ ha=e and lu tered telo ere end . The telo ere , ho>e?er, are not ne e aril8 at the =ole o==o ite to

entro ere ( 8 tri @8et al., 2005). The aCl orientationo; ro o=hila hro o o e >a in?e ti9ated inat8=i al nu lei: 9iant =ol8tene nu lei (#o h tra er et al.,1AB6) and e Cr8oni ell . The ;ir t 9rou= on i t o; endoredu=li ated hro o o e , >hile the latter la @ a

1 =ha e. -n other ro o=hila ell the hro o o edi =la8 a non aCl orientation ( in@ and #eni@o;;, 1AAB).

i ilarl8, o e ell in ri e, u h a "8le ?e el ell ,ho> a aCl on;i9uration o; hro o o e . Thi a8

Ce e"=lained C8 endoredu=li ation o; "8le ell (Prietoet al., 2004), re e Clin9 the =ol8teni or9ani ation o; the

ali?ar8 9land nu lei in ro o=hila.


9/21

&==arentl8, a=art ;ro hro o o e i e there are ore;a tor that a;;e t the lar9e ale or9ani ation o; hro o

o e .teri on traint due to li ited =a e ha?e Ceen =ro

=o ed to =la8 a ajor role in dire tin9 o?erall hro atinor9ani ation durin9 inter=ha e. in9 a no?el in ?i?olaCelin9 te hniGue in?ol?in9 =hotoa ti?ation, *uller et al.(2010) onitored an indi?idual hu an hro o o e inli?in9 ell and de on trated a ra=id o?erall de onden ation o; the itoti hro o o e u=on entran e into 1 C8 a;a tor o; 2.5. The Cul@ o; hro o o e ha=e and territor8>a ettled >ithin 2 h. Thi >a attriCuted to a Calan eCet>een e"=an ion o; the hro o o e and =atial on

traint i =o ed C8 urroundin9 hro o o e and thenu lear en?elo=e. i ilarl8, or=holo9i al ;eature , u h a

the nu leolar or9ani in9 re9ion (' ) ontainin9 riCo o al9ene , nu lear ha=e, endo=ol8=loid8 le?el and nu lear ?olu e >ere =ro=o ed to dire t hro o o e arran9e entin &raCido= i ( huCert and ud, 1AA7, err and huCert,2007). The e data >ere ;urther uC tantiated C8 o =utational i ulation o; &raCido= i hro o o e , ho>in9that nu lear =a e a;;e t the or9ani ation and =o ition o;

hro o o e (de 'ooijer et al., 200A). 'u lear i e ha al oCeen =ro=o ed to =la8 a role in a o t =e ial a e o;

hro o o e =o itionin9. hro o o e in the retina o; no turnal a al di =la8 an in?erted =attern o =ared>ith other ell ( olo?ei et al., 200A). -n tead o; ha?in9 a=eri=heral =o ition the hetero hro atin e9 ent lo ali ein the nu lear enter, >here the8 =roCaCl8 u==ort the;un tion o; the retinal ell in tran ittin9 the li9ht, C8tran ;or in9 the in?erted nu leu into olle tin9 len e .


10/21

hro o o e territor8 arran9e ent re;le t the linear or9ani ation o; the hro o o e

a ed on the nu lear =o ition o; the telo ere and entroere >e an in;er ;oldin9 =attern o; a hro o o e

a u in9 that inter in9lin9 o; di;;erent hro o o e territorie i aC ent or li ited to the =eri=her8 o; the territor8( ran o and Po Co, 2006D re er et al., 2006). The T o; a

aCl oriented hro o o e ha a tuCe li@e ha=e in >hi hthe hro o o e a"i run ;ro a telo ere at one =ole tothe o==o ite =ole >ith the entro ere and Ca @ to thetelo ere =ole ( i9ure 2). oth ar o; a hro o o e arerunnin9 =arallel in a + ha=e anner >ith their telo ere inrelati?el8 lo e ?i init8. -n to ato nu lei Coth telo ereand entro ere are on a hetero hro atin i land. Thi i=roCa Cl8 due to the a o iation o; the hetero hro atiClo @ around the entro ere and in the uCtelo erire9ion ( a anna and Pra@@en, 1A67DMhon9 et al., 1AAB).

-n &ra Cido= i the T lie Cet>een the nu lear en?elo=eand the nu leolu . The t>o ar are either =arallel in a +

ha=e or lo ate at o==o ite ide o; the entro ere.Thi i >ell illu trated in a T tud8, >here the t>o aro; hro o o e 2 are di;;erentl8 =ainted ( err and

huCert, 2007). -ntere tin9l8, lo e e"a ination o; thei a9e re?eal no inter in9lin9 o; the t>o ar territorie ,re e Clin9 the it uation in a alian ell >heredi;;erent =art o; the a e hro o o e ho> no or little

i"in9 ( iet el et al., 1AABD oet e et al., 2007). i eontain all hro o ere attered alon9 thehro o o e ar ( hen9 et al., 2001). Thi a8 Ce the

rea on >h8 ri e doe not di =la8 di rete hro o enterdurin9 inter=ha e (J#deJ, un=uCli hed data).

#o olo9ou re=eat re9ion rather than ho olo9ouhro o o e a o iate durin9 inter=ha e

The de?elo= ent o; hro o o e =aintin9 in &raCido= iha the a o iation ;reGuen ie o; hro o o e to Ce

onitored. in9 di;;erential =aintin9 o; all ;i?e hro oo e , Pe in@a et al. (2004) re=orted that ide C8 ide

arran9e ent o; heterolo9ou hro o o e territorieo ur rando l8 ;or hro o o e 1, 3 and 5, >hile hro

o o e 2 and 4 a o iate >ith ea h other ore thane"=e ted on the Ca i o; rando 9rou=in9. Thi i

=roCaCl8 due to the =re en e o; the ' >hi h io;ten lo el8 onne ted >ith the nu leolu . The e data

orroCorate the non rando a o iation o; hro o enterthat ontain the ' ( ran et al., 2002) and u==ortthe idea o; K ti @8L hetero hro atin. The hetero hro ati' at hro o o e 2 and 4, >hi h are a==ed

lo e to the di tal telo ere , indeed o lo ali e >iththe =eri entri hetero hro atin that ;lan@ their re =e ti?e entro ere ;or in9 a hro o enter.*oreo?er, ho olo9ou tande l8 re=etiti?e tran 9ene=re;erentiall8 a o iate >ith ea h other and >ithhetero hro atin rather than >ith nor al

eu hro atin re9ion (Pe in@a et al., 2005). The a o iation;reGuen ie , ho>e?er, a8 ?ar8 de=endin9 on on tru t,

hro o o al in ertion =o ition, ell t8=e and the nu Cer and re=etiti?ene o; in ert (Jo?t he? et al., 200B). -n all

a e hetero hro atin a o iation ha Ceen ho>n to Ce

an i =ortant ;a tor in the hi9her le?el or9ani ation o; hro o o e .

#etero hro atin in all 9eno e =lant =e ie i o;tenlu tered into hro o enter

hro o enter are di rete hetero hro atin do ain . The8are ea il8 di tin9ui haCle under the i ro o=e, due to the

har= tran ition to urroundin9 eu hro atin, >hi h =roCaCl8 re;le t the or9ani ation o; hetero hro atin andeu hro atin do ain alon9 the linear hro o o e (deJon9 et al., 1AAA). -n a tud8 o; 67 =lant =e ie ;ro di;;erent ;a ilie e arelli et al. (1AAB) oC er?ed di rete

hro o enter , the nu Cer and i e o; >hi h ?ariedCet>een =lant and durin9 de?elo= ent. -n o t =e iethe a"i u nu Cer o; hro o enter orre =ond to the

hro o o e nu Cer, =ointin9 at one ajor hetero hroati Clo @ =er hro o o e. in e an8 =lant ontaine?eral Clo @ o; hetero hro atin alon9 the linear hro oo e ar , >e an on lude that the e re=eat ri h re9ion

are a o iated >ith ea h other durin9 inter=ha e. *oreo?er,the a?era9e nu Cer o; hro o enter i al>a8 le thanthe hro o o e nu Cer, u99e tin9 that hro o enter o; di;;erent hro o o e are a o iated. Thi i >ell illutrated ;or &raCido= i , >hi h ha on a?era9e ei9ht di tin tand >ell de;ined hro o enter =er nu leu ( ran et al.,

2002). in e di=loid ell in &raCido= i ha?e 10 hro oo e (n N 5), three to ;our hro o enter are 9enerall8a o iated. -ntri9uin9l8, in BBO o; the a o iated hro o

enter the t>o entro ere o; the hro o o e ho> one- # i9nal at the ore o; the hro o enter in tead o; t>oe=arate =ot (P. Pa?lo?a, J. #. de Jon9 and P. . ran ,a9enin9en ni?er it8 e ear h and ni?er it8 o;

& terda , The 'etherland , un=uCli hed data). Thi=oint at the ;u ion o; the t>o hro o enter and

u99e t inti ate onta t Cet>een the orre =ondin9hro o o e territorie . hro o enter in &raCido=iontain the ajor it8 o; the 9eno i re=eat , in ludin9

tran =o on , the tande l8 arra8ed entro eri 1B0 C=re=eat and riCo o al 9ene ( ran et al., 2002).

on eGuentl8, hro o enter are hea?il8 de orated >itht8=i al e=i9eneti ar@ ;or ina ti?e hro atin u h a

'& eth8lation and hi tone #3HA di eth8lation andono eth8lation ( o==e et al.,

2002D Ja en a@o?a et al., 2003D ProC t et al., 2003) Cut al o>ith #3HA e1, #3H27 e1, #3H27 e2 and #4H20 e1(%indroth et al., 2004D *athieu et al., 2005D 'au ann et al.,2005). The re=re i?e ar@ #3H27 e3 i not in hro o

enter , Cut in the urroundin9 9ene ri h eu hro atin,in e it i in?ol?ed in the re=re ion o; 9ene , e =e iall8

9ene a o iated >ith de?elo= ent.


11/21

oe hro o o e territor8 or9ani ation orre =ond>ith 9eno e a ti?it8I

The nu lear or9ani ation o; the T ha i =li ation ;or theuCnu lear lo ation o; 9ene a ti?it8 and the or9ani ation o;

other o =onent in the nu leu . or e"a =le, a =e ieli@e Carle8 ha lar9e hro o o e that ainl8 on i t o; het ero hro atin e9 ent and a all uCtelo erere9ion a o odatin9 o t o; the 9ene . on eGuentl8,a ti?e hro atin and related ole ular ;a tor are lo atedto>ard the telo ere =ole, >herea hetero hro atinrelated ;a tor are =o itioned to>ard the o==o ite =ole.

e=li ation in Carle8 tart in the nu leolar re9ion and=ro eed ;ro telo ere =ole to entro ere =ole,;ollo>in9 the eu hro atin–hetero hro atin a"i(Ja en a@o?a et al., 2001). The di =la e ent o; re=li ationa ti?it8 in the nu leu i di;;erent in &raCido= i >herethe T urround the =eri=heral hro o enter

(Ja en a@o?a et al., 2003). &l o, the di triCution o; re=re i?e e=i9eneti ar@u h a '& eth8lation and #3HA e i di;;erent Cet>een=e ie that di;;er in 9eno e and/or hro o o e i e,

re;le tin9 the di;;erent nu lear =o ition o; a ti?e andina ti?e hro atin. & o =arati?e tud8 o; the di7triCutiono; e=i9eneti ar@ in 24 =lant =e ie re ulted in t>odi;;erent =attern o; hi ton #3HA e2: (i) tron9 #3HA e2re tri ted to on tituti?e hetero hro atin do ain , and(ii) uni;or nu lear di triCution o; #3HA e2 (#ouCen et al.,2003). The di triCution =attern o; #3HA e2 a==ear to

orre =ond to 9eno e i e. =e ie >ith a 9eno e i e

u= to a==ro"i atel8 500 *C ha?e a t8=e 1 =attern,>herea a t8=e 2 =attern i oC er?ed in =e ie >ith alar9er 9eno e. #o>e?er, the linear di triCution o; re=eat

eGuen e al o a;;e t the #3HA e2 =attern, in e ri e(4A0 *C), >ith di =er ed re=eat alon9 the hro o o ear , ho> a rando di triCution >herea i inu

o uni (515 *C), >ith di rete hetero hro atine9 ent , ho> di tin t do ain o; #3HA e2.-n &raCido= i 9ene ri h re9ion ho> e=i9eneti ar@

;or a ti?e hro atin u h a #3H4 e3, hi tonea et8lation ( o==e et al., 2002D Ja en a@o?a et al., 2003)and hi tone ?ariant #2&.M ( eal et al., 2007) Cut al oe=i9eneti ar@ ;or ilent 9ene u h a #3H27 e3

('au ann et al., 2005) and the hetero hro atin =rotein%#P1 (%iCault et al., 2005). -ndeed hro o o e =aintin9>ith 9ene ri h & o?erin9 al o t the entire 9eno e

ho>ed onl8 laCelin9 out ide hro o enter , indi atin9that the ajorit8 o; the &raCido= i 9ene , a ti?e and

ilent, are not in hro o enter ( ran et al., 2006).hether eu hro atin re9ion in other =e ie are al o

e =t8 ;or tran =o on re ain to Ce in?e ti9ated.

hro o o e ha?e a loo= or9ani ation and di =la8lon9 ran9e intera tion

& 9enerall8 a e=ted hara teri ti o; hro o o e or9ani ation i the ;or ation o; loo= tru ture . &ll =uCli hed


12/21

hro o o e odel in lude hro atin loo= on;i9uration at one or the other le?el o; hro o o eor9ani ation (*un@el et al., 1AAAD *ateo %an9era@a etal., 200A). hro atin loo= ha?e Ceen a o iated >ith

e?eral 9eno e ;eature , in =arti ular in the onte"t o; 9ene a ti?it8. hro atin re9ion an loo= out o; a

onden ed re9ion >hen 9ene Ce o e a ti?e, u h athe ho" 9ene in a al ( ha Ce8ron and i @ ore,2004D *ore8 et al.,200A). all loo= u= to 100 @C are ;or ed >hen enhan er and =ro oter =h8 i all8 intera t to ti ulate thee"=re ion o; 9ene u h a the b 9loCin lo u in a

al (Tolhui et al., 2002). The ;or ation o; loo=tru ture ha al o Ceen re=orted in re=re i?eituation and a8 =la8 an i =ortant role in 9eneilen in9. or e"a =le, Pol8 o C 9rou= (P ) o =le"eaintain the ilent tate o; de?elo= ental 9ene re9ion .

+ia lon9 ran9e intera tion , di tant P tar9et anlu ter into do ain o; re =re ed hro atin >hile the

re9ion in Cet>een ;or loo= (Ti>ari et al., 200B).i ilarl8, 9eno i lo i an intera t at the nu lear

la ina, a ;iCrillar net>or@ at the inner ide o; thenu lear e Crane in ani al , 9i?in9 ri e to a re=re i?een?iron ent ;or hro atin ( uelen et al.,200B).

hro atin loo= are di;;i ult to ?i uali e, >ith thee" e= tion o; la =Cru h hro o o e in a =hiCianoo 8te . nl8 >ith - # te hnolo98 and u;;i ient

re olution i it =o iCle to ?i uali e a hro atin loo=tru ture ( ran et al., 2002D 8rd and or e , 2003D

#en9 et al., 2004). -n 9eneral, the =re en e o; loo= idedu ed ?ia indire t e?iden e. or e"a =le, in

&raCido= i the uCtelo eri ' in hro o o ear 2 and 4 o lo ali e >ith their =eri entrihetero hro atin re9ion in hro o enter , >hile the9ene ri h re9ion in Cet>een are lar9el8 out ide the

hro o enter. #en e, the hort ar ;or a loo=tru ture o; a==ro"i atel8 2 *C i; inter ediate eGuen e

are out ide the hro o enter. -n an8 ell , ho>e?er,inter titial lo i al o a o iate >ith hro o enter , 9i?in9ri e to ulti=le aller loo= ( ran et al., 2002). a ed onthe e data the hro o enter loo= odel >a =ro=o edto de riCe the or9ani ation o; a hro o o e territor8 in

&raCido= i ( i9ure 3d): a re=eat ri h hro o enter ;ro>hi h eu hro atin loo= e anate. Thi or9ani ationre;le t the di triCution o; 9ene and re=eat alon9 thelinear hro o o e ar . The hro o o e ar are 9ene

ri h (20–35 =er 100 @C) and ontain ?er8 ;e> tran =o onele ent (;e>er than 5 =er 100 @C), >hile the =eri entro

eri re9ion are 9ene =oor (;e>er than 5 =er 100 @C)( i9ure 4). The loo= or9ani ation i =lie an hor =oint o; eu hro atin loo= to the hro o enter. -n thi ?ie> it ite =tin9 to =e ulate that the ;e> tran =o on alon9 thear a o iate >ith =eri entri re=eat and an hor theeu hro ati loo= to hetero hro atin do ain . -; thi itrue then the di triCution o; tran =o on ele ent alon9 the

hro o o e ar u99e t hro atin loo= i e =annin9


13/21

5 4

5 4

22

(a) (C) ( ) (d)

(e) (;)

(i) (j)

(9) (h)

(@) (l)

i9ure 3. hro o enter loo= or9ani ation han9e in &raCido= i nu lei >ith de onden ed hro atin in ultured =roto=la t .The i a9e (a, C, e, ;, i, j) ho> 4¢,6 dia idino 2 =hen8lindole ( &P-) tained nu lei and ;luore ent in itu h8Cridi ation ( - #) i9nal o; 45 r '& (9reen) and 5r '& (red) 9ene .(a–d) onden ed ituation >ith 45 r '& and 5 r '& o lo ali ed in hro o enter 4. hro o o e territor8 (d) ho> a t8=i al hro o enter loo= arran9e ento; re=eat ( olored) and eu hro atin loo= (li9ht 9ra8).(e–h) e onden ed ituation >ith ;e>er and aller hro o enter . The uCtelo eri 45 r '& and =eri entri 5 r '& lo i o; hro o o e 4 are nolon9er o lo ali in9. on eGuentl8, the 45 r '& doe not ;or a loo= an8 ore.(i–l) ull8 de onden ed hro o enter . nl8 the lon9 re=eat arra8 o; 45 r '& 9ene o; hro o o e 2 and 4 re ain =artiall8 onden ed and o lo ali e to onedo ain, Clue, entro ere re=eat, 9reen, 45 r '&, red, 5 r '&, =ur=le, tran =o on .

4035

30

25

20

15

10

5

00 20 40 60 B0 100 120 140 160 1B0

Po ition in 100 @C

i9ure 4. atter =lot ho>in9 the di triCution o; 9ene (Clue) and tran =o on (T$ , =in@) alon9 the linear hro o o e 4 o; &raCido= i . The riCo o al 9ene at the uCtelo eri end o; the hort ar are not in luded (data ;ro ;t=://araCido =i .or9).

100 @C to 2 *C, >hi h orre =ond to the - # data oninter=ha e nu lei o; &raCido= i ( ran et al., 2002).

%oo= tru ture i =l8 inti ate a o iation Cet>eendi tant lo i >ithout the in?ol?e ent o; inter?enin9

eGuen e . The hro o o e on;or ation a=ture (3 )te hnolo98 i a =o>er;ul tool ;or tud8in9 hro atin loo=;or ation, in e it identi;ie =h8 i al a o iation Cet>eendi tant lo i throu9hout the 9eno e ( e@@er et al., 2002DTolhui et al., 2002). The te hniGue i Ca ed on ro lin@

in9 intera tin9 or adja ent hro atin =rotein o =le"eC8 ;or aldeh8de ;i"ation, ;ollo>ed C8 uttin9 the '&

trand >ith re tri tion en 8 e and li9atin9 their ;reeend . The eGuen e o; li9ated '& ;ra9 ent re=re entt>o lo i that are =h8 i all8 a o iated in the =rotein

o =le". The read in lude =ro"i al and di tant 9eno ilo i. The 3 Ca ed te hniGue ha?e Ceen >idel8 ado=tedto in?e ti9ate not onl8 loo= and lon9 ran9e intera tionCut al o the lar9e ale ;oldin9 =attern o; hro atin

' u 5

C e r o

; 9 e n e 7 a n

d

T $ 7 = e r

1 0 0 @ C


14/21

( ull>ood and uan, 200AD %ieCer an &iden et al., 200A,Pal tra, 200A).

e entl8, the 3 te hniGue ha Ceen a==lied u e ;ull8in =lant to re?eal hro atin loo=in9 at the C1 lo u in

ai e (%ou>er et al., 200A). The C1 9ene, in?ol?ed in red

=i9 entation o; hu @ lea?e and other ti ue, i re9ulatedC8 a et o; e?en tande re=eat lo ated a==ro"i atel8100 @Cu= trea o; the C1 9ene. The re=eat ;un tion a atran ri=tional enhan er. #o>e?er, the ole ular e hani underl8in9 the e;;e t o; the re=eat on the C1 9ene>a not lear. in9 3 te hnolo98 the authorde on trated a =h8 i al intera tion Cet>een there9ulator8 re=eat and the C1 9ene. -n addition, aninter ediate eGuen e al o a==eared to Ce in?ol?ed inthe re9ulation o; C1. The re ult denote a ultiloo=

tru ture reGuired to in rea e the e"=re ion o; the C19ene.

#o> hro atin ite are tethered to one =la e and held

to9ether to ;or a loo= tru ture i till an unan >eredGue tion in ell Ciolo98. #o>e?er, tron9 e?iden e i no>a?ailaCle to indi ate that the nu lear atri" and a o iated

eGuen e =la8 a ajor role in loo= ;or ation. The nu lear atri" ha Ceen =ro=o ed a a hi9hl8 d8na i net>or@ o;

=rotein that intera t >ith hro atin to ;a ilitate do aino; lo al a ti?it8 or re=re ion. io he i all8, the nu lear

atri" i de;ined a the ;ra tion that re ain a;ter hi9halt e"tra tion, >hile the nu leo o e tru ture i di ru=ted.

The eGuen e that o =uri;8 >ith atri" =rotein are &Tri h and are ter ed the atri" atta h ent re9ion(*& ) or a;;old atta h ent re9ion ( & ). *& / &

o lo ali e >ith in ulator u h a the 98= 8 ele ent('aCiro h@in et al., 1AAB) and T Cindin9 eGuen e( unn et al.,2003), Coth o; >hi h ediate 9eno i intera tion ?iaa o iation >ith di tant eGuen e and ;or loo= truture . & a on eGuen e the re9ion in ide the loo= i

hielded ;ro the in;luen e o; ;lan@in9 hro atineGuen e . T i a ulti in ;in9er tran ri=tion ;a tor

that i @no>n to Clo @ enhan er a ti?it8 on hu an 9eneC8 Cindin9 to tar9et eGuen e in Cet>een the enhan er and the 9ene. e entl8, T ha Ceen ho>n tore ruit ohe in, >hi h i reGuired ;or i ter hro atid

ohe ion, to tar9et hro atin ite ( endt et al., 200BD

#adjur et al.,200AD 'ati?io et al., 200A). -t i =ro=o ed that the T –

ohe in o =le" onne t t>o '& eGuen e and taCili e a loo= tru ture.

& la t ear h did not re?eal T li@e=rotein in &raCido= i (#e9er et al., 200A). #o>e?er, the a tion o; the=lant tran ri=tion ;a tor & **$T - %$&+$ 1 (& 1)and & 2 in ilen in9 the H' ! 9ene re e Cle the Ta tion in hu an ell . The & 1–& 2 o =le" Cind to t>o

=e i;i eGuen e in the H' ! =ro oter to ;or a loo=tru ture that re=re e H' ! e"=re ion durin9 lea;

de?elo= ent ( uo et al., 200B). The intera tion in?ol?e

the hro atin re odelin9 ;a tor #- &. i ilarl8, Ta tion in?ol?e &TP de=endent hro atin re odelin9


15/21

;a tor ( u et al., 200B). #ere T =ro?ide an an hor =oint;or nu leo o e =o itionin9, thu lin@in9 t>o le?el o;

hro atin or9ani ation (nu leo o e and loo= ). in eT Cindin9 i en iti?e to '& eth8lation and '&eth8lation i dire ted C8 nu leo o e o u=an 8, it ;ollo>7

that hro atin loo=in9 i ontrolled C8 nu leo o e =o itionin9, >hi h in turn i re9ulated C8 '& eGuen e ande=i9eneti odi;i ation .

'&*- -' # *&T-' *P& T- '

e onden ation and re onden ation o; hetero hro atindo ain

hro o enter re=re ent the do ain o; one or ore hetero hro atin Clo @ and an Ce ?i uali ed >ith 4¢,6dia i dino 2 =hen8lindole ( &P-) and Candin9.

& ordin9 to ro>n (1A66) the8 ontain on tituti?ehetero hro atin, >hi h re ain onden ed throu9houtthe ell 8 le. &ra Cido= i hro o enter are the

Cand =o iti?e do ain (& Cro and h>ei er, 1A76) andare there;ore on idered on tituti?e hetero hro atin.#o>e?er, >hen di;;erentiated e o=h8ll ell aretran ;or ed into =roto=la t and Crou9ht into ulture,lar9e ale de onden ation o; hetero hro atin do aino ur in the ajorit8 o; nu lei a;ter a ;e> hour(Te adori et al., 2007a). The =ro e i a o =anied C8de onden ation o; all ajor re=eat arra8 >ith ade o =a tion rate u= to 14 ti e . $?en the tande l8

arran9ed entro eri 1B0 C= re=eat re9ion under9o dra tide onden ation. The =heno enon i re ini ent o; theK hort la tin9 di =er ion =ha eL >here all hetero hro atindi a==ear in the nu lei ( arlo>, 1A76). The e data u99e tthat on tituti?e hetero hro atin i not a =er anentl8

onden ed a >e a u ed ( i9ure 3). -; >e on ider ade9ree o; o =a tion ;or hetero hro atin do ain o;

a==ro"i atel8 1 *C l ) 1 ( ran et al., 2002), then in =ro

to=la t it an un;old to aCout 71 @C l ) 1, >hi h ;all>ithin the o =a tion ran9e o; the 30 n ;iCer (70–160 @Cl ) 1). & i ilar le?el o; o =a tion >a onitored ;or

o e eu hro atin re9ion in lea; nu lei. &==arentl8, allhro atin in a ell an ado=t di;;erent de9ree o; o =a tion ;ro the hi9hl8 onden ed eta=ha e (16

*C l ) 1) do>n to the le?el o; the 30 n ;iCer inde onden ed inter=ha e hro atin o; =roto=la t (70 @Cl ) 1). %ar9e ale de o =a tion o; hro atin i ,ho>e?er, not re tri ted to =roto=la t , in e i ilar oC er?ation o; hetero hro atin de onden ationalthou9h le =ronoun ed >ere ;ound durin9 de?elo= ental han9e u h a eedlin9 de?elo= ent (*athieuet al., 2003) and the ;loral tran ition (Te adori et al., 2007C),Cut al o in utant that a;;e t hro atin re odelin9 u h athe '& eth8lation utant dd 1, an &TP de=endent

hro atin re odeler, et1, a '& eth8ltran ;era e( o==e et al., 2002), and hda6, a hi tone dea et8la e (ProC tet al., 2004). The dd 1–5 utant, >hi h la @ dete taClele?el o; *1 tran ri=t di =la8 a e?ere hro atin


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=henot8=e, in >hi h all =eri entri hetero hro atin in ludin9 the 1B0 C= entro ere re=eat i de onden ed (*ittel

ten heid et al., 2002D ProC t et al., 2003). -t indi atethe i =ortant role o; the hro atin re odeler *1 in the;or ation o; hetero hro atin do ain . e entl8, hro atin

de onden ation ha Ceen oC er?ed under Cioti and aCiotitre ituation u h a Ca terial in;e tion (Pa?et et al.,2006), lo> li9ht (Te adori et al., 200AD ?an Manten et al.,2010a) and hi9h te =erature (Pe in@a et al., 2010). Thedata u99e t that lar9e ale hro atin de o =a tiona o =anie han9e in the nu lear =ro9ra inre =on e to a de?elo= ental tran ition or (a)Cioti

tre ondition . *oreo?er, hro atin de o =a tion i are?er iCle =ro e . hro o enter re on titution o ur>ithin a ;e> da8 or u=on re?er ion to the ori9inal

ituation. Thi i >ell illu trated in a lo> li9hte"=eri ent >here 3 >ee@ old =lant >ere de=ri?ed ;ro

nor al li9ht le?el (200 l ol ) 2 e ) 1), C8 tran ;errin9

to 15 l ol ) 2 e ) 1 ;or 4 da8 and returned to nor alli9ht ondition (?an Manten et al.,2010a). The =er enta9e o; nu lei >ith nor al hetero hro

atin ontent de rea ed ;ro B0 to 10O, in ;a?or o; aredu ed hetero hro atin =henot8=e, and returned to B0Oa;ter in rea in9 the li9ht to nor al ondition . &==arentl8,lar9e ale de onden ation i a tran ient tate o; hro

atin in re =on e to han9in9 ondition . -ntere tin9l8,re ;or ation o; hro o enter o ur ?ia a =ro e o;

eGuential te= , in >hi h the lon9e t arra8 o; tandere=eat (45 r '& 9ene ) are ;ir t onden ed, ;ollo>ed C8

aller tande arra8 ( entro ere re=eat and 5 r '&

9ene ) and ;inall8 the di =er ed tran =o on ele ent(Te adori et al., 2007a). -t u99e t that the re=eat len9thi an i =ortant ;a tor in hro o enter ;or ation.

%i9ht a;;e t hro atin o =a tion

%i9ht indu ed hro atin (de) o =a tion i ontrolled ?iar8=to hro e ( ) and =h8to hro e (P# ) =hotore e=

tor , in e their utant di =la8 no or li ited redu tion o; hetero hro atin under lo> li9ht tre (?an Manten etal.,2010a). The author u99e t that taCili ation o; 2 in lo>li9ht tri99er hro atin de onden ation. & i ilar role ;or

2 >a =ro=o ed durin9 the ;loral tran ition (Te adoriet al., 2007C). oth oC er?ation u99e t a relati?el8 hort

i9nalin9 =ath>a8, in e the Clue li9ht =hotore e=tor ion tituti?el8 lo ated in ide the nu leu ( uo et al., 1AAA).

*oreo?er, 2 i a o iated >ith hro atin ( utler et al.,2000) and intera t >ith - 1, a tran ri=tion ;a tor, >hi hCind to =ro oter eGuen e (%iu et al., 200B). -n addition,

2 re=re e the P1/ $T/ =hoto or=ho9ene io =le" ?ia the -' ;in9er uCiGuitin li9a e P1 ( an9

et al., 2001). -ntere tin9l8, the $T1 o =onent Cind to thenon a et8lated ' ter inal tail o; the ore hi tone #2 andi u==o ed to ;a ilitate a onden ed tate o; hro atin

( en?enuto et al., 2002). a ed on the e ;indin9 it i u99e ted that the =hotore e=tor ontrol hro atin o =a


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tion ?ia a hro atin =rotein o =le" (Te adori et al.,2007CD ?an Manten et al., 2010a) that a8 ontain

e Cer o; $3 li9a e o =le"e u h a P1, >hi hintera t >ith nu lear =hotore e=tor ( i and en9, 2005).The hro atin =rotein o =le" a8 al o ontain# &6, >hi h i al o in?ol?ed in li9ht re9ulated

hro atin o =a tion (Te a dori et al., 200A).

- hro atin o =a tion inde=endent o; e=i9enetiar@ I

han9e in hro atin are 9enerall8 a o =anied C8 e=i9eneti han9e in hi tone ar@ or '& eth8lation.

ur=ri in9l8, no lar9e ale alteration in #3HA e2 or 5 eth8l 8to ine >a oC er?ed durin9 hro atinde on den ation in =roto=la t (Te adori et al., 2007a),

u99e t in9 that hro atin o =a tion andde onden ation an o ur inde=endentl8 o; the e ar@ .

e entl8, three tudie ;ro di;;erent laC ha?e ho>nthat heat tre to &raCid o= i =lant rea ti?ate ilent

tran ri=tional ele ent >ith no or little alteration o; e=i9eneti ar@ ;or ilen in9 (%an9 *lade@ et al., 2010DPe in@a et al., 2010D Tittel $l er et al.,2010). -n all a e the a ti?ation o; tran 9ene andendo9e nou re=eat ele ent o urred >ithout lo o;

'& eth 8lation. -n addition, #3HA e2, #3H27 e2and #3H27 e3 re ained una;;e ted (Tittel $l er et al.,2010), >hile hi tone a et8lation in rea ed. tri@in9l8, thein rea e o; 9ene a ti? it8 C8 heat tre >a a o =aniedC8 lo o; hro o enter or9ani ation and de onden ation

o; hro atin. *oreo?er, a dra ati lo o; hi tone #3 and#4 >a oC er?ed, indi atin9 de=letion o; nu leo o e(%an9 *lade@ et al., 2010D Pe in@a et al., 2010). i ilar tothe lo> li9ht re =on e, the heat indu ed tate ire?er iCle, in e re o?er8 ;ro the heat tre re ult inre toration o; nu leo o e loadin9 and 9ene ilen in9.The e data u99e t that en?iron ental ondition ano?errule e=i9eneti ontrol o; 9ene a ti?it8, at lea ttran ientl8. The heat tre re =on e a8 Ce on idered a a

ole ular e hani >ith dire t ontrol o?er nu leo o e=o itionin9 >ithout i9ni;i ant inter;eren e o; e=i9enetire9ulator8 ;a tor .

e entl8 it ha Ceen ho>n that te =erature re9ulated9ene e"=re ion i ontrolled C8 the hi tone ?ariant#2&.M (Hu ar and i99e, 2010). &t lo> te =erature(17 ° ) #2&.M nu leo o e are Cound ju t do>n treao; the T in an8 a ti?e and ina ti?e 9ene o;

&raCido= i . -n thi ituation the tran ri=tional a ti?it8 o; a 9ene re ain un han9ed. ai in9 the te =erature to

27°

re ult in ther al in taCilit8 at the #2&.Mnu leo o e, leadin9 to a de rea e in #2&.M o u=an 8 atthe T and a han9e in 9ene a ti?it8. Thi o ur inte =erature re =on i?e 9ene u h a the T 9ene, >hi hi in?ol?ed in ;lo>erin9 ti e. Plant de;i ient in & P6, a

o =onent o; the 1 re odelin9 o =le", >hi he taCli he #2&.M de=o ition, are unaCle to re =ond tote =erature han9e , Ce au e the nu leo o e ontainthe anoni al hi tone #2&. -n the a e tud8 i ilar re ult >ere oCtained >ith


18/21

. ere?i iae. The data i =l8 that #2&.M nu leo o eediate the ther o en or8 re =on e in Coth =lant and

8ea t. o =ared >ith '& at nu leo o e ontainin9#2&, the '& at #2&.M nu leo o e i ore ti9htl8>ra==ed, Cut in a te =erature de=endent >a8. Thi

allo> a dire t e hani ;or hro atin to re =ond tote =erature ;lu tuation .-t i not lear i; there i a au al relation hi= Cet>een the

lo o; nu leo o e ;ro indi?idual tran ri=tion ele entand the lar9e ale de onden ation o; hro atin in?ol?in9entire hetero hro atin do ain . The t>o le?el o; hro atin or9ani ation are =h8 i all8 onne ted, Cut not ne e aril8 au all8 related. The re o?er8 o; the heat ho @did notlead to hetero hro atin re o =a tion (Pe in@a et al.,2010), >hile li9ht indu ed de onden ation o;

hro o enter did not han9e nu leo o e den it8 inre=eat re9ion (?an Manten et al., 2010C).

ell in a al are le re =on i?e to en?iron ental

han9e o =ared >ith =lant . et, >e a8 ;ind aneGui?alent o; hro o enter re ;or ation in ell di;;erentiation durin9 ajor de?elo= ental >it he . or e"a =le,;ollo>in9 the ;ertili ation o; the ou e e99 there i ad8na i reor9ani ation o; hetero hro atin do ain >ith

o =lete aC en e o; hro o enter . The han9ed on;i9uration in?ol?e the ajor and inor atellite re=eat ,>hi h a= to the =eri entro ere and entro ere re9ion,re =e ti?el8 (ProC t et al., 2007). e ;or ation o; hro o

enter tart in the t>o ell ta9e e Cr8o. -ntri9uin9l8,re onden ation o; the =eri entri hetero hro atin i a o

iated >ith tran ri=tional a ti?it8 o; the ajor atellite

re=eat (ProC t et al., 2010). *oreo?er, tran ri=tion o; the re=eat o ur e"a tl8 >hen hro o enter are Cein9;or ed and are e ential ;or =ro=er de?elo= ent o; the

ou e e Cr8o.

' % - ' &' P$ P$ T-+$

$u@ar8oti or9ani ha?e their 9eneti and e=i9enetiin;or ation tored in a =ol8 er on tru tion o; nu leo

o e that i ontinuou l8 eetin9 nu erou di;;erent=rotein o =le"e . The e intera t >ith the 9eno ieGuen e to =rote t, re=air and re=li ate the '& or to

retrie?e the orre t in;or ation at the =ro=er ti e and inthe ri9ht =la e. The Ca i o =onent u h a hi tone ,

hro atin odi;ier and other hro atin =rotein arehi9hl8 on er?ed a on9 all eu@ar8ote . The a e hold true;or the ole ular e hani that rule the a e iCilit8 o; the '& eGuen e. Thi i e"e =li;ied C8 the nu leo o etru ture, nu leo o e =o itionin9 and hi9her order ;oldin9=attern o; hro atin u h a loo= ;or ation, Cut al o the

nu leo o e ontrolled '& eth8lation in &raCido= i andhu an ell . The =re i e Ciolo9i al eanin9 o; lar9e ale

hro atin de o =a tion in =lant re ain to Ceelu idated, Cut i =roCaCl8 related to the reor9ani ation o;

hro atin and the rearran9e ent o; '& a e iCilit8 inre =on e to a de?el

o= ental >it h or a tre ituation. in e =lant aree ile or9ani and annot e a=e ;ro han9in9

en?iron ental ondition the8 u t re =ond in a ra=idand adeGuate >a8 ?ia the nu lear =ro9ra . hro atinde onden ation a8 Ce =art o; the e hani that ;a ili

tate u h a re =on e.i;;eren e in nu lear or9ani ation o; hro o o eCet>een or9ani are deter ined C8 9eno i eGuen e,Cut al o C8 9eno e i e and the di triCution o; re=eat and9ene alon9 the linear eGuen e. hro atin i hi9hl8d8na i at di;;erent le?el o; or9ani ation. #o> the di;;erent

on;i9uration , u h a loo= tru ture , relate >ith 9eno ea ti?it8 i urrentl8 Cein9 in?e ti9ated >ith di;;erent te hniGue . The de?elo= ent o; hro atin i uno=re i=itation eGuen in9 ( h-P eG), 3 and related ethod , in

o Cination >ith a i?e =arallel eGuen in9 te hnolo98enaCle u to anal8 e at a 9eno e >ide ale hro atin=ro;ile , lon9 ran9e hro atin intera tion and hro o

o e ;oldin9 =attern in lar9e 9eno e or9ani(%ieCer an &iden et al., 200A). The hu9e data et reGuiree"ten i?e Cioin;or ati tool in order to e;;i ientl8tran ;or data into in;or ation and uC eGuentl8 into

odel in order to ;ull8 under tand the tru ture–;un tionrelation o; hro o o e .

& H' %$ $*$'T

e >i h to a @no>led9e oP

ra ina8, !ian>en Ji, %a@ anaHanta a, Pen@a Pa?lo?a and ederi o Te adori ;or =ro?idin9 thei a9e o; Carle8, to ato, ri e and &raCido= i .

$ $ $' $

& Cro , P. and h>ei er, . (1A76) The ie a Canded @ar8ot8=e o; &raCido= i thaliana. &raCido= i -n;or . er?. 13, 167–171.

&nder on, J. ., %o>ar8, P.T. and ido , J. (2001) $;;e t o; hi tone a et8lation on the eGuiliCriu a e iCilit8 o; nu leo o al '& tar9et ite .J. *ol. iol. 307, A77–AB5.

&nder on, ., $nroth, ., ada -9le ia , &., adeliu , . and Ho oro> @i, J.(200A) 'u leo o e are >ell =o itioned in e"on and arr8

hara teri ti hi tone odi;i ation . eno e e . 1A,1732–1741. &ra9on &l aide, %., eader, ., e?en, &., ha>, P., *iller, T. and *oore, .

(1AA7) & o iation o; ho olo9ou hro o o e durin9 ;loral de?elo=ent. urr. iol. 7, A05–A0B.

&r8a, . and hli @, T. (2006) ole o; hi tone tail in hro atin ;oldin9re?ealed C8 a e o o=i oli9onu leo o e odel. Pro . 'atl & ad.

i. &, 103, 16236–16241. &r8a, . and hli @, T. (200A) & Tale o; Tail : #o> #i tone Tail *ediate

hro atin o =a tion in i;;erent alt and %in@er #i tone $n?iron ent .J. Ph8 . he . 113, 4045–405A.

&the8, . ., ith, *. ., an@ert, .&., illia , .P. and %an9 ore, J.P.(1AA0) the dia eter o; ;ro en h8drated hro atin ;iCer in rea e >ith

'& lin@er len9th: e?iden e in u==ort o; ?ariaCle dia eter odel ;or hro atin. J. ell iol. 111, 7A5–B06.

arlo>, P. (1A76) The relation hi= o; the di =er ion =ha e o; hro oentri nu lei in the itoti 8 le to '& 8nthe i . Proto=la a, A0, 3B1–

3A2.ednar, J., #oro>it , .&., ri9or8e?, .&., arruther , %.*., #an en, J. .,

Ho ter, &.J. and ood o @, .-. (1AAB)'u leo o e , lin@er '&, and lin@er hi tone ;or a uniGue tru tural oti; that dire t the hi9her order ;oldin9 and o =a tion o; hro atin. Pro . 'atl & ad. i. &, A5,14173–1417B.

en?enuto, ., or i99ini, ., %a;la e, P., *ala@ho?, *. and o>ler, .(2002) The =hoto or=ho9ene i re9ulator $T1 Cind the a ino ter inaltail o; hi tone #2 in a nu leo o e onte"t. urr. iol. 12, 152A–1534.


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err, &. and huCert, -. (2007) -nter=ha e hro o o e arran9e ent in &raCido= i thaliana i i ilar in di;;erentiated and eri te ati ti ueand ho> a tran ient irror 8 etr8 a;ter nu lear di?i ion.

eneti ,176, B53–B63.

err, &., Pe in@a, &., *ei ter, &., Hreth, ., u h , J., lattner, . ., %8 a@,*.&. and huCert, -. (2006) hro o o e arran9e ent and nu lear

ar hite ture Cut not entro eri eGuen e are on er?ed Cet>een &raCido= i thaliana and &raCido= i l8rata. Plant J. 4B, 771–7B3.o?eri, T. (1A0A) ie la to eren@erne ?on & ari e9alo e=hala und dieTheorie der hro o o enindi?idualitat. &r h. Mell;or h. 3, 1B1–26B.

ran o, *. . and Po Co, &. (2006) -nter in9lin9 o; hro o o e territoriein inter=ha e u99e t role in tran lo ation and tran ri=tion de=endenta o iation . P%o iol. 4, e13B.

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e@@er, J., i==e, H., e@@er, *. and Hle @ner, '. (2002) a=turin9 hro oo e on;or ation. ien e, 2A5, 1306–1311.

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