Functional Analysis of Plant Cis Elements

download Functional Analysis of Plant Cis Elements

of 50

Transcript of Functional Analysis of Plant Cis Elements

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    1/50

    *HQHWLF(QJLQHHULQJ9ROXPH(GLWHGE\-.6HWORZ

    .OXZHU$FDGHPLF3OHQXP3XEOLVKHUVSS

    )81&7,21$/$1$/

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    2/50

    LQFOXGHG\QDPLFIHHGEDFNORRSVWKDWSURYLGHIRUIXUWKHUUHJXODWLRQRIWKHQHWZRUN

    DUFKLWHFWXUHDQGRXWSXW

    &HQWUDOWRVSHFLILFDFWLYDWLRQDUH'1$UHFRJQLWLRQVHTXHQFHVZKLFKLQWHUDFWZLWK

    EDVLFWUDQVFULSWLRQLQLWLDWLRQFRPSOH[HVDQGQXPHURXVWUDQVFULSWLRQIDFWRUV,QSODQWV

    WKHVHDUH XVXDOO\IODQNLQJPRGXOHVWKDWLQFOXGHDFRUHSURPRWHUSUR[LPDOUHJXODWRU\

    HOHPHQWVDQGXSVWUHDPHQKDQFHUVHTXHQFHVORFDWHGFORVHWRWKHVWUXFWXUDOSRUWLRQRIWKH

    JHQH5HJXODWRU\HOHPHQWVFDQRIWHQEHSRVLWLRQHGTXLWHIDUIURPWKHWUDQVFULSWLRQ

    LQLWLDWLRQVLWH7,6LQPDPPDOLDQJHQRPHVZKHUHDVLQ\HDVWDQGSODQWVWKH\DUHORFDWHG

    ZLWKLQDIHZWKRXVDQGVEDVHSDLUVRIWKH7,6

    7KHFRQWUROUHJLRQVRISODQWJHQHVPD\LQFOXGHPXOWLSOHFLVDFWLQJHOHPHQWVWKDW

    FRQWULEXWHWRWKHFRPSOH[H[SUHVVLRQ SURILOHRIWKDWSDUWLFXODUJHQH0RUHRYHUWKHVDPH

    WUDQVFULSWLRQIDFWRUVFDQDFWDVDFWLYDWRUVRUUHSUHVVRUVGHSHQGLQJRQWKHLUFRQFHQWUDWLRQ

    DQGWKHSUHVHQFHRILQWHUDFWLQJSDUWQHUSURWHLQV(DUOLHULQWKH*HQHWLF(QJLQHHULQJ

    VHULHV*XLOIR\OHSXEOLVKHGDQH[FHOOHQWUHYLHZIRFXVHGRQWKHEDVLFVWUXFWXUHRISODQW

    SURPRWHUVDQGWKHFRQVHUYDWLRQRIVSHFLILFFLVDFWLQJHOHPHQWVZLWKLQSURPRWHUVWKDW

    UHVSRQGVLPLODUO\:KLOHPDQ\RIWKHVHUHJXODWRU\HOHPHQWVDUHZHOOGHILQHGWRGD\WKHUH

    LVOLWWOHORJLFDSSDUHQWLQWKHRUJDQL]DWLRQRIPXOWLSOHUHJXODWRU\HOHPHQWVDQGHYHQOHVV

    LQWKHZD\WKDWWKH\LQWHUDFWWRUHJXODWHJHQHH[SUHVVLRQ7KHUHIRUHWKLVFKDSWHULVDLPHG

    DWLOOXVWUDWLQJWKHGLYHUVLW\DQGLQWULFDFLHVRISODQWUHJXODWRU\VHTXHQFHVDQGKLJKOLJKWLQJ

    KRZWKHLULQWHUDFWLRQVJRYHUQWKHVWUXFWXUDODQGIXQFWLRQDOLQWHUSOD\RIVLJQDOSHUFHSWLRQ

    SDWKZD\V:HDOVRDWWHPSWWRSURYLGHDGHHSHULQVLJKWLQWRWKHUHJXODWRU\IXQFWLRQRI$7

    ULFKVHTXHQFHVIRXQGLQSODQWSURPRWHUV

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    3/50

    75$16&5,37,21$/$&7,9,7< ,13/$1718&/(86

    7KHHXNDU\RWLFQXFOHXVFRQWDLQVWKUHHGLIIHUHQWFODVVHVRI51$SRO\PHUDVHVSRO

    51$SRO,LVUHVSRQVLEOHIRUWKHWUDQVFULSWLRQRIULERVRPDO'1$JHQHVDQGLVDFWLYHRQO\

    LQWKHQXFOHROXVUHJLRQ51$SRO,,WUDQVFULEHVDOOSURWHLQHQFRGLQJJHQHVDQGVHYHUDO

    VPDOOQXFOHDU51$VZKLOH51$SRO,,,WUDQVFULEHV6ULERVRPDO51$JHQHVWUDQVIHU

    51$JHQHVDQGVRPHVPDOOQXFOHDU51$V7KHUHLVVWURQJHYLGHQFHWKDWIXQFWLRQDO

    VHSDUDWLRQEHWZHHQDOOWKUHHPDMRUFODVVHVRISRO\PHUDVHVLVIXUWKHUHQKDQFHGE\VSDWLDO

    FRPSDUWPHQWDOL]DWLRQRIWKHLUDFWLYLW\LQWKHGLIIHUHQWGRPDLQVRIWKHHXNDU\RWLFQXFOHXV

    3ODQWJHQHVWUDQVFULEHGE\51$SRO,,W\SLFDOO\FRQWDLQFRPPRQFRUHHOHPHQWV

    UHFRJQL]HGE\JHQHUDOWUDQVFULSWLRQIDFWRUVDQGJHQHVSHFLILF'1$HOHPHQWVUHFRJQL]HG

    E\UHJXODWRU\IDFWRUVZKLFKLQWXUQPRGXODWHWKHIXQFWLRQRIWKHJHQHUDOLQLWLDWLRQIDFWRUV

    7KHDYDLODELOLW\RIZKROHJHQRPHGDWDDQGVRSKLVWLFDWHGPLFURDUUD\WHFKQRORJ\KDV

    RSHQHGXSQHZDYHQXHVIRUWKHDQDO\VLVRIJHQHUHJXODWLRQDQGH[SUHVVLRQ8QUDYHOLQJ

    WKHUHJXODWRU\QHWZRUNVWKDWLQIOXHQFHH[SUHVVLRQRIDJLYHQJHQHRUJHQHIDPLO\LV

    W\SLFDOO\EDVHGRQWKHDSULRULDVVXPSWLRQWKDWFRUHJXODWHGJHQHVXVXDOO\KDYHFRPPRQ

    UHJXODWRU\HOHPHQWV)XQFWLRQDOGLVVHFWLRQRIWKHSURPRWHUUHJLRQXVXDOO\UHTXLUHV

    LGHQWLILFDWLRQDQGFKDUDFWHUL]DWLRQRIDPLQLPDOSURPRWHUORFDWLRQRIWKHSXWDWLYHELQGLQJ

    VLWHVRINQRZQDQGXQNQRZQWUDQVFULSWLRQIDFWRUVDQGVRUWLQJRXWWKHHIIHFWVRIGLVWDQW

    HQKDQFHU DQGUHSUHVVRUOLNHPRGXOHV/RFDOFKURPDWLQVWDWHVDQGWKHDYDLODELOLW\RI

    VFDIIROGDWWDFKPHQWUHJLRQVDQG'1$PHWK\ODWLRQVLWHVPD\IXUWKHUFRQWULEXWHWRWKH

    DFWLYLW\RIWKHIODQNLQJUHJLRQ

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    4/50

    7KHSULPDU\VWUDWHJ\IRUWKHIXQFWLRQDODQDO\VLVRIDQ\SURPRWHULVDFRPSXWHU

    DVVLVWHGVFDQRYHUWKHHQWLUHVHTXHQFHE\DFRQVHQVXVDSSURDFKZKLFKUHOLHVRQNQRZQRU

    FRQVHUYHG'1$HOHPHQWV7KLVLVJHQHUDOO\DFKLHYHGE\TXHU\LQJWKHVHTXHQFHRILQWHUHVW

    DJDLQVWWKHUHIHUHQWLDOGDWDEDVHVXVLQJVFDQQLQJVRIWZDUHWKDWGRHVQRWUHTXLUHGRZQORDG

    DQGLQVWDOODWLRQ7DEOH7KLVLQIRUPDWLRQDOORZVSUHOLPLQDU\DVVHVVPHQWRISURPRWHU

    VWUHQJWKVSHFLILFLW\DQGUHJXODWLRQ6XEVHTXHQWO\DVHULHVRIZHWODEH[SHULPHQWVPXVW

    EHSHUIRUPHGWRGLVVHFWWKHLQGLYLGXDODQGFRPELQDWRULDODFWLYLWLHVRIWKHSXWD WLYHPRWLIV

    ERWKLQ YLWUR DQGLQYLYRVHHEHORZIRUUHFHQWUHSRUWVDQGUHIHUHQFHV

    D SURPRWHUIXVLRQWRDUHSRUWHUJHQH

    D IXVLRQWRDPLQLPDOSURPRWHU

    D WUDQVLHQWRUVWDEOHH[SUHVVLRQDVVD\

    D SURPRWHUGHOHWLRQDQGEDVHVXEVWLWXWLRQ

    D LQVHUWLRQDOPXWDJHQHVLV

    D OLQNHUVFDQQLQJPXWDJHQHVLV

    D KLJKWKURXJKSXW6(/(;6$*(

    D RQHK\EULG\HDVWV\VWHP

    D '1$SURWHLQFURVVOLQNLQJ

    D HOHFWURSKRUHVLVPRELOLW\VKLIWDVVD\

    D SULPHUH[WHQVLRQ

    D '1DVH,IRRWSULQWLQJ

    D 51DVHSURWHFWLRQDVVD\

    D LQYLWUR WUDQVFULSWLRQV\VWHPV

    &25(352027(5

    (XNDU\RWLFWUDQVFULSWLRQLVUHJXODWHGE\WZRPDLQFODVVHVRIWUDQVFULSWLRQIDFWRUV

    JHQHUDOWUDQVFULSWLRQIDFWRUV*7)VDQGVHTXHQFHVSHFLILFWUDQVFULSWLRQIDFWRUVUHYLHZHG

    LQ*7)VELQGWRWKHFRUHSURPRWHUFORVHWRWKH7,6DQGWRJHWKHUZLWK51$SRO,,

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    5/50

    DVVHPEOHLQDQRUGHUHGIDVKLRQWRIRUPWKHSUHLQLWLDWLRQFRPSOH[,WKDVEHHQVXJJHVWHG

    WKDWDSSUR[LPDWHO\RIWKHJHQHVRI$UDELGRSVLV HQFRGHIRUWUDQVFULSWLRQUHODWHG

    SURWHLQVFRPSULVLQJPRUHWKDQWUDQVFULSWLRQIDFWRUVRIZKLFKDUHVSHFLILFWR

    SODQWV$ERXWRQHWKLUGRIDOOSODQWJHQHVDUHH[SUHVVHGWKURXJKRXWWKHHQWLUHSODQW

    DOEHLWDWYDULDEOHOHYHOV$QRWKHURQHWKLUGPD\KDYHWKHLUSURGXFWVSUHVHQWLQDIHZ

    RUJDQVDQGWKHUHVWPD\EHORQJWRDXQLTXHRUJDQDVIDUDVH[SUHVVLRQLVFRQFHUQHG

    &RUHSURPRWHUHOHPHQWVDUHGHILQHGDVPLQLPDO'1$HOHPHQWVWKDWDUHQHFHVVDU\DQG

    VXIILFLHQWIRUDFFXUDWHLQLWLDWLRQRIWUDQVFULSWLRQE\51$SRO,,LQDUHFRQVWLWXWHGFHOOIUHH

    V\VWHP6HYHUDOPDMRUHOHPHQWVDFWLQJLQGHSHQGHQWO\RUFROOHFWLYHO\PHGLDWHWKH

    GLUHFWELQGLQJRIWKH7),,'FRPSOH[WRDSURSHU7,67KHILUVWHOHPHQWGHVFULEHGDV

    UHJXODWLQJWKLVSURFHVVZDVDFODVVLFDO7$7$ER[7$7$$7$ORFDWHGWR

    EDVHSRVLWLRQVXSVWUHDPRI7,6+RZHYHUVXEVHTXHQWVWXGLHVVXJJHVWHGWKDW$7ULFK

    VHTXHQFHVFRPSOHWHO\XQUHODWHGWRWKH7$7$ER[VWLPXODWHWUDQVFULSWLRQZLWKHTXDORU

    LQFUHDVHGHIILFLHQF\)XUWKHUPRUHDOWKRXJKWKHILUVWVWHSRIWUDQVFULSWLRQLQLWLDWLRQLV

    KLJKO\VSHFLILF7),,'DOVRELQGVZLWKKLJKDIILQLW\WRVHYHUDO7$7$HOHPHQWVWKDWGRQRW

    PDWFKWKHFRQVHQVXVVHTXHQFHDQGLVDFWLYHLQSURPRWLQJWUDQVFULSWLRQLQYLWUR IURPWKHVH

    HOHPHQWV$QRWKHUZHDNO\FRQVHUYHGLQLWLDWRUHOHPHQW ZDVGHVFULEHGLQWKHGLUHFW

    YLFLQLW\RIWKH7,67KLVHOHPHQWDQFKRUVWKH7),,'FRPSOH[LQWKHDEVHQFHRIWKH

    7$7$ER[DQGPD\IXQFWLRQV\QHUJLVWLFDOO\LQ7$7$PHGLDWHGLQLWLDWLRQ

    0DPPDOLDQLQLWLDWRUHOHPHQWVVKDUHDFRQVHQVXV3\3\$17$3\3\FRUH$VLPLODU

    S\ULPLGLQHULFKLQLWLDWRUPRWLIKDVEHHQGHVFULEHGLQWKHSURPRWHURIWKHQXFOHDUSVD'E

    JHQHHQFRGLQJWKHIHUUHGR[LQELQGLQJVXEXQLWRISKRWRV\VWHP,DOWKRXJKWKHRYHUDOO

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    6/50

    IUHTXHQF\RI7$7$OHVVSURPRWHUVLQQRQSKRWRV\QWKHWLFSODQWJHQHVLVOHVVWKDQ

    7ZRPRUHHOHPHQWVWKDWFRQWULEXWHWRWKHEDVLFWUDQVFULSWLRQLQLWLDWLRQZHUHGHVFULEHG

    UHFHQWO\7KHGRZQVWUHDPSURPRWHUHOHPHQW$**$7&*7*ORFDWHGDWSRVLWLRQ

    ESGRZQVWUHDPRIWKH7$7$OHVV7,6ZDVDEOHWRGLUHFWWUDQVFULSWLRQLQLWLDWLRQLQ

    'URVRSKLOD DQGLQIOXHQFHWKHDFWLYLW\RIWKHWXQJUREDFLOOLIRUPYLUXVSURPRWHULQ

    WUDQVLHQWH[SUHVVLRQDVVD\VLQULFHSURWRSODVWV)LQDOO\DIRUWKFODVVRISRWHQWLDOO\

    DFWLYHFRUHSURPRWHUHOHPHQWVZLWKOLWWOHFRQVHQVXVKRPRORJ\RWKHUWKDQ*&ULFK

    FRPSRVLWLRQKDVEHHQUHSRUWHGLQWKHPDPPDOLDQV\VWHP(DUOLHUDKRPRORJRXV

    FRQVHUYHG*&ULFKHOHPHQWZDVGHVFULEHGLPPHGLDWHO\XSVWUHDPRIWKH7$7$ER[LQWKH

    EDUOH\SUSURPRWHU7KHVHILQGLQJVVWURQJO\VXJJHVWWKDWHYHQWKRXJKPRVWRIWKH

    NQRZOHGJHRIWKHFRUHSURPRWHUHOHPHQWVZDVLQLWLDOO\GHULYHGIURP\HDVWDQG

    PDPPDOLDQPRGHOVWKHPDMRUSULQFLSOHVRIWKHUHJXODWLRQRIJHQHH[SUHVVLRQDUH

    FRQVHUYHGLQSODQWVDVZHOO$SRVVLEOHH[SODQDWLRQIRUWKHREVHUYHGGLYHUVLW\LQWKHFRUH

    SURPRWHUHOHPHQWVFRXOGEHWKHLUFRQWULEXWLRQWRWKHFRPELQDWRULDOJHQHUHJXODWLRQ

    LQFOXGLQJWKHUHVWULFWLRQRIHQKDQFHUVWLPXODWRU\FDSDFLW\WRDVSHFLILFVHWRISURPRWHUV

    7ZRPRUHSUR[LPDOUHJXODWRU\HOHPHQWVQRWXQLYHUVDOO\UHTXLUHGIRUWKHDFWLYLW\RI

    WKHFRUHHXNDU\RWLFSURPRWHUVZKHQSUHVHQWVLJQLILFDQWO\DIIHFWWKHLULQLWLDWLRQ

    IUHTXHQF\7KHVHVHTXHQFHVDUHORFDWHGFORVHWR7,6DURXQGESDQGDSSHDUWR

    DVVLVWLQWKHUHFUXLWPHQWRIEDVLFWUDQVFULSWLRQIDFWRUVWRWKH7,6VLWHVRIKRXVHNHHSLQJDQG

    7$7$OHVVJHQHV7KH*&ER[***&**SOD\VDQLPSRUWDQWUHJXODWRU\UROHLQWKHFRUH

    SURPRWHUUHJLRQVRIPDPPDOLDQJHQHV&RWUDQVIHFWLRQRIH[SUHVVLRQFDVVHWWHV

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    7/50

    WRJHWKHUZLWKWKH*&ER[ELQGLQJSURWHLQXVXDOO\UHVXOWVLQDIRXUWRWHQIROGLQFUHDVHLQ

    *&ER[UHJXODWHGSURPRWHUDFWLYLW\*&ER[HVKDYHDOVREHHQORFDOL]HGLQWKH

    XSVWUHDPSURPRWHUUHJLRQVRIPDQ\SODQWJHQHV $QRWKHUZHOOFRQVHUYHG

    HOHPHQWWKH&&$$7ER[LVRIWHQSUHVHQWDWWRESXSVWUHDPRI7,6DQGPD\

    RSHUDWHFRRSHUDWLYHO\ZLWKRWKHUSXWDWLYHFRQVHUYHGPRWLIV+RZHYHUQRXQLI\LQJ

    H[SUHVVLRQSDWWHUQIRUSODQWJHQHVFRQWDLQLQJSXWDWLYH&&$$7HOHPHQWVKDVEHHQ

    REVHUYHG0RUHRYHUPXOWLSOHFRSLHVRIWKHJHQHVFRGLQJIRUWKHVXEXQLWVRIWKH

    &&$$7ELQGLQJSURWHLQH[LVWLQ$UDELGRSVLVVXJJHVWLQJWKHSRWHQWLDOIRUPXOWLSOH

    DOWHUQDWLYHIRUPVRIWKHVHFRPSOH[HVLQSODQWV

    83675($05(*8/$725

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    8/50

    +LJKHUSODQWVKDYHGHYHORSHGDFRPSOH[ELRFKHPLFDOV\VWHPWRSHUFHLYHDQGUHVSRQG

    WROLJKWZKLFKLVEDVHGRQWKUHHFODVVHVRISKRWRUHFHSWRUVSK\WRFKURPHVEOXHOLJKW

    UHFHSWRUVDQGUHFHSWRUVIRU89OLJKW/LJKWVLJQDOVDEVRUEHGE\WKHVH SKRWRUHFHSWRUV

    UHJXODWHWUDQVFULSWLRQRIDODUJHQXPEHURIJHQHVWKDWHQFRGHSURWHLQVLQYROYHGLQ

    SKRWRV\QWKHVLVDQGYDULRXVGHYHORSPHQWDOSURFHVVHVWKURXJKDFRPSOH[VLJQDO

    WUDQVGXFWLRQFDVFDGH,WLVJHQHUDOO\EHOLHYHGWKDWGLIIHUHQWOLJKWDFWLYDWHGSDWKZD\V

    WDUJHWGLIIHUHQW/5(VDQGWUDQVFULSWLRQIDFWRUVZLWKLQWKHSURPRWHUUHJLRQEXWWKH\PD\

    DOVRWDUJHWFRPPRQ/5(V ([WHQVLYHPXWDJHQHVLVDQGGHOHWLRQDQDO\VLVRIWKH

    SURPRWHUUHJLRQVRIOLJKWLQGXFHGJHQHVUHVXOWHGLQWKHLGHQWLILFDWLRQRIDQXPEHURIFLV

    DFWLQJHOHPHQWVLQYROYHGLQWKHFRQWURORIOLJKWUHJXODWHGWUDQVFULSWLRQ6HYHUDORIWKHVH

    PRWLIVVXFKDVWKH*7ER[**77$$,ER[*$7$$$*5*ER[&$&*7*DQG

    +ER[$&&7$$&&$&KDYHEHHQH[SHULPHQWDOO\VKRZQWREHLPSRUWDQW

    FRPSRQHQWVLQWKHOLJKWUHVSRQVH$OWKRXJKVLPLODU/5(VDUHSUHVHQWLQPDQ\GLIIHUHQW

    SURPRWHUVDQGDUHDVVHPEOHGLQDYDULHW\RIFRPELQDWLRQVQRXQLYHUVDOHOHPHQWKDVEHHQ

    IRXQGLQDOOSKRWRUHJXODWHGSURPRWHUV6RPHRIWKH/5(VDUHSUHVHQWLQSURPRWHUVWKDW

    DUHQRWOLJKWUHJXODWHG)XUWKHUPRUHWKHVDPH/5(LVIUHTXHQWO\IRXQGLQSURPRWHUV

    ZLWKRSSRVLWHOLJKWUHVSRQVLYHQHVVDVZDVVKRZQIRUWKH*7ER[1RQHRIWKH

    /5(VLGHQWLILHGVRIDUKDVEHHQVKRZQWRFRQIHUOLJKWUHVSRQVLYHQHVVE\LWVHOI)RU

    H[DPSOHZKLOHDWHWUDPHURIWKH*7ELQGLQJHOHPHQWZDVDEOHWRFRQIHUOLJKWUHJXODWLRQ

    RQDPLQLPDOES6SURPRWHUFRQWDLQLQJWKHDVHOHPHQWLWIDLOHGWRDFWLQWKH

    VDPHZD\ZKHQFRPELQHGZLWKDVKRUWHUYHUVLRQRIWKH6SURPRWHUESODFNLQJ

    DV,WKDVDOVREHHQVKRZQWKDWRQO\DUWLILFLDOVHTXHQFHVFRPSRVHGRISDLUHG

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    9/50

    FRPELQDWLRQVRIWHWUDPHULFUHSHDWVRI* DQG*$7$ER[HVRU*7 DQG*$7$ER[HV

    EXWQRWPXOWLPHUVRIDVLQJOHPRWLIFDQIXQFWLRQDV/5(V

    7KHVHDQGPDQ\RWKHUH[SHULPHQWDOGDWDUHVXOWHGLQDJHQHUDOK\SRWKHVLVWKDWSODQW

    /5(VDUHDFWXDOO\FRPSRVLWHHOHPHQWVLHFRPELQDWLRQVRIFLVUHJXODWRU\VHTXHQFHVLQ

    ZKLFKWKHLURYHUDOODFWLYLW\LVWKHUHVXOWRIV\QHUJHWLFLQWHUDFWLRQVEHWZHHQFRJQDWH

    WUDQVFULSWLRQIDFWRUV7KHPRGXODUFRPSRQHQWRI/5(VLVFRPSRVHGRIWZR

    JHQHUDOHOHPHQWVWKHOLJKWVSHFLILFHOHPHQWDQGDFRXSOLQJHOHPHQW/LJKWVSHFLILF

    HOHPHQWVDUHWDUJHWHGE\WUDQVFULSWLRQIDFWRUVWKDWDUHUHJXODWHGE\OLJKW&RXSOLQJ

    HOHPHQWVELQGSURWHLQ IDFWRUVWKDWGLUHFWWKHOLJKWVWLPXOXVWRWUDQVFULSWLRQLQDVSDWLDORU

    WHPSRUDOPDQQHURUGHWHUPLQHWKHUHODWLYHVWUHQJWKRIWKHOLJKWLQGXFHGJHQHH[SUHVVLRQ

    1XPHURXVSURWHLQIDFWRUVWKDWELQGWRFLVHOHPHQWVFRQWDLQLQJ*$7$ DQG*7FRUH

    VHTXHQFHVKDYHEHHQLGHQWLILHGDQGH[WHQVLYHO\FKDUDFWHUL]HG$OWKRXJKLQPDQ\

    VWXGLHVFOHDUGLIIHUHQFHVLQVSHFLILFLWLHVDQGVXJJHVWLYHFKDQJHVLQDFWLYLW\LQUHVSRQVHWR

    OLJKWZHUHGHVFULEHGWKHFRQFOXVLYHIXQFWLRQVRIWKHVH'1$ELQGLQJSURWHLQVLQOLJKW

    UHJXODWHGWUDQVFULSWLRQKDV\HWWREHGHWHUPLQHG7KHRQO\WZRWUDQVFULSWLRQIDFWRUV

    IRUZKLFKWKHUHLVVWURQJHYLGHQFHVXJJHVWLQJWKHLULPSRUWDQFHLQOLJKWPHGLDWHG

    UHJXODWLRQDUH$UDELGRSVLV IDFWRUV+

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    10/50

    0(7$%2/,&5(*8/$7,21

    +RUPRQHVSOD\DNH\UROHLQUHJXODWLQJSODQWJURZWKDQGGHYHORSPHQW5HFHQW

    HYLGHQFHKDVVXJJHVWHGWKDWVXJDUVFRQWUROJHQHH[SUHVVLRQDQGGHYHORSPHQWDOSURFHVVHV

    LQDPDQQHUVLPLODUWRFODVVLFDOSODQWKRUPRQHV7KHTXHVWLRQLVKRZGR UHODWLYHO\

    VLPSOHPROHFXOHVUHJXODWHDYDULHW\RIUHVSRQVHVZLWKLQDQDVVRUWPHQWRIFHOOVWLVVXHV

    DQGRUJDQVRISODQWV"7KHDQVZHUWRWKLVTXHVWLRQUHTXLUHVDQXQGHUVWDQGLQJRIKRUPRQH

    DQGVXJDUSHUFHSWLRQDQGVLJQDOWUDQVGXFWLRQDVDSDUWRIWKHPHWDEROLFUHJXODWLRQRIJHQH

    H[SUHVVLRQLQSODQWV

    $X[LQ5HVSRQVLYH(OHPHQWV$X[5(V

    $X[LQSOD\VDQLPSRUWDQWUROHLQURRWIRUPDWLRQDSLFDOGRPLQDQFHWURSLVPDQG

    VHQHVFHQFHDWWKHRUJDQLVPOHYHOZKLOHDFWLQJDVDVLJQDOIRUGLYLVLRQH[WHQVLRQDQG

    GLIIHUHQWLDWLRQLQVLGHWKHSODQWFHOO$X[LQPHGLDWHGUHVSRQVHVDWWKHJHQHOHYHOFDQEH

    GHWHFWHGDVHDUO\DVWZR WRILYH PLQXWHVDIWHUDX[LQDSSOLFDWLRQ7KHPRVW

    H[WHQVLYHO\VWXGLHGDX[LQUHVSRQVLYHSODQWJHQHSURPRWHUVDUHWKRVHIURPWKHSHD36

    ,$$ JHQHWKHVR\EHDQ*+ JHQHDQGWKHVR\EHDQ6PDOO$X[LQ8S

    51$6$85$ JHQH7KHVHVWXGLHVOHGWRWKHLGHQWLILFDWLRQRIWKHFLVDFWLQJPRWLIV

    *7*7&&&$7ZLWKLQDQ$X[5(RIWKHSHD36,$$ SURPRWHUDQG7*7&7&

    ZLWKLQWKHWKUHHVPDOO$X[5(VRIWKHVR\EHDQ*+ SURPRWHU$Q$X[5(RIWKH

    6$85$ SURPRWHUFRQWDLQHGERWKW\SHVRIWKHVHPRWLIV$IXQFWLRQDOVWXG\RI

    $X[5(VLQWKHVR\EHDQ*+ SURPRWHUVKRZHGWKDWWKH7*7&7&HOHPHQWUHTXLUHVD

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    11/50

    FORVHO\DVVRFLDWHGFRQVWLWXWLYHRUFRXSOLQJ'1$HOHPHQWWRIXQFWLRQDVDQ$X[5(

    6LPLODUO\7*7&7&DQG7*7&&&$7HOHPHQWVLQWKHVR\EHDQ6$85$ SURPRWHUDQG

    WKHSHD36,$$ SURPRWHUPD\DOVRIXQFWLRQDVFRPSRVLWH$X[5(VWKDWFRQWDLQ

    GLIIHUHQWFRXSOLQJHOHPHQWVWKDQWKRVHIRXQGLQFRPSRVLWH$X[5(VRIWKHVR\EHDQ*+

    SURPRWHU:LWKLQWKHFRPSRVLWH$X[5(VDX[LQUHVSRQVLYHHOHPHQWVUHSUHVVWKH

    WUDQVFULSWLRQVWLPXODWLQJDFWLYLW\RIWKHDGMDFHQWRURYHUODSSLQJFRQVWLWXWLYHHOHPHQW

    ZKHQDX[LQOHYHOLVORZ:KHQDX[LQOHYHOLVKLJKWKHUHSUHVVLRQLVUHOHDVHGDQGWKH

    FRPSRVLWHHOHPHQWLVDFWLYDWHG'HSHQGLQJRQWKHQDWXUHRIWKHFRQVWLWXWLYHRU

    FRXSOLQJHOHPHQWVRIGLIIHUHQW$X[5(VWKH\FRXOGSRWHQWLDOO\FRQIHUDYDULHW\RIWLVVXH

    VSHFLILFDQGGHYHORSPHQWDOO\UHJXODWHGH[SUHVVLRQSDWWHUQV

    %RWK7*7&7&DQG7*7&&&$7HOHPHQWVFDQIXQFWLRQDV$X[5(VLQWKHDEVHQFHRI

    DQ\FRXSOLQJHOHPHQWZKHQPXOWLPHUL]HGZLWKDSSURSULDWHVSDFLQJDQGRULHQWDWLRQ

    3URSHUO\VSDFHGDQGRULHQWHG7*7&7&$X[5(VDUHVHYHUDOIROGPRUHDFWLYH

    WKDQQDWXUDO$X[5(V$KLJKO\DFWLYHSDOLQGURPLFUHSHDWRIWKH7*7&7&

    HOHPHQWZDVXVHGDVEDLWLQD\HDVWRQHK\EULGV\VWHPWRLGHQWLI\WKHILUVWPHPEHURIWKH

    DX[LQUHVSRQVLYHIDFWRUV$5)IURP$UDELGRSVLV %RWKWKH$5)IDPLO\DQG WKH

    $X[,$$SURWHLQVKDYHEHHQLGHQWLILHGDVNH\UHJXODWRUVRIDX[LQPRGXODWHGJHQH

    H[SUHVVLRQKRZHYHUWKH'1$ELQGLQJDFWLYLW\RIWKH$X[,$$SURWHLQVKDVQRW

    EHHQFRQFOXVLYHO\GHPRQVWUDWHG$X[,$$SURWHLQVDUHEHOLHYHGWRUHJXODWH

    WUDQVFULSWLRQE\PRGXODWLQJWKHDFWLYLW\RI$5)V

    $QRWKHU$X[5(WKDWKDVUHFHLYHGFRQVLGHUDEOHDWWHQWLRQLVWKHRFVDVHOHPHQW

    2ULJLQDOO\IRXQGLQWKH&DXOLIORZHU0RVDLF9LUXV&D096SURPRWHUDFWLYDWLRQ

    VHTXHQFHPHGLDWHVERWKVDOLF\OLFDFLG DQGDX[LQLQGXFLEOHWUDQVFULSWLRQDFWLYDWLRQDQG

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    12/50

    FRQVLVWVRIWZRLPSHUIHFW7*$&*7&$SDOLQGURPHV:KHUHDVWKHVHTXHQFHFDQ

    GHYLDWHTXLWHVXEVWDQWLDOO\IURPLWVFRQVHQVXVWKHESVSDFHEHWZHHQWKHWZR

    SDOLQGURPLFFHQWHUVLVFRQVHUYHGLQDOORVFDVHOHPHQWVWKDWUHVSRQGWRDX[LQ7KLV

    HOHPHQWZDVDOVRGHWHFWHGLQVHYHUDOSODQWSURPRWHUVLQFOXGLQJWKHDX[LQLQGXFLEOH

    WREDFFR3DUJHQHV $QXFOHDUSURWHLQFRPSOH[$6)WKDWELQGVWRWKH

    7*$&*7&$SDOLQGURPH ZDVLGHQWLILHGE\XVLQJHOHFWURSKRUHWLFPRELOLW\VKLIWDVVD\

    $QXPEHURIF'1$VHQFRGLQJDVELQGLQJ7*$SURWHLQVKDYHEHHQGHVFULEHGLQ

    WREDFFR

    *LEEHUHOOLQ5HVSRQVLYH(OHPHQWV*$5(V

    7KHPHFKDQLVPE\ZKLFKWKHJLEEHUHOOLFDFLG*$VLJQDOLVSHUFHLYHGDQG

    WUDQVGXFHG LQSODQWVKDVEHHQVWXGLHGH[WHQVLYHO\XVLQJDOHXURQHVSHFLILFH[SUHVVLRQDVD

    PRGHO$QDO\VLVRI*$UHJXODWLRQRI,DP\ODVHSURPRWHUVXQFRYHUHGFLVDFWLQJ

    HOHPHQWVWKDWDUHVXIILFLHQWIRUJLEEHUHOOLQUHVSRQVLYHQHVV7KHVHLQFOXGHGWKH*$5(

    PRWLI7$$&$$*$7$7&&$&ER[DQGS\ULPLGLQHER[&7&7777&7

    )XUWKHUIXQFWLRQDODQDO\VLVRIWKHEDUOH\,DP\ODVHJHQHSURPRWHUVKRZHGWKDW

    7$$&$$*$LVYHU\VLPLODUWRWKHF0\EFRQVHQVXVELQGLQJVLWH6XEVHTXHQWO\D

    QRYHO0

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    13/50

    )XQFWLRQDODQDO\VLVRIWKH(3%SURPRWHUUHYHDOHGWKDWWKH*$5(DS\ULPLGLQHER[

    DQGDQXSVWUHDPHOHPHQWDUHDOOQHFHVVDU\IRU*$LQGXFWLRQ&RQVWLWXWLYHH[SUHVVLRQRI

    WKH*$0\EWUDQVFULSWLRQDOIDFWRULQWKHDEVHQFHRI*$OHGWRWKHWUDQVDFWLYDWLRQRI

    (3%H[SUHVVLRQLQDGRVDJHGHSHQGHQWPDQQHUZLWKWKHKLJKHVWOHYHOFRPSDUDEOHWR

    WKDWLQIXOO\*$LQGXFHGWLVVXH)XQFWLRQDODQDO\VLVRIDQRWKHU*$UHJXODWHGZKHDW

    ,DP\ODVHSURPRWHU,$P\KDVDOVRLQGLFDWHGWKDWWKUHHHOHPHQWVDUHHVVHQWLDOIRU

    *$LQGXFHGH[SUHVVLRQ7KH\LQFOXGHWKHSURSRVHG*$5(PRGXOHDQGDQHZSXWDWLYH

    HOHPHQW*$77*$&77*$&&,WLVLQWHUHVWLQJWRQRWHWKDWWKH*$UHVSRQVLYH,

    DP\ODVHJHQHZDVUHSRUWHGWREHVXJDUUHSUHVVHGLQULFHHPEU\RVDQGWKDWERWK*$5(

    DQGWKHS\ULPLGLQHER[KDYHEHHQSDUWLDOO\LQYROYHGLQVXJDULQGXFHGJHQHUHSUHVVLRQ

    $EVFLVLF$FLG5HVSRQVLYH(OHPHQWV$%5(V

    0XOWLSOH$%5(VDUHORFDWHGXSVWUHDPRIWKH$%$LQGXFHGJHQHV7KH*ER[ZLWK

    WKHVHTXHQFH&*7$&*7**&*LVSUREDEO\WKHPRVWVWXGLHGHOHPHQWVXEMHFWWR$%$

    UHJXODWLRQ0XOWLSOHWDQGHPFRSLHVRIWKLVPRGXOHFRQIHU$%$UHVSRQVLYHQHVVZKHQ

    IXVHGXSVWUHDPRIWKHPLQLPDO6SURPRWHU:KLOHWKHLVRODWHG*ER[IDLOHGWR

    FRQIHU$%$UHVSRQVLYHQHVVWRWKHPLQLPDOSURPRWHUDFRPSOH[PRGXOHFRPSULVLQJWKH

    *ER[DQGDFRXSOLQJHOHPHQWIXQFWLRQHGDVDQ$%5(LQYLYR 0XOWLSOH$%5(V

    ZHUHLGHQWLILHGLQWKHIODQNLQJUHJLRQRIWKHZKHDW(P JHQHDQGVKRZQWREH

    DFWLYDWHGLQWKHSUHVHQFHRI93WUDQVFULSWLRQDODFWLYDWRU7\SLFDOO\WKHSUHVHQFHRI

    93HQKDQFHV$%$LQGXFWLRQRIODWHHPEU\RJHQHVLVJHQHVEXWDOVRVXSSUHVVHV

    JHUPLQDWLRQVSHFLILFJHQHV$VZLWKDX[LQVRUJDQ DQGVSHFLHVVSHFLILFDFWLYDWLRQRI

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    14/50

    $%$UHVSRQVLYHJHQHVLVDFKLHYHGRQO\E\WKHFRRSHUDWLYHDFWLRQRIVHYHUDOFLVDFWLQJ

    HOHPHQWV

    (WK\OHQH5HVSRQVLYH(OHPHQWV(5(V

    7KHEHVWNQRZQHIIHFWRIHWK\OHQHLVWKHSURPRWLRQRIIUXLWULSHQLQJ2WKHUQRWDEOH

    SURFHVVHVUHJXODWHGE\HWK\OHQHLQFOXGHVHHGJHUPLQDWLRQVHQHVFHQFHDQGUHVSRQVHVWR

    VWUHVVIDFWRUVVXFKDVIORRGLQJZRXQGLQJRUSDWKRJHQDWWDFN,QFOLPDFWHULFIUXLWV

    VXFKDVWRPDWRHVDSSOHVEDQDQDVDQGDYRFDGRVWKHLQLWLDWLRQRIULSHQLQJLVDVVRFLDWHG

    ZLWKDEXUVWLQHWK\OHQHELRV\QWKHVLVDQGVLJQLILFDQWDOWHUDWLRQLQWKHH[SUHVVLRQSURILOH

    RIPDQ\JHQHV$IXQFWLRQDO(5(ZDVLGHQWLILHG LQWKHWRPDWRIUXLWULSHQLQJJHQHV

    ( DQG( 7UDQVFULSWLRQRI( LVUDSLGO\DFWLYDWHGE\HWK\OHQHLQERWKOHDYHV

    DQGIUXLWEXW( LVDFWLYDWHGE\HWK\OHQHRQO\LQIUXLWDQGLVDGGLWLRQDOO\UHJXODWHGE\

    VHSDUDWHIUXLWULSHQLQJGHYHORSPHQWDOVLJQDOV6HTXHQFHVUHTXLUHGIRUERWKHWK\OHQH

    UHVSRQVLYHQHVVDQGIUXLWULSHQLQJUHJXODWLRQZHUHLGHQWLILHGZLWKLQWKHESXSVWUHDP

    RIWKH( WUDQVFULSWLRQVWDUWDQGWKHVHTXHQFHIURPWRZDVVKRZQWREH

    HVVHQWLDOIRUHWK\OHQHUHVSRQVLYHJHQHWUDQVFULSWLRQEXWQRWVXIILFLHQWWRFRQIHUHWK\OHQH

    UHVSRQVLYHQHVVWRWKHPLQLPDO6SURPRWHU,WKDVEHHQFRQFOXGHGWKDWDWOHDVWWZR

    FRRSHUDWLYHFLVDFWLQJVHTXHQFHVDQXSVWUHDPWRDQGDGRZQVWUHDPWR

    UHJXODWRU\HOHPHQWVDUHUHTXLUHGIRUHWK\OHQHUHVSRQVLYHUHJXODWLRQRI( $

    QXFOHDUSURWHLQWKDWELQGVWRWKHIODQNLQJUHJLRQVRIERWK( DQG( JHQHV((%3

    ZDVLGHQWLILHGE\JHOVKLIWDVVD\DQG'1DVH,IRRWSULQWLQJDQGVXEVHTXHQWO\FORQHG

    $WUXQFDWHGYHUVLRQRI((%3ZDVVKRZQWRWUDQVDFWLYDWHWKH( SURPRWHULQD

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    15/50

    WUDQVLHQWDVVD\GHPRQVWUDWLQJWKDWWKLV'1$ELQGLQJSURWHLQFDQDFWLYDWHWKH(

    SURPRWHUWRVSHFLILFDOO\HQKDQFHJHQHWUDQVFULSWLRQLQYLYR

    7KHVHQHVFHQFHRIFDUQDWLRQIORZHUSHWDOVLQYROYHVDQLQFUHDVHGELRV\QWKHVLVRI

    HWK\OHQH$ ESVHTXHQFHZLWKLQWKHSURPRWHUUHJLRQRIWKHFDUQDWLRQJOXWDWKLRQH6

    WUDQVIHUDVHJHQHZDVVKRZQWREHQHFHVVDU\DQGVXIILFLHQWIRUHWK\OHQHUHJXODWLRQGXULQJ

    SHWDOVHQHVFHQFH$SURWHLQWKDWLQWHUDFWVZLWKWKDWVHTXHQFHZDVLGHQWLILHGDQG

    VKRZQWRKDYHVSHFLILF'1$ELQGLQJDFWLYLW\LQSUHVHQHVFHQWSHWDOVVHQHVFHQWSHWDOV

    DQGSHWDOVWUHDWHGZLWKHWK\OHQH'1DVH,IRRWSULQWLQJGHILQHGWKH'1$VHTXHQFH

    EHWZHHQDQGZLWKLQWKHUHJLRQVSHFLILFDOO\SURWHFWHGE\ERXQGSURWHLQV7KLV

    SURWHLQSURWHFWHGUHJLRQVKDUHVDQESVHTXHQFH$7$77&$$$ZLWKWKHSURWHLQ

    ELQGLQJVHTXHQFHRIWKH( SURPRWHUUDLVLQJWKHSRVVLELOLW\WKDWIORZHUSHWDOVHQHVFHQFH

    DQGIUXLWULSHQLQJPD\KDYHVRPHFRPPRQPHFKDQLVPVIRUHWK\OHQHJHQHUHJXODWLRQ

    6XJDU5HVSRQVLYH(OHPHQWV685(V

    %LRFKHPLFDOPROHFXODUDQGJHQHWLFH[SHULPHQWVDOOVXSSRUWDFHQWUDOUROHIRUVXJDUV

    LQWKHFRQWURORISODQWPHWDEROLVPJURZWKDQGGHYHORSPHQWDQGKDYHUHYHDOHG

    LQWHUDFWLRQVWKDWLQWHJUDWHOLJKWVWUHVVKRUPRQHVLJQDOLQJDQGFRRUGLQDWHFDUERQDQG

    QLWURJHQPHWDEROLVP ,WKDVEHHQSURSRVHGWKDWVXJDUWUDQVSRUWHUOLNHSURWHLQV

    DQGVRPHH[WUDFHOOXODUVXJDUELQGLQJSURWHLQVFDQVHUYHDVVXJDUVHQVRUVWRSHUFHLYHDQG

    WUDQVPLWVXJDUPHGLDWHGVLJQDOVZKLFKDOWHUQDWLYHO\PD\EHWULJJHUHGE\KRUPRQHVOLJKW

    DQGRWKHUHQYLURQPHQWDOVWLPXOLWKDWFURVVWDONZLWKVXJDUVLJQDOLQJSDWKZD\V

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    16/50

    6XFURVHUHVSRQVLYHHOHPHQWVZHUHIRXQGLQWKHSURPRWHUVRIJHQHVFRGLQJIRUFHUHDO

    ,DP\ODVHV SRWDWRWXEHUVWRUDJHSURWHLQVVZHHWSRWDWRYHJHWDWLYHVWRUDJH

    SURWHLQVSRWDWRVXFURVHV\QWKDVHEHDQSKRWRV\QWKHVLVSURWHLQ

    5%&6 DQGWKHFXFXPEHUPDODWHV\QWKDVH1RFRQVHUYHGFLVDFWLQJHOHPHQW

    FRPPRQWRDOOVXJDUUHJXODWHGSURPRWHUVKDVEHHQUHSRUWHGLQGLFDWLQJSHUKDSVWKH

    FRPSOH[QDWXUHRIVXJDUVLJQDOLQJSDWKZD\V$VXJDUUHVSRQVHVHTXHQFH656IRXQGLQ

    WKHSURPRWHURIDVXJDUVWDUYDWLRQLQGXFLEOHULFHDP\ODVHJHQH$P\ZDVVKRZQWR

    FRQIHUVXJDUUHVSRQVLYHQHVVWRDPLQLPDOSURPRWHU7KH656FRQWDLQVWKUHHHVVHQWLDO

    PRWLIVD*&ER[D*ER[DQGD7$7&&$HOHPHQWLGHQWLILHGDWWRESLQDOO

    SURPRWHUVRI,DP\ODVHJHQHVLVRODWHGIURPFHUHDOV7KH7$7&&$HOHPHQWERXQG

    WKUHHVWUXFWXUDOO\UHODWHGULFH2V0

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    17/50

    UHVSRQVLYHHOHPHQWVKDYHEHHQUHSRUWHGLQVXJDUUHVSRQVLYHDP\ODVHSURPRWHUV

    ([RJHQRXVDSSOLFDWLRQRI$%$ZDVVKRZQWRDFWLYDWHERWKWKH-DP\ODVHDQG

    -SKDVHROLQSURPRWHUVWKHODWWHUEHLQJPRGXODWHGE\H[WHUQDOO\VXSSOLHGVXFURVHDWWKH

    VDPHWLPH7RJHWKHUWKHVHGDWDSURYLGHVWURQJHYLGHQFHWKDWVXJDUKRUPRQHDQG

    GHIHQVHVLJQDOLQJPD\FRQYHUJHLQWKHWUDQVFULSWLRQDOFRQWURORIGLYHUVHSURPRWHUV

    WKURXJKDFWLYDWLRQRIWKH: DQG*ER[HOHPHQWV

    $%,27,&675(66

    +HDW6WUHVV5HVSRQVLYH(OHPHQWV+6(V

    7KHKHDWVKRFNUHVSRQVHLVZLGHO\FRQVHUYHGLQDOOOLYLQJFHOOVUHYLHZHGLQDQG

    KHDWVWUHVVWUDQVFULSWLRQIDFWRUVDUHWKHFHQWUDOSURWHLQVLQWKLVSURFHVV'HVSLWHWKHLU

    JHQHUDOYDULDELOLW\LQVHTXHQFHDQGVL]HWKHLUVWUXFWXUHDQGSURPRWHUUHFRJQLWLRQ

    VHTXHQFHVDUHUHPDUNDEO\FRQVHUYHGDPRQJWKHHXNDU\RWHV$OORIWKHPFRPSULVHDQ1

    WHUPLQDO'1$ELQGLQJGRPDLQWKHK\GURSKRELFFRUHRIZKLFKHQVXUHVWKHSUHFLVH

    ORFDWLRQRIWKHFHQWUDOKHOL[WXUQKHOL[PRWLIDWWKH+6(7KLVHOHPHQWFRQWDLQVD

    UHSHWLWLYHSDWWHUQRISDOLQGURPLFELQGLQJPRWLIVQ*$$QQ77&QQ*$$DQGSOD\VD

    PDMRUUROHLQWKHKHDWVKRFNUHVSRQVHLQWRPDWRVR\EHDQDQGVXQIORZHU

    )RUH[DPSOHH[SUHVVLRQ RIWKHDVFRUEDWHSHUR[LGDVHJHQHLVRIWHQLQGXFHGE\ERWK

    R[LGDWLYHVWUHVVDQGDVXEVHTXHQWKHDWVKRFNUHVSRQVHWKHODWWHUUHVXOWLQJIURPWKH

    DFFXPXODWLRQRIK\GUR[\ODQGVXSHUR[LGHUDGLFDOVDQGK\GURJHQSHUR[LGH

    6HTXHQFHFRPSDULVRQRIWKHSURPRWHUUHJLRQVXSVWUHDPRIWKHDVFRUEDWHSHUR[LGDVHJHQH

    IURPSHDDQG$UDELGRSVLV UHYHDOHGWKHSUHVHQFHRIRQO\RQHUHJLRQRIKLJK

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    18/50

    KRPRORJ\WKDWLVORFDWHGDURXQGWKH7$7$ER[DQGFRQWDLQVVHYHUDOVHTXHQFHPRWLIV

    FKDUDFWHULVWLFRIWKH+6(LGHQWLILHGLQSURPRWHUVRIDOOKHDWVKRFNLQGXFLEOHJHQHV7KLV

    SXWDWLYH+6(ZDVUHFRJQL]HGE\WKHWRPDWRKHDWVKRFNIDFWRULQYLWUR DQGFRQWULEXWHV

    SDUWLDOO\WRWKHLQGXFWLRQRIWKHDVFRUEDWHSHUR[LGDVHJHQHE\R[LGDWLYHVWUHVV

    6RPHSODQWJHQHVXVHPRUHWKDQD+6(WRUHJXODWHWKHLUWKHUPRLQGXFHGH[SUHVVLRQ)RU

    H[DPSOHWKHVR\EHDQKHDWVKRFNJHQH*PKVS% LVUHJXODWHGYLDWKHFODVVLFDO+6(

    EXWIXOOSURPRWHUDFWLYLW\UHTXLUHVDGGLWLRQDOVHTXHQFHVORFDWHGXSVWUHDPRI+6(

    6WUXFWXUDOIHDWXUHVZLWKLQWKLVSXWDWLYHHQKDQFHUUHJLRQLQFOXGHDUXQRIVLPSOHVHTXHQFHV

    ZKLFKDUHDOVRSUHVHQWXSVWUHDPRIWKH+6(OLNHVHTXHQFHVRIRWKHUVR\EHDQKHDWVKRFN

    JHQHVDQGWKUHHSHUIHFW&&$$7ER[HVORFDWHGLPPHGLDWHO\XSVWUHDPIURPWKHPRVW

    GLVWDO+6(RIWKHSURPRWHU:KLOHWKH$7ULFKGRPDLQRIWKHIODQNLQJUHJLRQ

    ZDVXQDEOHWRGLUHFWWUDQVFULSWLRQIURPWKH7$7$ER[RIDWUXQFDWHG6SURPRWHUKHDW

    LQGXFLEOHWUDQVJHQHDFWLYLW\ZDVGHWHFWDEOHZKHQDGGLWLRQDOVHTXHQFHVIURPWKHQDWLYH

    SURPRWHUFRQWDLQLQJWKUHH&&$$7ER[HVDQGDVLQJOH+6(ZHUHSUHVHQWLQWKH

    FRQVWUXFWV

    2[LGDWLYH6WUHVV5HVSRQVLYH(OHPHQWV

    ,QFUHDVLQJHYLGHQFHLQGLFDWHVWKDW+2 IXQFWLRQVDVDVWUHVVVLJQDOLQSODQWV

    PHGLDWLQJDGDSWLYHUHVSRQVHVWRYDULRXVVWUHVVHVE\PRGXODWLQJH[SUHVVLRQRIPDQ\

    JHQHVLQFOXGLQJWKRVHFRGLQJIRUDQWLR[LGDQWHQ]\PHVDQGPRGXODWRUVRI+2

    SURGXFWLRQ$JOREDOPLFURDUUD\DQDO\VLVRIJHQHH[SUHVVLRQLQUHVSRQVHWR

    +2 VKRZHGWKDWDSSUR[LPDWHO\RIWKH$UDELGRSVLV WUDQVFULSWRPHLVUHJXODWHGE\

    +22IWKHVHJHQHVVRPHZHUHDOVRUHJXODWHGE\YDULRXVVWLPXOLVXFKDV89OLJKW

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    19/50

    HOLFLWRUWUHDWPHQWDQGGURXJKWVWUHVV'HVSLWHWKHIDFWWKDW+2UHVSRQVLYH

    SURPRWHUVZHUHLGHQWLILHGLQWKDWVWXG\QHLWKHUVLJQDOLQJSDWKZD\VQRUWUDQVFULS WLRQ

    IDFWRUVRU+2UHJXODWRU\'1$VHTXHQFHVKDYH\HWEHHQLVRODWHGDQGFKDUDFWHUL]HG

    +RZHYHUVHYHUDOSURPRWHUHOHPHQWVVXFKDV:*DQG+ER[HVDQGWKHHWK\OHQH

    UHVSRQVLYH*&&HOHPHQWZKLFKDUHSUHVHQWLQWKHR[LGDWLYHVWUHVVUHVSRQVLYHSDUWRI

    SODQWSURPRWHUVKDYHEHHQSXWIRUZDUGDVFDQGLGDWHVIRU+2UHVSRQVLEOHPRWLIV

    7KHUHLVVWURQJHYLGHQFHWKDWHWK\OHQH$%$6$DQGFDOFLXPFRQWULEXWHWRWKH

    FRPELQDWRULDOUHJXODWLRQRIWKHUHVSRQVHDJDLQVWWRR[LGDWLYHGDPDJHLQ$UDELGRSVLV

    %RWKLQKLELWRUDQGJHQHWLFGDWDVXJJHVWHGWKDWHWK\OHQH6$DQG$%$DUHDFWXDOO\XVHG

    E\$UDELGRSVLV LQYLYR WRSURWHFWSODQWWLVVXHVDJDLQVWKHDWLQGXFHGR[LGDWLYHVWUHVV

    7KHIXWXUHFKDOOHQJHZLOOEHWRGHWHUPLQHZKDWVLJQDOLQJSDWKZD\VWKHVHIRXUFRPSRQHQWV

    DUHLQYROYHGLQDQGWRLGHQWLI\WKHRWKHUVLJQDOLQJFRPSRQHQWVLQWKHVHSDWKZD\V

    &ROG'URXJKWDQG2VPRWLF6WUHVV 5HVSRQVLYH(OHPHQWV

    :KHQH[SRVHGWRORZWHPSHUDWXUHVSODQWFHOOVHQFRXQWHUWKUHHPDMRUSUREOHPV

    FKDQJHVLQWKHVSDWLDORUJDQL]DWLRQRIELRORJLFDOPHPEUDQHVUHWDUGDWLRQRIELRFKHPLFDO

    DQGFKHPLFDOUHDFWLRQVDQGDOWHUDWLRQVLQWKHDYDLODELOLW\DQGVWDWXVRIZDWHU7KHODWWHU

    SK\VLRORJLFDOVWDWHLVRIWHQLQGXFHGE\WKHGLUHFWHIIHFWRIGURXJKWDQGRVPRWLFVWUHVVDV

    ZHOO&RQVHTXHQWO\WROHUDQFHRIIUHH]LQJDQGGURXJKWPD\KDYHFHUWDLQSURVSHFWLYH

    PHFKDQLVPVLQFRPPRQEHFDXVHWKHPDMRULW\RIIUHH]LQJLQMXULHVXVXDOO\UHVXOWIURP

    IUHH]HLQGXFHGGHK\GUDWLRQRISODQWV6HYHUDOFROGUHVSRQVLYHSURPRWHUVZHUHVKRZQWR

    FRQWDLQWKHGHK\GUDWLRQUHVSRQVHHOHPHQW'5(ZLWKD&&*$&FRQVHUYHGPRWLI&

    UHSHDWUHSHDWHGVHYHUDOWLPHV7KHUHJLRQRIWKHFRUD JHQHRI$UDELGRSVLV

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    20/50

    KDUERULQJWKH&UHSHDWHOHPHQWEHWZHHQDQGEDVHSRVLWLRQLVLQDFWLYHRUYHU\

    ZHDNO\DFWLYHLQPRVWRIWKHWLVVXHVDQGRUJDQVRISODQWVJURZQDWQRUPDOWHPSHUDWXUH

    EXWEHFRPHVDFWLYDWHGWKURXJKRXWPRVWRIWKHSODQWLQUHVSRQVHWRORZWHPSHUDWXUH*HQH

    IXVLRQH[SHULPHQWVLQGLFDWHGWKDWWKLVUHJLRQLQDGGLWLRQWRLPSDUWLQJFROGUHJXODWHGJHQH

    H[SUHVVLRQFDQLPSDUW$%$ DQGGURXJKWUHJXODWHGJHQHH[SUHVVLRQ0RUHUHFHQW

    HIIRUWVKDYHGHILQHGDQ$UDELGRSVLV '5(WUDQVFULSWLRQDFWLYDWRU&%)

    0XWDWLRQRIWKHFRUHSHQWDPHU&&*$&RIWZRSXWDWLYHORZWHPSHUDWXUHUHVSRQVLYH

    HOHPHQWVLQWKHSUR[LPDOUHJLRQRIWKHZLQWHU%UDVVLFDQDSXV FROGLQGXFHGJHQH

    %1 UHVXOWHGLQFRPSOHWHORVVRIORZWHPSHUDWXUHUHJXODWLRQE\WKHSURPRWHU7KLV

    LQGLFDWHVWKDWWKH&&*$&VHTXHQFHLVFULWLFDOWRWKHORZWHPSHUDWXUHUHVSRQVHLQWKH

    %1 JHQH,QFRQWUDVWPXWDWLRQRIWZR*ER[HV&$&*7*VWDJJHUHGEHWZHHQWKHVH

    HOHPHQWVLQWKHVDPHUHJLRQRIWKHSURPRWHUGLGQRWDOWHUFROGLQGXFLEOHJHQHH[SUHVVLRQ

    6LPLODUO\D*ER[LQFRPELQDWLRQZLWKDQDQDHURELFUHVSRQVHHOHPHQWLVUHTXLUHG

    IRUFROGVWUHVVLQGXFWLRQRIWKH$UDELGRSVLV DOGHK\GHGHK\GURJHQDVHSURPRWHUEXW$%$

    DSSHDUVWRSOD\QRUROHLQFROGUHVSRQVLYHH[SUHVVLRQRIWKLVJHQH7KXVPDQ\RI

    WKHFKDQJHVLQWKHJHQHH[SUHVVLRQWKDWRFFXULQUHVSRQVHWRORZWHPSHUDWXUHDQGGURXJKW

    DSSHDUWRUHTXLUH$%$VLJQDOLQJYLDDVHFRQGLQGHSHQGHQWVLJQDOWUDQVGXFWLRQSDWKZD\

    'URXJKWDQGFROGVWUHVVLQGXFLEOHJHQHVWKDWDUHDFWLYDWHGLQWKLVSDWKZD\XVXDOO\FRQWDLQ

    DSRWHQWLDO$%5(7&$&*7***LQWKHLUSURPRWHUUHJLRQV$VLPLODUFRUUHODWLRQFDQ

    EHREVHUYHGLQWKHFORVHO\UHODWHG$UDELGRSVLVUG$ DQGUG% JHQHV(YHQWKRXJK

    WKHVHJHQHVDUHFORVHO\OLQNHGLQWKH$UDELGRSVLV JHQRPHWKH\DUHGLIIHUHQWLDOO\LQGXFHG

    XQGHUWKHFRQGLWLRQVRIGHK\GUDWLRQORZWHPSHUDWXUHKLJKVDOLQLW\RUWUHDWPHQWZLWK

    H[RJHQRXV$%$,WDSSHDUVWKDWUG$ KDVDWOHDVWWZRFLVDFWLQJHOHPHQWVRQHLQYROYHG

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    21/50

    LQWKH$%$DVVRFLDWHGUHVSRQVHWRGHK\GUDWLRQDQGWKHRWKHULQGXFHGE\FKDQJHVLQ

    RVPRWLFSRWHQWLDODQGWKDWUG% FRQWDLQVDWOHDVWRQHFLVDFWLQJ$%5(WKDWLVLQYROYHG

    LQ$%$UHVSRQVLYHVORZLQGXFWLRQ7KHPDL]HUDE JHQHKDVDOVREHHQLGHQWLILHG

    DV$%$LQGXFLEOHLQHPEU\RVDQGYHJHWDWLYHWLVVXHVDQGLWLVDFWLYDWHGE\H[SRVXUHWR

    ZDWHUVWUHVVLQ\RXQJOHDYHV7KHSUR[LPDOSURPRWHUUHJLRQRIWKLVJHQHFRQWDLQVDZHOO

    FRQVHUYHG$%5(PRGXOH7UDQVLHQWH[SUHVVLRQDVVD\VLQULFHSURWRSODVWVLQGLFDWHGWKDWD

    ESIUDJPHQWWRIXVHGWRDWUXQFDWHG6SURPRWHUZDVVXIILFLHQWWRFRQIHU

    $%$UHVSRQVLYHQHVVXSRQWKHJXV UHSRUWHUJHQH7KHVHGDWDVXJJHVWVWKDWFRPSOH[

    PROHFXODUUHVSRQVHVWRYDULRXVGHK\GUDWLRQ DQGFROGUHODWHGVWUHVVHVPD\EHPHGLDWHG

    E\ERWKUHJXODWRU\V\VWHPVZKHUHWKH$%$VLJQDOOLQJSDWKZD\GRHVQRWLQGXFHDQ

    LPPHGLDWHUHVSRQVHEXWSOD\VDQLPSRUWDQWUROHLQSURORQJHGORQJWHUPDGDSWLYH

    UHVSRQVHWRFROGVWUHVVLQGXFHGE\GHK\GUDWLRQRISODQWWLVVXHV

    $QDHURELF5HVSRQVLYH(OHPHQWV$5(V

    7KHORZR[\JHQUHVSRQVHRIKLJKHUSODQWVLVFRPSOH[DQGLQYROYHVLQGXFWLRQRI

    VSHFLILFJHQHVHWV7KHSULPDU\WDUJHWRIWKLVUHVSRQVHLVDSDWKZD\OHDGLQJWRLQFUHDVHG

    H[SUHVVLRQRIWKHDOFRKROGHK\GURJHQDVHJHQH$GKDQGHWKDQROLFIHUPHQWDWLRQ

    7KH$GK JHQHIURP$UDELGRSVLV FDQEHLQGXFHGE\GHK\GUDWLRQDQGFROGDVZHOODVE\

    K\SR[LDVWUHVV'HOHWLRQPDSSLQJRIWKHHQGDQGVLWHVSHFLILFPXWDJHQHVLVLGHQWLILHG

    IRXUUHJLRQVRIWKHSURPRWHUHVVHQWLDOIRUH[SUHVVLRQXQGHUDOOWKUHHVWUHVVFRQGLWLRQV

    7KHPRVWFULWLFDOUHJLRQHVVHQWLDOIRUH[SUHVVLRQRIWKH$GK SURPRWHUXQGHU

    DQDHURELFFRQGLWLRQVFRQWDLQHGVHTXHQFHVKRPRORJRXVWRWKH*7PRWLI7&**777

    DQGWKH*&PRWLI*&&*&&UHSRUWHGLQPDL]H2QWKHRWKHUKDQGERWK*ER[

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    22/50

    UHJLRQVFORVHWRWKH$5(GLGQRWDIIHFWH[SUHVVLRQXQGHUK\SR[LFFRQGLWLRQVEXW

    VLJQLILFDQWO\UHGXFHGLQGXFWLRQE\FROGVWUHVVDQGWRDOHVVHUH[WHQWE\GHK\GUDWLRQ

    VWUHVV7KHIXQFWLRQDOSURSHUWLHVRIWKH$5(SRVLWLRQHGLQWKHPDL]H$GKJHQH

    KDYHEHHQDQDO\]HGXVLQJDWUDQVLHQWH[SUHVVLRQDVVD\LQHOHFWURSRUDWHGPDL]H

    SURWRSODVWV$5(IXQFWLRQHGLQERWKRULHQWDWLRQVDQGWKHSURPRWHUDFWLYLW\XQG HU

    DQDHURELFFRQGLWLRQVZDVSURSRUWLRQDOWRWKHQXPEHURIFRPSOHWH$5(VHTXHQFHVQHVWHG

    LQWKH$GKSURPRWHU7KH0

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    23/50

    -$DQG0H-$DUHIDWW\DFLGGHULYDWLYHVZKLFKDUHFRQVLGHUHGWREHJOREDOVLJQDOVRI

    GHIHQVHJHQHH[SUHVVLRQVLQFHPDQ\GHIHQVHUHODWHGJHQHVKDYHEHHQVKRZQWRUHVSRQGWR

    MDVPRQDWHV(LWKHUSDWKRJHQHOLFLWRUVRUH[RJHQRXVDSSOLFDWLRQRI-$DFWLYDWHVGH

    QRYR V\QWKHVLVRISK\WRDOH[LQV$WWKHVDPHWLPH-$DQGHWK\OHQHDFW

    V\QHUJLVWLFDOO\LQLQGXFLQJPHPEHUVRIWKH35DQG35JHQHIDPLOLHVRISDWKRJHQHVLV

    UHODWHGSURWHLQVDQG$UDELGRSVLV SODQWVLPSDLUHGLQ-$SHUFHSWLRQRUELRV\QWKHVLV

    DUHXQDEOHWRPRXQWDSSURSULDWHGHIHQVHUHVSRQVHV

    $0H-$UHVSRQVLYHUHJLRQ-$5(KDVEHHQLGHQWLILHGLQWKHSURPRWHURIWKHYVS%

    JHQHZKLFKLVVWLPXODWHGE\0H-$DQGVXJDUVLQVR\EHDQ$'1$GRPDLQWKDW

    PHGLDWHVWKH0H-$UHVSRQVHZDVORFDOL]HGEHWZHHQDQGESDQGFRQWDLQHGD

    *ER[DQGD&ULFKHOHPHQW6LPLODUUHJLRQVFRQWDLQLQJWKHE=,3SURWHLQELQGLQJ

    7*$&*PRWLIVRU*ER[HVDUHSUHVHQWLQWKHSURPRWHUVRIEDUOH\OLSR[\JHQDVH

    SRWDWR3LQSURWHLQDVHLQKLELWRU,,DQGQHVWHGLQWKHDVOLNHHOHPHQWV0RUH

    UHFHQWO\0HQNHDQGFRZRUNHUVGHVFULEHGWKHHOLFLWRULQGXFHGVWULFWRVLGLQH

    V\QWKDVHVWUJHQHLQ&DWKDUDQWKXVWKDWUHTXLUHG-$DVDVHFRQGPHVVHQJHU$ES

    UHJLRQLQWKHVWUSURPRWHUFRQWDLQHGD*&&ER[OLNHHOHPHQWDQGZDVERWKQHFHVVDU\

    DQGVXIILFLHQWIRU-$ DQGHOLFLWRUUHVSRQVLYHH[SUHVVLRQ7\SLFDOO\WKH*&&ER[

    FRPPRQO\IRXQGLQWKHIODQNLQJUHJLRQVRIHWK\OHQHLQGXFLEOHGHIHQVHJHQHVLV

    EHOLHYHGWREHWKHFRUHVHTXHQFHIRUHWK\OHQHUHVSRQVLYHWUDQVFULSWLRQ7KH(5)

    HWK\OHQHUHVSRQVLYHHOHPHQWELQGLQJIDFWRUSURWHLQVZHUHILUVWLVRODWHGDV*&&ER[

    ELQGLQJSURWHLQVIURPWREDFFR(5)DQG(5)HQKDQFHGWKH*&&ER[PHGLDWHG

    WUDQVFULSWLRQRIDUHSRUWHUJHQHLQWREDFFRSURWRSODVWVVXJJHVWLQJWKDWWKH\DFWDV

    WUDQVFULSWLRQDODFWLYDWRUVZKLOH(5)IXQFWLRQVDVDUHSUHVVRU2YHUH[SUHVVLRQRI

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    24/50

    3WLDWRPDWRWUDQVFULSWLRQIDFWRUWKDWEHORQJVWRWKH(5)IDPLO\LQWUDQVJHQLF

    $UDELGRSVLVSODQWVLQGXFHGDPRUHWKDQIROGKLJKHUH[SUHVVLRQRIWZHQW\HLJKW35

    JHQHVFRQWDLQLQJD*&&ER[(WK\OHQHLVDOVRUHTXLUHGLQWKHWUDQVGXFWLRQSDWKZD\

    OHDGLQJIURPLQMXU\DQGHWK\OHQHDQG-$VHHPWRDFWWRJHWKHUWRUHJXODWHSURWHLQDVH

    LQKLELWRUJHQHH[SUHVVLRQGXULQJWKHZRXQGUHVSRQVH2QWKHRWKHUKDQG*&&ER[

    PHGLDWHGWUDQVFULSWLRQRIGHIHQVHJHQHVGRHVQRWDOZD\VUHTXLUHVHWK\OHQH

    WKHUHIRUHLWDSSHDUVWKDWPLQRUYDULDWLRQVLQWKHFRUHVHTXHQFHVRIWKH*&&HOHPHQW

    LPSDUWUHVSRQVLYHQHVVWRGLIIHUHQWHQYLURQPHQWDOVWLPXOL

    7KHUHLVLQFUHDVLQJHYLGHQFHWKDW:ER[HVDUHDPDMRUFODVVRIFLVDFWLQJHOHPHQWV

    UHVSRQVLEOHIRUWKHSDWKRJHQLQGXFLELOLW\RIPDQ\SODQWJHQHV7KHLPSRUWDQFHRI:

    ER[HVZDVLOOXVWUDWHGUHFHQWO\E\VWXGLHVRIWKH$UDELGRSVLV WUDQVFULSWRPHGXULQJ

    V\VWHPLFDFTXLUHGUHVLVWDQFH6$57KHVLJQLILFDQWRYHUUHSUHVHQWDWLRQRI:ER[

    PRWLIVDQGWKHLUFOXVWHULQJRQ35VXEVHWJHQHSURPRWHUVVXJJHVWVWKDW:ER[ELQGLQJ

    SURWHLQV:5.

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    25/50

    $QXPEHURISURPRWHUHOHPHQWVLQFOXGLQJWKH5

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    26/50

    PRWLIVDUHUHFRJQL]HGE\VSHFLILF'1$ELQGLQJSURWHLQV7KH$$&$PRWLILVUHFRJQL]HG

    E\0

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    27/50

    )UXLWVSHFLILFSURPRWHUVVXFKDVWRPDWRSRO\JDODFWXURQDVHDQG(

    SURPRWHUVKDYHDWWUDFWHGPXFKLQWHUHVWEHFDXVHRIWKHLUSUDFWLFDOXVHLQWKHPDQLSXODWLQJ

    IUXLWPHWDEROLVPDQGWKHSURGXFWLRQRIYDOXDEOHSKDUPDFHXWLFDOSURWHLQVVXFKDV

    DQWLERGLHVDQGHGLEOHYDFFLQHVLQJHQHWLFDOO\HQJLQHHUHGIUXLWV+RZHYHUWKH

    GHWDLOHGPHFKDQLVPVRIIUXLWVSHFLILFWUDQVFULSWLRQDUHSRRUO\XQGHUVWRRGDQGPDQ\RI

    WKHHVVHQWLDOFLVHOHPHQWVKDYHQRWEHHQLGHQWLILHG5HFHQWO\DQRYHOFLVDFWLQJHOHPHQW

    WKDWGHWHUPLQHVIUXLWVSHFLILFKLJKOHYHOH[SUHVVLRQRIFXFXPLVLQZDVLGHQWLILHGDQG

    IXQFWLRQDOO\FKDUDFWHUL]HGLQPHORQ*DLQRIIXQFWLRQH[SHULPHQWVUHYHDOHGWKDWWKH

    ESVHTXHQFH*$&$&*7*7&$&$$&&7$$7ZKLFKFRQWDLQVWKHSHUIHFW

    SDOLQGURPLF*ER[LQLWVILUVWKDOILQFOXGHVDIUXLWVSHFLILFHQKDQFHUHOHPHQW

    7*7&$&$)RXUWDQGHPUHSHDWVRIWKHIXOOPRGXOHLQHLWKHURULHQWDWLRQZHUHVXIILFLHQW

    WRGLUHFWIUXLWVSHFLILFH[SUHVVLRQZKHQIXVHGWRDPLQLPDOSURPRWHU6WUHVVLQJWKH

    LPSRUWDQFHRIWKH7*7&$&$PRWLIJHOPRELOLW\VKLIWDVVD\VVKRZHGWKDWWKHHQKDQFHU

    HOHPHQWLWVHOIEXWQRWWKH*ER[ZDVDQHVVHQWLDOWDUJHWIRUDIUXLWVSHFLILFSURWHLQ

    ELQGLQJWRWKDWUHJLRQRIWKHFXFXPLVLQSURPRWHU1RHWK\OHQHUHVSRQVLYHHOHPHQWVVXFK

    DVWKH*&&ER[WKDWLVFRQVHUYHGLQWKHSURPRWHUVRIPDQ\ULSHQLQJLQGXFHGJHQHV

    KDYHEHHQIRXQGLQWKHFXFXPLVLQSURPRWHULQGLFDWLQJ WKDWLWVH[SUHVVLRQLV

    SUREDEO\UHJXODWHGLQDGHYHORSPHQWDODQGRUJDQVSHFLILFPDQQHU7KLVILQGLQJ

    GHPRQVWUDWHVWKDWFLVHOHPHQWVUHVSRQVLEOHIRUIUXLWVSHFLILFLW\FRXOGEHVXFFHVVIXOO\

    VHSDUDWHGIURPWKRVHWKDWPHGLDWHULSHQLQJDVVRFLDWHGGHYHORSPHQWDO DQGHWK\OHQH

    PHGLDWHGUHJXODWLRQ

    3ROOHQ

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    28/50

    $QXPEHURIJHQHVVSHFLILFDOO\H[SUHVVHGGXULQJYDULRXVVWDJHVRISROOHQ

    GHYHORSPHQWDQGJHUPLQDWLRQKDYHEHHQLVRODWHGDQGFKDUDFWHUL]HGERWKIRUGLFRWDQG

    PRQRFRWSODQWV7KHSROOHQUHODWHGJHQHVDUHGLYLGHGLQWRHDUO\DQGODWHJURXSV

    DFFRUGLQJWRWKHLUPD[LPDOH[SUHVVLRQEHIRUHRUDIWHUSROOHQPLWRVLV,ZKHQWKHUHLVD

    WUDQVLWLRQIURPPLFURVSRUHGHYHORSPHQWWRSROOHQPDWXUDWLRQ3URPRWHUDQDO\VLVRI

    JHQHVWKDWDUHFRRUGLQDWHO\H[SUHVVHGGXULQJSROOHQGHYHORSPHQWLQWRPDWRWREDFFRDQG

    PDL]HUHYHDOHGHQKDQFHUVHTXHQFHVDQGVKDUHGUHJXODWRU\HOHPHQWVUHTXLUHGIRUSROOHQ

    VSHFLILFWUDQVFULSWLRQ3URPRWHUGHOHWLRQDQDO\VLVLQWUDQVJHQLFSODQWV

    GHPRQVWUDWHGWKDWUHODWLYHO\VKRUWSUR[LPDOUHJLRQVDUHUHTXLUHGIRUGHYHORSPHQWDOO\

    UHJXODWHGH[SUHVVLRQLQSROOHQDQGLQVSHFLILFFHOOW\SHVRIWKHVSRURSK\WH&LVDFWLQJ

    UHJXODWRU\HOHPHQWVRIWKUHHWRPDWRODWHJHQHSURPRWHUV/$7/$7DQG

    /$7 WREDFFRJHQHVJDQG173DQGWKHPRQRFRWSROOHQVSHFLILF

    SURPRWHU=0IURPPDL]HZHUHFKDUDFWHUL]HGLQGHWDLOXVLQJWUDQVLHQWDQGVWDEOH

    H[SUHVVLRQDQDO\VLV7KHUHLVDVWULNLQJDUFKLWHFWXUDOVLPLODULW\EHWZHHQWKHSURPRWHUV

    IURPPDL]H=0WRPDWR/$7/$7DQGWKHWREDFFR173JHQH$OORIWKHP

    FRQWDLQDESPRGXOHORFDWHGESXSVWUHDPIURPWKH7$7$ER[UHVSRQVLEOH

    IRUSROOHQVSHFLILFH[SUHVVLRQ,QDGGLWLRQVKRUWHOHPHQWVUHTXLUHGIRUWKHHQKDQFHPHQW

    RISROOHQVSHFLILFH[SUHVVLRQWKH4HOHPHQW$**7&$ DQGDQ$$$7*$PRWLIKDYH

    EHHQLGHQWLILHGLQWKHPDL]H=0DQGWREDFFR173SURPRWHUVUHVSHFWLYHO\7KH

    PDL]H4HOHPHQWZDVUHSRUWHGWRSRVLWLYHO\PRGXODWHWKHH[SUHVVLRQRIWKHSUR[LPDO

    SURPRWHUUHJLRQEXWVKRZHGQRDELOLW\WRFDXVHH[SUHVVLRQLQSRO OHQRQLWVRZQ$VLPLODU

    HQKDQFHUOLNHQRQVSHFLILFDFWLYLW\RIWKHVKRUWFLVHOHPHQWVKDVEHHQUHSRUWHGIRUWKH

    SROOHQVSHFLILFH[SUHVVLRQLQWRPDWR$UDELGRSVLVDQG%UDVVLFD

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    29/50

    :KLOHPDQ\SROOHQVSHFLILFSURPRWHUVDUHLQWHUFKDQJHDEOHDPRQJDZLGHYDULHW\RI

    SODQWVSHFLHVWKHESFLVHOHPHQWVHVVHQWLDOIRUWKHH[SUHVVLRQLQSROOHQVKRZQRRU

    OLWWOHVHTXHQFHVLPLODULWLHVWRHDFKRWKHU)RUH[DPSOHWKHWRPDWR/$7

    SURPRWHULVDFWLYHLQVHYHUDORWKHUGLFRWSODQWVVWXGLHG)XUWKHUPRUHWKH

    PDL]H=0SURPRWHUIXQFWLRQVZHOOZKHQVWDEO\WUDQVIRUPHGLQWRWREDFFRDQG

    $UDELGRSVLV 7KLVGDWDVXJJHVWWKDWWKHUHVKRXOGEHVRPHFRQVHUYHGIHDWXUHVLQWKH

    YDULRXVSROOHQSURPRWHUVWKDWLVQRW\HWDSSDUHQWDWOHDVWLQWHUPVRIFRQVHQVXV

    VHTXHQFHV

    ([WHQVLYHDQDO\VLVRIWKHWRESUHJLRQLQWKHWRPDWRSROOHQVSHFLILF/$7

    SURPRWHUUHYHDOHGDFRUH3%,PRWLI7*7**77DSXWDWLYHELQGLQJWDUJHWIRUWKH*7

    UHODWHGWUDQVDFWLQJIDFWRUV0XWDWLRQRIWKHFHQWUDO**UHVLGXHVLQ3%,UHGXFHGSROOHQ

    VSHFLILFH[SUHVVLRQDSSUR[LPDWHO\WHQIROG7KH3%,PRWLIWRJHWKHUZLWKWZRRWKHU

    UHJXODWRU\HOHPHQWV*$$$DQG7&&$&&$7$EXLOGVDVWURQJSROOHQVSHFLILF

    WUDQVFULSWLRQDODFWLYDWLRQXQLW)XUWKHUPXWDJHQHVLVDQGIXQFWLRQDOFRPELQDWRULDODQDO\VLV

    GHPRQVWUDWHGWKDW3%,*$$$DQG*$$$7&&$&&$7$IXQFWLRQDOSDLUVFRXOGDFWLQD

    SROOHQVSHFLILFPDQQHUZKLOHWKH3%,7&&$&&$7$XQLWZDVQRWDFWLYH7KLVGDWD

    WRJHWKHUZLWKWKHIXQFWLRQDODQDO\VLVRIRWKHUSROOHQVSHFLILFSURPRWHUVVXJJHVWVWKH

    LQWHUSOD\RIVHYHUDOWUDQVFULSWLRQIDFWRUVRQHRUPRUHRIZKLFKLVUHVSRQVLEOHLQ

    HVWDEOLVKLQJSROOHQVSHFLILFH[SUHVVLRQ$OWKRXJKVHYHUDOF'1$VHQFRGLQJSXWDWLYH

    WUDQVFULSWLRQIDFWRUVVSHFLILFDOO\H[SUHVVHGLQDQWKHUVDQGRU SROOHQKDYHEHHQLVRODWHG

    WKHLUIXQFWLRQDODFWLYLW\DQGWDUJHWSURPRWHUFLVHOHPHQWVUHPDLQWREH

    FKDUDFWHUL]HG

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    30/50

    48$17,7$7,9(75$16&5,37,21(1+$1&(56

    $QHQKDQFHULVGHILQHGDVDFLVDFWLQJPRGXOHFDSDEOHRIVWLPXODWLQJJHQHH[SUHVVLRQ

    ZKHQSODFHGLQHLWKHURULHQWDWLRQXSVWUHDPRUGRZQVWUHDPRIWKHJHQH)LUVWGHVFULEHGLQ

    DQLPDOYLUXVHVIRUWKHLUUHPDUNDEOHDELOLW\WRGUDPDWLFDOO\LQFUHDVHJHQHH[SUHVVLRQXSRQ

    69VHTXHQFHVDFWLQJLQFLV WRWKHEHWDJORELQJHQHHQKDQFHUVZHUHVKRZQWRDFW

    RYHUFRQVLGHUDEOHGLVWDQFHVLQWKHJHQRPH:KLOHPDQ\HQKDQFHUOLNHVHTXHQFHV

    RIWHQGLUHFWWLVVXHVSHFLILFRUUHJXODWHGH[SUHVVLRQVHHDERYHQXPHURXVSODQWJHQHV

    KDYHEHHQUHSRUWHGWRLQFOXGHQRQWLVVXHVSHFLILFXSVWUHDPUHJXODWRU\HOHPHQWV ZLWK

    TXDQWLWDWLYHHQKDQFHUOLNHTXDOLWLHV'HDQHWDOKDYHUHSRUWHGWKDWVHTXHQFHV

    GRZQVWUHDPRIWKHFRGLQJUHJLRQFRQWULEXWHWRTXDQWLWDWLYHGLIIHUHQFHVLQH[SUHVVLRQRI

    WZRSHWXQLDUEF6JHQHV6LPLODU$7ULFKVHTXHQFHVKDYHORQJEHHQREVHUYHGWR GLUHFW

    TXDQWLWDWLYHH[SUHVVLRQHQKDQFHPHQWGXHWRWKHSRWHQWLDOFRPELQDWRULDOHIIHFWRIPXOWLSOH

    FLV HOHPHQWV%XVWRVHWDOKDYHVWXGLHGDNEIUDJPHQWIURPWKHIODQNLQJ

    UHJLRQRID)UHQFKEHDQEHWDSKDVHROLQJHQH*HOUHWDUGDWLRQDQGIRRWSULQWLQJDVVD\V

    XVLQJQXFOHDUH[WUDFWVIURPLPPDWXUHEHDQFRW\OHGRQVUHYHDOHGVWURQJELQGLQJRIWKH

    QXFOHDUSURWHLQVWRDQXSVWUHDPUHJLRQWRWKDWFRQWDLQHGWZRLQYHUWHG$7

    ULFKPRWLIV)XVLRQRIDEDVHSDLUIUDJPHQWRUDEDVHSDLUV\QWKHWLF

    ROLJRQXFOHRWLGHFRQWDLQLQJWKHVHPRWLIVWRDPLQLPDO6SURPRWHU*86FDVVHWWH\LHOGHG

    KLJKJXV H[SUHVVLRQLQVHYHUDOWLVVXHV,QDQRWKHUUHSRUWDESGRXEOHVWUDQGHG

    ROLJRQXFOHRWLGHKRPRORJRXVWRWZR$7ULFKVHTXHQFHVORFDWHGXSVWUHDPWR

    DQGWRWRWKH7,6RIWKHVR\EHDQKHDWVKRFNJHQH*PKVS(VWLPXODWHG

    WUDQVFULSWLRQZKHQSODFHGWRDWUXQFDWHGPDL]H$GKSURPRWHU6WUXFWXUDO

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    31/50

    IHDWXUHVZLWKLQWKLVSXWDWLYHHQKDQFHUUHJLRQLQFOXGHGDUXQRI$7ULFKVHTXHQFHV DQG

    WKUHHSHUIHFW&&$$7ER[HVORFDWHGLPPHGLDWHO\XSVWUHDPIURPWKHPRVWGLVWDO+6(RI

    WKHSURPRWHU7KH$7ULFKSRVLWLYHUHJXODWRU\UHJLRQWRRIWKHSHD

    SODVWRF\DQLQJHQHSURPRWHUFRQIHUVHQKDQFHGJXV H[SUHVVLRQLQOHDYHVRIWUDQVJHQLF

    WREDFFRSODQWVZKHQIXVHGLQHLWKHURULHQWDWLRQWRDPLQLPDOSHDSURPRWHU

    ,QPDQ\FDVHVWKHHQKDQFHUOLNHDFWLYLW\RIWKH$7ULFKVHTXHQFHVLQWKHXSVWUHDP

    SURPRWHUPRGXOHRIWKHJHQHFDQEHUHODWHGWRWKHSUHVHQFHRIWKHPDWUL[DWWDFKPHQW

    UHJLRQ0$5DWWKLVORFDWLRQ0$5VDSSHDUWRRUJDQL]HWKHHXNDU\RWLFJHQRPHLQWR

    ODUJHORRSVIRUPHGE\WKHELQGLQJRIGLVSHUVHG$7ULFKVHTXHQFHVWRQRQKLVWRQHSURWHLQV

    RIWKHQXFOHDUVFDIIROGUHYLHZHGLQ,QGLYLGXDO'1$ORRSVDUHOLNHO\WRGHILQH

    IXQFWLRQDOXQLWVDVZHOODVWRSRORJLFDOGRPDLQVFRQWULEXWLQJWRWKHUHJXODWLRQRIJHQH

    H[SUHVVLRQDQG'1$UHSOLFDWLRQLQJHQHUDO&RPSDULVRQRIWKHODUJHQXPEHURIWKH0$5

    VHTXHQFHVVKRZHGQRFOHDUUHODWLRQVKLSVDPRQJWKHPDQGQRVWULFWFRQVHQVXVVHTXHQFHV

    +RZHYHUWKH\VKDUHWKHSURSHUW\RIEHLQJDV\PPHWULFDOO\$7ULFKDQGFRQWDLQ

    G$G7VWUHWFKHVZKLFKDUHUHVSRQVLEOHIRUDGLVWLQFWLYHO\QDUURZPLQRUJURRYHWRWKH

    GRXEOHKHOL[7KHUHLVDOVRDFOHDUVL]HUHTXLUHPHQWIRULQWHUDFWLRQRI0$5

    VHTXHQFHVZLWKWKHQXFOHDUVFDIIROGIRUH[DPSOHWLJKWELQGLQJUHTXLUHVQHDUO\ESRI

    $7ULFK'1$LQ'URVRSKLOD ,QDGGLWLRQWRWKH'1$EHQWLQJSURSHUWLHVWKH$7

    ULFKUHJLRQVUHDGLO\EHFRPHEDVHXQSDLUHGDQGDUHRIDJUHDWELRORJLFDOVLJQLILFDQFHWR

    WKH0$5IXQFWLRQ$VHWRIRWKHUFLVDFWLQJHOHPHQWVFKDUDFWHULVWLFRI0$5V

    SURYLGHWKHELQGLQJVLWHVIRUDQFKRULQJWKHFRUHSURPRWHUDQGRULJLQRIUHSOLFDWLRQ

    FRPSOH[HVWRWKHQXFOHDUPDWUL[7KHVHLQFOXGH$ DQG7ER[HVEHQW'1$

    PRWLI WRSRLVRPHUDVH,,ER[XQZLQGLQJWUDFWPRWLIDQGDXWRQRPRXVO\

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    32/50

    UHSOLFDWLQJVHTXHQFHV,QWKHLQWDFWSODQWQXFOHXVWKH0$5VGHILQHLQGLYLGXDOORRSV

    DQGFDQEHLVRODWHGXVLQJORZFRQFHQWUDWLRQVRIFKDRWURSLFDJHQWVWRDFKLHYHVHOHFWLYH

    H[WUDFWLRQXQGHUFRQGLWLRQVLQZKLFKSUHFLSLWDWLRQDUWLIDFWVDUHPLQLPL]HG7KH

    GLVWULEXWLRQRIWKHGLIIHUHQWFODVVHVRI'1$ZLWKLQWKLVFRQWLQXXPZLWKUHVSHFWWRWKH

    SUHGLFWHGVWUXFWXUDOORRSVUHYHDOVDQLQWHUHVWLQJFRUUHODWLRQWKHORQJVWUHWFKHVRI PL[HG

    FODVVHVRIKLJKO\UHSHWLWLYH'1$VDUHRIWHQVHJUHJDWHGLQWRWRSRORJLFDOO\VHTXHVWHUHG

    XQLWVZKHUHDVORZFRS\QXPEHU'1$VDUHSRVLWLRQHGLQVHSDUDWHORRSV0$5V

    LQFUHDVHUHSRUWHUJHQHH[SUHVVLRQERWKLQVWDEO\WUDQVIRUPHGSODQWFHOOVDQG

    WUDQVJHQLFSODQWVDQGDUHZLGHO\XVHGWRPLQLPL]HWUDQVJHQHVLOHQFLQJUHYLHZHGLQ

    7KHQRQUDQGRPGLVWULEXWLRQRI0$5VDFFRUGLQJWRORFDOL]DWLRQRIWUDQVFULSWLRQ

    XQLWVDQGWKHLUFRPDSSLQJZLWK'1$VHTXHQFHVVXSSRUWLQJWKHRULJLQRIUHSOLFDWLRQLQ

    \HDVWDQGSHDVWUHQJWKHQVWKHLGHDWKDW0$5VSOD\DUROHLQUHSOLFDWLRQ

    PHFKDQLVPVDVZHOO7KHSRWHQWLDOUHODWLRQVKLSEHWZHHQDQFKRUDJHRI'URVRSKLOD

    ULERVRPDO'1$WRDQXFOHDUVXEVWUXFWXUHDQGUHSOLFDWLRQPHFKDQLVPVLQWKHHQKDQFHU

    OLNHXSVWUHDPUHJLRQRIWKHULERVRPDO'1$SURPRWHUKDYHEHHQVXJJHVWHG,QGHHG

    WKHWR$7ULFKUHJLRQLPPHGLDWHO\XSVWUHDPRIWKHWREDFFRULERVRPDO'1$

    SURPRWHUFRPSULVHVDYDULHW\RIFLVDFWLQJHOHPHQWVZLWKDW\SLFDOTXDQWLWDWLYHHQKDQFHU

    OLNHPRGXOH7KLVDPSOLILFDWLRQSURPRWLQJVHTXHQFHDSVVLJQLILFDQWO\LQFUHDVHGWKH

    FRS\QXPEHUDQGH[SUHVVLRQDFWLYLW\RIWKHDGMDFHQWUHSRUWHUJHQHVZKHQFORQHGLQERWK

    XSVWUHDPDQGGRZQVWUHDPSRVLWLRQLQUHJDUGVWRWKHH[SUHVVLRQFDVVHWWH6LPLODUO\

    DQXSVWUHDP6DOUHSHDWV865VHTXHQFHORFDWHGXSVWUHDPIURPWKHULERVRPDO'1$

    SURPRWHURI$UDELGRSVLVWKDOLDQD ZDVWHVWHGIRULWVLQIOXHQFHRQWKHLQYLYR DFWLYLW\RI

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    33/50

    QHDUE\SURWHLQFRGLQJJHQHV2QDYHUDJHWKHSUHVHQFHRIWKH865HOHPHQWOHGWRDIRXU

    IROGLQFUHDVHLQWKHH[SUHVVLRQRIDUHSRUWHUJHQH

    &21&/86,216$1'3(563(&7,9(6

    2YHUWKHODVWIHZ\HDUVDFRQVLGHUDEOHERG\RIHYLGHQFHKDVDFFXPXODWHGRQWKH

    VWUXFWXUDORUJDQL]DWLRQDQGUHJXODWLRQRISODQWSURPRWHUVPDQ\DVSHFWVRIZKLFKKDYH

    EHHQSUHYLRXVO\UHYLHZHG,QWKLVFKDSWHUZHKDYHWULHGWRVXPPDUL]HERWK

    WKHZHOONQRZQDQGQHZO\GHVFULEHGFLVDFWLYHHOHPHQWVQHVWHGLQWKHSODQWSURPRWHUV

    GHOLEHUDWHO\HPSKDVL]LQJWKHPRVWUHFHQWVWXGLHVWKDWLOOXPLQDWHWKHLUIXQFWLRQDODFWLYLW\

    LQWKHPXOWLOHYHOUHJXODWLRQRISODQWJHQHH[SUHVVLRQ

    7KHRUJDQL]DWLRQRISODQWSURPRWHUVIROORZVWKHJHQHUDOVWUXFWXUHFRPPRQIRURWKHU

    HXNDU\RWHVDWRESFRUHSURPRWHUDGMDFHQWWRWKH7,6IROORZHGE\DQXSVWUHDP

    UHJLRQRIDERXWNEFRQWDLQLQJWKHSUR[LPDODQGXSVWUHDPFLVDFWLQJHOHPHQWVDQGWKH

    RXWVLGHHQKDQFHUOLNHVHTXHQFHV)LJ:KLOHPDQ\SODQWFRUHSURPRWHUVVKDUH

    FRPELQDWLRQVRIZHOOGHILQHGHOHPHQWVVXFKDV7$7$ER[LQLWLDWRU'3(DQG&&$$7

    ER[WKHLUFRQVHQVXVVHTXHQFHVDQGVSDFLQJPD\YDU\VLJQLILFDQWO\VRWKDWQRWZRFRUH

    SURPRWHUVDUHLGHQWLFDO7KHUHIRUHWKHFRPSRVLWLRQRIWKHWUDQVFULSWLRQLQLWLDWLRQ

    FRPSOH[WKDWELQGVWRWKHFRUHSURPRWHULVYDULDEOHDQGWKLVRIIHUVDGGLWLRQDO

    RSSRUWXQLWLHVIRUWKHUHJXODWLRQRIEDVLFWUDQVFULSWLRQ1HYHUWKHOHVVWKHPDMRU

    OHYHORIWUDQVFULSWLRQDOFRQWUROLVPHGLDWHGE\WUDQVDFWLQJIDFWRUVELQGLQJWRWKHXSVWUHDP

    UHJXODWRU\HOHPHQWV,Q$UDELGRSVLVWKHUHJXODWLRQRIJHQRPHH[SUHVVLRQUHTXLUHVWKH

    SURGXFWVRIDERXWRIWKHSUHGLFWHGJHQHVUHIOHFWLQJWKHFRPSOH[LW\RIWKLV

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    34/50

    WUDQVFULSWLRQUHJXODWLRQQHWZRUN$WDQ\JLYHQWLPHDGLVWLQFWVHWRIWUDQVFULSWLRQ

    IDFWRUVLVDYDLODEOHWRIRUPWKHKLJKHURUGHUQXFOHRSURWHLQFRPSOH[HVDWWKHDFWLYH

    SURPRWHU7KHFRPSRVLWLRQRILQGLYLGXDOWUDQVDFWLQJIDFWRUVZLWKLQWKHVH

    FRPSOH[HVPD\RIWHQFKDQJHZKHQDVSHFLILFVLJQDOLVSHUFHLYHGVRWKDWDJLYHQ

    WUDQVFULSWLRQIDFWRUFDQSOD\PXOWLSOHUROHVDQGDIIHFWPXOWLSOHJHQHVHWVGHSHQGLQJRQ

    LWVORFDOFRQFHQWUDWLRQDQGDYDLODELOLW\

    ,WVKRXOGEHPHQWLRQHGWKDWRQHRIWKHPRVWVXFFHVVIXOVWUDWHJLHVIRUIXQFWLRQDO

    FKDUDFWHUL]DWLRQRIPDQ\FLVDFWLQJHOHPHQWVLVWKHJDLQRIIXQFWLRQIXVLRQRIGHILQHG

    LQGLYLGXDOHOHPHQWVWRDPLQLPDOSODQWSURPRWHUWKHUHE\UHGXFLQJWKHFRPSOH[LW\RIWKH

    H[SUHVVLRQSURILOH5HFHQWDGYDQFHVLQWKHGHYHORSPHQWRIVWDEOHLQYLWUR WUDQVFULSWLRQ

    V\VWHPVEDVHGRQULFHZKROHFHOODQGWREDFFRQXFOHDUH[WUDFWVLQFRPELQDWLRQ

    ZLWKDUDQJHRIDYDLODEOHSODQWQDWXUDODQGV\QWKHWLFSURPRWHUVSURYLGHVIXUWKHU

    RSSRUWXQLWLHVIRUWKHGHWHUPLQDWLRQRIWKHPROHFXODUPHFKDQLVPVXQGHUO\LQJVHOHFWLYH

    JHQHH[SUHVVLRQLQUHVSRQVHWRYDULRXVVLJQDOVWKDWFRXOGEHPRGHOHGLQYLWUR

    )XQFWLRQDOVWXGLHVRISODQWSURPRWHUVKDYHDOVRJLYHQULVHWRDJHQHUDOFRQFHSWWKDW

    XSVWUHDPUHJXODWRU\HOHPHQWVDUHFRPSRVLWHDQGQRWLQGLYLGXDOZKHUHHDFKFLVDFWLQJ

    HOHPHQWFRQWULEXWHVWRWKHRYHUDOODFWLYLW\RIWKHPRGXOHWKURXJKV\QHUJLVWLFLQWHUDFWLRQV

    EHWZHHQFRJQDWHWUDQVFULSWLRQIDFWRUV 6WLPXOLVSHFLILFHOHPHQWV

    ZLWKLQDPRGXOHDUHWDUJHWHGE\WUDQVFULSWLRQIDFWRUVWKDWDUHUHJXODWHGE\VLJQDO

    SHUFHSWLRQSDWKZD\VZKLOHFRXSOLQJHOHPHQWVELQGSURWHLQIDFWRUVWKDWGHWHUPLQHVSDWLDO

    WHPSRUDORUTXDQWLWDWLYHH[SUHVVLRQ)RUH[DPSOH*ER[HVVHUYHDVWKHFRXSOLQJ

    HOHPHQWVLQPDQ\PRGXODUUHJXODWRU\XQLWVWKDWUHVSRQGWRDYDULHW\RIFKHPLFDODQG

    HQYLURQPHQWDOVLJQDOV6XFKIOH[LELOLW\LVDFKLHYHGERWKE\WKHGLIIHUHQW*ER[IODQNLQJ

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    35/50

    VHTXHQFHVDQGFORVHLQWHUDFWLRQZLWKLPPHGLDWHFLVDQGWUDQVDFWLQJIDFWRUV7R

    XQGHUVWDQGWKHLQWHUSOD\RIWUDQVFULSWLRQDOQHWZRUNVLQSODQWVZHXOWLPDWHO\QHHGWRNQRZ

    WKHH[SUHVVLRQSDWWHUQVRIDOOWUDQVDFWLQJIDFWRUVDVZHOO,GHQWLILFDWLRQDQGIXQFWLRQDO

    FKDUDFWHUL]DWLRQRIWKHFLVDFWLQJ HOHPHQWLVQRORQJHUHQRXJK RQO\WKRURXJKDQG

    FUHDWLYHVWXGLHVWKDWFDQVRUWRXWWKHFURVVWDONRISOHLRWURSLFRUVLJQDOVSHFLILFHIIHFWVLQ

    PXWDQWVZLOOGHILQHWKHSK\VLRORJLFDOUROHVRIGLIIHUHQWVLJQDOVDQGHVWDEOLVKFRQQHFWLRQV

    EHWZHHQGLIIHUHQWSDWKZD\VLQWKHUHJXODWLRQRISODQWJHQHWUDQVFULSWLRQ

    7KHSUDFWLFDOLPSRUWDQFHRIEHWWHUXQGHUVWDQGLQJWKHUHJXODWLRQRISODQWSURPRWHUVLV

    WKHSRWHQWLDOWRLQIOXHQFHJHQHH[SUHVVLRQWRPDQLSXODWHSODQWPHWDEROLVPDQG

    DFKLHYHFRPSDUWPHQWDOL]HGSURGXFWLRQRIYDOXDEOHSKDUPDFHXWLFDOSURWHLQVIURPVHHGV

    OHDYHVURRWVRUIUXLWV

    $.12:/('*(0(176

    :HZLVKWRWKDQN3HWHU'D\0LFKDHO/DZWRQDQG1LU

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    36/50

    7DEOH2QOLQHWRROVIRUVWUXFWXUDODQGIXQFWLRQDODQDO\VLVRISODQWSURPRWHUV

    2QOLQH5HVRXUFH 'HVFULSWLRQ

    3ODQW&$5(KWWSREHURQUXJDFEH3ODQW&$5(

    5HIHUHQWLDOGDWDEDVHZLWKSODQWFLVDFWLQJ

    HOHPHQWVGHVFULELQJSODQWSURPRWHUV

    3/$&(

    KWWSZZZGQDDIIUFJRMSKWGRFV3/$&(

    'DWDEDVHRIFLVDFWLQJUHJXODWRU\'1$

    HOHPHQWVUHSRUWHGLQYDVFXODUSODQWV

    75$16)$&

    KWWSWUDQVIDFJEIGH75$16)$&

    'DWDEDVHRQHXNDU\RWLFFLVDFWLQJUHJXODWRU\

    '1$HOHPHQWVDQGWUDQVDFWLQJIDFWRUV

    (XNDU\RWLF3URPRWHU'DWDEDVH(3'

    KWWSZZZHSGLVEVLEFK

    (3'LVDVSHFLDOL]HGDQQRWDWLRQGDWDEDVHRI

    HXNDU\RWLFSURPRWHUVIURP(0%/

    1HXUDO1HWZRUN3URPRWHU3UHGLFWLRQ

    KWWSZZZIUXLWIO\RUJVHTBWRROVSURPRWHUKWPO

    3UHGLFWLRQRIWKHSXWDWLYHSURPRWHUVLQ

    SURNDU\RWLFDQGHXNDU\RWLF'1$VHTXHQFHV

    6LJQDO6FDQKWWSELPDVGFUWQLKJRYPROELRVLJQDO

    +RPRORJ\VHDUFKIRUSXEOLVKHG FLVHOHPHQWV

    EDVHGRQ75$16)$&VLJQDOGDWDEDVH

    0$5:L]

    KWWSZZZIXWXUHVRIWRUJ0$5:L]

    'HWHFWLRQRISXWDWLYHPDWUL[DWWDFKPHQWUHJLRQV

    LQHXNDU\RWLF'1$VHTXHQFHV

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    37/50

    7DEOH &RPPRQFLVDFWLQJHOHPHQWVLQYROYHGLQWHPSRUDODQGRUVSDWLDOUHJXODWLRQRI

    JHQHH[SUHVVLRQLQSODQWV2QO\WUDQVFULSWLRQIDFWRUVIRUZKLFKWKHUHLVVWURQJHYLGHQFH

    VXJJHVWLQJWKHLULPSRUWDQFHLQJHQHUHJXODWLRQDUHLQFOXGHGLQWKLVWDEOH

    5HVSRQVHV &LVHOHPHQWV&RQVHQVXV 7UDQVDFWLQJ)DFWRUV

    /LJKW

    /LJKW

    *7ER[**77$$

    ,ER[*$7$$$*5

    *ER[&$&*7*

    +ER[$&&7$$&&$&

    +

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    38/50

    5()(5(1&(6

    .DWDJLUL)DQG&KXD1+7UHQGV*HQHW

    &KDQGOHU9/DQG9DXFKHUHW+3ODQW3K\VLRO

    5REHUWV6*DQG*UHHQ051DWXUH

    *XLOIR\OH7*HQHWLF(QJLQHHULQJ3ULQFLSOHVDQG0HWKRGV

    6SHFWRU'/$QQX5HY&HOO%LRO

    5RHGHU5*7UHQGV%LRFKHP6FL

    'YLU$&RQDZD\-:DQG&RQDZD\5&&XUU2SLQ*HQHW'HY

    5RJHUV+-%DWH1&RPEH-6XOOLYDQ-6ZHHWPDQ -6ZDQ&/RQVGDOH

    '0DQG7ZHOO'3ODQW0RO%LRO

    5XVKWRQ35HLQVWDGOHU$/LSND9/LSSRN%DQG6RPVVLFK,(

    3ODQW&HOO

    +RHUHQ)8'ROIHUXV5:X

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    39/50

    &DQWRQ)5DQG4XDLO3+3ODQW3K\VLRO

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    40/50

    0LQDPL(,2]HNL

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    41/50

    2\DPD76KLPXUD

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    42/50

    7KRUQWRQ706ZDLQ60DQG2OV]HZVNL1(7UHQGV3ODQW6FL

    6NULYHU.2OVHQ)/5RJHUV-&DQG0XQG\-3URF1DWO$FDG6FL

    86$

    *XEOHU).DOOD55REHUWV-.DQG-DFREVHQ-93ODQW&HOO

    &HUFRV0*RPH]&DGHQDV$DQG+R7+'3ODQW-

    7UHJHDU-:3ULPDYHVL/)DQG+XWWO\$.3ODQW0RO%LRO

    0RULWD$8PHPXUD7.XUR\DQDJL0)XWVXKDUD

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    43/50

    5ROODQG)0RRUH%DQG6KHHQ-3ODQW&HOO6XSSO

    +ZDQJ

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    44/50

    0F'XIIHH$76HQLVWHUUD*+XQWOH\6/HSRFN-56HNKDU.5

    0HUHGLWK0-%RUUHOOL0-0RUURZ-'DQG)UHHPDQ0/-&HOO

    3K\VLRO

    0LWWOHU5DQG=LOLQVNDV%$-%LRO&KHP

    .XER$6DML+7DQDND.DQG.RQGR1)(%6/HWW

    6WRUR]KHQNR6'H3DXZ39DQ0RQWDJX0,Q]H'DQG.XVKQLU6

    3ODQW3K\VLRO

    5LHSLQJ0DQG6FKRIIO)0RO*HQ*HQHW

    1HLOO65DGKLND'HVLNDQ5DQG+DQFRFN-&XUU2SLQ3ODQW%LRO

    %D[WHU%XUUHOO$

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    45/50

    'ROIHUXV5-DFREV03HDFRFN:-DQG'HQQLV(63ODQW3K\VLRO

    2OLYH05:DONHU-&6LQJK.'HQQLV(6DQG3HDFRFN:-3ODQW

    0RO%LRO

    +RHUHQ)8'ROIHUXV5:X

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    46/50

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    47/50

    :DVKLGD+:X&

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    48/50

    7ZHOO'

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    49/50

    $PDWL%3LFN//DURFKH7DQG*DVVHU60(0%2-

    %RGH-.RKZL

  • 7/30/2019 Functional Analysis of Plant Cis Elements

    50/50

    6XJLXUD0$QQX5HY3ODQW3K\VLRO3ODQW0RO%LRO

    =KX42UGL]0,'DELD7%HDFK\51DQG/DPE& 3ODQW&HOO

    ,VKLJH)7DNDLFKL0)RVWHU5&KXD1+DQG2HGD.3ODQW-

    .XVQDGL$5+RRG((:LWFKHU'5+RZDUG-$DQG1LNRORY=/

    %LRWHFKQRO3URJ

    .RPDUQ\WVN\6%RULVMXN19%RULVMXN/*$ODP0=DQG5DVNLQ,

    3ODQW3K\VLRO

    %RULVMXN19%RULVMXN/*/RJHQGUD63HWHUVHQ)*OHED