`
`Replacement Sheet
`
`Sheet 1 of 13
`
`MRO REFS 4(768bp)
`
`MIRBOALBFS 1485p
`
`
`
`MIR6O4 WELBFS 4IRBES 1
`1582 bp
`
`FIG. 1
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet 2 of 13
`
`Donor DNA
`
`
`
`Homology Arn
`
`
`_ Cecaos |_ pityNos
`
`
`
`
`Safe harborlocus#4 faReo4 evevent insertion site}
`
`Qf Site-directed nuclease (e.g. TALEN
`J\ and CRISPR-Cas9}
`
` pr
`HomologyArm| prOMPeCrySANos
`|_itchNos
`| prUbit-oPillos
`{pgmLACEINETSESINOEAe
`a wnprabe (rCMP)
`Probe {cPsae
`ecm i
`
`
`A
`ANINT Probe (native sequences
`Bsu36i
`flanking homology ars }
`
`
`A
`Bsu3Gl
`
`\
`
`Targeted insertion event in the safe harbor locus #1
`
`FG. 2
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet 3 of 13
`
`
`
`FG.3
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet 4 of 13
`
`
`
`oOAIQWICaG{}JOdsanig#GAY
`
` axeontmM——_—
`
`FIG. 4
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
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`Replacement Sheet
`
`Sheet 5 of 13
`
`12345678
`
`
`
`Probe 1
`
`ase
`
`veut
`MKD
`
`
`
`
`
`12343678
`
`12345678
`
`FG. 5
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
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`Replacement Sheet
`
`Sheet6 of 13
`
`She-ditactad tuclaase
`dleavage al the Mlarget
`
`
`
`eachallele
`
`{
`
`0
`
`0
`
`Small inDel in one
`aliale
`
`Small InDelinboth
`alleles,
`
`Small InDel and
`large deletion in
`
`FIG. 6
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet 7 of 13
`
`Detecting targeted mutagenesis: Taqman assay design
`
`
`
`
`ea mnemympainn
`spree
`.
`eeNUedlagste~ nameenananes
`
` ANY ANY
`CTOONGR CACTCST TMAGRAGGTN ASSAGTAGTCAGGHG AGROTIGITINGA CMGRTNTS
`GUGACOCETT GTEGGAQCA BCGSTTTOR CGIRGGGACG THACGTAACG TUACGIOCTS TOCTGRanh ANCAAATCOT GOCTACGAC
`aviare
`
` ERE RT CO ERR*5%‘
`
`:
`
`‘‘%‘‘%
`$
`SAS‘‘;
`:
`:
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`gag tt me wea
`eS Qe TE
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`eed
`:
`ot
`i
`fh
`f
`y.
`‘
`i
`:
`.
`Baarauinniinnniiiiniiiiiiiiniiiinittiint iiniitttitinnnintiie eitetttbnntitinttitnttithettUE GSUULERASURERUNGHENNSCUSAR GuaGEAR
`:::
`‘..
`:
`:
`‘
`gt
`oe
`:
`:
`7
`‘
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`2.
`.
`*
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`5
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`SASKANAGAANRGAESAEAAASASCAAGANEE HSEGACSHEGEASGERGAARECGEGHEE
`
`:
`NENW}NNERANNESSNNER
`
`NSSNNNRERN
`
`SNSS
`
`;
`
`’
`
`ANNAN
`
`SSS
`
`ANNREAD
`
`rat
`
`ag
`
`sEAN
`
`FG.7
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet 8 of 13
`
`(A) Target sequence status in different types of events
`
`I, Event without targeted insertion
`
`i], Event with targeted insertion
`
`t
`
` a0)
`
`al
`
`
`
`cn
`AC
`
`
`
`
`~
`
`seesseecenseneenseney,
`
`Lindel | Large deletion
`
`EOI
`
`largeted insertion
`
`FIG. 8A
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet 9 of 13
`
`(B) Copy numbercall of different types of events
`
`
`Event with no targetedinsertion
`
`a} WT no mutation in both allies
`
`b} Small inde! n one allele
`
`©} Sinall indelin both alleles
`
`df} Small indel in oneallele
`and largedeletion in anotherallele
`¢} Large insertion in both alleles
`
`Event with targeted insertion
`
`i} No mutation i one aliais, targeted
`insertion in another allela
`
`g} Small indel in each alieie, targeted
`msenion in anotherallele
`
`h} Large deletion in in each allele,
`targeted insertion in another allele
`
`{i Targeted insertion in both alleles
`
`é
`
`2
`
`2
`
`{
`
`Q
`
`‘
`
`,
`
`Q
`
`oe
`
`FIG.8B (cont'd.)
`
`2
`
`{
`
`0
`
`(
`
`}
`
`j
`
`}
`
`Q
`
`ma
`
`>
`
`>d
`
`>d
`
`>)
`
`>
`
`>4
`
`of
`
`if
`
`$3
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet 10 of 13
`
`NOS (253 bp)
`|
`piZmlbit (1998 bp)
`|
`cPM-O1 (1176 bp)
`(
`INOS (253 bp)
`LBFS (1786 bp)
`
`©
`
`7
`
`
`prZmNfTL (2556 bp)
`RBFS(1451 bp}
`
`\
`
`menGA (1797 bp)
`
`|
`|
`
`
`
`MIR604 RBFS_pNOV2130 T-DNA insert_LBFS
`{1622 bp
`
`FG. 9
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet 11 of 13
`
`TALEN cul
`yi
`<
`
` MIR604 transgenic locus
`em(nsa | PM
`
`sesaarieeessdonniePivaGeUs WY
`
`y11y11
`
`
`\
`
`\
`\
`
`
`oveenesennensennmnogeniny enanennrnnanennnnanennannanensen MARANA
`EBES
`oa
`Bovwnnnnneny
`fevercecee.
`Benen.why
`_hasnnennnnnnnnnnnnasinnnniNSIS NILe.me
`| orbit|cP
`~
`IC Exp. Cass,
`| EPSPS Exp, cass.
`| MI
`Sorceteranatsts
`Donor DNA
`4
`\
`(22872)
`\
`\
`‘\wassvunnsunnnnennans,aassennnsonnnnnnnnne?
`
`SOSAKneAKRAM
`
`sarahiniNNNRNAROANA
`‘
`:
`;
`‘
`Lassasanaunnninn!
`
`\
`
`LS bp
`
`Targeted integration
`
`utUra
`
`
`
`
`
`12 Kb
`
`«i
`
`PA (FE35034)
`P2 {FE4793}
`&NY
`i4444‘MS
`
`prUbil|cP) ICEyp.Cass / EPSPS Ep. Cass, |
`| mCry T7
`MTL
`peewerereceBeeccceece
`fom
`dmnnsey,
`%
`:
`ny
`:
`&
`‘
`
`
`oofcommnanmemneaneinemenancnnnemenanenteatReenTwlehomonnrconndOMRON AAA
`soon
`ay
`PL{FEATIG |
`Targeted insertionvia
`P3(FE35035)
` ae
`
`homologous recombination9“yn ”
`LAK
`20K
`
`Note: Drawing not to scale
`
`Fig. 10
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet12 of 13
`
`Site-directed nuclease cut(s}
`
`:
`
`|RBESnnnen~nnan ges~MIR604transgeniclocus ToTFatty
`
`$t$pnCPM
`casera
`ARRONKERARALAEOARAtoSEENSRW RA ARS:
`
`
`
`.
`
`
`
`-AWWANANAMANAARIVARARATANAAAAARARABARARAAAAAN,
`
`IC Exp. Cass,
`SAAAAEAAAARASAGEAAAAHASAISANABAENAALMA
`
`Beececeeeedtae
` PAT Exp, Cass.
`Percerercery
`
`Donor DNA
`
`LEGEPPEEEOLOEEEEEEUEEELOEEEEEEEOUEEEE,
`
`Targeted insertion via
`homologous recombination
`
`eeunbtnnaneitinahhnaahinehAARNEnNNNAAN
`
`—
`
`steeeneneneseennaneeaneneenenen
`
`asenaGRUGAGREARAEAA
`
`
`
`
` mibp.Casszpores
`PrMTL | mCn3A |to _t Exp, Cass,
`
`
`ARAN
`
`ay aad
`
`sannannaanneannnennnn! -sonnannnnnnsnnnnnnntSOR
`
`Targeted recombinant event
`
`Note: Drawing not to scale
`
`Fig, 14
`
`
`
`ATTY DOCKET NO.: 80484-US-REG-D-NAT-2
`
`Replacement Sheet
`
`Sheet13 of 13
`
`“klte-Cirected nuclease cutis) MN
`tt,4Naty DS RR ARE RRA RES
`+ _'
`i
`_pasencecnsuensentnncenesensuencea eeeeneTCHGUESSEREERE
`$
`{BFS
`ytiyt
`
`
`MiR604 transgenic locus
`
`Sy
`
`ihoee aRY RAE ARH RAE AE
`
`AWAY ANAKEAE AY >
`‘\
`we
`
`
`
` Donor DNA
`
`Targeted integration via
`+ homologous recombination
`
`
`
`Targeted recombinant event
`
`Note: Drawing not to scale
`
`Fig. 12
`
`