Methods and compositions for modification of a HLA locus

1. A protein comprising an engineered zinc finger DNA-binding domain, wherein the engineered zinc finger DNA-binding domain comprises four, five or six zinc finger DNA recognition regions designated and ordered F1 to F4, F1 to F5 or F1 to F6 from N-terminus to C-terminus and further wherein the engineered zinc finger DNA-binding domain comprises the zinc finger DNA recognition regions selected from the group consisting of:

(i) F1: QSSHLTR (SEQ ID NO:1);

F2: RSDHLTT (SEQ ID NO:2);

F3: RSDTLSQ (SEQ ID NO:3);

F4: RSADLSR (SEQ ID NO:4);

F5: QSSDLSR (SEQ ID NO:5); and

F6: RSDALTQ (SEQ ID NO:6), wherein the protein binds to the target site set forth in SEQ ID NO:97 in an endogenous human leukocyte antigen (HLA) A2 gene;

(ii) F1: QKTHLAK (SEQ ID NO:7);

F2: RSDTLSN (SEQ ID NO:8);

F3: RKDVRIT (SEQ ID NO:9);

F4: RSDHLST (SEQ ID NO:10); and

F5: DSSARKK (SEQ ID NO:11), wherein the protein binds to the target site set forth in SEQ ID NO:98 in an endogenous HLA A2 gene;

(iii) F1: QNAHRKT (SEQ ID NO:12);

F2: RSDSLLR (SEQ ID NO:13);

F3: RNDDRKK (SEQ ID NO:14);

F4: RSDHLST (SEQ ID NO:10); and

F5: DSSARKK (SEQ ID NO:11), wherein the protein binds to the target site set forth in SEQ ID NO:99 in an endogenous HLA A2 gene;

(iv) F1: DRSHLSR (SEQ ID NO:15);

F2: RSDDLTR (SEQ ID NO:16);

F3: DRSDLSR (SEQ ID NO:17); and

F4: QSGHLSR (SEQ ID NO:18), wherein the protein binds to the target site set forth in SEQ ID NO:100 in an endogenous HLA A3 gene;

(v) F1: DRSALSR (SEQ ID NO:19);

F2: QSSDLRR (SEQ ID NO:20);

F3: DRSALSR (SEQ ID NO:19);

F4: DRSHLAR (SEQ ID NO:21);

F5: RSDDLSK (SEQ ID NO:22); and

F6: DRSHLAR (SEQ ID NO:21), wherein the protein binds to the target site set forth in SEQ ID NO:101 in an endogenous HLA A3 gene;

(vi) F1: SSELLNE (SEQ ID NO:23);

F2: TSSHLSR (SEQ ID NO:24);

F3: QSGDRNK (SEQ ID NO:25);

F4: RSANLAR (SEQ ID NO:26); and

F5: RSDNLRE (SEQ ID NO:27), wherein the protein binds to the target site set forth in SEQ ID NO:102 in an endogenous HLA B gene;

(vii) F1: QSGDLTR (SEQ ID NO:28);

F2: RSDDLTR (SEQ ID NO:16);

F3: DQSTLRN (SEQ ID NO:29);

F4: DRSNLSR (SEQ ID NO:30); and

F5: DAFTRTR (SEQ ID NO:31), wherein the protein binds to the target site set forth in SEQ ID NO:103 in an endogenous HLA B gene;

(viii) F1: RSDNLSE (SEQ ID NO:32);

F2: ASKTRKN (SEQ ID NO:33);

F3: TSGNLTR (SEQ ID NO:34); and

F4: RSDALAR (SEQ ID NO:35), wherein the protein binds to the target site set forth in SEQ ID NO:104 in an endogenous HLA B gene;

(ix) F1: DRSALSR (SEQ ID NO:19);

F2: QSGNLAR (SEQ ID NO:36);

F3: DRSALSR (SEQ ID NO:19);

F4: QSGHLSR (SEQ ID NO:18), wherein the protein binds to the target site set forth in SEQ ID NO:105 in an endogenous HLA B gene;

(x) F1: RSDNLSE (SEQ ID NO:32);

F2: ASKTRKN (SEQ ID NO:33);

F3: QSGHLSR (SEQ ID NO:18);

F4: TSGHLSR (SEQ ID NO:37); and

F5: QSGHLSR (SEQ ID NO:18), wherein the protein binds to the target site set forth in SEQ ID NO:106 in an endogenous HLA B gene;

(xi) F1: RSADLTR (SEQ ID NO:38);

F2: QSGDLTR (SEQ ID NO:28);

F3: QSGNLAR (SEQ ID NO:36); and

F4: QSGDLTR (SEQ ID NO:28), wherein the protein binds to the target site set forth in SEQ ID NO:107 in an endogenous HLA B gene;

(xii) F1: QSGHLSR (SEQ ID NO:18);

F2: RSDHLST (SEQ ID NO:10);

F3: QSADRTK (SEQ ID NO:39);

F4: TSGSLSR (SEQ ID NO:40); and

F5: QSADRTK (SEQ ID NO:39), wherein the protein binds to the target site set forth in SEQ ID NO:108 in an endogenous HLA C gene;

(xiii) F1: QSGDLTR (SEQ ID NO:28);

F2: RSDHLST (SEQ ID NO:10);

F3: QSADRTK (SEQ ID NO:39);

F4: RSDNLSA (SEQ ID NO:41); and

F5: RSDNRTT (SEQ ID NO:42), wherein the protein binds to the target site set forth in SEQ ID NO:109 in an endogenous HLA C gene;

(xiv) F1: QRSNLVR (SEQ ID NO:43);

F2: DRSALAR (SEQ ID NO:44);

F3: QSSDLRR (SEQ ID NO:20);

F4: RSDDLTR (SEQ ID NO:16); and

F5: RSDDLTR (SEQ ID NO:16), wherein the protein binds to the target site set forth in SEQ ID NO:110 in an endogenous HLA C gene;

(xv) F1: RSDDLTR (SEQ ID NO:16);

F2: DRSDLSR (SEQ ID NO:17);

F3: QSGHLSR (SEQ ID NO:18);

F4: RSDHLSA (SEQ ID NO:45); and

F5: ESRYLMV (SEQ ID NO:46), wherein the protein binds to the target site set forth in SEQ ID NO:111 in an endogenous HLA C gene;

(xvi) F1: RSDHLST (SEQ ID NO:10);

F2: DNANRTK (SEQ ID NO:47);

F3: QSGDLTR (SEQ ID NO:28);

F4: RSDALST (SEQ ID NO:48); and

F5: ASSNRKT (SEQ ID NO:49), wherein the protein binds to the target site set forth in SEQ ID NO:112 in an endogenous DBP2 gene;

(xvii) F1: TSGNLTR (SEQ ID NO:34);

F2: DRSDLSR (SEQ ID NO:17);

F3: RSDNLSE (SEQ ID NO:32);

F4: RSANLTR (SEQ ID NO:50); and

F5: QSGHLSR (SEQ ID NO:18), wherein the protein binds to the target site set forth in SEQ ID NO:113 in an endogenous DBP2 gene;

(xviii) F1: RSDNLSE (SEQ ID NO:32);

F2: TSGSLTR (SEQ ID NO:51);

F3: TSGHLSR (SEQ ID NO:37);

F4: RSDNLSQ (SEQ ID NO:52); and

F5: ASNDRKK (SEQ ID NO:53), wherein the protein binds to the target site set forth in SEQ ID NO:114 in an endogenous DRA gene;

(xix) F1: RSDNLSR (SEQ ID NO:54);

F2: DNNARIN (SEQ ID NO:55);

F3: RSDSLSV (SEQ ID NO:56);

F4: QNQHRIN (SEQ ID NO:57); and

F5: RSDHLSR (SEQ ID NO:58), wherein the protein binds to the target site set forth in SEQ ID NO:115 in an endogenous DRA gene;

(xx) F1: DSSDRKK (SEQ ID NO:59);

F2: DRSHLTR (SEQ ID NO:60);

F3: RSDALAR (SEQ ID NO:35);

F4: QSSDLSR (SEQ ID NO:5); and

F5: RSDNLTT (SEQ ID NO:61), wherein the protein binds to the target site set forth in SEQ ID NO:116 in an endogenous transporter associated with antigen processing 1 (TAP1) gene;

(xxi) F1: RSANLAR (SEQ ID NO:26);

F2: QSGHLSR (SEQ ID NO:18);

F3: TSGNLTR (SEQ ID NO:34);

F4: QSGALVI (SEQ ID NO:62);

F5: RSDHLSE (SEQ ID NO:63); and

F6: RKHDRTK (SEQ ID NO:64), wherein the protein binds to the target site set forth in SEQ ID NO:117 in an endogenous TAP1 gene;

(xxii) F1: QSSDLSR (SEQ ID NO:5);

F2: QSGDLTR (SEQ ID NO:28);

F3: QSSHLTR (SEQ ID NO:1):

F4: RSDDRKT (SEQ ID NO:65);

F5: TSGNLTR (SEQ ID NO:34); and

F6: RSDDLTR (SEQ ID NO:16), wherein the protein binds to the target site set forth in SEQ ID NO:118 in an endogenous transporter associated with antigen processing 2(TAP2) gene;

(xxiii) F1: RSDNLST (SEQ ID NO:66);

F2: RSDALAR (SEQ ID NO:35);

F3: RSDVLSA (SEQ ID NO:67);

F4: DRSNRIK (SEQ ID NO:68);

F5: RREDLIT (SEQ ID NO:69); and

F6: TSSNLSR (SEQ ID NO:70), wherein the protein binds to the target site set forth in SEQ ID NO:119 in an endogenous TAP2 gene;

(xxiv) F1: RSDNLSE (SEQ ID NO:32);

F2: KRCNLRC (SEQ ID NO:71);

F3: DRSDLSR (SEQ ID NO:17);

F4: QTTHRNR (SEQ ID NO:72);

F5: DRSDLSR (SEQ ID NO:17), and

F6: QSSTRAR (SEQ ID NO:73), wherein the protein binds to the target site set forth in SEQ ID NO:120 in an endogenous tapasin gene;

(xxv) F1: QSSDLR (SEQ ID NO:5);

F2: RSDNLTR (SEQ ID NO:74);

F3: QSSHLTR (SEQ ID NO:1);

F4: QSSDLTR (SEQ ID NO:75);

F5: RSDNLAR (SEQ ID NO:76); and

F6: QKVNLMS (SEQ ID NO:77), wherein the protein binds to the target site set forth in SEQ ID NO:121 in an endogenous tapasin gene;

(xxvi) F1: TSGNLTR (SEQ ID NO:34);

F2: LSQDLNR (SEQ ID NO:78);

F3: RSDSLSA (SEQ ID NO:79);

F4: DRSHLAR (SEQ ID NO:21);

F5: RSDHLST (SEQ ID NO:10); and

F6: QSGHLSR (SEQ ID NO:18), wherein the protein binds to the target site set forth in SEQ ID NO:122 in an endogenous tapasin gene;

(xxvii) F1: RSDDLTR (SEQ ID NO:16);

F2: SSSNLTK (SEQ ID NO:80);

F3: TSGSLSR (SEQ ID NO:40);

F4: QSGDLTR (SEQ ID NO:28);

F5: RSDHLSE (SEQ ID NO:63); and

F6: RNRDRIT (SEQ ID NO:81), wherein the protein binds to the target site set forth in SEQ ID NO:123 in an endogenous tapasin gene;

(xxviii) F1: RSDDLTR (SEQ ID NO:16);

F2: RSDHLSE (SEQ ID NO:63);

F3: NSRNRKT (SEQ ID NO:82);

F4: RSDNLSQ (SEQ ID NO:52); and

F5: ASNDRKK (SEQ ID NO:53), wherein the protein binds to the target site set forth in SEQ ID NO:124 in an endogenous class 2 transactivator (CTIIA) gene;

(xxvix) F1: RSDDLSR (SEQ ID NO:83);

F2: RNDDRKK (SEQ ID NO:14);

F3: DRSDLSR (SEQ ID NO:17);

F4: RSDHLSE (SEQ ID NO:63); and

F5: ARSTRTN (SEQ ID NO:84), wherein the protein binds to the target site set forth in SEQ ID NO:125 in an endogenous CTIIIA gene;

(xxx) F1: TSGNLTR (SEQ ID NO:34);

F2: QSGNLAR (SEQ ID NO:36);

F3: RSDHLTQ (SEQ ID NO:85);

F4: ASMALNE (SEQ ID NO:86); and

F5: TSSNLSR (SEQ ID NO:70), wherein the protein binds to the target site set forth in SEQ ID NO:126 in an endogenous regulatory factor X protein 5 (RXF5) gene;

(xxxi) F1: RSDVLSE (SEQ ID NO:87);

F2: RNQHRKT (SEQ ID NO:88);

F3: RSDHLST (SEQ ID NO:10);

F4: QSSDLRR (SEQ ID NO:20);

F5: RSDNLST (SEQ ID NO:66); and

F6: RSADRKN (SEQ ID NO:89), wherein the protein binds to the target site set forth in SEQ ID NO:127 in an endogenous RXF5 gene;

(xxxii) F1: QSGDLTR (SEQ ID NO:28);

F2: QWGTRYR (SEQ ID NO:90);

F3: ERGTLAR (SEQ ID NO:91);

F4: RSDNLRE (SEQ ID NO:27);

F5: QSGDLTR (SEQ ID NO:28); and

F6: TSGSLTR (SEQ ID NO:51), wherein the protein binds to the target site set forth in SEQ ID NO:128 in an endogenous T-cell receptor alpha (TRAC) gene;

(xxxiii) F1: QSGDLTR (SEQ ID NO:28);

F2: WRSSLAS (SEQ ID NO:92);

F3: QSGDLTR (SEQ ID NO:28);

F4: HKWVLRQ (SEQ ID NO:93); and

F5: DRSNLTR (SEQ ID NO:94), wherein the protein binds to the target site set forth in SEQ ID NO:129 in an endogenous TRAC gene;

(xxxiv)F1: RSDVLSA (SEQ ID NO:67);

F2: DRSNRIK (SEQ ID NO:68);

F3: RSDVLSE (SEQ ID NO:87);

F4: QSGNLAR (SEQ ID NO:36); and

F5: QSGSLTR (SEQ ID NO:95), wherein the protein binds to the target site set forth in SEQ ID NO:130 in an endogenous T-cell receptor beta (TRBC) gene; and

(xxxv) F1: RSDHLST (SEQ ID NO:10);

F2: RSDNLTR (SEQ ID NO:74);

F3: DRSNLSR (SEQ ID NO:30);

F4: TSSNRKT (SEQ ID NO:96);

F5: RSANLAR (SEQ ID NO:26); and

F6: RNDDRKK (SEQ ID NO:14), wherein the protein binds to the target site set forth in SEQ ID NO:131 in an endogenous TRBC gene.

2. A fusion protein comprising the engineered zinc finger DNA-binding domain of claim 1 and a transcriptional regulatory domain or a nuclease domain.

3. The fusion protein of claim 2 wherein the transcriptional regulatory domain comprises an activation domain or a repression domain.

4. An isolated cell comprising the fusion protein of claim 2 .

5. The fusion protein 2 , wherein the nuclease domain comprises a cleavage domain or cleavage half-domain.

6. A polynucleotide encoding the protein of claim 1 .

7. A gene delivery vector comprising the polynucleotide according to claim 6 .

8. An isolated cell comprising the protein according to claim 1 .

9. The isolated cell of claim 8 , wherein the cell is selected from the group consisting of a stem cell, a progenitor cell, a T-cell or a Natural Killer (NK) cell.