0 13 Transcription Transcription NNP 14 20 factor factor NN 21 28 binding binding NN 29 34 sites site NNS 35 45 downstream downstream JJ 46 48 of of IN 49 52 the the DT 53 58 human human JJ 59 75 immunodeficiency immunodeficiency NN 76 81 virus virus NN 82 86 type type NN 87 88 1 1 CD 89 102 transcription transcription NN 103 108 start start NN 109 113 site site NN 114 117 are be VBP 118 127 important important JJ 128 131 for for IN 132 137 virus virus NN 138 149 infectivity infectivity NN 149 150 . . . 152 156 When when WRB 157 174 transcriptionally transcriptionally RB 175 181 active active JJ 181 182 , , , 183 186 the the DT 187 192 human human JJ 193 209 immunodeficiency immunodeficiency NN 210 215 virus virus NN 216 217 ( ( ( 217 220 HIV HIV NNP 220 221 ) ) ) 222 230 promoter promoter NN 231 239 contains contain VBZ 240 241 a a DT 242 257 nucleosome-free nucleosome-free JJ 258 264 region region NN 265 277 encompassing encompass VBG 278 282 both both CC 283 286 the the DT 287 304 promoter/enhancer promoter/enhancer NN 305 311 region region NN 312 315 and and CC 316 317 a a DT 318 323 large large JJ 324 330 region region NN 331 332 ( ( ( 332 335 255 255 CD 336 347 nucleotides nucleotide NNS 348 349 [ [ ( 349 351 nt nt NN 351 352 ] ] ) 352 353 ) ) ) 354 364 downstream downstream JJ 365 367 of of IN 368 371 the the DT 372 385 transcription transcription NN 386 391 start start NN 392 396 site site NN 396 397 . . . 398 400 We we PRP 401 405 have have VBP 406 416 previously previously RB 417 427 identified identify VBN 428 431 new new JJ 432 439 binding bind VBG 440 445 sites site NNS 446 449 for for IN 450 463 transcription transcription NN 464 471 factors factor NNS 472 482 downstream downstream RB 483 485 of of IN 486 489 the the DT 490 503 transcription transcription NN 504 509 start start NN 510 514 site site NN 515 516 ( ( ( 516 518 nt nt NNS 519 522 465 465 CD 523 525 to to TO 526 529 720 720 CD 529 530 ) ) ) 530 531 : : : 532 537 three three CD 538 542 AP-1 ap-1 NN 543 548 sites site NNS 549 550 ( ( ( 550 551 I i NN 551 552 , , , 553 555 II ii CD 555 556 , , , 557 560 and and CC 561 564 III iii CD 564 565 ) ) ) 565 566 , , , 567 569 an an DT 570 578 AP3-like ap3-like JJ 579 584 motif motif NN 585 586 ( ( ( 586 591 AP3-L AP3-L NNP 591 592 ) ) ) 592 593 , , , 594 595 a a DT 596 606 downstream downstream JJ 607 614 binding binding NN 615 621 factor factor NN 622 623 ( ( ( 623 626 DBF DBF NNP 626 627 ) ) ) 628 632 site site NN 632 633 , , , 634 637 and and CC 638 648 juxtaposed juxtapose VBN 649 652 Sp1 sp1 NN 653 658 sites site NNS 658 659 . . . 660 664 Here here RB 664 665 , , , 666 668 we we PRP 669 673 show show VBP 674 678 that that IN 679 682 the the DT 683 686 DBF DBF NNP 687 691 site site NN 692 694 is be VBZ 695 697 an an DT 698 719 interferon-responsive interferon-responsive JJ 720 726 factor factor NN 727 728 ( ( ( 728 731 IRF IRF NNP 731 732 ) ) ) 733 740 binding binding NN 741 745 site site NN 746 749 and and CC 750 754 that that IN 755 758 the the DT 759 764 AP3-L AP3-L NNP 765 770 motif motif NN 771 776 binds bind VBZ 777 780 the the DT 781 796 T-cell-specific t-cell-specific JJ 797 803 factor factor NN 804 809 NF-AT nf-at NN 809 810 . . . 811 820 Mutations mutation NNS 821 825 that that WDT 826 833 abolish abolish VBP 834 837 the the DT 838 845 binding binding NN 846 848 of of IN 849 853 each each DT 854 860 factor factor NN 861 863 to to TO 864 867 its its PRP$ 868 875 cognate cognate JJ 876 880 site site NN 881 884 are be VBP 885 895 introduced introduce VBN 896 898 in in IN 899 901 an an DT 902 912 infectious infectious JJ 913 918 HIV-1 HIV-1 NNP 919 928 molecular molecular JJ 929 934 clone clone NN 935 937 to to TO 938 943 study study VB 944 949 their their PRP$ 950 956 effect effect NN 957 959 on on IN 960 965 HIV-1 HIV-1 NNP 966 979 transcription transcription NN 980 983 and and CC 984 995 replication replication NN 995 996 . . . 997 1007 Individual individual JJ 1008 1016 mutation mutation NN 1017 1019 of of IN 1020 1023 the the DT 1024 1027 DBF DBF NNP 1028 1030 or or CC 1031 1036 AP3-L AP3-L NNP 1037 1041 site site NN 1042 1044 as as RB 1045 1049 well well RB 1050 1052 as as IN 1053 1056 the the DT 1057 1063 double double JJ 1064 1072 mutation mutation NN 1073 1088 AP-1(III)/AP3-L AP-1(III)/AP3-L NNP 1089 1092 did do VBD 1093 1096 not not RB 1097 1103 affect affect VB 1104 1109 HIV-1 HIV-1 NNP 1110 1121 replication replication NN 1122 1130 compared compare VBN 1131 1133 to to TO 1134 1138 that that DT 1139 1141 of of IN 1142 1145 the the DT 1146 1155 wild-type wild-type JJ 1156 1161 virus virus NN 1161 1162 . . . 1163 1165 In in IN 1166 1174 contrast contrast NN 1174 1175 , , , 1176 1186 proviruses provirus NNS 1187 1195 carrying carry VBG 1196 1205 mutations mutation NNS 1206 1208 in in IN 1209 1212 the the DT 1213 1216 Sp1 sp1 NN 1217 1222 sites site NNS 1223 1227 were be VBD 1228 1235 totally totally RB 1236 1245 defective defective JJ 1246 1248 in in IN 1249 1254 terms term NNS 1255 1257 of of IN 1258 1269 replication replication NN 1269 1270 . . . 1271 1276 Virus virus NN 1277 1287 production production NN 1288 1296 occurred occur VBD 1297 1301 with with IN 1302 1310 slightly slightly RB 1311 1318 delayed delay VBN 1319 1327 kinetics kinetic NNS 1328 1331 for for IN 1332 1339 viruses virus NNS 1340 1350 containing contain VBG 1351 1359 combined combined JJ 1360 1369 mutations mutation NNS 1370 1372 in in IN 1373 1376 the the DT 1377 1386 AP-1(III) ap-1(iii) NN 1386 1387 , , , 1388 1393 AP3-L AP3-L NNP 1393 1394 , , , 1395 1398 and and CC 1399 1402 DBF DBF NNP 1403 1408 sites site NNS 1409 1412 and and CC 1413 1415 in in IN 1416 1419 the the DT 1420 1425 AP3-L AP3-L NNP 1426 1429 and and CC 1430 1439 DBF-sites DBF-site NNP 1439 1440 , , , 1441 1448 whereas whereas IN 1449 1456 viruses virus NNS 1457 1464 mutated mutate VBN 1465 1467 in in IN 1468 1471 the the DT 1472 1486 AP-1(I,II,III) AP-1(I,II,III) NNP 1487 1490 and and CC 1491 1496 AP3-L ap3-l NN 1497 1502 sites site NNS 1503 1506 and and CC 1507 1509 in in IN 1510 1513 the the DT 1514 1528 AP-1(I,II,III) ap-1(i,ii,iii) NN 1528 1529 , , , 1530 1535 AP3-L AP3-L NNP 1535 1536 , , , 1537 1540 and and CC 1541 1544 DBF DBF NNP 1545 1550 sites site NNS 1551 1560 exhibited exhibit VBD 1561 1562 a a DT 1563 1571 severely severely RB 1572 1581 defective defective JJ 1582 1593 replicative replicative JJ 1594 1603 phenotype phenotype NN 1603 1604 . . . 1605 1607 No no DT 1608 1621 RNA-packaging rna-packaging JJ 1622 1628 defect defect NN 1629 1634 could could MD 1635 1637 be be VB 1638 1646 measured measure VBN 1647 1650 for for IN 1651 1654 any any DT 1655 1657 of of IN 1658 1661 the the DT 1662 1668 mutant mutant JJ 1669 1676 viruses virus NNS 1677 1679 as as IN 1680 1690 determined determine VBN 1691 1693 by by IN 1694 1708 quantification quantification NN 1709 1711 of of IN 1712 1717 their their PRP$ 1718 1721 HIV HIV NNP 1722 1729 genomic genomic JJ 1730 1733 RNA RNA NNP 1733 1734 . . . 1735 1746 Measurement Measurement NNP 1747 1749 of of IN 1750 1753 the the DT 1754 1769 transcriptional transcriptional JJ 1770 1778 activity activity NN 1779 1781 of of IN 1782 1785 the the DT 1786 1791 HIV-1 HIV-1 NNP 1792 1800 promoter promoter NN 1801 1806 after after IN 1807 1816 transient transient JJ 1817 1829 transfection transfection NN 1830 1832 of of IN 1833 1836 the the DT 1837 1842 HIV-1 HIV-1 NNP 1843 1851 provirus provirus NN 1852 1855 DNA dna NN 1856 1858 or or CC 1859 1861 of of IN 1862 1866 long long JJ 1867 1875 terminal terminal JJ 1876 1893 repeat-luciferase repeat-luciferase NN 1894 1904 constructs construct NNS 1905 1911 showed show VBD 1912 1913 a a DT 1914 1922 positive positive JJ 1923 1934 correlation correlation NN 1935 1942 between between IN 1943 1946 the the DT 1947 1962 transcriptional transcriptional JJ 1963 1966 and and CC 1967 1970 the the DT 1971 1982 replication replication NN 1983 1990 defects defect NNS 1991 1994 for for IN 1995 1999 most most JJS 2000 2007 mutants mutant NNS 2007 2008 . . .