| Genome-wide mapping of ORC and Mcm2p binding sites on tiling arrays and identification of essential ARS consensus sequences in S. cerevisiae. |
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Weihong Xu, Jennifer G Aparicio, Oscar M Aparicio, Simon Tavaré |
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BMC Genomics (2006), 7():276 |
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| BACKGROUND: Eukaryotic replication origins exhibit different initiation efficiencies and activation times within S-phase. Although local chromatin structure and function influences origin activity, the exact mechanisms remain poorly understood. A key to understanding the exact features of chromatin that impinge on replication origin function is to define the precise locations of the DNA sequences that control origin function. In S. cerevisiae, Autonomously Replicating Sequences (ARSs) contain a consensus sequence (ACS) that binds the OriginRecognition Complex (ORC) and is essential for origin function. However, an ACS is not sufficient for origin function and the majority of ACS matches do not function as ORC binding sites, complicating the specific identification of these sites. RESULTS: To identify essential origin sequences genome-wide, we utilized a tiled oligonucleotide array (NimbleGen) to map the ORC and Mcm2p binding sites at high resolution. These binding sites define a set of potential Autonomously Replicating Sequences (ARSs), which we term nimARSs. The nimARS set comprises 529 ORC and/or Mcm2p binding sites, which includes 95% of known ARSs, and experimental verification demonstrates that 94% are functional. The resolution of the analysis facilitated identification of potential ACSs (nimACSs) within 370 nimARSs. Cross-validation shows that the nimACS predictions include 58% of known ACSs, and experimental verification indicates that 82% are essential for ARS activity. CONCLUSION: These findings provide the most comprehensive, accurate, and detailed mapping of ORC binding sites to date, adding to the emerging picture of the chromatin organization of the budding yeast genome. |
OriDB annotation of this paper:
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Origin site(s) analysed by ARS assay:
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ARS102, ARS102.5, ARS103, ARS104, ARS105, ARS106, ARS107, ARS107.5, ARS108, ARS111, ARS112, ARS113, ARS200, ARS201, ARS202, ARS203, ARS206, ARS207, ARS207.1, ARS207.8, ARS208, ARS210.5, ARS211, ARS212, ARS213, ARS214, ARS215, ARS215.5, ARS216, ARS217, ARS218, ARS219, ARS219.5, ARS220, ARS221, ARS221.5, ARS222, ARS222.5, ARS223, ARS224, ARS225, ARS227, ARS228, ARS228.5, ARS229, ARS400, ARS402.5, ARS405.5, ARS413.5, ARS426.5, ARS427.5, ARS429.5, ARS430.5, ARS603.1, ARS608.5, ARS1007.5, ARS1009.5, ARS1016, ARS1017, ARS1017.5, ARS1018.5. |
Origin site(s) analysed by 2D gel analysis: |
None curated. |
Predicted ACS element: |
ARS107, ARS108, ARS109, ARS110, ARS111, ARS112, ARS109, ARS110, ARS111, ARS113, ARS201, ARS202, ARS206, ARS207, ARS208, ARS209, ARS211, ARS212, ARS at , ARS at , ARS216, ARS217, ARS218, ARS219, ARS at II-587, ARS220, ARS221, ARS221.5, ARS222, ARS219.5, ARS224, ARS at , ARS229, ARS228.5, ARS300, ARS at , ARS320, ARS301, ARS304, ARS305, ARS306, ARS307, ARS at , ARS309, ARS at , ARS310, ARS314, ARS313, ARS315, ARS319, ARS316, ARS at III-138, ARS at IV-9, ARS403, ARS400, ARS404, ARS402.5, ARS406, ARS409.5, ARS409, ARS412, ARS413, ARS405.5, ARS415, ARS413.5, ARS416, ARS417, ARS417.5, ARS418, ARS419, ARS420, ARS421, ARS422, ARS422.5, ARS423, ARS425, ARS at IV-444, ARS at IV-899, ARS102, ARS102.5, ARS104, ARS105, ARS106, ARS428, ARS429, ARS430, ARS429.5, ARS431, ARS431.5, ARS at , ARS432.5, ARS433, ARS435, ARS at , ARS at IV-1380, ARS440, ARS441, ARS442, ARS446, ARS447, ARS at IV-1524, ARS at , ARS at IV-1531, ARS at , ARS at V-12, ARS507, ARS508, ARS510, ARS511, ARS at V-68, ARS512, ARS at V-256, ARS513.5, ARS513.5, ARS514, ARS at V-302, ARS at V-317, ARS516, ARS518, ARS519, ARS520, ARS521, ARS522, ARS523, ARS at V-184, ARS600.1, ARS600.1, ARS600.2, ARS600.4, ARS602, ARS603, ARS at VII-33, ARS604, ARS605, ARS606, ARS607, ARS608, ARS609, ARS610, ARS at , ARS at , ARS at VII-17, ARS at VII-553, ARS702, ARS704, ARS at , ARS706, ARS at VII-187, ARS710, ARS at VII-241, ARS714, ARS716, ARS at , ARS at , ARS719, ARS721, ARS722, ARS at VII-654, ARS727, ARS728, ARS731.5, ARS733, ARS734, ARS at VII-1002, ARS at VII-1063, ARS at VIII-111, ARS131a, ARS131a, ARS at VII-1090, ARS at VIII-452, ARS131n, ARS802, ARS at VIII-46, ARS805, ARS810, ARS810, ARS813, ARS at VIII-381, ARS818, ARS820, ARS822, ARS823, ARS823.5, ARS at IX-190, ARS at , ARS824, ARS at IX-226, ARS at IX-407, ARS at IX-8, ARS at IX-17, ARS at IX-34, ARS at IX-81, ARS909, ARS at , ARS911.5, ARS912, ARS913, ARS1009.5, ARS913.5, ARS914, ARS916, ARS at , ARS920, ARS at , ARS922, ARS at IX-433, ARS1018.5, ARS1001, ARS1002, ARS1003, ARS1004, ARS1005, ARS1006, ARS1007, ARS1007.5, ARS at , ARS at , ARS at X-702, ARS at , ARS at , ARS1015, ARS at , ARS at XI-200, ARS at , ARS at XI-236, ARS at , ARS1021, ARS1023, ARS at , ARS at , ARS at XI-1, ARS1103, ARS1104.5, ARS1106.3, ARS1106.7, ARS at XII-7, ARS at XI-302, ARS1109, ARS1112, ARS1114, ARS1114.5, ARS at XI-463, ARS1116, ARS at XI-530, ARS1118, ARS1120, ARS at XI-633, ARS1123, ARS at XI-662, ARS at XI-662, ARS at XII-1, ARS at XII-607, ARS at XII-12, ARS at XII-52, ARS1206, ARS at XII-140, ARS1209, ARS at XII-645, ARS1211, ARS1211.5, ARS1212.5, ARS1213, ARS1215, ARS1216, ARS1216.5, ARS at XII-786, ARS1217, ARS1218, ARS at XII-839, ARS at XII-623, ARS1220, ARS1223, ARS at XIII-1, ARS1226, ARS1227.5, ARS at XII-928, ARS at , ARS at XII-1043, ARS1235, ARS at XII-1064, ARS at XII-1071, ARS at XIII-74, ARS at XIII-269, ARS at XIII-6, ARS1304, ARS at XIII-342, ARS1305, ARS1307, ARS1307.5, ARS at , ARS1310, ARS at XIV-1, ARS at XIV-253, ARS1312, ARS1316, ARS1320, ARS at XIV-705, ARS at , ARS1325, ARS1327, ARS at , ARS1330, ARS at XIII-837, ARS1331.5, ARS at XIII-879, ARS at , ARS at XIII-923, ARS at XV-24, ARS at XIV-9, ARS at XIV-9, ARS at XIV-15, ARS1405, ARS1406, ARS1407, ARS at XIV-127, ARS1411, ARS1412, ARS1413, ARS1414, ARS1415, ARS at XV-160, ARS1419, ARS at , ARS1421, ARS1422, ARS1424, ARS1426, ARS at , ARS at XIV-764, ARS at XIV-783, ARS at XV-1, ARS at XV-11, ARS at XV-19, ARS1506.5, ARS1507, ARS1508, ARS1509, ARS1509.5, ARS1510, ARS at XV-309, ARS at XV-445, ARS1513, ARS at XV-497, ARS at XV-459, ARS at XV-464, ARS1514, ARS at XV-521, ARS at XV-618, ARS at XV-1023, ARS at XV-682, ARS1521, ARS1523, ARS1524, ARS at XV-1058, ARS1528, ARS1529.5, ARS at XVI-242, ARS at XVI-274, ARS at XV-1081, ARS at XV-1081, ARS at XV-1091, ARS at XVI-377, ARS1601, ARS at XVI-19, ARS1604, ARS1605, ARS1607, ARS1614, ARS at XVI-569, ARS at XVI-332, ARS at XVI-701, ARS1618, ARS1619, ARS1620.5, ARS1621, ARS1622, ARS at XVI-584, ARS1624, ARS at , ARS at IX-308, ARS1626, ARS1626.5, ARS1627, ARS1628, ARS805.5, ARS1630, ARS1630, ARS at , ARS1631, ARS at XVI-942, ARS at XII-1056, ARS at , ARS at , ARS209, ARS at , ARS at , ARS216, ARS219, ARS220, ARS221, ARS227, ARS229, ARS303, ARS309, ARS310, ARS at , ARS at , ARS409, ARS413.5, ARS417.5, ARS419, ARS420, ARS421, ARS at , ARS422.5, ARS447, ARS508, ARS513.5, ARS514, ARS at V-302, ARS at , ARS520, ARS522, ARS600.1, ARS601, ARS603, ARS610, ARS at VII-17, ARS704, ARS718, ARS at , ARS at , ARS731.5, ARS734, ARS at VII-1063, ARS131a, ARS at , ARS823.5, ARS at , ARS911, ARS919, ARS920, ARS at , ARS1004, ARS1005, ARS1006, ARS1007, ARS at , ARS at , ARS1104.5, ARS1112, ARS at , ARS at XII-52, ARS1206, ARS1211.5, ARS at , ARS1216, ARS1216.5, ARS at XII-786, ARS at XII-928, ARS1233, ARS at XII-1043, ARS1235, ARS at XII-1071, ARS1304, ARS at , ARS at , ARS1323, ARS1329, ARS at , ARS at XV-160, ARS1421, ARS1422, ARS1426, ARS1427, ARS at , ARS at , ARS1509, ARS at , ARS at , ARS at , ARS at XV-1081, ARS at , ARS1622, ARS at , ARS at IX-308, ARS1628, ARS at , ARS at , ARS at , ARS310, ARS403, ARS at , ARS at V-302, ARS at , ARS719, ARS823.5, ARS at , ARS1006, ARS1023, ARS at , ARS at , ARS at XII-786, ARS at , ARS310, ARS1006. |
Experimentally confirmed ACS element: |
ARS1001, ARS1002, ARS1003, ARS1004, ARS1007, ARS1007.5, ARS1009, ARS1011, ARS1014, ARS1015, ARS1018, ARS1019, ARS1020, ARS1005. |
Activation ('firing') time determined: |
None curated. |
Activation ('firing') efficiency determined: |
None curated. |
Analysed by microarray: |
ARS102, ARS102.5, ARS103, ARS104, ARS105, ARS106, ARS107, ARS107.5, ARS108, ARS109, ARS110, ARS111, ARS112, ARS113, ARS200, ARS201, ARS201.5, ARS202, ARS203, ARS206, ARS207, ARS207.1, ARS207.5, ARS207.8, ARS208, ARS209, ARS at II-279, ARS210.5, ARS211, ARS212, ARS213, ARS214, ARS215, ARS215.5, ARS at II-479, ARS216, ARS217, ARS218, ARS219, ARS219.5, ARS220, ARS221, ARS221.5, ARS222, ARS222.5, ARS223, ARS224, ARS225, ARS227, ARS228, ARS228.5, ARS229, ARS at II-812, ARS300, ARS301, ARS302, ARS303, ARS320, ARS304, ARS305, ARS306, ARS307, ARS308, ARS309, ARS at III-138, ARS310, ARS313, ARS314, ARS315, ARS316, ARS318, ARS319, ARS400, ARS at IV-9, ARS403, ARS402.5, ARS404, ARS405, ARS405.5, ARS406, ARS at IV-138, ARS at IV-158, ARS409, ARS409.5, ARS410, ARS412, ARS413, ARS413.5, ARS414, ARS415, ARS at IV-444, ARS416, ARS at IV-477, ARS417, ARS417.5, ARS418, ARS419, ARS420, ARS421, ARS422, ARS at IV-721, ARS422.5, ARS423, ARS425, ARS426.5, ARS at IV-899, ARS427.5, ARS428, ARS429, ARS429.5, ARS430, ARS430.5, ARS431, ARS431.5, ARS432, ARS432.5, ARS433, ARS434, ARS435, ARS437, ARS at IV-1380, ARS440, ARS441, ARS442, ARS446, ARS447, ARS at IV-1524, ARS at IV-1531, ARS at V-1, ARS503, ARS at V-12, ARS at V-18, ARS507, ARS at V-68, ARS508, ARS at V-110, ARS510, ARS511, ARS at V-184, ARS512, ARS at V-256, ARS513.5, ARS514, ARS at V-302, ARS at V-317, ARS516, ARS517, ARS518, ARS519, ARS520, ARS521, ARS522, ARS523, ARS at V-576, ARS at VI-1, ARS600.1, ARS600.2, ARS600.3, ARS600.4, ARS601, ARS602, ARS at VI-53, ARS603, ARS603.1, ARS603.5, ARS604, ARS605, ARS606, ARS607, ARS608, ARS608.5, ARS609, ARS610, ARS at VII-0, ARS at VII-8, ARS at VII-17, ARS at VII-33, ARS702, ARS704, ARS706, ARS707, ARS at VII-171, ARS at VII-187, ARS710, ARS at VII-241, ARS at VII-275, ARS714, ARS716, ARS717, ARS718, ARS at VII-481, ARS719, ARS720, ARS at VII-553, ARS721, ARS722, ARS at VII-608, ARS at VII-621, ARS at VII-654, ARS727, ARS728, ARS729, ARS731, ARS at VII-847, ARS at VII-883, ARS731.5, ARS at VII-917, ARS733, ARS734, ARS at VII-1002, ARS at VII-1005, ARS at VII-1063, ARS at VII-1074, ARS131a, ARS at VII-1090, ARS at VIII-1, ARS131n, ARS802, ARS at VIII-46, ARS at VIII-58, ARS805, ARS at VIII-88, ARS at VIII-111, ARS at VIII-116, ARS at VIII-135, ARS809, ARS810, ARS813, ARS815, ARS at VIII-360, ARS at VIII-381, ARS818, ARS820, ARS at VIII-452, ARS at VIII-475, ARS822, ARS at VIII-505, ARS823, ARS823.5, ARS at VIII-551, ARS824, ARS at VIII-562, ARS at IX-1, ARS at IX-8, ARS at IX-17, ARS at IX-31, ARS at IX-34, ARS907, ARS at IX-81, ARS909, ARS911, ARS911.5, ARS912, ARS at IX-190, ARS913, ARS at IX-226, ARS913.5, ARS914, ARS916, ARS at IX-323, ARS919, ARS920, ARS at IX-407, ARS922, ARS at IX-433, ARS at IX-439, ARS1001, ARS1002, ARS1003, ARS1004, ARS1005, ARS1006, ARS1007, ARS at X-121, ARS1007.5, ARS1008, ARS1009, ARS1009.5, ARS1010, ARS1011, ARS at X-355, ARS1012, ARS1013, ARS1014, ARS1015, ARS1016, ARS1017, ARS1017.5, ARS1018, ARS1018.5, ARS1019, ARS at X-644, ARS1020, ARS1021, ARS at X-702, ARS1022, ARS1023, ARS1024, ARS1025, ARS at XI-1, ARS at XI-8, ARS1103, ARS1104.5, ARS at XI-114, ARS1106, ARS at XI-164, ARS1106.3, ARS at XI-200, ARS1106.7, ARS at XI-236, ARS at XI-257, ARS at XI-302, ARS at XI-327, ARS1109, ARS at XI-344, ARS1112, ARS1113, ARS1114, ARS1114.5, ARS at XI-463, ARS1116, ARS at XI-520, ARS at XI-530, ARS1118, ARS1120, ARS at XI-633, ARS1123, ARS at XI-662, ARS at XII-1, ARS at XII-7, ARS at XII-12, ARS at XII-31, ARS at XII-52, ARS at XII-77, ARS1206, ARS at XII-140, ARS1209, ARS at XII-199, ARS1210, ARS1211, ARS1211.5, ARS1212, ARS1212.5, ARS1213, ARS1215, ARS1216, ARS1216.5, ARS at XII-468, ARS at XII-494, ARS1217, ARS1218, ARS at XII-607, ARS at XII-623, ARS at XII-638, ARS at XII-645, ARS1220, ARS at XII-731, ARS1223, ARS at XII-786, ARS1226, ARS at XII-806, ARS at XII-822, ARS at XII-839, ARS1227.5, ARS at XII-928, ARS at XII-948, ARS1233, ARS1234, ARS at XII-1043, ARS1235, ARS at XII-1064, ARS at XII-1071, ARS at XII-1078, ARS at XIII-1, ARS at XIII-6, ARS at XIII-25, ARS1303, ARS1304, ARS at XIII-45, ARS at XIII-74, ARS1305, ARS1307, ARS1307.5, ARS at XIII-227, ARS1309, ARS at XIII-269, ARS1310, ARS at XIII-340, ARS at XIII-342, ARS1312, ARS at XIII-417, ARS at XIII-433, ARS1316, ARS at XIII-482, ARS1319, ARS1320, ARS1322, ARS at XIII-569, ARS1323, ARS1324, ARS1325, ARS at XIII-689, ARS1327, ARS1328, ARS1329, ARS1330, ARS at XIII-837, ARS1331.5, ARS at XIII-879, ARS1332, ARS at XIII-919, ARS at XIII-923, ARS at XIV-1, ARS at XIV-9, ARS at XIV-15, ARS1405, ARS1406, ARS1407, ARS at XIV-127, ARS1411, ARS1412, ARS1413, ARS at XIV-253, ARS1414, ARS1415, ARS at XIV-344, ARS1417, ARS1419, ARS1420, ARS1421, ARS1422, ARS1424, ARS1426, ARS1427, ARS at XIV-705, ARS at XIV-714, ARS at XIV-739, ARS at XIV-764, ARS at XIV-783, ARS at XV-1, ARS at XV-11, ARS at XV-19, ARS at XV-24, ARS1506.5, ARS1507, ARS1508, ARS at XV-104, ARS1509, ARS1509.5, ARS at XV-160, ARS1510, ARS1511, ARS at XV-309, ARS at XV-332, ARS1513, ARS at XV-348, ARS at XV-354, ARS at XV-372, ARS at XV-398, ARS at XV-445, ARS at XV-459, ARS at XV-464, ARS1514, ARS at XV-497, ARS at XV-521, ARS1516, ARS at XV-577, ARS1517, ARS at XV-618, ARS1519, ARS at XV-663, ARS at XV-682, ARS1521, ARS1523, ARS1524, ARS at XV-855, ARS1526, ARS at XV-900, ARS at XV-902, ARS1528, ARS1529, ARS at XV-999, ARS at XV-1020, ARS at XV-1023, ARS1529.5, ARS at XV-1058, ARS at XV-1072, ARS at XV-1081, ARS at XV-1091, ARS at XVI-1, ARS1601, ARS1602, ARS at XVI-19, ARS1604, ARS1605, ARS at XVI-91, ARS1607, ARS at XVI-163, ARS at XVI-179, ARS at XVI-191, ARS at XVI-196, ARS1609, ARS at XVI-242, ARS at XVI-262, ARS at XVI-274, ARS1614, ARS at XVI-299, ARS at XVI-304, ARS at XVI-318, ARS at XVI-332, ARS at XVI-369, ARS at XVI-377, ARS1618, ARS1619, ARS at XVI-428, ARS at XVI-440, ARS at XVI-454, ARS1620.5, ARS at XVI-500, ARS1621, ARS at XVI-553, ARS1622, ARS1622.5, ARS at XVI-569, ARS at XVI-584, ARS at XVI-589, ARS1623, ARS1624, ARS1625, ARS at XVI-701, ARS at XVI-729, ARS1626, ARS1626.5, ARS1627, ARS at XVI-824, ARS1628, ARS at XVI-864, ARS1630, ARS1631, ARS at XVI-942, ARS at XVI-947. |
Other analysis: |
None curated. |
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