OriDB Curated Paper

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Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication.

Wenyi Feng, David Collingwood, Max E Boeck, Lindsay A Fox, Gina M Alvino, Walton L Fangman, Mosur K Raghuraman, Bonita J Brewer

Nat. Cell Biol. (2006), 8(2):148-55Data to DownloadPubMed | PubMed Central | Nat. Cell Biol.

During DNA replication one or both strands transiently become single stranded: first at the sites where initiation of DNA synthesis occurs (known as origins of replication) and subsequently on the lagging strands of replication forks as discontinuous Okazaki fragments are generated. We report a genome-wide analysis of single-stranded DNA (ssDNA) formation in the presence of hydroxyurea during DNA replication in wild-type and checkpoint-deficient rad53 Saccharomyces cerevisiae cells. In wild-type cells, ssDNA was first observed at a subset of replication origins and later 'migrated' bi-directionally, suggesting that ssDNA formation is associated with continuously moving replication forks. In rad53 cells, ssDNA was observed at virtually every known origin, but remained there over time, suggesting that replication forks stall. Telomeric regions seemed to be particularly sensitive to the loss of Rad53 checkpoint function. Replication origins in Schizosaccharomyces pombe were also mapped using our method.

OriDB annotation of this paper:

ARS assay

None curated.

2D gel

ARS314.5, ARS1007.5

ChIP of replication origin proteins

None curated.

Replication timing

None curated.

Replication in hydroxyurea

ARS102.5, ARS103, ARS at I-10, ARS104, ARS105, ARS106, ARS107, ARS108, ARS109, ARS at I-166, ARS at I-166, ARS at I-166, ARS110, ARS at I-198, ARS at I-206, ARS200, ARS201.7, ARS202, ARS203, ARS at II-96, ARS206, ARS207, ARS207.5, ARS at II-229, ARS208, ARS at II-246, ARS at II-246, ARS209, ARS211, ARS213, ARS214, ARS216, ARS217, ARS218, ARS at II-584, ARS219, ARS220, ARS at II-695, ARS222, ARS222.5, ARS223, ARS at II-732, ARS at II-732, ARS224, ARS225, ARS at II-761, ARS227, ARS228, ARS301, ARS302, ARS303, ARS320, ARS302, ARS305, ARS306, ARS at III-85, ARS307, ARS309, ARS at III-163, ARS310, ARS at III-193, ARS313, ARS314, ARS314.5, ARS at III-224, ARS315, ARS316, ARS317, ARS318, ARS at IV-9, ARS403, ARS404, ARS at IV-51, ARS405, ARS406, ARS408, ARS409, ARS at IV-220, ARS409.5, ARS409.3, ARS410, ARS at IV-257, ARS412, ARS413, ARS414, ARS415, ARS416, ARS417, ARS417.5, ARS418, ARS419, ARS420, ARS421, ARS at IV-645, ARS422, ARS at IV-721, ARS423, ARS425, ARS at IV-879, ARS428, ARS at IV-991, ARS430, ARS431, ARS431.5, ARS432.5, ARS433, ARS434, ARS at IV-1275, ARS435, ARS at IV-1306, ARS at IV-1308, ARS437, ARS at IV-1356, ARS at IV-1380, ARS439.5, ARS440, ARS441, ARS442, ARS446, ARS447, ARS at IV-1506, ARS at IV-1499, ARS at IV-1524, ARS502, ARS503, ARS504, ARS507, ARS508, ARS510, ARS511, ARS512, ARS at V-256, ARS513.5, ARS513.7, ARS at V-317, ARS516, ARS517, ARS518, ARS519, ARS520, ARS at V-510, ARS at V-510, ARS521, ARS522, ARS at V-563, ARS523, ARS600.1, ARS at VI-1, ARS600.3, ARS600.4, ARS601, ARS602, ARS603, ARS at VI-99, ARS603.5, ARS605, ARS606, ARS607, ARS608, ARS609, ARS608.5, ARS at VII-8, ARS700.5, ARS at VII-26, ARS at VII-33, ARS702, ARS704, ARS at VII-115, ARS707, ARS at VII-167, ARS709, ARS710, ARS712, ARS714, ARS at VII-288, ARS716, ARS717, ARS718, ARS719, ARS at VII-481, ARS720, ARS722, ARS at VII-576, ARS727, ARS728, ARS729, ARS731, ARS731.5, ARS732, ARS733, ARS734, ARS735, ARS735.5, ARS at VII-1090, ARS131n, ARS802, ARS at VIII-11, ARS804, ARS805, ARS at VIII-116, ARS805.7, ARS807, ARS at VIII-135, ARS809, ARS813, ARS815, ARS816, ARS at VIII-367, ARS818, ARS820, ARS821, ARS822, ARS at VIII-505, ARS823, ARS at IX-17, ARS905, ARS at IX-31, ARS907, ARS909, ARS911, ARS912, ARS at IX-183, ARS at IX-190, ARS at IX-205, ARS913, ARS at IX-220, ARS at IX-238, ARS913.5, ARS914, ARS at IX-249, ARS916, ARS at IX-308, ARS919, ARS920, ARS922, ARS at IX-407, ARS at IX-439, ARS1003, ARS1004, ARS1005, ARS1007, ARS1007.5, ARS1008, ARS at X-212, ARS1009, ARS1010, ARS at X-305, ARS1011, ARS1012, ARS1013, ARS1014, ARS1015, ARS1016, ARS1017, ARS1018, ARS1019, ARS1018.5, ARS1020, ARS1021, ARS1021, ARS1022, ARS at X-719, ARS1023, ARS1025, ARS at XI-16, ARS at XI-24, ARS1102.5, ARS1103, ARS1104.5, ARS at XI-114, ARS1106, ARS1106.3, ARS1106.5, ARS1106.7, ARS1107, ARS1107.5, ARS1109, ARS at XI-327, ARS1112, ARS1113, ARS1114, ARS1113.5, ARS1116, ARS1117, ARS1118, ARS at XI-584, ARS1120, ARS at XI-617, ARS1123, ARS at XII-1, ARS at XII-7, ARS at XII-12, ARS at XII-7, ARS at XII-31, ARS1203, ARS1205, ARS1206, ARS1206.5, ARS at XII-140, ARS1209, ARS1211, ARS1211.5, ARS1212, ARS at XII-316, ARS1212.5, ARS1213, ARS1215, ARS1216, ARS1217, ARS at XII-599, ARS1218, ARS at XII-607, ARS1219, ARS at XII-618, ARS1220, ARS1220.5, ARS1222, ARS1223, ARS at XII-749, ARS1226, ARS1227, ARS1227.5, ARS1229, ARS at XII-931, ARS1231, ARS1232, ARS at XII-1020, ARS1234, ARS at XII-1064, ARS at XII-1071, ARS at XIII-6, ARS at XIII-10, ARS at XIII-1, ARS1303, ARS1305, ARS1307, ARS1307.5, ARS1308, ARS at XIII-227, ARS1309, ARS1310, ARS at XIII-290, ARS1312, ARS at XIII-373, ARS1315, ARS1316, ARS1319, ARS1320, ARS1322, ARS at XIII-574, ARS1323, ARS1324, ARS1325, ARS1326, ARS1327, ARS at XIII-763, ARS1328, ARS1330, ARS1331.7, ARS1332, ARS at XIII-919, ARS at XIII-923, ARS at XIV-9, ARS at XIV-1, ARS at XIV-9, ARS1405, ARS at XIV-36, ARS1406, ARS1407, ARS at XIV-85, ARS1410, ARS at XIV-159, ARS1411, ARS at XIV-180, ARS1412, ARS1413, ARS at XIV-253, ARS1414, ARS1415, ARS at XIV-325, ARS1311.7, ARS at XIV-358, ARS1417, ARS at XIV-416, ARS1419, ARS at XIV-459, ARS1420, ARS1421, ARS1422, ARS at XIV-556, ARS at XIV-577, ARS1424, ARS1426, ARS1427, ARS1428, ARS1428.5, ARS1429, ARS at XV-11, ARS at XV-19, ARS at XV-24, ARS1506.5, ARS at XV-45, ARS1507, ARS at XV-79, ARS1508, ARS at XV-79, ARS1509, ARS1510, ARS1510.5, ARS1511, ARS1512, ARS1513, ARS at XV-354, ARS1513.5, ARS at XV-464, ARS at XV-495, ARS1515.5, ARS1516, ARS1517, ARS at XV-605, ARS at XV-618, ARS1519, ARS1520, ARS1521, ARS at XV-737, ARS at XV-763, ARS1523, ARS1524, ARS1525, ARS1526, ARS1528, ARS1529, ARS1529.5, ARS at XV-1058, ARS at XV-1081, ARS at XV-1091, ARS1601, ARS1602, ARS1604, ARS1605, ARS at XVI-91, ARS1607, ARS at XVI-163, ARS at XVI-191, ARS1609, ARS at XVI-262, ARS1614, ARS at XVI-318, ARS at XVI-324, ARS1617, ARS at XVI-324, ARS1618, ARS1619, ARS at XVI-423, ARS1618.5, ARS1620.5, ARS at XVI-454, ARS at XVI-477, ARS1621, ARS at XVI-553, ARS at XVI-560, ARS1622, ARS1622.5, ARS1622.7, ARS at XVI-589, ARS1623, ARS at XVI-653, ARS1624, ARS at XVI-691, ARS at XVI-691, ARS1625, ARS1626, ARS1626.5, ARS1627, ARS at XVI-824, ARS1628, ARS at XVI-873, ARS1630, ARS1631, ARS at XVI-930, ARS at XVI-942, ARS at XVI-947

Predicted origins

None curated.

Confirmed sequence element

None curated.

Predicted sequence element

None curated.

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