Publication Information

{'id': 'https://openalex.org/W3136565871', 'doi': 'https://doi.org/10.7554/elife.62161.sa1', 'title': 'Decision letter: Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones', 'display_name': 'Decision letter: Human ORC/MCM density is low in active genes and correlates with replication time but does not delimit initiation zones', 'publication_year': 2020, 'publication_date': '2020-09-30', 'ids': {'openalex': 'https://openalex.org/W3136565871', 'doi': 'https://doi.org/10.7554/elife.62161.sa1', 'mag': '3136565871'}, 'language': 'en', 'primary_location': {'is_oa': True, 'landing_page_url': 'https://doi.org/10.7554/elife.62161.sa1', 'pdf_url': None, 'source': None, 'license': None, 'license_id': None, 'version': 'publishedVersion', 'is_accepted': True, 'is_published': True}, 'type': 'peer-review', 'type_crossref': 'peer-review', 'indexed_in': ['crossref'], 'open_access': {'is_oa': True, 'oa_status': 'gold', 'oa_url': 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'https://openalex.org/W3134744679', 'https://openalex.org/W3045607205', 'https://openalex.org/W2083152795', 'https://openalex.org/W2057896961', 'https://openalex.org/W2031154391', 'https://openalex.org/W1979452570', 'https://openalex.org/W1966435085', 'https://openalex.org/W1547945395'], 'abstract_inverted_index': {'Article': [0, 18], 'Figures': [1], 'and': [2, 9, 19, 54, 61, 69, 77, 85, 95, 124, 162, 176, 209, 228, 251, 275, 283, 307, 349, 378, 405, 420, 454, 504, 508, 527, 538, 547, 562, 582, 586, 653, 694, 718, 733, 755, 805, 829, 847, 859, 881, 916, 974, 1007, 1030, 1033, 1079, 1120, 1137, 1154, 1182, 1195, 1238, 1328, 1334, 1374, 1407, 1415, 1436, 1444, 1466, 1519, 1563, 1625, 1628, 1702, 1704, 1709, 1761, 1786, 1800, 1827, 1871, 1884, 1903, 1912, 1975, 2002, 2046, 2072, 2083, 2110, 2165, 2189, 2271, 2273, 2354, 2480, 2552, 2575, 2634, 2638, 2644, 2671, 2684, 2723, 2737, 2764, 2836, 2889, 2907, 2971, 3027, 3098, 3121, 3129, 3159, 3166, 3232, 3256, 3304, 3328, 3339, 3359, 3375, 3455, 3540, 3573, 3617, 3650, 3693, 3721, 3725, 3767, 3788, 3797, 3869, 3886, 3894, 3976, 3996, 4012, 4023, 4067, 4119, 4130, 4150, 4187, 4229, 4239, 4250, 4296, 4308, 4331, 4357, 4373, 4409], 'data': [3, 1141, 1852, 2121, 2130, 2947, 3204, 3846, 3880], 'Abstract': [4, 23], 'Introduction': [5, 183], 'Results': [6, 1365], 'Discussion': [7], 'Materials': [8, 2270, 2353, 4249], 'methods': [10, 675], 'Data': [11], 'availability': [12], 'References': [13], 'Decision': [14], 'letter': [15], 'Author': [16], 'response': [17], 'author': [20], 'information': [21], 'Metrics': [22], 'Eukaryotic': [24], 'DNA': [25, 187, 246, 273, 390, 402, 556, 835], 'replication': [26, 59, 133, 143, 167, 178, 188, 194, 386, 421, 449, 518, 685, 692, 710, 772, 976, 1016, 1034, 1093, 1115, 1313, 1324, 1345, 1363, 1584, 2253, 2276, 2368, 2613, 2873, 2890, 3760, 3962, 4116, 4133, 4200, 4268, 4279], 'initiates': [27, 179, 189, 422, 520, 773, 1094], 'during': [28, 229, 391], 'S': [29, 346, 434, 464, 839], 'phase': [30, 232, 465, 840], 'from': [31, 88, 190, 197, 389, 423, 810, 940, 1177, 2136, 2976, 3125, 3285, 3314, 3337, 3348, 3379, 3512, 3562, 3634, 3698, 3829, 3881, 4426], 'origins': [32, 195, 207, 396, 428, 437, 526, 533, 603, 623, 1064, 2292, 3796, 3819], 'that': [33, 368, 382, 481, 517, 771, 986, 1091, 1230, 1239, 1254, 1275, 1289, 1613, 1626, 1943, 2178, 2290, 2446, 3211, 3354, 3462, 3691, 3752, 3782, 3812, 3930, 3938, 3955, 4079], 'have': [34, 296, 658, 666, 3403, 3847], 'been': [35, 297, 418, 616, 659, 667, 3810, 3849], 'licensed': [36, 1066, 1322], 'in': [37, 98, 101, 111, 158, 180, 225, 353, 459, 604, 618, 774, 837, 842, 924, 982, 1017, 1095, 1122, 1149, 1258, 1284, 1294, 1451, 1526, 1537, 1573, 1683, 1716, 1723, 1791, 1805, 1822, 1890, 1925, 1968, 2035, 2237, 2258, 2296, 2303, 2439, 2573, 2727, 2948, 2955, 2986, 3021, 3033, 3056, 3205, 3226, 3472, 3568, 3710, 3715, 3872, 3911, 3920, 3966, 4000, 4027, 4033, 4071, 4178, 4320, 4371, 4399, 4439], 'the': [38, 48, 72, 78, 140, 230, 234, 240, 258, 262, 305, 445, 522, 596, 611, 640, 670, 678, 708, 843, 991, 1011, 1023, 1089, 1106, 1123, 1126, 1160, 1244, 1309, 1315, 1353, 1423, 1471, 1522, 1582, 1599, 1614, 1621, 1689, 1714, 1730, 1734, 1752, 1764, 1776, 1838, 1861, 1864, 1873, 1876, 1896, 1932, 1937, 1962, 2015, 2055, 2061, 2148, 2245, 2267, 2283, 2357, 2361, 2379, 2402, 2481, 2524, 2657, 2718, 2770, 2884, 2894, 2930, 2940, 3068, 3146, 3172, 3212, 3463, 3619, 3671, 3793, 3813, 3861, 3967, 4084, 4128, 4169, 4189, 4404], 'preceding': [39], 'G1': [40, 231, 926], 'phase.': [41], 'Here,': [42, 1103], 'we': [43, 591, 1104, 1251, 1438, 1858, 1929, 1944, 1995, 2008, 2019, 2146, 2196, 2265, 2371, 2385, 2444, 2892, 2935, 3209, 3875], 'compare': [44, 1028, 2127], 'ChIP-seq': [45, 934, 979, 1554, 1577, 1746, 1892, 2129, 2135, 3203], 'profiles': [46, 64, 1720, 2107, 2112, 2287, 2653, 3826, 3854], 'of': [47, 142, 165, 203, 233, 261, 364, 598, 601, 626, 703, 766, 780, 845, 935, 966, 980, 990, 999, 1062, 1110, 1125, 1198, 1203, 1243, 1263, 1278, 1343, 1356, 1388, 1411, 1427, 1434, 1492, 1555, 1564, 1700, 1707, 1733, 1744, 1757, 1811, 1863, 1880, 1934, 2012, 2048, 2060, 2065, 2105, 2152, 2159, 2201, 2214, 2249, 2282, 2367, 2393, 2401, 2414, 2450, 2510, 2611, 2632, 2667, 2676, 2735, 2791, 2831, 2866, 2898, 2932, 3071, 3082, 3150, 3157, 3161, 3254, 3258, 3270, 3283, 3294, 3330, 3453, 3457, 3479, 3571, 3615, 3779, 3795, 3799, 3815, 3906, 3946, 3973, 3980, 4088, 4144, 4147, 4171, 4193, 4314], 'licensing': [49, 597, 1025, 1350], 'factors': [50, 358, 548, 1329], 'Orc2,': [51, 1441, 2668], 'Orc3,': [52, 1442, 1703, 2669], 'Mcm3,': [53, 1443, 2670], 'Mcm7': [55, 981, 1445, 1801, 2672, 3305, 3694, 4332], 'with': [56, 132, 249, 304, 355, 863, 969, 1069, 1162, 1168, 1650, 1954, 1987, 2001, 2039, 2181, 2193, 2218, 2389, 2431, 2472, 2583, 2694, 2709, 2810, 2961, 3015, 3035, 3134, 3276, 3326, 3427, 3484, 3704, 3769, 3785, 3821, 4098, 4115, 4344], 'gene': [57, 93, 163, 1180, 1186, 2498, 2863, 3127, 3174, 3286, 3315, 3333, 3380, 3421, 3555, 3620, 3700, 3786, 4002, 4039, 4047], 'expression,': [58], 'timing,': [60], 'fork': [62, 168, 711, 2614, 2874, 4134], 'directionality': [63], 'obtained': [65, 1615, 1904, 2000, 2034, 2117], 'by': [66, 400, 489, 628, 673, 681, 801, 827, 830, 873, 1132, 1361, 1401, 1512, 1581, 1638, 1675, 1763, 1771, 1832, 2054, 2424, 2455, 2539, 2628, 2650, 2827, 2842, 3657, 3661, 3708, 3736, 3993, 4077, 4185, 4378], 'RNA-seq,': [67, 1136], 'Repli-seq,': [68], 'OK-seq.': [70], 'Both,': [71], 'origin': [73, 154, 241, 317, 415, 491, 551, 1292, 1474, 1585, 1666, 1691, 1735, 1939, 2017, 3800, 3831], 'recognition': [74, 242, 1667, 2593, 3494, 4108], 'complex': [75, 81, 221, 243, 1670, 2596, 3495, 3508, 4111], '(ORC)': [76, 244, 3496], 'minichromosome': [79, 254, 3506], 'maintenance': [80, 255, 1669, 2595, 3507, 4110], '(MCM)': [82, 3509], 'are': [83, 314, 387, 397, 483, 793, 912, 995, 1156, 1175, 1256, 1337, 1711, 1721, 2235, 2308, 2626, 3123, 3566, 3576, 3666, 3695, 3754, 3765, 4123, 4183, 4211], 'significantly': [84, 1966, 3218, 3251, 3335, 3696], 'homogeneously': [86, 4125], 'depleted': [87, 1176, 3124, 3336, 3378, 3511, 3697], 'transcribed': [89, 803, 1179, 1319, 2457, 2483, 2497, 2695, 2715, 2775, 2977, 3126, 3296, 3332, 3514, 3699], 'genes,': [90, 804, 3368, 4441], 'enriched': [91, 157, 1183, 1257, 1283, 2236, 2912, 3020, 3130, 3219, 3372, 3498], 'at': [92, 430, 441, 521, 621, 669, 677, 896, 1184, 1494, 1521, 1688, 1751, 1867, 1907, 1916, 1936, 1973, 1976, 2014, 2186, 2203, 2432, 2673, 2697, 2717, 2994, 3040, 3086, 3109, 3131, 3220, 3307, 3366, 3373, 3410, 3467, 3499, 3600, 3818, 4091, 4197, 4413], 'promoters,': [94], 'more': [96, 913, 2309, 2536, 3318, 3425, 3473, 4390], 'abundant': [97], 'early-': [99, 4372], 'than': [100, 1171, 2474, 3260, 3477, 3549, 4354, 4394], 'late-replicating': [102, 159, 602, 4001], 'domains.': [103], 'Surprisingly,': [104], 'after': [105, 1692, 1747, 2654], 'controlling': [106], 'these': [107, 2194, 2306], 'variables,': [108], 'no': [109, 411, 2861, 3641, 4290, 4292], 'difference': [110, 4405], 'ORC/MCM': [112, 129, 1174, 1188, 1209, 1231, 1493, 1745, 1901, 1935, 2013, 2234, 2250, 2887, 2899, 2963, 2990, 3003, 3022, 3057, 3202, 3369, 3408, 3418, 3450, 3518, 3596, 3610, 3741, 3753, 3762, 3870, 3890, 4352, 4422], 'density': [113, 130, 1165, 1189, 3742, 3871, 4086, 4191], 'is': [114, 1019, 1190, 1248, 1282, 1321, 1368, 1736, 1888, 2052, 2742, 2825, 3032, 3497, 3510, 3702, 3775, 3783, 4083, 4205, 4318], 'detected': [115, 1516, 1931, 3006, 3037], 'between': [116, 823, 1784, 1798, 1816, 1900, 2081, 2477, 2523, 2886, 3863, 4406], 'initiation': [117, 160, 717, 789, 1035, 1074, 1116, 1221, 1346, 2254, 2369, 3974, 3995, 4307], 'zones,': [118, 120, 1096, 1215], 'termination': [119, 719, 1214, 3163, 3526, 4241], 'unidirectionally': [121, 3957, 4283], 'replicating': [122, 126, 1217, 1225, 2565, 3958, 3992, 4284], 'regions,': [123, 973, 1972, 4304, 4375], 'randomly': [125, 1224], 'regions.': [127, 1226], 'Therefore,': [128], 'correlates': [131, 3820], 'timing': [134, 450, 977, 3798, 4117], 'but': [135, 776, 905, 994, 1575, 1611, 2302, 3067, 3101, 3250, 3312, 3437, 3771, 4122, 4432], 'does': [136, 300], 'not': [137, 301, 384, 1234, 1642, 1946, 2520, 3090, 3377, 3402, 3470, 3755, 3772, 4246], 'solely': [138, 1235], 'regulate': [139], 'probability': [141, 4085, 4190], 'initiation.': [144, 1325], 'Interestingly,': [145], 'H4K20me3,': [146, 1285], 'a': [147, 198, 460, 599, 646, 964, 1207, 1240, 1276, 1369, 1384, 1529, 1535, 1662, 1724, 1955, 2198, 2365, 2496, 2972, 3053, 3776, 3971, 4092, 4198], 'histone': [148, 558, 560, 612, 629], 'modification': [149], 'proposed': [150, 592, 3714], 'to': [151, 192, 200, 439, 530, 550, 594, 650, 661, 715, 878, 891, 910, 942, 1027, 1059, 1071, 1339, 1382, 1506, 1634, 1846, 2131, 2211, 2251, 2293, 2342, 2347, 2377, 2419, 2495, 2714, 2774, 2778, 2916, 3207, 3301, 3350, 3670, 3679, 3732, 3757, 3851, 3889, 4063, 4132, 4168, 4262, 4335, 4428], 'facilitate': [152], 'late': [153, 226, 860, 925, 1280, 2564, 4429], 'licensing,': [155, 217], 'was': [156, 821, 876, 1965, 2959, 3005, 3217, 3248, 3288, 3345, 3423, 3439, 3638, 4176, 4368, 4389, 4412, 4436], 'zones': [161, 778, 790, 1342, 3941], 'deserts': [164, 4003], 'stochastic': [166, 490, 1354, 3830], 'direction.': [169], 'We': [170, 1006, 1146, 1272, 1378, 1515, 1597, 1894, 2242, 2335, 3901, 4008, 4053], 'discuss': [171], 'potential': [172, 204, 945, 1063], 'mechanisms': [173], 'specifying': [174], 'when': [175, 919, 2018, 3431], 'where': [177, 3961], 'human': [181, 185, 767, 932, 1024, 1092, 1127, 1389, 3233, 3722, 3842, 3873], 'cells.': [182], 'In': [184, 393, 408, 885, 931, 1952, 2191, 2383, 2410, 2485, 2984, 3364, 3739, 3806, 3841, 4402, 4419], 'cells,': [186, 933, 2443, 3843, 3874], '20,000': [191], '50,000': [193], 'selected': [196, 485, 2386], 'five-': [199, 1058], 'tenfold': [201, 1060], 'excess': [202, 1061], 'or': [205, 513, 676, 798, 1223, 1265, 2040, 2219, 2855, 3524, 3564, 4045, 4060, 4260], "'licensed'": [206], '(Moiseeva': [208], 'Bakkenist,': [210, 379], '2018;': [211, 376, 2330], 'Papior': [212, 1045, 1082, 1452, 1546], 'et': [213, 279, 320, 326, 330, 334, 338, 342, 374, 467, 471, 496, 500, 542, 566, 570, 574, 578, 607, 633, 698, 721, 725, 729, 738, 744, 748, 752, 758, 762, 814, 850, 867, 902, 928, 949, 953, 957, 1003, 1038, 1042, 1046, 1050, 1054, 1083, 1143, 1269, 1299, 1303, 1394, 1453, 1457, 1461, 1497, 1547, 1551, 1590, 1594, 1604, 1608, 1959, 1992, 2143, 2174, 2262, 2299, 2316, 2320, 2324, 2328, 2332, 2578, 3044, 3139, 3143, 3229, 3236, 3240, 3718, 3803, 3834, 3838, 3856, 3883, 3898, 3922], 'al.,': [214, 280, 321, 327, 331, 335, 339, 343, 375, 468, 472, 497, 501, 543, 567, 571, 575, 579, 608, 634, 699, 722, 726, 730, 739, 745, 749, 753, 759, 763, 815, 851, 868, 903, 929, 950, 954, 958, 1004, 1039, 1043, 1047, 1051, 1055, 1084, 1144, 1270, 1300, 1304, 1395, 1454, 1458, 1462, 1498, 1548, 1552, 1591, 1595, 1605, 1609, 1960, 1993, 2144, 2175, 2263, 2300, 2317, 2321, 2325, 2329, 2333, 2579, 3045, 3140, 3144, 3230, 3237, 3241, 3719, 3804, 3835, 3839, 3857, 3884, 3899, 3923], '2012).': [215, 735, 1085, 1396], 'Origin': [216, 2592, 3493, 4107], 'also': [218, 3103, 3848], 'called': [219], 'pre-replicative': [220, 1150, 1386], '(pre-RC)': [222], 'formation,': [223], 'occurs': [224], 'mitosis': [227], 'cell': [235, 1130, 1424], 'cycle.': [236], 'During': [237, 345], 'this': [238, 477, 2937, 3072, 3438, 4433], 'step,': [239], 'binds': [245, 889], 'and,': [247], 'together': [248], 'Cdt1': [250, 313], 'Cdc6,': [252, 311], 'loads': [253, 290], 'complexes': [256, 3361], '(MCM),': [257], 'core': [259], 'motor': [260], 'replicative': [263], 'helicase,': [264], 'as': [265, 554, 688, 1476, 1540, 1579, 1738, 1887, 2278, 2364, 2570, 3116, 3118, 3186, 3223, 3392, 3640, 3712, 3917, 4376, 4396, 4445], 'inactive': [266, 3542], 'head-to-head': [267], 'double': [268], 'hexamers': [269], '(MCM-DHs)': [270], 'around': [271, 2156, 2900, 3522], 'double-stranded': [272], '(Bell': [274], 'Kaguni,': [276], '2013;': [277, 506, 727, 951, 2322, 3238], 'Evrin': [278], '2009;': [281, 332], 'Remus': [282, 329], 'Diffley,': [284], '2009).': [285, 3805], 'A': [286, 511, 1057, 3076], 'single': [287, 936], 'ORC': [288, 299, 619, 880, 887, 937, 944, 1029, 1153, 1164, 1373, 1435, 1505, 1518, 1559, 1627, 2082, 2109, 2154, 2202, 2736, 2906, 3099, 3120, 3213, 3244, 3284, 3358, 3465, 3572, 3844], 'reiteratively': [289], 'multiple': [291], 'MCM-DHs.': [292], 'However,': [293], 'once': [294], 'MCM-DHs': [295, 361, 381, 987, 3816], 'assembled,': [298], 'maintain': [302], 'contact': [303], 'MCM-DH': [306, 1375, 1513, 3360], 'neither': [308], 'ORC,': [309, 911, 3302, 4395], 'nor': [310, 312], 'required': [315, 1338, 2373], 'for': [316, 414, 476, 486, 639, 1312, 1323, 1372, 1558, 1567, 1665, 1851, 2656, 2759, 2783, 2939, 3291, 3433, 3529, 3593, 3684, 4021, 4213, 4328, 4340, 4392, 4443], 'activation': [318, 1355], '(Fragkos': [319], '2015;': [322, 328, 498, 572, 3836], 'Hyrien,': [323], '2016;': [324, 580, 584, 731, 760, 2326], 'Powell': [325], 'Rowles': [333], '1999;': [336], 'Sun': [337], '2014;': [340, 469, 502], 'Yeeles': [341], '2015).': [344, 930], 'phase,': [347, 435], 'CDK2': [348], 'CDC7': [350], 'kinase': [351], 'activities': [352], 'conjunction': [354], 'other': [356], 'origin-firing': [357, 641], 'convert': [359], 'some': [360], 'into': [362, 447], 'pairs': [363], 'active': [365, 811, 1000, 1185, 1264, 1332, 2187, 2252, 2605, 3151, 3173, 3221, 3262, 3480, 3500, 3531, 3706, 3737, 4046], 'CDC45-MCM-GINS': [366], 'helicases': [367], 'nucleate': [369], 'bidirectional': [370], 'replisome': [371], 'establishment': [372], '(Douglas': [373], 'Moiseeva': [377], '2018).': [380, 852, 1005, 1145, 1305, 2334, 3727, 3900], 'do': [383, 1233, 1945], 'initiate': [385], 'dislodged': [388], 'replication.': [392], 'Saccharomyces': [394], 'cerevisiae,': [395], 'genetically': [398], 'defined': [399, 3919], 'specific': [401, 1241], 'sequences': [403, 3085, 3093], '(Marahrens': [404], 'Stillman,': [406], '1992).': [407], 'multicellular': [409], 'organisms,': [410], 'consensus': [412], 'sequence': [413, 3077], 'activity': [416, 922, 1293, 2954, 3017, 3185, 3390, 3605, 3625, 3637, 4121], 'has': [417, 615, 3809], 'identified': [419, 856, 939], 'flexible': [424], 'locations.': [425], 'Although': [426], 'mammalian': [427, 663, 2304], 'fire': [429, 440], 'different': [431, 1112, 1868, 2525, 2792, 2941, 3904], 'times': [432], 'through': [433, 463, 624], 'neighboring': [436], 'tend': [438], 'similar': [442, 1204, 1208, 2031], 'times,': [443], 'partitioning': [444], 'genome': [446, 1068, 1124, 1161, 1317, 2403, 3780, 4129], '~5,000': [448], 'domains': [451, 494], '(RTDs)': [452], '(Rivera-Mulia': [453], 'Gilbert,': [455, 505, 509], '2016a).': [456], 'RTDs': [457, 482, 1978], 'replicate': [458], 'reproducible': [461], 'order': [462, 1829], '(Pope': [466], 'Zhao': [470], '2017).': [473, 609], 'One': [474], 'model': [475, 515, 1090, 1311], 'temporal': [478], 'regulation': [479], 'suggests': [480, 516], 'first': [484, 519, 1107], 'initiation,': [487, 2891, 4269, 4291], 'followed': [488, 872, 1400, 1511, 1674, 1770, 2538, 2649, 3660], 'firing': [492, 3801, 3832, 3867], 'within': [493, 534, 2350, 2556, 2599, 2847, 2913, 3007, 3261, 3420, 3556, 3618], '(Boulos': [495], 'Pope': [499], 'Rhind': [503], 'Rivera-Mulia': [507], '2016b).': [510], 'cascade': [512, 1310], 'domino': [514], 'most': [523, 1891, 2380], 'efficient': [524, 532, 2381], '(master)': [525], 'then': [528, 2543], 'spreads': [529], 'less': [531, 2473, 3310, 3440], 'an': [535, 818, 1489, 1645, 2157, 2390, 2612, 3190], 'RTD': [536], '(Boos': [537], 'Ferreira,': [539], '2019;': [540, 723, 2318, 3141], 'Guilbaud': [541], '2011).': [544], 'Various': [545], 'processes': [546], 'contribute': [549], 'specification': [552], 'such': [553, 687], 'transcription,': [555, 3208], 'sequences,': [557], 'variants,': [559], 'modifications,': [561], 'nucleosome': [563, 3096], 'dynamics': [564], '(Akerman': [565], '2020;': [568, 576, 955], 'Cayrou': [569], 'Long': [573, 952], 'Petryk': [577, 728, 2323, 3142, 3921], 'Prioleau': [581], 'MacAlpine,': [583], 'Smith': [585, 732], 'Aladjem,': [587], '2014).': [588], 'For': [589, 2006, 2761], 'example,': [590, 2007], 'H4K20me3': [593, 1290], 'support': [595, 1088, 1308], 'subset': [600, 1277], 'heterochromatin': [605], '(Brustel': [606, 1298], 'Recently,': [610, 817], 'variant': [613], 'H2A.Z': [614], 'implicated': [617], 'recruitment': [620], 'early': [622, 838, 858, 975, 1169, 1977, 2557, 4427], 'deposition': [625], 'H4K20me2': [627], 'methyltransferase': [630], 'SUV420H1': [631], '(Long': [632], '2020).': [635, 655, 700, 869], 'Furthermore,': [636, 853, 1201], 'binding': [637, 946, 968, 1032, 3845], 'sites': [638, 899, 947, 1036, 2184, 3503, 3527, 4238, 4242], 'factor': [642], 'Treslin-MTBP': [643], 'often': [644, 888], 'feature': [645], 'nucleosome-free': [647], 'gap': [648], 'adjacent': [649, 1331, 3554], 'H3K4me2': [651], '(Kumagai': [652], 'Dunphy,': [654], 'Different': [656], 'approaches': [657], 'developed': [660], 'characterize': [662], 'origins.': [664], 'Origins': [665], 'mapped': [668, 1073, 1731], 'single-molecule': [671, 741], 'level': [672, 680], 'optical': [674], 'cell-population': [679], 'sequencing': [682, 702, 874, 1676, 2651], 'various': [683], 'purified': [684], 'intermediates,': [686], 'short': [689], 'nascent': [690, 834], 'strands,': [691], 'bubbles,': [693], 'Okazaki': [695, 704, 3105], 'fragments': [696, 705], '(Hulke': [697], 'Strand-oriented': [701], '(OK-seq)': [706], 'reveals': [707], 'population-averaged': [709], 'direction': [712, 2615, 4135], '(RFD)': [713, 2616, 4136], 'allowing': [714, 1488, 2341], 'map': [716, 879], '(Chen': [720, 2315, 3138], 'McGuffee': [724, 2319], 'Whitehouse,': [734], 'Bubble-seq': [736], '(Mesner': [737], '2013),': [740, 2301], 'analyses': [742, 1410, 2037, 3685], '(Demczuk': [743], '2012;': [746, 1048, 1455, 1549, 1606], 'Lebofsky': [747], '2006;': [750], 'Norio': [751, 1078], '2005),': [754, 1994], 'OK-seq': [756, 785, 828, 864, 2257, 3136], '(Petryk': [757, 813, 1268, 2577, 3043], 'Wu': [761, 2331], '2018)': [764], 'studies': [765, 961, 3137], 'cells': [768, 841, 984, 1392, 1483, 1533, 2140, 2260, 2305, 3234, 3723], 'all': [769, 1654, 1817, 2415, 2451, 2587, 2678, 2901, 3488, 4056, 4102, 4256, 4420], 'suggest': [770, 1229], 'broad': [775, 3766], 'circumscribed': [777], 'consisting': [779], 'multiple,': [781, 1099], 'individually': [782, 1100], 'inefficient': [783, 1101], 'sites.': [784, 1102], 'revealed': [786, 3079, 3153], 'both,': [787], 'early-firing': [788, 824], '(IZs),': [791], 'which': [792, 832, 1097, 2396, 3791], 'precisely': [794], 'flanked': [795, 2454, 2841, 3735], 'on': [796, 1022, 1620, 2102, 2240, 2427, 2466, 2533, 2604, 2618, 2822, 2850, 2910, 3183, 3407, 3603, 3623, 4207], 'one': [797, 2434, 2492, 2856], 'both': [799, 857, 1517, 2428, 2467, 2698, 2823, 2851, 3026, 3065], 'sides': [800, 2429, 2468, 2824, 2852], 'actively': [802, 1178, 2456, 3295, 3513], 'late-firing': [806], 'IZs': [807, 825, 861, 865, 1237, 1255, 1281, 2238, 2277, 3734, 3773], 'distantly': [808], 'located': [809, 2417, 2555], 'genes': [812, 1194, 2458, 2512, 2696, 2716, 2844, 3152, 3188, 3263, 3297, 3532, 3543, 3547, 4219, 4231, 4349, 4356, 4408], '2016).': [816, 959, 1271, 2580, 3046, 3242, 3858], 'excellent': [819], 'agreement': [820], 'observed': [822, 2572, 3210, 3999], 'determined': [826, 1831, 2445], 'EdUseq-HU,': [831], 'identifies': [833], 'synthesized': [836], 'presence': [844], 'EdU': [846], 'hydroxyurea': [848], '(Tubbs': [849], 'high-resolution': [854], 'Repli-seq': [855, 1140, 3879], 'consistent': [862, 3703], '(Zhao': [866], 'Chromatin': [870], 'immunoprecipitation': [871, 1673, 2648, 4154], '(ChIP-seq)': [875, 1677, 2652], 'used': [877, 1010, 1379, 3850, 3876], 'MCM': [882, 1031, 1155, 1172, 1520, 1538, 1568, 1629, 2084, 2111, 2738, 2908, 2974, 3122, 3474, 3574, 4393], 'chromatin': [883, 893, 972, 992, 1246, 1260, 1296, 1672, 2647, 3789, 4153], 'binding.': [884], 'Drosophila,': [886], 'next': [890, 909, 2243], 'open': [892, 971, 1259], 'marks': [894, 1261, 1336], 'found': [895, 1612, 2166, 2197], 'transcription': [897, 1118, 1333, 2241, 3355, 3429, 3501, 3709], 'start': [898, 3502, 4237], '(TSSs)': [900, 3504], '(MacAlpine': [901, 3228], '2010),': [904], 'MCMs,': [906], 'initially': [907], 'loaded': [908, 915, 3817], 'abundantly': [914], 'widely': [917], 'redistributed': [918], 'cyclin': [920], 'E/CDK2': [921], 'rises': [923], '(Powell': [927, 3717], 'subunits': [938, 1560], '13,000': [941], '101,000': [943], '(Dellino': [948, 3235], 'Miotto': [956, 2142, 2173, 3239], 'These': [960, 1086, 1227, 1306, 2228, 3266], 'consistently': [962], 'demonstrated': [963, 3225, 4377], 'correlation': [965, 1813, 1839, 1898, 2058, 2104], 'ORC-DNA': [967], 'TSSs,': [970, 1974, 3222], '(RT).': [978], 'HeLa': [983, 2576], 'suggested': [985], 'bind': [988], 'regardless': [989], 'environment,': [993], 'preferentially': [996], 'activated': [997], 'upstream': [998, 3156, 3253, 3452, 3476, 3614], 'TSSs': [1001, 3132, 3158, 3255, 3308, 3374, 3411, 3454, 3468, 3523, 3563, 3601, 3616, 3629], '(Sugimoto': [1002], 'others': [1008], 'previously': [1009, 1138, 1252, 2132, 2571, 3036, 3713, 3918], 'Epstein–Barr': [1012], 'virus': [1013], '(EBV),': [1014], 'whose': [1015], 'latency': [1018], 'entirely': [1020], 'dependent': [1021, 1619, 2239, 3602, 3622], 'machinery,': [1026], '(Chaudhuri': [1037], '2001;': [1040, 1044, 1077], 'Dhar': [1041], 'Ritzi': [1049, 1456, 1550], '2003;': [1052, 1459], 'Schepers': [1053, 1460], '2001).': [1056, 1463], 'were': [1065, 1468, 1617, 1631, 1759, 1830, 2033, 2085, 2116, 2453, 2508, 2532, 2562, 2814, 3018, 3268, 3309, 3317, 3370, 3376, 3459, 3559, 3655, 4075, 4245], 'per': [1067, 1694, 2460, 2462, 2878, 2880, 3534, 3536, 4221, 4223, 4316], 'respect': [1070], '1–3': [1072], 'event(s)': [1075], '(Norio,': [1076], 'Schildkraut,': [1080], '2004;': [1081], 'findings': [1087, 1228, 1307], 'comprise': [1098], 'present': [1105, 2185, 2288], 'comparative': [1108], 'survey': [1109], 'four': [1111, 3903], 'pre-RC': [1113], 'components,': [1114], 'events,': [1117], 'activity,': [1119, 2934], 'RT': [1121, 1170, 1205, 3770, 3774, 3825, 3853, 3888, 4032, 4094, 4160, 4172, 4430, 4434], 'lymphoblastoid': [1128, 1390], 'Raji': [1129, 1391, 1482, 2259, 2442, 3877], 'line': [1131, 1828, 1953, 2192, 2753, 3034, 3587], 'combining': [1133], 'ChIP-seq,': [1134], 'OK-seq,': [1135], 'published': [1139, 2133], '(Sima': [1142, 3897], 'find': [1147], 'that,': [1148], '(G1)': [1151], 'chromatin,': [1152], 'broadly': [1157], 'distributed': [1158, 1349, 4126], 'over': [1159, 1192, 2312, 3952, 3988, 4163], 'high': [1163, 2056, 3651, 3947], 'better': [1166], 'correlating': [1167], 'density.': [1173], 'bodies': [1181, 3128, 3175, 3287, 3316, 3334, 3381, 3422, 3701, 4040, 4048], 'promoters.': [1187], 'homogeneous': [1191, 3347], 'non-transcribed': [1193, 2995], 'intergenic': [1196, 4034, 4214, 4358, 4410], 'regions': [1197, 1202, 1218, 1985, 1990, 2206, 2212, 2421, 2729, 2918, 2958, 2978, 3959, 3983, 4035, 4215, 4244, 4359, 4411], 'comparable': [1199], 'RT.': [1200], 'show': [1206, 1274, 4254], 'density,': [1210], 'be': [1211, 1635], 'they': [1212], 'IZs,': [1213], 'undirectionally': [1216], '(presumably': [1219], 'lacking': [1220], 'events),': [1222], 'densities': [1232, 2888, 4353, 4423], 'determine': [1236], 'contribution': [1242], 'local': [1245, 3054, 3464], 'environment': [1247], 'required.': [1249], 'Indeed,': [1250], 'showed': [1253, 3052, 4350], 'typical': [1262], 'poised': [1266], 'enhancers': [1267], 'further': [1273, 2036, 2230, 2372], 'non-genic': [1279, 2544, 2560, 2725, 3008, 3048, 3746, 3759], 'confirming': [1286], 'previous': [1287, 1956, 3135, 3672], 'finding': [1288], 'enhances': [1291], 'certain': [1295], 'environments': [1297], '2017;': [1301], 'Shoaib': [1302], 'initiation:': [1314], 'entire': [1316], '(except': [1318], 'genes)': [1320], 'Additional': [1326], 'process': [1327, 3730], 'like': [1330], 'epigenetic': [1335], 'specify': [1340], 'master': [1341], 'higher': [1344, 3252], 'efficiency.': [1347], 'The': [1348, 1500, 1719, 1742, 1755, 2044, 2079, 2517, 2733, 2749, 3281, 3583, 4174, 4202, 4252, 4312, 4387], 'pattern': [1351, 3908], 'allows': [1352], 'secondary': [1357], 'origins,': [1358], 'possibly': [1359], 'triggered': [1360], 'approaching': [1362], 'forks.': [1364], 'Moderate': [1366, 1659], 'averaging': [1367, 1660], 'suitable': [1370], 'approach': [1371, 1664], 'distribution': [1376, 3216, 3247], 'analysis': [1377, 2784, 3078, 4175], 'centrifugal': [1380], 'elutriation': [1381], 'obtain': [1383], 'G1-enriched,': [1385], 'population': [1387, 1530], '(Papior': [1393], 'Propidium': [1397], 'iodide': [1398], 'staining': [1399], 'FACS': [1402], '(Figure': [1403, 1418, 1478, 1542, 1587, 1919, 1940, 1979, 2023, 2122, 2169, 2223, 2404, 2546, 2566, 2919, 2944, 2979, 2998, 3010, 3023, 3059, 3112, 3176, 3195, 3264, 3320, 3362, 3382, 3412, 3435, 3445, 3749, 4004, 4014, 4360, 4381], '1—figure': [1404, 1419, 1479, 1543, 1848, 1920, 1980, 2024, 2123, 2170, 2224], 'supplement': [1405, 1420, 1480, 1544, 1849, 1921, 1981, 2025, 2124, 2171, 2225, 2548, 2568, 2781, 2923, 2951, 3114, 3178, 3197, 3279, 3324, 3386, 3416, 3447, 3486, 3682, 3914, 4006, 4018, 4326, 4338, 4364, 4383], '1a)': [1406, 3115], 'western': [1408], 'blot': [1409], 'cyclins': [1412], 'A,': [1413], 'B,': [1414], 'H3S10': [1416], 'phosphorylation': [1417], '1b)': [1421], 'confirmed': [1422], 'cycle': [1425], 'stages': [1426], 'elutriated': [1428], 'fractions.': [1429], 'To': [1430, 2126, 2882, 2928, 3859], 'ensure': [1431], 'unbiased': [1432], 'mapping': [1433], 'MCM,': [1437, 4444], 'simultaneously': [1439], 'targeted': [1440], 'using': [1446, 1470, 1837, 2118], 'validated': [1447], 'ChIP-grade': [1448], 'antibodies': [1449], '(validated': [1450], 'ChIP': [1464, 1767, 1818, 1865, 1882, 2050, 2106, 2344, 2664, 4089, 4194], 'efficiencies': [1465], 'qualities': [1467], 'measured': [1469], 'EBV': [1472, 1486], 'latent': [1473], 'oriP': [1475, 1495], 'reference': [1477], '1c).': [1481, 3387, 4007], 'contain': [1484], '50–60': [1485], 'episomes,': [1487], 'easy': [1490], 'detection': [1491, 3108], '(Adams': [1496], '1973).': [1499], 'viral': [1501], 'protein': [1502], 'EBNA1': [1503], 'recruits': [1504], "oriP's": [1507], 'dyad': [1508, 1523], 'symmetry': [1509, 1524], 'element,': [1510], 'loading.': [1514], 'element': [1525], 'G1,': [1527, 3711], 'whereas': [1528], 'containing': [1531], 'S-G2-M-phased': [1532], 'depict': [1534], 'reduction': [1536], 'levels,': [1539], 'expected': [1541], '1c;': [1545], '2003).': [1553], 'two': [1556, 1698], 'replicates': [1557, 1566, 1758, 1866], '(Orc2,': [1561], 'Orc3)': [1562], 'three': [1565, 1705, 1717], 'proteins': [1569], '(Mcm3,': [1570], 'Mcm7)': [1571, 4024], 'resulted': [1572], 'reproducible,': [1574], 'dispersed,': [1576], 'signals': [1578, 1874, 2345], 'exemplified': [1580], 'well-characterized': [1583], 'Mcm4/PRKDC': [1586, 1690], '1a;': [1588], 'Ladenburger': [1589], '2002;': [1592], 'Schaarschmidt': [1593], '2002).': [1596], 'employed': [1598], 'MACS2': [1600], 'peak-calling': [1601], 'program': [1602, 1623], '(Feng': [1603], 'Zhang': [1607], '2008),': [1610], 'results': [1616, 1999, 2115, 2229], 'too': [1618, 1632], 'chosen': [1622], 'settings': [1624], 'distributions': [1630, 3081, 3764], 'dispersed': [1633], 'efficiently': [1636], 'captured': [1637], 'peak': [1639], 'calling': [1640], '(data': [1641, 3089], 'shown),': [1643], 'requiring': [1644], 'alternative': [1646], 'approach.': [1647], 'Figure': [1648, 1847, 2070, 2077, 2097, 2581, 2779, 2921, 2949, 2968, 3063, 3274, 3277, 3322, 3384, 3414, 3482, 3680, 3912, 4016, 4096, 4324, 4336, 4345, 4362, 4400], '1': [1649, 1748, 1792, 1806, 1823, 1843, 1908, 1926, 2208, 2470, 2530, 2551, 2692, 2763, 2789, 2802, 2835, 3485, 3683, 4327], '3': [1651, 1850, 3483, 3631, 4140], 'supplements': [1652, 2585, 4100], 'see': [1653, 2586, 3487, 4101], 'Download': [1655, 2588, 3489, 4103], 'asset': [1656, 1658, 2589, 2591, 3490, 3492, 4104, 4106], 'Open': [1657, 2590, 3491, 4105], 'represents': [1661, 1775], 'valid': [1663], 'complex/minichromosome': [1668, 2594, 4109], '(ORC/MCM)': [1671, 2597, 4112], 'analysis.': [1678], '(a)': [1679, 2607, 3530, 4149], 'Sequencing': [1680], 'profile': [1681, 1743, 2617, 3149, 3194], 'visualization': [1682], 'UCSC': [1684], 'Genome': [1685], 'Browser': [1686], '(hg19)': [1687], 'reads': [1693, 1756, 1862], 'genomic': [1695, 3763], 'content': [1696], 'normalization:': [1697], 'samples': [1699, 1706], 'Orc2': [1701, 1785, 2134, 2161, 2179, 2645, 4011, 4148], 'Mcm3': [1708, 1799, 2642, 3303, 3338, 3692, 4013, 4151], 'Mcm7,': [1710, 3340], 'plotted': [1712], 'against': [1713, 1875, 1885, 4031], 'input': [1715, 1772, 1855, 1963, 2004, 2021, 2042, 2221, 2786, 2926, 3271, 3434, 3443, 3687], 'replicates.': [1718], 'shown': [1722, 2743, 3577], '10': [1725, 2348, 4028, 4179], 'kb': [1726, 1749, 1793, 1807, 1824, 1909, 1927, 2314, 2349, 2426, 2476, 2683, 2809, 2821, 2849, 2865, 3551, 3558, 3632, 4029, 4165, 4180], 'window': [1727], '(chr8:': [1728], '48,868,314–48,878,313);': [1729], 'position': [1732], 'indicated': [1737, 3567, 3667, 4206, 4319], 'green': [1739, 2406, 2629], 'line.': [1740], '(b)': [1741, 2677, 3541, 4152], 'binning': [1750, 1869, 2655], 'same': [1753, 2658, 3968], 'locus.': [1754], 'summed': [1760, 1859], 'normalized': [1762, 1872, 3432, 4076, 4184], 'total': [1765], 'genome-wide': [1766], 'read': [1768, 1779, 1789, 1803, 1820, 1878, 2063, 2150, 2247, 2665, 2740, 2756, 2896, 3215, 3246, 3520, 3590, 3598, 3612, 3892, 4025, 4157], 'frequency': [1769, 2757, 3591, 4090, 4158], 'division.': [1773, 1856, 2787, 3688], 'Y-axis': [1774], 'resulting': [1777], 'relative': [1778, 1788, 1802, 1819, 2062, 2149, 2246, 2663, 2739, 2755, 2895, 3214, 3245, 3519, 3589, 3597, 3611, 3891, 4010, 4156, 4195], 'frequency.': [1780], '(c)': [1781, 2690, 3595], 'Correlation': [1782, 1796], 'plot': [1783, 1797], 'Orc3': [1787, 4022, 4330], 'frequencies': [1790, 1804, 1821, 1879, 2064, 2151, 2248, 2666, 2741, 2897, 3521, 3575, 3599, 3613, 3893, 4026, 4196], 'bins.': [1794, 1808, 1825, 4181], '(d)': [1795, 2704, 3609], '(e)': [1809, 2724], 'Heatmap': [1810], 'Pearson': [1812, 1897, 2057, 2103], 'coefficients': [1814, 1899, 2059], 'r': [1815, 2090, 2094], 'Column': [1826], 'complete': [1833], 'linkage': [1834], 'hierarchical': [1835], 'clustering': [1836, 2100], 'distance': [1840], '(d': [1841], '=': [1842, 2068, 2075, 2091, 2095, 2688, 2702, 2721, 2731], 'r).': [1844], 'Refer': [1845, 2777, 3678, 4334], 'representation': [1853], 'without': [1854, 2003, 2041, 2220, 2785, 2925, 3442, 3552, 3686], 'Consequently,': [1857], 'up': [1860, 2346], 'sizes': [1870, 1918], 'mean': [1877, 2734], 'each': [1881, 4081, 4321], 'sample': [1883], 'input,': [1886], 'standard': [1889], 'analyses.': [1893, 4333], 'computed': [1895, 2893, 4212], 'ChIPs': [1902, 2155], 'good': [1905], 'correlations': [1906, 2080], 'bin': [1910], 'size': [1911, 2392], 'only': [1913, 2086, 2491, 3051], 'marginal': [1914], 'improvement': [1915], 'larger': [1917, 3548], '2a).': [1922], 'When': [1923, 3199], 'working': [1924], 'bins,': [1928], 'still': [1930, 2009], 'enrichment': [1933, 2011, 2168, 2200, 2598, 3004, 3466], 'MCM/PRKDC': [1938, 2016], '1b),': [1941, 2569, 3325], 'indicating': [1942, 3461], 'lose': [1947], 'local,': [1948], 'biologically': [1949], 'relevant': [1950], 'signals.': [1951], 'report': [1957], '(Teytelman': [1958], '2009),': [1961], 'control': [1964], 'underrepresented': [1967], 'DNase': [1969, 1988, 2182, 2204, 2215], 'hypersensitive': [1970], '(HS)': [1971], '2b–d).': [1982, 2952], 'As': [1983, 2027], 'sonication-hypersensitive': [1984], 'correlate': [1986, 3768, 4114], 'HS': [1989, 2183, 2205, 2216], '(Schwartz': [1991], 'carefully': [1996], 'compared': [1997, 2210, 2244, 2915], 'our': [1998, 2049, 2128, 2153, 2232, 3201], 'normalization.': [2005, 2043], 'detect': [2010], 'omit': [2020], 'normalization': [2022, 2222, 3272, 3444], '3).': [2026], 'will': [2028], 'become': [2029], 'apparent,': [2030], 'conclusions': [2032], 'performed': [2038, 3656, 4177], 'reliability': [2045], 'reproducibility': [2047], 'experiments': [2051], 'reflected': [2053], 'Orc2/Orc3': [2066], '(r': [2067, 2074], '0.866,': [2069], '1c)': [2071], 'Mcm3/Mcm7': [2073], '0.879,': [2076], '1d).': [2078, 3417], 'slightly': [2087, 2535, 3424], 'lower': [2088, 4351], '(Mcm3/Orc2/3:': [2089], '0.775/0.757;': [2092], 'Mcm7/Orc2/3:': [2093], '0.821/0.800,': [2096], '1e).': [2098, 3448], 'Hierarchical': [2099], 'based': [2101], 'clustered': [2108], 'together.': [2113], 'Similar': [2114], 'non': [2119], 'input-normalized': [2120, 2662], '3b–d).': [2125], 'asynchronously': [2137, 2440], 'cycling': [2138, 2441], 'K562': [2139, 2160], '(GSE70165;': [2141], '2016),': [2145, 3145], 'calculated': [2147, 2266, 4009], 'aggregate': [2158, 2903], 'peaks': [2162], '(>1': [2163], 'kb)': [2164], 'substantial': [2167], '3e).': [2172], '2016': [2176], 'reported': [2177, 3811], 'co-localizes': [2180], 'promoters': [2188], 'enhancers.': [2190], 'observations,': [2195], 'significant': [2199, 3290, 4370, 4416], '>': [2207, 2338, 2375, 2681, 2812, 3950], 'kb,': [2209, 2340, 2395], 'deprived': [2213], 'sites,': [2217], '3f,': [2226], 'g).': [2227], 'validate': [2231], 'data.': [2233], 'units.': [2255], 'Using': [2256, 2356], '(Wu': [2261], '2018),': [2264], 'RFD': [2268, 2284, 2286, 2358, 2635, 3148, 3168, 3193, 3895, 3907, 3927, 3935, 3982, 4298, 4303], '(see': [2269, 2352, 4248], 'Methods)': [2272], 'delineated': [2274], 'preferential': [2275], 'ascending': [2279, 2600, 2870, 3926, 4263], 'segments': [2280, 2601, 3169, 3928, 3936, 3945, 3979], '(ASs)': [2281, 2602], 'profile.': [2285], 'upshifts': [2289], 'define': [2291], 'kilobase': [2294, 2461, 2879, 3535, 4222], 'resolution': [2295], 'yeast': [2297], '(McGuffee': [2298], 'transitions': [2307], 'gradual,': [2310], 'extending': [2311], '10–100': [2313], 'Tubbs': [2327], 'analyzed': [2336, 3902], 'ASs': [2337, 2351, 2362, 2448, 2488, 2506, 2531, 2545, 2554, 2561, 2625, 2693, 2707, 2726, 2818, 2840, 2914, 2966, 3009, 3155], '20': [2339, 2425, 2475, 2682, 2820, 2848], 'assess': [2343], 'Methods).': [2355], 'shift': [2359], 'across': [2360, 3171, 3745], '(ΔRFD)': [2363], 'measure': [2366], 'efficiency,': [2370], 'ΔRFD': [2374, 2685, 2811], '0.5': [2376, 2813], 'select': [2378], 'IZs.': [2382, 3761], 'total,': [2384, 2411, 2486], '2957': [2387], 'ASs,': [2388, 2542, 2766, 2989, 4064], 'average': [2391, 2534, 3147], '52.3': [2394], 'covered': [2397], '4.9%': [2398], '(155': [2399], 'Mb)': [2400], '2a,': [2405, 4384], 'bars,': [2407], 'Table': [2408, 2788], '1).': [2409, 2516, 3299, 3343], '2451': [2412], '(83%)': [2413], 'AS': [2416, 2478, 2526, 2674, 2679, 2699, 2711, 2771, 2793, 2807, 2867, 2902, 2942, 2956, 2996, 3012, 3041, 3049, 3087, 3747], 'close': [2418], 'genic': [2420, 2828], '(ASs': [2422], 'extended': [2423, 2819], 'overlapped': [2430, 2826], 'least': [2433], 'annotated': [2435, 2862], 'gene).': [2436], 'Performing': [2437], 'RNA-seq': [2438], '673': [2447], '(22.8%': [2449], 'ASs)': [2452], '(transcripts': [2459, 3533, 4220], 'million': [2463, 3537, 4224], '[TPM]': [2464, 3538], '>3)': [2465, 3539], '(type': [2469, 2499, 2853, 2858], 'AS),': [2471], 'borders': [2479, 2675, 2700, 2772, 2997, 3013, 3029, 3042, 3050, 3088, 3748], 'closest': [2482], 'gene.': [2484], '1026': [2487], '(34.7%)': [2489], 'had': [2490], 'border': [2493, 2712, 3107], 'associated': [2494, 2713, 2773, 2960, 3014], '2': [2500, 2541, 2553, 2582, 2584, 2706, 2765, 2782, 2804, 2838, 2988, 4099], 'AS;': [2501], 'TPM': [2502, 4225], '>3).': [2503], 'Also,': [2504], '506': [2505], '(17.1%)': [2507], 'devoid': [2509], 'proximal': [2511, 4243], '(non-genic': [2513], 'AS)': [2514], '(Table': [2515, 3298, 3342], 'slope': [2518, 3896], 'did': [2519, 3401, 3469], 'change': [2521], 'considerably': [2522], 'types,': [2527], 'although': [2528], 'type': [2529, 2540, 2691, 2705, 2762, 2834, 2837, 2987], 'efficient,': [2537], '2—figure': [2547, 2567, 2780, 2922, 2950, 3113], '1a).': [2549, 3179, 3198], 'Type': [2550], 'RTDs,': [2558], 'while': [2559, 3505], 'predominantly': [2563], 'GM06990': [2574], 'depends': [2603], 'transcription.': [2606], 'Top': [2608], 'panel:': [2609], 'example': [2610], 'chr1:': [2619], '178,400,000–182,800,000,': [2620], 'covering': [2621], '4': [2622, 4097], 'Mb.': [2623], 'Detected': [2624], 'labeled': [2627], 'rectangles': [2630], '(irrespective': [2631], 'length': [2633, 2798], 'shift).': [2636], 'Middle': [2637], 'bottom': [2639, 4310], 'panels:': [2640], 'representative': [2641], '(blue)': [2643], '(red)': [2646], 'region.': [2659], '(b–e)': [2660], 'Average': [2661], '(L': [2680], '>0.5;': [2686], 'n': [2687], '2957),': [2689], '(n': [2701, 2720, 2730], '673),': [2703], 'oriented': [2708], 'their': [2710, 3705], 'right': [2719, 2982, 3028, 4051, 4234], '1026),': [2722], 'gene-deprived': [2728], '506).': [2732], '±2': [2744, 3578], '×': [2745, 3579, 3607, 3627, 4141], 'SEM': [2746, 3580], '(lighter': [2747, 3581], 'shadows).': [2748, 3582], 'dashed': [2750, 3584], 'grey': [2751, 3585], 'horizontal': [2752, 3586], 'indicates': [2754, 3588], '1.0': [2758, 3592], 'reference.': [2760, 3594], 'yellow': [2767], 'bars': [2768], 'mark': [2769], 'genes.': [2776, 3481, 3515, 3738], 'Characterization': [2790], 'subtypes.': [2794], 'NumberGenome': [2795], 'coverage': [2796], '(%)Average': [2797], '(kb)All': [2799], 'AS29574.952.3Genic': [2800], 'AS24514.152.3Type': [2801], 'AS6731.150.7Type': [2803], 'AS10265.250.2Non-genic': [2805], 'AS5060.850.7Only': [2806], '≥20': [2808], 'considered.': [2815, 3560], 'Genic': [2816], 'ASs:': [2817], 'region(s)': [2829], 'irrespective': [2830], 'transcriptional': [2832, 2933, 3016, 3162, 3184, 3389, 3525, 3604, 3624, 3673, 4120, 4240], 'activity;': [2833], 'AS:': [2839, 2869], 'expressed': [2843, 4230, 4348, 4440], '(TPM': [2845, 3544, 3642, 3645, 3648, 3652, 4041, 4049, 4232], '≥3)': [2846], '1)': [2854], 'side': [2857], '2);': [2859], 'non-genic:': [2860], '±20': [2864], 'borders;': [2868], 'segment;': [2871], 'RFD:': [2872], 'direction;': [2875], 'TPM:': [2876], 'transcripts': [2877], 'million.': [2881], 'study': [2883], 'relationship': [2885], 'borders.': [2904], 'Both': [2905], 'were,': [2909], 'average,': [2911], 'flanking': [2917, 2957], '2b,': [2920, 2969], '2a': [2924, 4339], 'division).': [2927], 'resolve': [2929], 'impact': [2931, 3406], 'repeated': [2936], 'calculation': [2938], 'types': [2943, 3905], '2c-e;': [2945], 'non-input-normalized': [2946], 'Transcriptional': [2953, 3636], 'increased': [2962], 'levels': [2964, 2991, 3058, 3430, 3451, 4113], 'inside': [2965], '(compare': [2967, 3273], 'c)': [2970], 'prominent': [2973], 'depletion': [2975, 3282, 3419, 3729, 4388], '2c,': [2980, 3024], 'd,': [2981, 3025], 'border).': [2983, 3001], 'contrast,': [2985, 3365, 3740, 4403], 'remained': [2992, 3743], 'elevated': [2993], '2d,': [2999, 3060], 'left': [3000, 3061], 'No': [3002], '2e).': [3011], 'locally': [3019], 'respectively).': [3030], 'This': [3031, 3180, 3728, 4367], 'Orc1': [3038], 'accumulation': [3039], 'Reciprocally,': [3047], 'dip': [3055], 'border;': [3062], '2e,': [3064], 'borders),': [3066], 'biological': [3069], 'significance': [3070], 'observation': [3073, 3690], 'remains': [3074], 'unclear.': [3075], 'biased': [3080], 'homopolymeric': [3083], 'repeat': [3084], 'shown).': [3091], 'Such': [3092], 'may': [3094, 3102], 'affect': [3095], 'formation': [3097], 'binding,': [3100], 'bias': [3104], 'fragment/AS': [3106], 'small': [3110], 'scales': [3111], 'well': [3117], 'mappability.': [3119], 'Consistent': [3133], 'strong': [3154], 'downstream': [3160, 3257, 3456, 3478], 'site': [3164], '(TTSs),': [3165], 'descending': [3167, 3934, 4072, 4272], '(DSs)': [3170], '3—figure': [3177, 3196, 3278, 3323, 3385, 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