Strand‐specific, high‐resolution mapping of modified RNA polymerase II

Name: Work Video:
Duration: 3 min 30 s
Laura Milligan; Vân Anh Huynh‐Thu; Clémentine Delan‐Forino; Alex Tuck; Elisabeth Petfalski; Rodrigo Lombraña; Guido Sanguinetti; Grzegorz Kudla; David Tollervey
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1204, 1805, 1950, 2558, 3310, 3623, 4181, 4249, 4305, 4337], 'mapped': [663, 755, 857, 2084, 2103, 2204, 2344, 2559, 2690, 4135], 'location': [665, 1228, 2272], 'carrying': [668, 823], 'five': [670, 825], 'types': [671, 826], 'CTD': [673, 828, 949, 1003, 1054, 1586, 3654, 3788, 4365], 'phosphorylation': [674, 829, 999, 1029, 1088, 1816, 3651, 3671, 3804, 3818, 3847, 3867, 3891, 3928, 3938, 3959, 3968, 3997, 4013, 4204, 4228], 'on': [675, 811, 1316, 1603, 1753, 1831, 1860, 2396, 2417, 2438, 2475, 2541, 2675, 2716, 2742, 3498, 3805, 3835, 3929, 3939], 'transcript,': [678], 'providing': [679], 'strand-specific,': [680], 'nucleotide-resolution': [681], 'information,': [682], 'used': [685, 865, 1103, 1184, 1322, 1414, 2225], 'machine': [687, 1323], 'learning-based': [688], 'approach': [689, 1261, 1853], 'define': [691, 1416], 'states.': [693, 1393], 'This': [694, 1835, 2432, 4265], 'revealed': [695, 1726], 'enrichment': [696, 2062, 2976, 3672, 3714, 3845, 3868, 3892, 3995, 4014, 4193, 4284, 4317, 4329, 4339, 4354], 'Ser5P,': [698, 3648], 'depletion': [700, 720, 3432, 4041, 4298], 'Tyr1P,': [702, 3645, 3709], 'Ser2P,': [703, 3646, 3710, 3742], 'Thr4P,': [704, 3647, 3711, 3743], 'Ser7P': [706, 3650, 3713, 3745, 3773, 4297, 4319, 4328, 4366, 4380], 'in': [707, 911, 937, 940, 944, 958, 984, 1004, 1058, 1066, 1090, 1116, 1124, 1137, 1154, 1200, 1207, 1274, 1312, 1378, 1488, 1646, 1656, 1692, 1722, 1802, 1910, 1916, 2020, 2051, 2157, 2251, 2281, 2311, 2329, 2466, 2481, 2519, 2527, 2532, 2570, 2664, 2668, 2747, 2809, 2822, 2835, 2859, 3006, 3014, 3099, 3150, 3153, 3179, 3208, 3259, 3367, 3454, 3472, 3529, 3629, 3652, 3759, 3776, 3793, 3827, 3877, 3970, 4018, 4083, 4100, 4103, 4142, 4159, 4309, 4325], 'start': [710, 1766, 1877, 2404, 3896], 'site': [711, 1878, 2405, 2892, 2986, 3036, 3615, 4050, 4212], '(TSS)': [712, 1879, 2406], 'proximal': [713, 4316], '~150': [714, 3374], 'nt': [715, 2383, 2710, 2842, 2901, 3178, 3375, 3521, 3541, 3765, 3782, 3906], 'most': [717, 1760, 2424, 2717], 'genes,': [718, 2399, 3106, 3879, 3976], 'all': [722, 1799, 2221, 2355, 2397, 2566, 2685, 2909, 3515, 3747, 3900, 3974, 4016, 4043, 4189], 'modifications': [723, 1111, 2177], 'close': [724, 1762, 1873, 3032, 3143, 3189, 3306, 3433, 3494, 3609], 'poly(A)': [727, 2973], 'site.': [728, 3862], 'The': [729, 780, 905, 1052, 1338, 1577, 1885, 2039, 2161, 2267, 2293, 2336, 2358, 2456, 2573, 2679, 2738, 2804, 2819, 2888, 2904, 2937, 2950, 3114, 3381, 3419, 3526, 3538, 3903, 4002, 4155], 'TSS': [730, 787, 3192, 3245, 3378, 3436, 3497, 3612], 'region': [731, 2779, 3116, 3457, 3542, 4102], 'also': [732, 1033, 1238, 1614, 1681, 1771, 2946, 4081], 'showed': [733, 2434, 2974, 3056, 3197, 3362], 'elevated': [734, 3188], 'relative': [736, 1232, 1659, 2323, 2551, 2627, 3412, 3848, 3869, 3893, 3998, 4252, 4332, 4340, 4357], 'regions': [738, 1795, 2813, 3102], 'further': [739, 2218, 3737], '3′,': [740], 'high': [742, 1194, 2061, 2436, 2486, 3121], 'recruitment': [743], 'termination': [748, 2886, 2895, 3035, 3345, 3453], 'factors,': [749, 3429], 'correlated': [751, 3717], 'previously': [754, 3148, 4059, 4134], '3′': [756, 2811, 3085, 3101, 3211, 3464, 3564, 4066, 4216, 4231], 'ends': [757, 3086, 3465, 3565], 'short,': [759, 3256, 3567], 'unstable': [760, 800, 1449, 1905], 'ncRNA': [761, 1634, 1930, 3095, 3570, 3808], 'transcripts.': [762], 'hidden': [764, 847, 1334, 1351], 'Markov': [765, 848, 1335], 'model': [766, 1336, 1373, 1556, 2757], 'identified': [767, 844, 1163, 3880], 'distinct': [768, 3027, 3607], 'states': [770, 809, 834, 1369, 1817], 'associated': [771, 835, 876, 2065, 2761], 'initiating,': [773, 837], 'early': [774, 838, 1886], 'elongating': [775, 778, 841], 'later': [777], 'RNAPII.': [779, 3851, 4001], 'initiation': [781], 'state': [782, 1380, 1833, 1888], 'was': [783, 1262, 1770, 1964, 1979, 1991, 2007, 2415, 2580, 2651, 2688, 2705, 2825, 3081, 3240, 3423, 3673, 3726, 4058, 4330, 4355], 'enriched': [784, 2626, 3305, 3493, 3727, 3911], 'near': [785, 3728, 3750, 4299], 'protein-coding': [789, 812, 1064, 1657, 1684, 1754, 1800, 2249, 2277, 2356, 2398, 2686, 2817, 2910, 3105, 3118, 3135, 3253, 3459, 3499, 3820, 3975, 4190], 'genes': [790, 1065, 1307, 1658, 1685, 1801, 1903, 2105, 2250, 2278, 2463, 2687, 2719, 2744, 2911, 3119, 3136, 3172, 3254, 3460, 3500, 3517, 3693, 3809, 3821, 3857, 4017, 4191], 'persisted': [792], 'throughout': [793, 1683], 'exon': [794], 'intron-containing': [797, 1861], 'genes.': [798, 813, 2357, 2656, 2818, 3902, 4278], 'Notably,': [799, 3225, 4295], 'ncRNAs': [801, 883, 1477, 1665, 1747, 1788, 3220, 3258, 3411], 'apparently': [802], 'failed': [803], 'transition': [805, 1366, 1426], 'into': [806], 'elongation': [808, 2666, 3030], 'seen': [810, 4206], 'Synopsis': [814], 'new': [816], 'technique': [817], 'transcriptome-wide': [819, 3618], 'is': [830, 875, 900, 1167, 1881, 1892, 2004, 2342, 2464, 2534, 2588, 2597, 2610, 2837, 2912, 3004, 3020, 3073, 3186, 3303, 3393, 3408, 3491, 3543, 3910, 3918, 4090, 4266, 4307], 'presented.': [831], 'Distinct': [832], 'late': [840], 'are': [843, 1023, 1031, 1453, 1483, 1559, 1641, 1654, 1714, 2279, 2299, 2426, 2516, 2714, 2745, 2945, 3097, 3272, 3445, 3916, 4080], 'using': [845, 1078, 1332, 2026, 2207, 3813], 'model.': [849], 'Multiple': [850], 'forms': [852, 1247, 4246], 'can': [855, 863, 950, 973, 1075, 1300, 1365, 1580, 1613, 1837, 2202, 3469, 3810], 'be': [856, 864, 1076, 1162, 1774, 1790, 1839, 2083, 2203, 2525, 2753, 3470, 3791, 3811, 4062], 'nucleotide': [859, 921], 'resolution.': [860], 'Machine': [861], 'learning': [862, 1324], 'extract': [867], 'biological': [868, 1282, 1408], 'insights': [869, 1283], 'from': [870, 1284, 1792, 1966, 1993, 2230, 2789, 2932, 3376, 3410, 3426, 3534, 3767, 3783, 4368], 'these': [871, 998, 1255, 1701, 1713, 2100, 3356, 3467, 3787, 4074], 'datasets.': [872], 'Initiating': [873], 'distinct,': [879], 'surveillance-prone': [880], 'state.': [881, 1912], 'Unstable': [882], 'fail': [884], 'exit': [886], 'state,': [888], 'potentially': [889], 'linked': [890], 'rapid': [892, 1575, 2536], 'degradation.': [893, 1576], 'Introduction': [894], 'Eukaryotic': [895], '(RNAPII)': [899], 'large,': [902], 'multisubunit': [903], 'complex.': [904, 1961, 3293], 'largest': [906], 'subunit,': [908], 'termed': [909], 'Rpo21': [910, 1933, 1963, 1984, 2006, 2071, 2146, 2915, 3546], 'yeast,': [912, 938], 'has': [913, 2500], 'catalytic': [915, 3316], 'N-terminal': [916], '(NTD)': [918], 'that': [919, 1019, 1083, 1514, 1557, 1629, 1712, 1727, 1786, 1807, 1872, 2000, 2081, 2298, 2423, 2435, 2647, 2660, 2758, 3093, 3182, 3198, 3251, 3786, 4077, 4088, 4364], 'performs': [920], 'polymerization,': [922], 'regulatory': [925], '(CTD),': [928], 'consisting': [929], 'multiple': [931, 977], 'heptad': [932], '(consensus': [933], 'YSPTSPS)': [934], 'repeats': [935], '(26': [936], '52': [939], 'humans).': [941], 'Each': [942, 3502], 'position': [943, 2882, 4256], 'heptads': [946], 'undergo': [951], 'independent,': [952], 'reversible': [953], 'post-translational': [954], '(PTM)': [956], '(reviewed': [957, 983, 1089, 1199], 'Heidemann': [959, 1095], 'et': [960, 1009, 1013, 1037, 1041, 1045, 1049, 1071, 1096, 1217, 1278, 1429, 1433, 1459, 1479, 1528, 1532, 1536, 1540, 1544, 1548, 1590, 1608, 1624, 1667, 1687, 1704, 1708, 2508, 2546, 2725, 3016, 3041, 3053, 3163, 3167, 3350, 3400, 3479, 3586, 3598, 4070, 4115, 4119, 4152, 4321, 4350], 'al,': [961, 1010, 1014, 1038, 1042, 1046, 1050, 1072, 1097, 1218, 1279, 1430, 1434, 1460, 1480, 1529, 1533, 1537, 1541, 1545, 1549, 1591, 1609, 1625, 1668, 1688, 1705, 1709, 2509, 2547, 2726, 3017, 3042, 3054, 3164, 3168, 3351, 3401, 3480, 3587, 3599, 4071, 4116, 4120, 4153, 4322, 4351], '2013).': [962, 1098, 1669, 1751, 2936, 2999, 3224, 3418, 3442], 'In': [963, 1176, 2220, 2257, 3075, 3739, 4219, 4238, 4346], 'particular,': [964], 'phosphorylation/dephosphorylation': [965], 'Tyr1,': [967, 4223], 'Ser2,': [968, 4224], 'Thr4,': [969, 4225], 'Ser5,': [970], 'Ser7': [972, 4227], 'regulate': [974], 'interactions': [975], 'factors': [982, 3127, 3361, 3490], 'Buratowski,': [985], '2009;': [986, 2723, 3051], 'Hsin': [987, 1040], 'Manley,': [989], '2012).': [990], 'Two': [991], 'recent': [992, 1178], 'studies': [993, 1017], 'addressed': [994], 'sites': [1000, 1030, 1649, 1698, 2795, 3876, 4034, 4165, 4187, 4235], 'heptad-specific': [1006], 'manner': [1007], '(Schüller': [1008], '2016;': [1011], 'Suh': [1012], '2016).': [1015], 'Both': [1016], 'indicate': [1018, 4076], 'Ser5P': [1020, 3725, 3909, 4369], 'Ser2P': [1022, 3756, 3913], 'major': [1025, 1500, 2155, 3329, 3357, 3382, 4156], 'modifications;': [1026], 'however,': [1027, 1371, 4324], 'other': [1028, 1437, 1843, 3267, 3720, 4078], 'clearly': [1032, 2517], 'functionally': [1034, 2503], 'important': [1035, 1135, 2504, 4063, 4267], '(Egloff': [1036], '2007;': [1039], '2011;': [1043, 1706, 3161, 4113], 'Mayer': [1044, 1070, 3040, 3162, 4114], '2012;': [1047], 'Rosonina': [1048], '2014).': [1051, 1435, 2548], 'shows': [1055, 2164, 2296, 2361, 2391, 2484, 2495, 2952, 3092, 3120, 3504, 3606, 4007], 'dynamic': [1056], 'changes': [1057, 2663], 'PTMs': [1059], 'as': [1060, 2315, 2582, 2897, 2918, 2920, 3147, 3232, 3234, 3325, 3327, 3675, 3732, 3826, 3830, 3931, 3941, 3969, 4257], 'traverses': [1063], 'yeast': [1067, 1419, 1439, 1948, 2533, 2718, 2836, 3154, 4143, 4160], '(see,': [1068], 'e.g.,': [1069], '2010),': [1073, 2727, 4352], 'which': [1074, 1452, 1846, 2378, 2499, 2834, 3107, 3637], 'detected': [1077, 2429, 3098], 'set': [1080, 1349], 'antibodies': [1082, 1100, 2174], 'each': [1084, 1354, 2369, 3354, 3523, 3530, 3719, 4005, 4019, 4255], 'recognize': [1085], 'specific': [1087, 2131], 'Eick': [1091], 'Geyer,': [1093], '2013;': [1094, 1534, 1538], 'Such': [1099], 'have': [1101, 1128, 1133, 1183, 1205, 1320, 1411, 1734, 3205], 'been': [1102, 1129, 1413], 'assess': [1105, 1940, 3295, 4171], 'distribution': [1107, 1942, 2457, 2650, 2730, 2853, 3131, 3227, 3313, 3420, 3643, 3667, 4241, 4291], 'different': [1110, 1368, 1391, 1639, 1929, 3425, 4037, 4196, 4244], 'across': [1112, 1120, 1256, 1306, 1818, 2236, 2248, 2354, 2460, 2684, 3134, 3514, 3819, 3960, 3973, 4276], 'individual': [1113, 1691, 2462, 2655, 2743, 3524], 'units': [1115, 1123, 1421], 'ChIP': [1117, 1146, 2528, 3076, 3112], 'analyses,': [1118, 3077], 'or': [1119, 1289, 1503, 1664, 1798, 2179, 3281, 3649], 'many': [1121, 1797, 3104, 3252], 'ChIP-Seq.': [1125], 'These': [1126, 1445, 1551, 1783, 2750, 3443], 'analyses': [1127, 1179, 1314, 1725, 2224, 2242, 3152, 3196, 3834, 4107], 'highly': [1130, 2043], 'informative': [1131], 'played': [1134], 'roles': [1136], 'our': [1138], 'current': [1139], 'understanding': [1140], 'eukaryotic': [1142], 'gene': [1143, 1310, 2876, 3698], 'expression.': [1144], 'However,': [1145, 1627, 1670, 3089], 'ChIP-Seq': [1148], 'map': [1149, 1225, 1254, 3641], 'formaldehyde': [1152], 'crosslinking': [1153, 1186, 1210, 2147, 2683, 2907], 'sonicated': [1155], 'chromatin,': [1156], 'so': [1157], 'transcribed': [1159, 2106], 'strand': [1160, 2441, 2450, 2487], 'cannot': [1161], 'spatial': [1165, 1197, 1376], 'resolution': [1166, 1198], 'limited': [1168], 'fragment': [1171], 'sizes—typically': [1172], 'around': [1173, 2827, 2880], '200–300': [1174], 'nt.': [1175], 'contrast,': [1177, 3740, 4220], 'RNA-binding': [1181, 3200], 'proteins': [1182, 1730, 3201], 'UV': [1185, 1209, 2012], 'sequence': [1188, 1317], 'small': [1189, 2121, 2126], 'fragments,': [1191], 'giving': [1192], 'degree': [1195, 3450], 'Darnell,': [1201], '2010).': [1202, 3043], 'Here,': [1203, 1804], 'applied': [1206, 1951], 'vivo': [1208, 1693], 'analysis': [1212, 2433, 2791, 2799, 2969, 3045, 3864, 3888, 3925, 3935, 4010, 4327], 'cDNA': [1214], '(CRAC)': [1215], '(Granneman': [1216], '2009)': [1219, 2353], 'generate': [1221, 3255], 'high-resolution,': [1223, 1811], 'strand-specific': [1224, 1812], 'transcribing': [1230, 4127], 'nascent': [1235, 1520, 1936, 2543, 2641, 4131], 'transcript.': [1236, 1901], 'We': [1237, 1319, 1850, 1870, 1913, 2645, 4086], 'incorporated': [1239], 'an': [1240, 1346, 1398, 1822, 2380, 3625, 3794], 'additional': [1241, 3626], 'immunoprecipitation': [1242, 3627], 'step': [1243, 3628], 'separate': [1245], '(modification': [1250], 'CRAC;': [1251], 'mCRAC)': [1252], 'transcriptome.': [1258], 'related': [1260, 4091], 'recently': [1263, 1412], 'reported': [1264, 4162, 4185], 'identify': [1266, 1302, 1926], 'locations': [1268, 2375, 2739, 3707], 'Ser5P-': [1270], 'Ser2P-modified': [1272], 'human': [1275, 3156, 4149], 'cells': [1276, 2023, 3157, 4150], '(Nojima': [1277, 4151], '2015).': [1280, 1550, 1626, 3169, 3352, 3588, 4121, 4154], 'Extracting': [1281], 'large': [1285, 1441, 1956], 'complex': [1287, 1513, 1573, 1579, 3031, 3287, 3334, 3346], 'transcriptomic': [1288], 'genomic': [1290], 'datasets': [1291], 'remain': [1292, 2760], 'challenging.': [1293], 'address': [1295], 'problem,': [1297], 'modeling': [1298, 1327], 'approaches': [1299], 'help': [1301], 'significant': [1303], 'common': [1304], 'features': [1305, 1417, 1628, 3608], 'between': [1309, 1367, 1631, 1858, 1866, 4174], 'classes': [1311, 2113, 2238, 3984], 'metagene': [1313, 4009], 'based': [1315, 1830], 'analyses.': [1318, 2529], 'therefore': [1321, 2689], 'probabilistic': [1326], 'segment': [1329], 'genome': [1331, 1388, 1663, 1829], '(HMM).': [1337], 'HMM': [1339, 1392, 1823], 'explains': [1340], 'mCRAC': [1342, 2159, 2212, 3631, 3814, 3833], 'data': [1343, 1848, 2751, 3008, 3475, 3579], 'postulating': [1345], 'underlying,': [1347], 'finite': [1348], 'states,': [1353], 'characterized': [1355], 'noisy': [1358], 'signature': [1359], 'PTM': [1361], 'log-enrichments': [1362], '(emissions).': [1363], 'stochastically;': [1370], 'assumptions': [1374], 'enforce': [1375], 'coherence': [1377], 'distribution,': [1381], 'effectively': [1382], 'yielding': [1383, 2076], 'partitioning': [1385], 'according': [1389], 'See': [1394, 2214], 'Eddy': [1395], '(2004)': [1396], 'accessible': [1399], 'overview': [1400], 'use': [1403, 1851], 'HMMs': [1405, 1410], 'analyze': [1407], 'data.': [1409, 2492], 'initiation–elongation': [1425], '(de': [1427], 'Boer': [1428], '2014;': [1431, 1542, 1546], 'Zacher': [1432], 'Like': [1436], 'eukaryotes,': [1438], 'transcribes': [1440], 'numbers': [1442], 'ncRNAs.': [1444], 'include': [1446], 'cryptic': [1448], 'transcripts': [1450, 1466, 1567, 1635, 1891, 1938, 2135, 2642, 2956, 3096, 3174, 3571], '(CUTs),': [1451], 'normally': [1454, 1882], 'very': [1455, 2060, 2535], 'rapidly': [1456, 3268], 'degraded': [1457, 3269], '(Wyers': [1458], '2005),': [1461, 3406], 'stable': [1464, 1476], 'untranslated': [1465, 2812], '(SUTs)': [1467], 'class': [1469], 'generally': [1471, 2838, 3304], 'nuclear': [1472, 1496, 1779, 2127, 3236, 3270, 3300, 3320, 3330, 3358, 3390, 3397], 'retained,': [1473], 'but': [1474, 2523, 3068, 3392, 3734, 3855, 4073], '(Xu': [1478], '2009).': [1481, 3481, 3600], 'CUTs': [1482, 1558, 3265, 3930], 'strongly': [1484, 1553, 2625, 3492, 3716, 3748, 4275], 'stabilized': [1485, 3273], 'mutations': [1487], 'exosome': [1490, 1501, 1526, 1622, 3278], 'nuclease': [1491, 3279], 'complex,': [1492, 1498, 3280], 'Trf4/5-Air1/2-Mtr4': [1494], '(TRAMP)': [1495], 'polyadenylase': [1497], 'cofactor,': [1502], 'Nrd1': [1505, 1588, 1651, 1672, 1694], 'Nab3': [1507, 1612, 1653, 1674, 1696, 3348], 'components': [1508, 3317, 3335], 'Nrd1/Nab3/Sen1': [1511], '(NNS)': [1512], 'terminates': [1515], 'targets': [1518], 'transcript': [1521, 2237, 2410, 2506, 2544, 4132], 'TRAMP': [1523, 3285, 3333], '(Arigo': [1527], '2006;': [1530], 'Heo': [1531], 'Schulz': [1535], 'Tudek': [1539], 'Webb': [1543], 'Fasken': [1547], 'observations': [1552, 1784, 3444, 4313], 'support': [1554], 'transcriptionally': [1560], 'terminated': [1561], 'NNS,': [1563], 'released': [1566, 1900], 'being': [1568], 'targeted': [1569], 'TRAMP/exosome': [1572], 'NNS': [1578, 1720, 3290, 3343], 'associate': [1581], 'Ser5': [1583, 4203, 4372], 'phosphorylated': [1584], 'via': [1587], '(Vasiljeva': [1589], '2008)': [1592], 'histone': [1596], 'H3,': [1597], 'lysine': [1598], '4': [1599, 2052], 'trimethylation': [1600], '(H3K4me3)': [1601], 'present': [1602], 'promoter-proximal': [1605, 3456], 'nucleosome(s)': [1606], '(Terzi': [1607], '2011),': [1610, 1710], 'directly': [1615], 'recruit': [1616], 'Rrp6': [1618, 3322], 'component': [1619, 3347], '(Fasken': [1623], 'discriminate': [1630], 'mRNAs': [1632, 1867, 2425, 3414, 3961, 4304], 'confer': [1637], 'their': [1638], 'fates': [1640], 'not': [1642, 1715, 1922, 2443, 4308], 'fully': [1643], 'understood.': [1644], 'Consensus': [1645], 'vitro': [1647], 'binding': [1648, 1697, 2050, 2331, 2394, 2414, 2985, 3297, 3372, 3512], 'depleted': [1655, 3409, 3749, 3758, 3775], 'total': [1662, 1944, 2472, 3850, 4000, 4098, 4262, 4343, 4359], '(Schulz': [1666], 'while': [1671], 'show': [1675, 2374, 2379, 2890], 'strong': [1677, 2708, 2975, 3364, 3431, 4040], '5′': [1678, 1794, 2190, 2348, 3115, 3365, 3730, 3752, 4208, 4283, 4301, 4315], 'bias,': [1679], 'they': [1680], 'bind': [1682], '(Webb': [1686], '2014)': [1689], 'frequently': [1699, 2652], 'lack': [1700], 'motifs': [1702], '(Jamonnak': [1703], 'Wlotzka': [1707], 'indicating': [1711, 1999, 2130], 'sole': [1717], 'determinants': [1718], 'function': [1721], 'vivo.': [1723], 'Systematic': [1724], 'pre-mRNA-binding': [1729], 'Hrp1': [1731, 1756, 2991, 3202, 3229], 'Nab2': [1733, 1758, 3204], 'dual': [1735, 3206], 'roles,': [1736], 'promoting': [1737, 3209], 'both': [1738], 'pre-mRNA': [1739, 3368], 'cleavage': [1740], 'polyadenylation,': [1742], 'degradation': [1744, 1897, 2928, 3489], 'CUT': [1746, 1906, 3219], '(Tuck': [1748, 2996, 3221, 3415, 3439, 3592], 'Tollervey,': [1750, 2935, 2998, 3223, 3417, 3441, 3594], 'Surprisingly,': [1752], 'transcripts,': [1755, 1864], 'were': [1759, 2072, 2102, 2442, 2624, 2787, 3688, 3695, 3715, 3746, 3757, 3774, 4133, 4161, 4205, 4229, 4381], 'abundant': [1761], 'site,': [1767], 'found': [1772, 2416], 'case': [1776], 'factor': [1781, 2929, 2990, 3238, 3385], 'Mtr4.': [1782], 'suggested': [1785], 'short': [1787], 'might': [1789, 3790], 'generated': [1791, 3812], 'yeast.': [1803], 'report': [1806], 'combination': [1809], 'transcriptome': [1820], 'allowed': [1824, 3638], 'segmentation': [1826, 1836], 'changes.': [1834], 'readily': [1838], 'compared': [1840, 3311, 3977, 4213], 'any': [1842], 'feature': [1844], 'genome-wide': [1847], 'exist.': [1849], 'reveal': [1855], 'systematic': [1856], 'differences': [1857], 'intronless': [1863], 'lncRNAs.': [1869], 'propose': [1871], '"surveillance': [1883], 'ready".': [1884], 'post-initiation': [1887], 'prone': [1893], 'termination,': [1895, 3216], 'On': [1902], 'encoding': [1904], 'ncRNAs,': [1907], 'remains': [1909], 'postulate': [1914], 'that,': [1915], 'consequence,': [1917], 'system': [1920, 3302], 'does': [1921], 'need': [1923], 'specifically': [1925], 'thousands': [1927], 'species.': [1931], 'Results': [1932], 'CRAC': [1934, 1952, 2208, 2241, 2454, 2491, 2521, 3536, 4104], 'recovers': [1935], 'along': [1946, 2654, 3668], 'genome,': [1949, 3670], 'Rpo21,': [1954, 2172], 'subunit': [1957], 'HTP-tagged': [1962], 'expressed': [1965, 2427, 4250], 'endogenous': [1968], 'locus': [1969], 'His6-TEV-protein': [1972], 'tag': [1974], '(Rpo21-HTP,': [1975], 'Fig': [1976, 2215, 2389, 2860, 3090, 3828, 3971], 'EV1).': [1977, 2038], 'Rpo21-HTP': [1978], 'only': [1981], 'source': [1982], 'growth': [1986], 'resulting': [1989], 'strains': [1990, 2228], 'indistinguishable': [1992], 'parental': [1995], 'wild': [1996], 'type': [1997], '(BY4741),': [1998], 'tagged': [2002], 'construct': [2003], 'functional.': [2005], 'crosslinked': [2008, 2069, 2193], 'irradiation': [2013], 'at': [2014, 2290, 3083, 3823, 3859, 4254], '254': [2015], 'nm': [2016], 'min': [2019], 'actively': [2021], 'growing': [2022], 'purified': [2025], 'multistep,': [2028], 'tandem-affinity': [2029], 'protocol,': [2030], 'followed': [2031], 'gel': [2033, 2057, 2163, 2169], 'purification': [2034, 2149, 2170], '(Figs': [2035, 3633, 3657, 3700], '1A': [2036, 3634], 'protocol': [2040], 'includes': [2041], 'two': [2042, 2165, 3527], 'denaturing': [2044], 'steps': [2045, 2156], '(incubation': [2046], 'nickel': [2048], 'column': [2049], 'M': [2053], 'guanidinium–HCl': [2054], 'SDS': [2056], 'electrophoresis)': [2058], 'ensuring': [2059], 'covalently': [2064], 'RNAs.': [2066], 'fragments': [2068, 4140], 'amplified': [2073], 'sequenced,': [2075], '1.5': [2077], 'million': [2078], 'unique': [2079], 'reads': [2080, 2235, 2297, 2561, 2579, 2592, 2601, 2614], 'could': [2082], 'genome.': [2087], 'After': [2088], 'quality': [2089], 'filtering': [2090], 'removal': [2092], 'PCR': [2094], 'duplicates,': [2095], 'than': [2097, 2780, 3176, 3519], '90%': [2098], 'sequences': [2101, 2319], 'RNAPII,': [2108, 4248, 4360], 'mRNAs,': [2110, 2421], 'several': [2111], 'lncRNAs': [2112], '(CUTs,': [2114], 'SUTs,': [2115], 'NUTs,': [2116], 'XUTs,': [2117], 'antisense': [2119, 2255, 2300, 2446, 2505, 2514, 3094], 'transcripts),': [2120], 'nucleolar': [2122], 'RNAs': [2123, 2128, 2310, 2630, 3271, 3468], '(snoRNAs),': [2124], '(snRNAs),': [2129], 'recovery': [2132, 2636], '(Fig': [2136, 2643, 2696, 2832, 2994, 3046, 3137, 3193, 3246, 3379, 3437, 3476, 4051, 4108, 4236], '1B).': [2137], 'Click': [2138, 2862, 3948], 'here': [2139, 2863, 3949], 'expand': [2141, 2865, 3951], 'figure.': [2143, 2867, 3953], 'Figure': [2144, 2199, 2868, 3482, 3799, 3954], 'EV1.': [2145, 2468, 2749], 'during': [2150, 2765, 3797], 'mCRACThe': [2151], 'schematic': [2152], 'indicates': [2153, 2264, 2270, 3839, 3844, 3989, 3994], 'protocol.': [2160, 2213], 'inset': [2162], 'replicates': [2166], 'against': [2175], 'indicated': [2178, 2850, 3139, 3919], 'no': [2181], 'antibody': [2182], 'control': [2183], '(NAb),': [2184], 'visualized': [2185], 'autoradiography': [2187], '[32P]': [2191], 'labeled,': [2192], 'RNA.': [2194], 'Download': [2195, 2197, 2385, 2387, 2964, 2966, 3601, 3603, 3944, 3946, 4021, 4023], 'figure': [2196, 2386, 2965, 3602, 3945, 4022], 'PowerPoint': [2198, 2388, 2967, 3604, 3947, 4024], '1.': [2200], 'Outline': [2209], 'EV1': [2216], 'details.': [2219], 'figures,': [2222], 'S.': [2226], 'cerevisiae': [2227], 'derived': [2229], 'BY4741.': [2231], 'Distribution': [2232, 2245, 2870, 3561, 3815, 3956], 'determined': [2239, 2796, 3831], 'Rpo21-HTP.': [2244, 3836], 'sense': [2253, 2283, 2440], 'orientations.': [2256], 'upper': [2259], 'panel,': [2260], 'vertical': [2262, 2340], 'line': [2263, 2269, 2360], 'TSS.': [2266], 'curved': [2268], 'poly(A).': [2275], 'All': [2276], 'shown': [2280, 2465, 2746, 2913, 4060], 'orientation,': [2284], 'ordered': [2285, 3795], 'shortest': [2288], 'ORF': [2289], 'top.': [2292], 'lower': [2294], 'panel': [2295, 3503, 3531, 3853, 4006], 'same': [2303], 'regions.': [2304, 2903], 'Ratio': [2305], 'spliced': [2307, 2554, 2576], 'unspliced': [2309, 2556, 2578], 'RNAPII-bound': [2312], 'RNAs,': [2313], 'calculated': [2314, 2581, 3898, 4331, 4338, 4356], 'ratio': [2317], 'spanning': [2320, 2593, 2602, 2615], 'exon–exon': [2321, 2594], '(spliced)': [2322], 'intron–exon': [2325, 2616], '(unspliced)': [2326], 'junctions.': [2327], 'Peaks': [2328], 'correlate': [2332], 'nucleosome': [2334, 2347, 2370, 2694, 2736, 2959, 3060], 'positions.': [2335], 'zero': [2337], 'point': [2338], '(solid': [2339], 'line)': [2341], 'positions': [2345], 'boundaries': [2349, 2695], '(Jiang': [2350, 2720, 3048], 'Pugh,': [2352, 2722, 3050], 'red': [2359], 'overall': [2363], 'density': [2365, 2680, 2704, 2824, 2905, 3080], 'respect': [2367, 2692, 2874], 'boundary.': [2371], 'Dashed': [2372], 'lines': [2373, 3528], 'maxima,': [2377], 'apparent': [2381, 4290], '150': [2382, 2709, 3540, 3905], 'periodicity.': [2384, 2711], '1C': [2390, 3091, 3829], 'profile': [2395], 'aligned': [2400, 3822, 3858, 4182], 'arranged': [2408], 'length.': [2411], 'Robust': [2412], 'majority': [2419], 'suggesting': [2422, 3248, 3785], 'CRAC.': [2431], 'signals': [2437, 2474, 2878], 'accompanied': [2444], 'signals,': [2447, 2941], 'confirming': [2448], 'specificity': [2451, 2488], 'technique.': [2455], 'selected': [2461], 'Dataset': [2467, 2493, 2748], 'Inspection': [2469], 'plus': [2477, 2899], 'minus': [2479], 'strands': [2480], 'panels': [2482], 'A–C': [2483], 'EV1D': [2494], 'PHO84': [2497], 'gene,': [2498], 'well-characterized,': [2502], '(Camblong': [2507], '2007).': [2510], 'Sense': [2511], 'resolved': [2518], 'data,': [2522], 'would': [2524, 2752], 'conflated': [2526], 'Pre-mRNA': [2530], 'splicing': [2531], 'largely': [2538], 'takes': [2539], 'place': [2540], '(Moehle': [2545], 'calculate': [2550], 'abundances': [2552], 'reads,': [2557], 'database': [2564], 'containing': [2565], 'known': [2567], 'splice': [2568, 2606, 2619], 'junctions': [2569, 2604, 2617], 'mRNA': [2571, 3210, 3516, 3692, 3729, 3806, 3878, 3901, 4065], 'sequences.': [2572], 'proportion': [2574], '(2': [2583], '×': [2584], 'ExEx)/(ExI+IEx),': [2585], 'where': [2586, 2957, 3908, 4353], 'ExEx': [2587], 'number': [2590, 2599, 2612], 'junctions,': [2595], 'ExI': [2596], 'exon–intron': [2603], '(5′': [2605], 'sites),': [2607], 'IEx': [2609], '(3′': [2618, 2814], 'sites).': [2620], 'Pre-mRNAs': [2621], '(ExI+IEx': [2622], 'reads)': [2623], 'mature': [2629], '(ExEx': [2631], 'reads),': [2632], 'consistent': [2633, 2754, 3021, 3446], 'bona': [2638], 'fide': [2639], 'RNAPII-associated,': [2640], '1D).': [2644], 'noted': [2646, 4363], 'uneven': [2653], 'It': [2657], 'seemed': [2658], 'possible': [2659], 'reflected': [2662], 'rates': [2667], 'response': [2669], 'presence': [2672], 'nucleosomes': [2674, 2741, 2759], 'DNA': [2677, 2764, 2778], 'template.': [2678], '1E).': [2697], 'striking': [2699], 'pattern': [2700], 'f': [2701], 'hit': [2703, 3506], 'observed,': [2706], 'Nucleosome': [2712, 2948, 3044], 'arrays': [2713], 'formed': [2715], 'Weiner': [2724, 3052], 'peaks': [2733], 'matches': [2734, 2960], 'spacing.': [2737], 'transcription,': [2766], 'moving': [2769], 'slowly': [2771], 'through': [2772], 'center': [2774], 'nucleosome-bound': [2777], 'outside': [2782], 'spacers.': [2784], 'Similar': [2785, 3000], 'conclusions': [2786], 'drawn': [2788], 'pause': [2794, 3875, 4186, 4211, 4234], 'NET-seq': [2798, 3151, 4157], '(Churchman': [2800, 3158, 3883, 4144], 'Weissman,': [2802, 3160, 3885, 4112, 4146], '2011).': [2803, 3886], 'signal': [2806, 2981, 3185, 4287], 'dropped': [2807], 'sharply': [2808, 3735], 'UTRs)': [2815], 'principal': [2820, 2846], 'drop': [2821, 2879], 'centered': [2826], 'translation': [2829, 2885], 'stop': [2830, 3066], 'codon': [2831, 2896], 'EV2),': [2833], 'located': [2839, 4230], 'approximately': [2840], '50–100': [2841], 'upstream': [2843, 2970, 3063, 4046], 'polyadenylation': [2847, 2940, 2980, 2989, 3286, 3861], 'p(A)': [2848], 'sites,': [2849, 3897], 'poly(A)-binding': [2856, 2922], 'protein': [2857, 2923], '(Pab1)': [2858], 'EV2.': [2861, 2869], 'featuresRNAPII': [2877], 'codon.': [2887], 'graphs': [2889], '0': [2898], '500': [2900, 3177, 3520], 'flanking': [2902, 4217], 'over': [2908, 4188], '(total': [2916], 'RNAPII),': [2917], 'well': [2919, 3233, 3326], 'Pab1': [2924], 'cytoplasmic': [2927], 'Xrn1': [2930], '(data': [2931], 'frequency': [2938], 'AWTAAA': [2942], 'TATATA,': [2944], 'indicated.': [2947], 'distribution:': [2949], 'curve': [2951], 'fraction': [2954, 4259], 'corresponding': [2962], 'position.': [2963], 'Motif': [2968], 'canonical': [2979], 'AWUAAA': [2982], '(Nab4),': [2992], 'AUAUAU': [2993], 'EV2)': [2995, 3047], 'reduced': [3001, 4094], 'occupancy': [3003, 3061, 3122, 4095], 'visible': [3005], 'NET-Seq': [3007, 3882], '(see': [3009, 3037, 3682], 'figures': [3010], '2': [3011], 'Nojima': [3015, 3166, 4118], '2015)': [3018], 'formation': [3024, 3213, 4068], 'Pol': [3028, 3665, 3678, 3680], 'below': [3038, 4004], '2010)': [3055], 'peak': [3058, 3371], 'immediately': [3062, 3395, 4045, 4207], 'codon,': [3067], 'significance': [3070], 'unclear.': [3074], 'increased': [3078], 'observed': [3082, 3149, 3471, 4096, 4306], 'mRNAs.': [3088], 'will': [3108], 'contribute': [3109], 'signals.': [3113], 'Analysis': [3128], '1C)': [3138], 'systematically': [3140], 'higher': [3141, 4200], 'levels': [3142, 4201], 'TSS,': [3146, 3309, 3769, 3825], '2015;': [3165, 4117], 'Filtering': [3170], 'longer': [3175, 3518], 'length': [3180, 3699], 'confirmed': [3181], 'indeed': [3187], '2A).': [3194], 'Previous': [3195], 'functions': [3207], 'end': [3212, 4067, 4302], 'destabilizing': [3218], 'Nab2,': [3231], 'Mtr4,': [3239], 'heavily': [3241], 'skewed': [3242], 'toward': [3243], '2),': [3247], 'possibility': [3250], 'truncated': [3257], 'addition': [3260], 'full-length': [3263], 'mRNA.': [3264], 'loss': [3275], 'its': [3282, 3328], 'cofactors': [3283], 'termination/surveillance': [3292], 'whether': [3296], 'exosome,': [3321], 'Rrp44,': [3324], 'cofactors,': [3331], 'Trf4': [3336], 'Air2': [3338], '(this': [3339, 3582], 'work),': [3340, 3583], '(Holmes': [3349, 3585], 'Strikingly': [3353], 'bias': [3366], 'association,': [3369], 'within': [3373], '2B–F).': [3380], 'export': [3384, 3398], 'Mex67': [3386, 3422], 'binds': [3387], 'newly': [3388], 'synthesized': [3389], 'pre-mRNAs': [3391], 'dissociated': [3394], 'following': [3396], '(Segref': [3399], '1997;': [3402], 'Lund': [3403], 'Guthrie,': [3405], 'strikingly': [3424], 'showing': [3430], '2G)': [3438], 'substantial': [3449], 'and,': [3461], 'indeed,': [3462], 'published': [3473], 'RNAseq': [3474], '2H)': [3477], '(Neil': [3478, 3597], '2.': [3483], 'Binding': [3484], 'A–J.': [3501], 'density,': [3507], 'normalized': [3508], 'maximal': [3511], 'value': [3513], 'inside': [3522], 'experiment.': [3525], 'represent': [3532, 4164], 'results': [3533], 'independent': [3535, 3696], 'experiments.': [3537], 'TSS-proximal': [3539, 3904], 'shaded.': [3544], '(A)': [3545, 3854], '(RNAPII);': [3547], '(B)': [3548], 'Rrp44;': [3549], '(C)': [3550], 'Rrp6;': [3551], '(D)': [3552], 'Trf4;': [3553], '(E)': [3554], 'Air2;': [3555], '(F)': [3556, 3584], 'Nab3;': [3557], '(G)': [3558], 'Mex67;': [3559], '(H)': [3560, 3596], 'promoter-proximal,': [3568], 'sense-orientated': [3569], '(S': [3572], 'CUTs);': [3573], '(I)': [3574], 'Nab2;': [3575], '(J)': [3576], 'Hrp1.': [3577], 'Sequence': [3578], 'source:': [3580], '(A-E)': [3581], '(G,': [3589], 'I,': [3590], 'J)': [3591], '2013),': [3595], 'pA': [3614, 4033, 4049], 'examine': [3617], 'profiles': [3619, 3687, 4030, 4378], 'phosphorylation,': [3622], 'included': [3624], 'procedure': [3632], 'EV1),': [3636], 'us': [3639], '3A': [3658, 3701], 'EV3).': [3660, 3705], 'account': [3662], 'unequal': [3664], 'quantified': [3674], 'log2': [3676], '(phosphorylated': [3677], 'II/total': [3679], 'II)': [3681], 'Materials': [3683], 'Methods).': [3685], 'Phosphorylation': [3686], 'remarkably': [3689], 'similar': [3690], 'among': [3691], 'B,': [3703], 'Genome-wide': [3706], 'anticorrelated': [3722], 'Ser5P.': [3724], 'ends,': [3731], 'expected,': [3733], 'declined': [3736], '3′.': [3738], 'Tyr1p,': [3741], 'end.': [3753], 'Tyr1P': [3754, 3915], 'narrow': [3761], 'window': [3762], '0–150': [3764], 'downstream': [3766], 'whereas': [3770, 4336, 4376], 'Thr4P': [3771], 'relatively': [3778, 4374], 'broader': [3779], 'area': [3780], '(0–300': [3781], 'TSS),': [3784], 'phosphorylations': [3789], 'placed': [3792], 'fashion': [3796], 'transcription.': [3798], '3.': [3800], 'Profiles': [3801], 'Red': [3837, 3987], 'color': [3838, 3843, 3988, 3993], 'depletion,': [3840, 3990], 'green': [3842, 3992], 'As': [3852], 'Metagene': [3863, 3887, 3924, 3934], '5,000': [3872], 'strongest': [3873, 4184], 'region,': [3907], 'depleted,': [3917], 'dashed': [3922], 'line.': [3923], '(D).': [3933, 3943], 'SUTs': [3940], 'EV3.': [3955], 'non-coding': [3963], 'genesDistribution': [3965], '3A,': [3972], 'SUT,': [3980], 'CUT,': [3981], 'snoRNA': [3983], 'ncRNA.': [3986], 'graph': [4003], 'class.': [4020], 'Alignment': [4025], 'gave': [4035], 'result,': [4038], '3B).': [4052], 'Dephosphorylation': [4053], 'Tyr1': [4055], 'Glc7': [4057], '(Schreieck': [4069], '2014),': [4072], 'findings': [4075], 'residues': [4079], 'dephosphorylated': [4082], 'region.': [4085, 4218], 'speculate': [4087], 'NETseq': [4106], 'EV2;': [4109], 'Churchman': [4110], 'Sites': [4122], 'interaction': [4124], 'sequencing': [4137], 'protected': [4139], '(NET-seq)': [4141], '2011)': [4147], 'products': [4158], 'pausing.': [4169], 'relationship': [4173], 'patterns': [4177], 'transcriptional': [4179], 'pausing,': [4180], 'modifications.': [4198, 4294], 'Notably': [4199], 'maxima': [4221], '3C).': [4237], 'analyzing': [4239], 'abundance': [4253], 'signal.': [4264, 4345], 'because': [4268], 'absolute': [4270], 'amount': [4271], 'varies': [4274], 'Without': [4279], 'normalization,': [4281], 'skews': [4288], 'agreement': [4310], 'prior': [4312], '(Mayer': [4320], '2010);': [4323], 'input': [4334], 'DNA,': [4335], 'another': [4347], 'study': [4348], '(Kim': [4349], 'authors': [4362], 'differs': [4367], '5′peak': [4373], 'constant,': [4375], 'varia': [4382]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2418692346', 'counts_by_year': [{'year': 2023, 'cited_by_count': 1}, {'year': 2021, 'cited_by_count': 7}, {'year': 2020, 'cited_by_count': 9}, {'year': 2019, 'cited_by_count': 8}, {'year': 2018, 'cited_by_count': 11}, {'year': 2017, 'cited_by_count': 14}, {'year': 2016, 'cited_by_count': 4}], 'updated_date': '2024-12-25T20:39:57.900978', 'created_date': '2016-06-24'}
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