DNA Substrate Length and Surrounding Sequence Affect the Activation-induced Deaminase Activity at Cytidine

Name: Work Video:
Duration: 3 min 30 s
Kefei Yu; Feng‐Ting Huang; Michael R. Lieber
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70, 160, 209, 1089, 1181, 1344, 1766, 2487, 2598, 2696, 3734, 4024, 4232, 4311, 4344], 'DNA,': [22, 161, 1182], 'but': [23, 115, 162, 254, 1681, 1838, 2492, 2626, 3006, 3354, 4360], 'the': [24, 30, 44, 51, 66, 69, 76, 81, 86, 89, 107, 121, 124, 134, 163, 169, 183, 190, 205, 208, 215, 220, 225, 228, 246, 260, 263, 273, 292, 295, 300, 369, 404, 420, 426, 432, 447, 485, 503, 726, 818, 893, 937, 965, 968, 1004, 1069, 1267, 1313, 1351, 1356, 1410, 1467, 1506, 1546, 1733, 1742, 1749, 1762, 1765, 1772, 1777, 1782, 1785, 1789, 1799, 1809, 1817, 1830, 1844, 1847, 1853, 1857, 1874, 1914, 1946, 1956, 1973, 1982, 2048, 2230, 2274, 2415, 2423, 2427, 2440, 2486, 2546, 2568, 2573, 2579, 2585, 2589, 2594, 2597, 2603, 2613, 2616, 2623, 2647, 2665, 2684, 2690, 2695, 2701, 2727, 2732, 2737, 2742, 2745, 2783, 2809, 2821, 2841, 2845, 2848, 2890, 2898, 2918, 2922, 2930, 2934, 2939, 2943, 2947, 2969, 2993, 3049, 3055, 3067, 3081, 3090, 3103, 3118, 3136, 3142, 3158, 3162, 3167, 3174, 3190, 3194, 3220, 3228, 3238, 3250, 3268, 3287, 3292, 3330, 3358, 3368, 3375, 3402, 3414, 3424, 3429, 3435, 3445, 3450, 3454, 3478, 3484, 3499, 3512, 3517, 3546, 3582, 3611, 3622, 3629, 3636, 3682, 3692, 3701, 3710, 3717, 3721, 3727, 3730, 3737, 3767, 3777, 3807, 3810, 3835, 3881, 3885, 3918, 3928, 3941, 3952, 3961, 3998, 4002, 4020, 4027, 4049, 4125, 4193, 4204, 4210, 4267, 4274, 4280, 4314], 'relationship': [25, 164], 'of': [26, 46, 50, 68, 78, 88, 165, 185, 189, 207, 217, 227, 294, 299, 422, 431, 450, 488, 643, 720, 733, 810, 940, 948, 967, 1040, 1053, 1068, 1269, 1277, 1318, 1350, 1359, 1435, 1474, 1489, 1606, 1659, 1735, 1744, 1748, 1764, 1774, 1784, 1995, 1998, 2030, 2072, 2089, 2209, 2217, 2221, 2232, 2235, 2243, 2276, 2279, 2293, 2355, 2442, 2578, 2581, 2587, 2596, 2605, 2615, 2683, 2694, 2741, 2744, 2811, 2820, 2824, 2839, 2850, 2866, 2883, 2889, 2897, 2909, 2924, 3001, 3039, 3084, 3144, 3157, 3169, 3189, 3300, 3309, 3377, 3413, 3426, 3584, 3614, 3624, 3729, 3780, 3809, 3917, 4192, 4203, 4207, 4214, 4317, 4358, 4362], 'this': [27, 166, 949, 1185, 2673, 3020, 3060, 3121, 3482, 3554, 3594, 3604, 3765, 3818, 3888], 'step': [28, 167, 2425], 'or': [33, 172, 377, 412, 1516, 1521, 2497, 2692, 2903, 2975, 2980, 3030, 3626, 4059, 4339], 'hypermutation': [35, 174, 441, 3337, 3372, 3572], 'processes': [36, 175, 473], 'not': [38, 177, 475, 650, 1597, 2493, 2503, 2712, 2720, 2789, 3115, 3198, 3265, 3443, 3524, 3560, 3574, 3698, 3947, 3978, 4006, 4134], 'entirely': [39, 178], 'clear.': [40, 179], 'We': [41, 63, 180, 202, 1759, 1806, 1822, 2852, 2962, 3013, 3290, 3506, 4300], 'have': [42, 181, 729, 1303, 1495, 1807, 3208, 3472, 3733, 3948, 4042, 4296], 'studied': [43, 182], 'activity': [45, 184, 961, 1743, 2124, 2506, 2604, 2849, 3026, 3542, 4342], 'a': [47, 59, 95, 113, 186, 198, 234, 252, 401, 526, 636, 903, 941, 1065, 1391, 1403, 1439, 1471, 1511, 1600, 1745, 1755, 1836, 1993, 2028, 2111, 2195, 2254, 2337, 2356, 2608, 2641, 2651, 2837, 2881, 2907, 3004, 3016, 3023, 3063, 3107, 3201, 3297, 3352, 3495, 3527, 3531, 3556, 3567, 3585, 3679, 3699, 3770, 3829, 3974, 4035, 4231, 4263, 4288, 4292, 4302, 4352], 'recombinant': [48, 187, 1084, 1490, 1746, 2077], 'form': [49, 188, 1201, 1747, 3623, 3842, 3991], 'mouse': [52, 191, 1750, 2372], 'protein': [54, 193, 406, 528, 1752, 2078, 2109, 2394, 2477], 'that': [55, 65, 194, 204, 648, 890, 1082, 1176, 1198, 1266, 1276, 1305, 1402, 1505, 1653, 1686, 1761, 1816, 1824, 2026, 2419, 2545, 2672, 2753, 2964, 2967, 3015, 3046, 3059, 3080, 3152, 3249, 3279, 3284, 3308, 3329, 3408, 3466, 3475, 3539, 3558, 3726, 3823, 3828, 3927, 3933, 3976, 4019, 4044, 4124, 4271, 4286, 4323], 'was': [56, 195, 632, 953, 1075, 1921, 1934, 1942, 1964, 1970, 2038, 2052, 2061, 2079, 2246, 2271, 2379, 2395, 2409, 2719, 2869, 3839, 3876, 3891], 'purified': [57, 196, 1083, 1753], 'from': [58, 197, 305, 372, 407, 635, 646, 1003, 1492, 1550, 1936, 1978, 2139, 3511, 3644], 'baculovirus': [60, 199, 1756, 1968, 1975], 'expression': [61, 200, 809, 1757, 1976], 'system.': [62, 201, 1758], 'find': [64, 203, 1760, 1823], 'length': [67, 87, 206, 226, 1763, 1783, 1878, 2595, 2659, 2674, 2717, 2743, 2786, 2865, 4305, 4348], 'DNA': [71, 92, 210, 231, 1090, 1307, 1345, 1440, 1767, 1800, 1948, 2140, 2149, 2190, 2362, 2488, 2496, 2576, 2599, 2697, 3740, 3963, 4303], 'target': [72, 211, 504, 1393, 1509, 1768, 4036], 'critical': [74, 213, 962, 1770], 'action': [77, 216, 1608, 1773, 4309], 'at': [80, 120, 219, 259, 282, 1312, 1776, 1843, 1992, 2040, 2151, 2160, 2240, 2250, 2288, 2302, 2550, 2565, 2583, 2607, 2677, 2815, 3019, 3045, 3070, 3120, 3135, 3357, 3474, 3481, 4026, 4129], 'Cs': [82, 105, 221, 244, 1778, 1828], 'positioned': [83, 222, 1779], 'anywhere': [84, 223, 1780], 'along': [85, 224, 1781], 'DNA.': [90, 229, 1050, 1786, 2405, 2617, 4312, 4345], 'The': [91, 230, 285, 311, 415, 470, 1384, 1928, 1960, 2035, 2058, 2107, 2201, 2269, 2430, 2714, 2779, 2864, 2998, 3212, 3244, 3410, 4277], 'sequence': [93, 232, 900, 950, 1801, 1810, 1933, 2621, 2843, 3501, 3568, 3600, 4268, 4281], 'surrounding': [94, 233, 1811, 2622, 2844, 3547], 'given': [96, 235, 3351, 3576, 3725, 4285], 'C': [97, 236, 1087, 1813, 2402, 2482, 2610, 2624, 2685, 2846, 2913, 3126, 3150, 3159, 3195, 3214, 3230, 3252, 3282, 3437, 3519], 'influences': [98, 237, 1803, 2847], 'deamination': [100, 239, 1508, 2421, 2434, 2547, 2557, 2634, 2709, 2734, 2860, 2960, 3011, 3153, 3168, 3210, 3259, 3275, 3461, 3535, 4226], 'efficiency.': [101, 240, 2961, 3211, 3536], 'preferentially': [103, 242, 1826, 4046], 'deaminates': [104, 243, 1047, 1086, 1178, 1827, 3224, 3241, 3434], 'WRC': [108, 247, 1512, 1831, 3175, 3202, 3221, 3239, 3269, 3513, 3528, 3586, 3607, 3693, 3711, 3718, 3811, 3919, 3938, 3956, 4275], 'motif,': [109, 248, 3203, 3240, 3529], 'additionally': [111, 250, 1834], 'has': [112, 251, 1196, 1308, 1398, 1502, 1651, 1835, 3003, 3062, 3106, 3826, 3977, 4016], 'small': [114, 253, 1837, 3108, 3353, 4315], 'consistent': [116, 255, 1839, 2513, 3007, 3355, 3775], 'preference': [117, 256, 1840, 3295, 3356, 3446, 3486, 3569, 3587, 4282], 'purine': [119, 258, 1842], 'position': [122, 261, 1845, 2941, 2945, 2952, 3000, 3021, 3061, 3105, 3360], 'after': [123, 262, 1846, 2004], 'WRC,': [125, 264, 1848], 'thereby': [126, 265, 1849, 3689], 'favoring': [127, 266, 1850], 'WRCr': [128, 267, 3288], '(the': [129, 268], 'lowercase': [130, 269, 1854, 3056], 'r': [131, 270, 1855, 3057], 'corresponds': [132, 271], 'smaller': [135, 274, 1858, 3064, 3479], 'impact': [136, 275, 3008, 3065, 3109], 'on': [137, 276, 477, 1476, 1797, 2110, 2319, 2481, 2494, 2498, 2708, 2757, 2826, 2886, 3009, 3110, 3374, 3628, 3716, 3720, 3736, 3951, 3960, 4048, 4237, 4279, 4310, 4343], 'activity).': [138, 277], 'Three': [278], 'genetic': [279, 417, 4234], 'modifications': [280], 'occur': [281, 483], 'loci.': [284], 'first': [286, 2940, 3213], 'V(D)J': [288, 3986, 4003, 4194], 'recombination,': [289], 'which': [290, 366, 1542, 2566, 3235, 3522, 3706, 3943, 4030], 'involves': [291, 367], 'assembly': [293], 'variable': [296, 428], 'domain': [297, 429], 'exon': [298], 'heavy': [301, 370, 433], 'light': [303, 435, 3916], 'chains': [304], 'V,': [306], 'D,': [307], 'J': [309], 'subexons.': [310], 'second': [312, 2944, 3229, 3251, 3518], '(CSR),': [317], '1The': [318, 342], 'abbreviations': [319, 343], 'used': [320, 344, 1871, 1910, 1943, 3931, 4224], 'are:': [321, 345, 1894], 'CSR,': [322, 346, 735], 'recombination;': [325, 349], 'AID,': [326, 350, 4359], 'activation-induced': [327, 351, 530], 'cytidine': [328, 352, 531, 904, 2199, 2876], 'deaminase;': [329, 353], 'SHM,': [330, 354], 'hypermutation;': [332, 356], 'GST,': [333, 357], 'glutathione': [334, 358, 1929, 2055, 2059], 'S-transferase;': [335, 359], 'UNG,': [336, 360, 2142, 2723], 'uracil': [337, 361, 2236, 2407], 'nucleotide': [338, 362, 3119], 'glycosylase;': [339, 363], 'nt,': [340, 364, 2871], 'nucleotide.': [341, 365], 'changing': [368, 964, 2700], 'chain': [371], 'Igμ': [373], 'Igγ,': [375], 'Igα,': [376], 'Igϵ': [378], '(1Dunnick': [379, 3784], 'W.': [380, 3785], 'Hertz': [381, 3786], 'G.Z.': [382, 3787], 'Scappino': [383, 3788], 'L.': [384, 3789], 'Gritzmacher': [385, 3790], 'C.': [386, 1119, 3101, 3791, 3851, 3898, 4137, 4172, 4372], 'Nucleic': [387, 1164, 1232, 1638, 1721, 3792, 4073], 'Acids': [388, 1165, 1233, 1639, 1722, 3793, 4074], 'Res.': [389, 1166, 1234, 1640, 1723, 3794, 4075], '1993;': [390, 3795], '21:': [391, 3796], '365-372Crossref': [392, 3797], 'PubMed': [393, 465, 519, 555, 611, 626, 676, 713, 794, 842, 865, 884, 932, 995, 1018, 1032, 1109, 1130, 1149, 1170, 1225, 1238, 1258, 1295, 1338, 1379, 1457, 1537, 1567, 1587, 1623, 1644, 1676, 1706, 1727, 2184, 2470, 2536, 2774, 3323, 3395, 3671, 3759, 3798, 3863, 3910, 4079, 4113, 4152, 4184, 4255, 4383, 4419], 'Scopus': [394, 466, 520, 556, 612, 627, 677, 714, 795, 843, 866, 885, 933, 996, 1019, 1033, 1110, 1131, 1150, 1171, 1239, 1259, 1296, 1339, 1380, 1430, 1458, 1538, 1568, 1588, 1624, 1645, 1677, 1707, 1728, 2185, 2471, 2537, 2775, 3324, 3396, 3672, 3760, 3799, 3864, 3911, 4080, 4097, 4114, 4153, 4185, 4256, 4384, 4420], '(235)': [395, 3800], 'Google': [396, 468, 522, 558, 614, 629, 679, 716, 797, 845, 868, 887, 935, 998, 1021, 1035, 1112, 1133, 1152, 1173, 1226, 1241, 1261, 1298, 1341, 1382, 1432, 1460, 1540, 1570, 1590, 1626, 1647, 1679, 1709, 1730, 2187, 2473, 2539, 2777, 3326, 3398, 3674, 3762, 3801, 3866, 3913, 4082, 4099, 4116, 4155, 4187, 4258, 4386, 4422], 'Scholar).': [397, 469, 630, 680, 717, 798, 999, 1174, 1262, 1299, 1342, 1383, 1433, 1591, 1648, 2188, 2540, 2778, 3399, 3675, 3763, 3802, 3867, 3914, 4117, 4188, 4259, 4423], 'This': [398, 437, 1073, 2905, 3032, 3537, 3634, 4346], 'results': [399], 'change': [402], 'Ig': [405, 427], 'IgM': [408], 'IgG,': [410], 'IgA,': [411], 'IgE,': [413], 'respectively.': [414, 3074], 'third': [416], 'modification': [418], 'introduction': [421], 'point': [423], 'mutations': [424, 724, 4229], 'exons': [430], 'chains.': [436], 'called': [439, 529], '(SHM)': [442], 'responsible': [445], 'affinity': [448], 'maturation': [449], 'antibodies': [451], '(2Papavasiliou': [452, 506], 'F.N.': [453, 507, 1142, 1616, 1699], 'Schatz': [454, 508, 1450], 'D.G.': [455, 509, 1451], 'Cell.': [456, 510, 546, 602, 704, 785], '2002;': [457, 511, 623, 839, 862, 881, 1015, 1029, 1564, 3392, 4176], '109:': [458, 512], 'S35-S44Abstract': [459, 513], 'Full': [460, 462, 514, 516, 550, 552, 606, 608, 671, 673, 708, 710, 789, 791, 927, 929, 1222, 1253, 1255, 2179, 2181, 3754, 3756, 4179, 4181], 'Text': [461, 463, 515, 517, 551, 553, 607, 609, 672, 674, 709, 711, 790, 792, 928, 930, 1223, 1254, 1256, 2180, 2182, 3755, 3757, 4180, 4182], 'PDF': [464, 518, 554, 610, 675, 712, 793, 931, 1224, 1257, 2183, 3758, 4183], '(163)': [467, 521], 'latter': [471], 'two': [472, 1593, 1682, 2360, 2926, 3722, 3962], 'are': [474, 684, 738, 1819, 1879, 1911, 2805, 3285, 3988], 'dependent': [476], 'each': [478, 1812, 2446, 2867], 'other,': [479], 'although': [480, 3540], 'they': [481, 498, 737], 'germinal': [486], 'centers': [487], 'peripheral': [489], 'lymphoid': [490], 'tissues': [491], 'share': [493], 'some': [494, 1497, 3509], 'common': [495, 3609], 'features.': [496], 'Specifically,': [497], 'require': [500, 525], 'transcription': [501, 1203, 1404, 4028, 4053], 'through': [502, 1204], 'region': [505, 1412, 1963, 2489, 3838, 3930, 4004, 4195], 'Scholar)': [523, 1036, 3327], '24-kDa': [527], '(3Muramatsu': [534, 692], 'M.': [535, 575, 591, 652, 658, 693, 758, 774, 833, 856, 875, 908, 914, 980, 982, 1117, 1159, 1244, 1422, 1633, 1716, 3661, 3745, 3849, 3896, 4068, 4089, 4370, 4405, 4411], 'Kinoshita': [536, 594, 659, 694, 777, 853, 872, 915, 977, 4408], 'K.': [537, 595, 660, 695, 778, 848, 854, 873, 877, 916, 978, 1121, 1281, 1324, 1365, 1557, 1577, 3385, 3651, 3853, 3900, 4166, 4374, 4399, 4409], 'Fagarasan': [538, 696], 'S.': [539, 541, 656, 697, 699, 912, 990, 1104, 2465, 2531, 3657, 3663, 4147, 4401, 4407], 'Yamada': [540, 698], 'Shinkai': [542, 700], 'Y.': [543, 565, 701, 748], 'Honjo': [544, 596, 663, 702, 779, 859, 878, 919, 983, 4412], 'T.': [545, 563, 597, 664, 703, 746, 780, 852, 860, 879, 920, 976, 984, 1579, 2170, 2904, 4413], '2000;': [547, 603, 705, 786, 1250, 3668, 3751], '102:': [548, 604, 706, 787], '553-563Abstract': [549, 707], '(2642)': [557, 715], 'Scholar,': [559, 615, 846, 869, 1022, 1113, 1134, 1153, 1227, 1242, 1571, 1627, 1710, 4083, 4100, 4156, 4387], '4Revy': [560], 'P.': [561, 744, 1094, 1420, 1526, 1665, 2455, 2521, 3312, 4087, 4102, 4168, 4244], 'Muto': [562, 745], 'Levy': [564, 747], 'Geissmann': [566, 749], 'F.': [567, 583, 750, 766, 1283, 1326, 1367], 'Plebani': [568, 751], 'A.': [569, 579, 599, 601, 752, 762, 782, 784, 827, 991, 1105, 1155, 1161, 1629, 1635, 1712, 1718, 2466, 2532, 3665, 4064, 4070, 4148, 4395, 4397], 'Sanal': [570, 753], 'O.': [571, 754], 'Catalan': [572, 755, 4392], 'N.': [573, 589, 756, 772, 3655, 4158, 4164, 4393], 'Forveille': [574, 757], 'Dufourcq-Labelouse': [576, 759], 'R.': [577, 760, 1092, 1528, 1667, 2453, 2519, 3314, 3847, 3894, 4104, 4141, 4246], 'Gennery': [578, 761], 'Tezcan': [580, 763], 'I.': [581, 764], 'Ersoy': [582, 765], 'Kayserili': [584, 767], 'H.': [585, 617, 768, 858, 3647, 3649, 3653, 3659, 4170, 4391], 'Ugazio': [586, 769], 'A.G.': [587, 770], 'Brousse': [588, 771], 'Muramatsu': [590, 773, 855, 874, 981, 4410], 'Notarangelo': [592, 775], 'L.D.': [593, 776], 'Fischer': [598, 781, 4396], 'Durandy': [600, 783, 4394], '565-575Abstract': [605, 788], '(1310)': [613, 796], '5Arakawa': [616], 'Hauschild': [618], 'J.': [619, 665, 921, 1025, 1115, 1143, 1157, 1213, 1216, 1247, 1530, 1559, 1562, 1617, 1631, 1669, 1700, 1714, 2173, 3316, 3387, 3390, 3748, 4066, 4106, 4248, 4368, 4403], 'Buerstedde': [620], 'J.M.': [621], 'Science.': [622, 861], '295:': [624], '1301-1306Crossref': [625], '(381)': [628], 'initially': [633, 954], 'identified': [634, 1549], 'cDNA': [637, 1920], 'subtraction': [638], 'between': [639, 1955], 'B': [640, 806, 1321, 1361, 2091], 'cells': [641, 647, 1322, 1986, 2384], 'capable': [642], 'spontaneous': [644], 'CSR': [645, 689, 823, 969, 1070, 1191, 1445, 1468], 'were': [649, 1863, 1988, 2007, 2295, 2300, 2317, 2332, 2559, 2956, 3128, 3766, 3944], '(6Muramatsu': [651, 907], 'Sankaranand': [653, 909], 'V.S.': [654, 910], 'Anant': [655, 911], 'Sugai': [657, 913], 'Davidson': [661, 917], 'N.O.': [662, 918], 'Biol.': [666, 922, 1217, 1248, 2174, 3749], 'Chem.': [667, 923, 1218, 1249, 2175, 3750], '1999;': [668, 924], '274:': [669, 925], '18470-18476Abstract': [670, 926], '(927)': [678, 934], 'null': [682], 'mice': [683], 'completely': [685], 'deficient': [686, 740], 'SHM': [691, 742, 825, 972, 1416, 1447, 4132], 'A': [718, 1515, 1520, 1663, 1688, 1939, 2011, 2074, 2352, 2509, 2541, 2638, 2974, 2979, 3029, 3132, 3139, 4221], 'group': [719, 1501, 1650], 'human': [721, 3645], 'patients': [722], 'with': [723, 1950, 1990, 2054, 2065, 2081, 2346, 2374, 2449, 2514, 2619, 2736, 3028, 3097, 3130, 3146, 3182, 3776, 4209], 'gene': [728], 'hyper-IgM': [730], 'syndrome': [731], 'because': [732, 2724, 3432], 'blocked': [734], 'also': [739, 1399, 2704, 2751, 3236, 3507, 3707], '(4Revy': [743], 'normally': [801], 'only': [802, 894, 2480, 2628, 3044, 3242], 'expressed': [803, 2380], 'stimulated': [805, 1319, 1360], 'cells.': [807], 'Ectopic': [808], 'non-lymphoid': [813], 'cell': [814, 1362, 2036, 2050], 'types': [815], 'can': [816, 2136, 2154, 2192, 2755, 2894, 3086], 'confer': [817], 'ability': [819, 2399, 3870], 'carry': [821], 'out': [822, 2561, 4056], '(7Martin': [826], 'Bardwell': [828], 'P.D.': [829], 'Woo': [830], 'C.J.': [831], 'Fan': [832], 'Shulman': [834], 'M.J.': [835], 'Scharff': [836, 1095, 2456, 2522], 'M.D.': [837, 1096, 2457, 2523], 'Nature.': [838, 880, 1014, 1028, 1126, 1533, 1672, 3319, 4109, 4251, 4379], '415:': [840], '802-806Crossref': [841], '(225)': [844, 886], '8Yoshikawa': [847], 'Okazaki': [849], 'I.M.': [850, 871], 'Eto': [851], 'Nagaoka': [857, 4390], '296:': [863], '2033-2036Crossref': [864], '(323)': [867], '9Okazaki': [870], 'Yoshikawa': [876], '416:': [882], '340-345Crossref': [883], 'Scholar),': [888, 936, 1461, 1541, 1680, 1731, 2474], 'indicating': [889], 'lymphoid-specific': [895], 'factor': [896, 2796], 'required.': [897], 'shares': [899], 'homology': [901], 'deaminase,': [905, 1044], 'Apobec-1': [906], 'catalytic': [938], 'subunit': [939], 'large': [942], 'mRNA': [943, 959], 'editing': [944, 960], 'enzyme': [945, 3344], 'complex.': [946], 'Because': [947, 3102], 'homology,': [951], 'thought': [955, 1388], 'represent': [957], 'an': [958, 1042, 1055, 1278, 1309, 1347, 1463, 1951, 2082, 2145, 2311, 2375, 2499, 2515, 2794, 3131, 4010, 4238], 'property': [966, 1349], 'recombinase': [970, 1071], 'and/or': [971], 'mutagenesis': [973], 'machinery': [974], '(10Doi': [975], 'Ikegawa': [979, 4404], 'Proc.': [985, 1099, 2460, 2526, 4142], 'Natl.': [986, 1100, 2461, 2527, 4143], 'Acad.': [987, 1101, 2462, 2528, 4144], 'Sci.': [988, 1102, 2463, 2529, 4145], 'U.': [989, 1103, 2464, 2530, 2765, 4146, 4174], '2003;': [992, 1106, 1127, 1146, 1167, 1292, 1335, 1376, 1427, 1454, 1534, 1620, 1641, 1673, 1703, 1724, 2467, 2533, 3320, 3860, 3907, 4076, 4094, 4110, 4252, 4380, 4416], '100:': [993, 1107, 2468, 2534], '2634-2638Crossref': [994], '(99)': [997], 'However,': [1000, 1592, 2791, 3227, 3440, 3868], 'key': [1001, 1066, 1392], 'observations': [1002], 'Neuberger': [1005, 1012, 1026, 4138], 'co-workers': [1007], '(11Petersen-Mahrt': [1008], 'S.K.': [1009, 1136, 1610, 1693], 'Harris': [1010], 'R.S.': [1011], 'M.S.': [1013, 1027, 4139], '418:': [1016], '99-103Crossref': [1017], '(733)': [1020], '12Di': [1023], 'Noia': [1024], '419:': [1030], '43-48Crossref': [1031], '(461)': [1034], 'indicated': [1037, 1912], 'that,': [1038], 'instead': [1039, 1052], 'being': [1041, 1054], 'RNA': [1043, 1056, 1660], 'actually': [1046, 1059], 'cytosines': [1048, 1179], 'Therefore,': [1051, 2189, 2555, 4189], 'modifier,': [1057], 'appeared': [1060], 'more': [1061, 2983, 3098, 3147], 'likely': [1062], 'be': [1064, 1390, 1482, 2137, 2155, 2798, 2895, 3087, 3339, 3503, 3581, 3966, 4007, 4197, 4327], 'component': [1067], 'machinery.': [1072], 'hypothesis': [1074], 'further': [1076, 1795, 2663, 3170, 4219], 'strengthened': [1077], 'by': [1078, 1657, 1661, 1865, 1924, 2134, 2141, 2157, 2273, 2334, 2722, 3488, 3545, 3563, 4009], 'biochemical': [1079, 1604, 4294], 'evidence': [1080], 'demonstrating': [1081], '(13Bransteitter': [1091, 2452, 2518], 'Pham': [1093, 2454, 2520], 'Goodman': [1097, 1531, 1670, 2458, 2524, 3317, 4107, 4249], 'M.F.': [1098, 1532, 1671, 2459, 2525, 3318, 4108, 4250], '4102-4107Crossref': [1108, 2469, 2535], '(565)': [1111, 2472, 2538], '14Chaudhuri': [1114], 'Tian': [1116, 3848, 3895, 4369], 'Khuong': [1118, 3850, 3897, 4371], 'Chua': [1120, 3852, 3899, 4373], 'Pinaud': [1122, 3854, 3901, 4375], 'E.': [1123, 1138, 1140, 1612, 1614, 1695, 1697, 3855, 3902, 4376], 'Alt': [1124, 1245, 3746, 3856, 3903, 4377], 'F.W.': [1125, 1246, 3747, 3857, 3904, 4378], '422:': [1128, 4381], '726-730Crossref': [1129, 4382], '(604)': [1132, 4385], '15Dickerson': [1135], 'Market': [1137, 1611, 1694], 'Besmer': [1139, 1613, 1696], 'Papavasiliou': [1141, 1615, 1698], 'Exp.': [1144, 1618, 1701], 'Med.': [1145, 1619, 1702], '197:': [1147, 1621, 1704], '1291-1296Crossref': [1148, 1622, 1705], '(379)': [1151, 1625, 1708], '16Sohail': [1154, 1628, 1711], 'Klapacz': [1156, 1630, 1713, 4065], 'Samaranayake': [1158, 1632, 1715, 4067], 'Ullah': [1160, 1634, 1717, 4069], 'Bhagwat': [1162, 1636, 1719, 4071], 'A.S.': [1163, 1637, 1720, 4072], '31:': [1168, 1642, 1725, 4077], '2990-2994Crossref': [1169, 1643, 1726, 4078], '(233)': [1172, 1646, 1729, 4081], 'Given': [1175, 4313], 'how': [1183, 1798, 2840], 'does': [1184, 3264, 3523], 'permit': [1186], 'it': [1187, 2725, 2792, 3263, 3467, 3820, 3924], 'function': [1189], 'SHM?': [1193], 'Previous': [1194], 'work': [1195, 3825], 'shown': [1197, 1304, 1496, 1652, 2117, 2127, 2365, 3827, 4043], 'RNA:DNA': [1199, 1273, 2500, 3992], 'hybrids': [1200, 1274, 3993], 'upon': [1202, 3994], 'regions': [1207, 1317, 1358, 3613, 3987], 'vitro': [1209, 1272, 3845, 4058], '(17Reaban': [1210], 'M.E.': [1211], 'Lebowitz': [1212], 'Griffin': [1214], 'J.A.': [1215], '1994;': [1219], '269:': [1220], '21850-21857Abstract': [1221], '18Daniels': [1228], 'G.A.': [1229], 'Lieber': [1230, 1288, 1331, 1372], 'M.R.': [1231, 1289, 1332, 1373], '1995;': [1235], '23:': [1236], '5006-5011Crossref': [1237], '(181)': [1240], '19Tian': [1243], '275:': [1251, 3752], '24163-24172Abstract': [1252, 3753], '(167)': [1260, 3761], 'Recently,': [1263], 'we': [1264, 1302, 1740, 1793, 2591, 2937, 3094, 3113, 3441, 3464, 3596, 4321], 'showed': [1265, 2544, 2671, 2705], 'conformation': [1268, 1311], 'these': [1270, 1436, 3183, 3205], 'R-loop': [1279, 1310, 1352, 1385, 1464, 3731], '(20Yu': [1280, 1323, 1364], 'Chedin': [1282, 1325, 1366], 'Hsieh': [1284, 1327, 1368], 'C.L.': [1285, 1328, 1369], 'Wilson': [1286, 1329, 1370], 'T.E.': [1287, 1330, 1371, 4160], 'Nat.': [1290, 1333, 1374, 1425, 1452, 1582, 4092, 4414], 'Immunol.': [1291, 1334, 1375, 1426, 1453, 1563, 1583, 3391, 3667, 3859, 3906, 4093, 4415], '4:': [1293, 1336, 1377, 1455, 3861, 3908, 4417], '442-451Crossref': [1294, 1337, 1378], '(539)': [1297, 1340, 1381], 'More': [1300], 'importantly,': [1301], 'chromosomal': [1306], 'vivo': [1315, 1552], 'primary': [1320, 3564], 'Interestingly,': [1343], 'intrinsic': [1348], 'structure': [1353, 1386, 1465], 'found': [1354, 2963, 3014, 3334, 3465, 4128], 'chromosomes': [1363], 'element': [1394], 'CSR.': [1396], 'It': [1397, 2749, 3075, 3419, 3617, 4015, 4118], 'been': [1400, 3979, 4017], 'suggested': [1401], 'bubble': [1405], 'provides': [1406], 'enough': [1407], 'single-strandedness': [1408, 4000], 'VDJ': [1411], 'allow': [1414], 'AID-mediated': [1415, 2198, 2420, 2433, 2875], '(21Ramiro': [1417], 'A.R.': [1418, 4085], 'Stavropoulos': [1419, 4086], 'Jankovic': [1421, 4088], 'Nussenzweig': [1423, 4090], 'M.C.': [1424, 4091], '5:': [1428, 4095], '452-456Crossref': [1429, 4096], '(359)': [1431, 4098], 'All': [1434, 1907], 'findings': [1437], 'favor': [1438], 'model': [1442], '(22Fugmann': [1448], 'S.D.': [1449], '429-430Crossref': [1456], '(15)': [1459], 'substrate.': [1469, 2932], 'Despite': [1470], 'recent': [1472, 3824, 4040, 4222], 'series': [1473], 'reports': [1475], 'biochemistry,': [1478], 'much': [1479], 'remains': [1480], 'learned': [1483], 'concerning': [1484, 3141], 'function.': [1486], 'Different': [1487], 'forms': [1488], 'various': [1493], 'laboratories': [1494], 'contradictory': [1498], 'properties.': [1499], 'One': [1500, 1649, 2348], 'provided': [1503, 1923], 'data': [1504, 3306], '(W': [1513, 2972], '=': [1514, 1519, 2973, 2978], 'T;': [1517], 'R': [1518, 2977, 3455, 3473], 'G)': [1522, 2981], 'hotspot': [1523, 1548, 1601, 3332, 3369, 3416, 3431, 3485], 'motif': [1524, 1832, 2971, 3222, 3270, 3333, 3458, 3497, 3812, 3920, 4127], '(23Pham': [1525, 1664, 3311, 4243], 'Bransteitter': [1527, 1666, 3313, 4103, 4245], 'Petruska': [1529, 1668, 3315, 4105, 4247], '424:': [1535, 1674, 3321, 4111, 4253], '103-107Crossref': [1536, 1675, 3322, 4112, 4254], '(528)': [1539, 1678, 3325, 4115, 4257], 'similar': [1544, 4264, 4298], 'RGYW/WRCY': [1547], 'studies': [1553, 1605, 2451, 2670, 2835, 4041], '(24Shapiro': [1554, 3382], 'G.S.': [1555, 3383], 'Aviszus': [1556, 3384], 'Murphy': [1558, 3386], 'Wysocki': [1560, 3388], 'L.J.': [1561, 3389], '168:': [1565, 3393], '2302-2306Crossref': [1566, 3394], '(53)': [1569, 3397], '25Rogozin': [1572], 'I.B.': [1573], 'Pavlov': [1574], 'Y.I.': [1575], 'Bebenek': [1576], 'Matsuda': [1578, 3658], 'Kunkel': [1580], 'T.A.': [1581], '2001;': [1584, 2176], '2:': [1585], '530-536Crossref': [1586], '(263)': [1589], 'other': [1594, 1683, 1908, 3245], 'groups': [1595, 1684, 3038], 'did': [1596, 1794, 3442, 3946], 'observe': [1598, 3444], 'such': [1599], 'predilection': [1602], '(15Dickerson': [1609, 1692], 'activated': [1656], 'removal': [1658], 'RNase': [1662, 1687, 1736, 2222, 2508], 'reported': [1685], 'had': [1689, 2880, 3935], 'no': [1690], 'effect': [1691, 2675, 2707, 2718, 2787, 3480], 'leaving': [1732], 'issue': [1734], 'A-activation': [1737], 'unclear.': [1738], 'Here,': [1739], 'examined': [1741], 'using': [1754, 1972, 2336, 3296], 'Having': [1787], 'established': [1788], 'minimum': [1790], 'optimal': [1791, 3050], 'length,': [1792, 2630, 2703], 'analyses': [1796], 'context': [1802], 'activity.': [1805, 3012], 'kept': [1808], 'identical': [1814, 2620], 'so': [1815], 'sites': [1818, 2153, 2861], 'fully': [1820, 1965, 3301, 3561], 'comparable.': [1821], 'WRCr,': [1851, 3053, 3350], 'where': [1852, 3054], 'designates': [1856], 'impact.': [1859], 'Oligonucleotide': [1860], 'Substrate—All': [1861], 'oligonucleotides': [1862, 1909, 2730, 2758, 2855, 3145], 'synthesized': [1864, 2853], 'Qiagen/Operon': [1866], 'Technologies': [1867], '(Richmond,': [1868], 'CA).': [1869], 'Oligonuleotides': [1870], 'determine': [1873, 2857], 'suitable': [1875], 'substrate': [1877, 2600, 2658, 2716, 2746, 2785, 2817, 2830, 2868, 2879, 3051, 3216, 3232, 3254, 4205, 4242, 4304], 'as': [1880, 2194, 2759, 2761, 2808, 3367, 3494, 3640, 3642, 3687, 3742, 4034], 'follows:': [1881], 'KY333': [1882], '(5′-TTTTTTTTTACGATTTTTTT-3′,': [1883], '20mer);': [1884], 'KY334': [1885], '(5′-TTTTTTTTTTTACGATTTTTTTTT-3′,': [1886], '24mer);': [1887], 'KY335': [1888], '(5′-TTTTTTTTTTTTTTACGATTTTTTTTTTTT-3′,': [1889], '30mer).': [1890], 'Uracil-DNA-glycosylase': [1891], '(UDG)': [1892], 'substrates': [1893, 2363, 2804, 2955, 2995, 3096, 3127, 3184, 3206, 4217], 'KY414': [1895], '(5′-TTTTTTTAUGATTTTT-3′,': [1896], '16': [1897], 'mer);': [1898, 1902], 'KY415': [1899], '(5′-TTTTTTTTTAUGATTTTTTT-3′,': [1900], '20': [1901], 'KY416': [1903], '(5′-TTTTTTTTTTTAUGATTTTTTTTT-3′,': [1904], '24': [1905, 4332], 'mer).': [1906], 'specified': [1915], 'figures.': [1916], 'Recombination': [1917], 'Protein—Mouse': [1918], 'kindly': [1922], 'Dr.': [1925], 'Tasuku': [1926], 'Honjo.': [1927], 'S-transferase': [1930], '(GST)': [1931], 'coding': [1932, 1962], 'obtained': [1935], 'pAcG2T': [1937], '(Pharmingen).': [1938], 'PCR': [1940], 'reaction': [1941, 2202, 2270, 2358, 2548, 2569, 2649], 'construct': [1945], 'GST-mAID': [1947, 1961, 2076, 2393, 2476, 2505], 'fragment': [1949], 'enterokinase': [1952], 'recognition': [1953], 'site': [1954, 3294, 3345], 'GST': [1957, 2377], 'mAID.': [1959], 'sequenced.': [1966], 'Recombinant': [1967], '(vKY9)': [1969], 'made': [1971], 'Bac-to-Bac': [1974], 'system': [1977], 'Invitrogen': [1979], 'according': [1980], "manufacturer's": [1983], 'instructions.': [1984], 'SF21': [1985], '(Invitrogen)': [1987, 2245], 'infected': [1989], 'vKY9': [1991], 'multiplicity': [1994], 'infection': [1996], '(MOI)': [1997], '10': [1999, 2020, 2066, 2100, 2563], 'harvested': [2001], '3': [2002, 2899], 'days': [2003], 'infection.': [2005], 'Cells': [2006], 'resuspended': [2008], 'buffer': [2010, 2073, 2090, 2255], '(50': [2012, 2092], 'mm': [2013, 2018, 2021, 2024, 2093, 2098, 2101, 2105, 2258, 2263, 2267], 'Tris-Cl,': [2014, 2094, 2259], 'pH': [2015, 2095, 2260], '8.0,': [2016, 2096, 2261], '250': [2017], 'NaCl,': [2019, 2099, 2264], 'NaF,': [2022], '5': [2023, 2063, 2266, 2286, 2306], '2-mercaptoethanol)': [2025], 'contains': [2027], 'mixture': [2029, 2203], 'proteinase': [2031], 'inhibitors': [2032], 'sonicated.': [2034], 'lysate': [2037], 'ultracentrifuged': [2039], '100,000': [2041], '×': [2042], 'g': [2043], '1': [2045, 2104, 2233, 2277], 'h,': [2046], 'clear': [2049], 'extract': [2051], 'mixed': [2053], 'agarose': [2056, 2060], '(Sigma).': [2057], 'washed': [2062], 'times': [2064], 'volumes': [2067], '(relative': [2068, 2085], 'bed': [2070, 2087], 'volume)': [2071, 2088], 'eluted': [2080], 'equal': [2083], 'volume': [2084], '100': [2097, 2219, 2303], 'reduced': [2102], 'glutathione,': [2103], 'dithiothreitol).': [2106], 'Coomassie': [2112], 'stained': [2113], 'SDS-polyacrylamide': [2114], 'gel': [2115], 'Fig.': [2119, 2130, 2367], '1A.': [2120], 'Deamination': [2121], 'Assay—The': [2122], 'assay': [2125, 2416, 3490], 'schematically': [2128], '1B.': [2131], 'Uracil': [2132], 'generated': [2133, 4008], 'removed': [2138], 'resulting': [2143], 'abasic': [2146], '(AP)': [2147], 'site.': [2148], 'cleavage': [2150, 2191], 'AP': [2152], 'introduced': [2156], 'alkali': [2158], 'treatment': [2159, 2510], 'elevated': [2161], 'temperatures': [2162], '(95': [2163], '°C)': [2164, 2242], '(26Abner': [2165], 'C.W.': [2166], 'Lau': [2167], 'A.Y.': [2168], 'Ellenberger': [2169], 'Bloom': [2171], 'L.B.': [2172], '276:': [2177], '13379-13387Abstract': [2178], '(54)': [2186], 'serve': [2193, 4033], 'readout': [2196, 4290], 'deamination.': [2200, 2877], '(10': [2204], 'μl)': [2205], 'containing': [2206, 2256], '200': [2207], 'fmol': [2208], 'radioisotope-labeled': [2210], 'oligonucleotide': [2211, 2702, 2803, 3303], 'substrate,': [2212, 2698], '50': [2213, 2262], 'ng': [2214, 2220], '(1': [2215, 2227], 'pmol)': [2216], 'GST-mAID,': [2218], 'A,': [2223, 2901], '0.1': [2225], 'unit': [2226, 2228], 'catalyzes': [2229], 'release': [2231], 'nmol': [2234], 'one': [2238, 3100, 3149, 3949, 4295], 'h': [2239], '37': [2241, 2251], 'UNG': [2244, 2754], 'incubated': [2247], '10min': [2249], '°C': [2252, 2304], '25': [2257], 'EDTA.': [2268], 'stopped': [2272], 'addition': [2275], 'μl': [2278], '2': [2280], 'm': [2281], 'NaOH': [2282], 'heated': [2284, 2301], 'min': [2287, 2307, 2552, 2564], '95': [2289], '°C.': [2290], 'Eleven': [2291], 'microliters': [2292], 'formamide': [2294], 'then': [2296, 3769, 4032], 'added': [2297, 2410], 'samples': [2299], 'plunged': [2309], 'ice': [2312], 'water': [2313], 'bath.': [2314], 'Reaction': [2315], 'products': [2316], 'separated': [2318], '10%': [2320], 'denaturing': [2321], 'polyacrylamide': [2322], 'gels': [2323], 'running': [2324], '1×': [2326], 'Tris': [2327], 'borate-EDTA': [2328], '(TBE)': [2329], 'buffer.': [2330], 'Gels': [2331], 'visualized': [2333], 'autoradiography': [2335], 'phosphor-imager': [2338], 'FX': [2339], '(BioRad': [2340], 'Laboratories,': [2341], 'Hercules,': [2342], 'CA)': [2343], 'quantified': [2345], 'Quantity': [2347], 'software': [2349], '(version': [2350], '4.2).': [2351], 'time': [2353, 2542, 2567], 'course': [2354, 2543, 2586], 'typical': [2357], 'different': [2361, 2633], '2.': [2368], 'Activity': [2370], 'Assay—Recombinant': [2371], 'N-terminal': [2376], 'fusion': [2378], 'baculovirus-infected': [2382], 'insect': [2383], 'affinity-purified': [2386], 'near': [2388], 'homogeneity': [2389], '(Fig.': [2390, 2490, 2511, 2553, 2636, 2680, 2747, 2862, 2996, 3185, 3271], '1A).': [2391], 'Purified': [2392], 'tested': [2396, 2957, 3095, 3129], 'its': [2398, 3869, 4215], 'residues': [2403, 3196, 3283], 'Excess': [2406], 'glycosylase': [2408], '(see': [2411], '"Experimental': [2412], 'Procedures")': [2413], 'ensure': [2418], 'rate-limiting': [2424], 'complete': [2428], 'reaction.': [2429, 2447], 'difference': [2431], 'efficiency': [2435, 2666, 2710, 3890], 'directly': [2437], 'reflected': [2438], 'percentage': [2441], 'cleaved': [2443], 'product': [2444], 'Consistent': [2448], 'earlier': [2450, 2516], 'our': [2475, 2834, 2988, 3274, 3460, 3489], 'active': [2479], 'nucleotides': [2483, 2763], 'located': [2484, 4236], '3),': [2491], 'double-stranded': [2495, 4240], 'hybrid': [2501], '(data': [2502, 2711], 'shown).': [2504, 2713], 'requires': [2507], '3A),': [2512], 'study': [2517, 3934, 4223, 4261], 'plateaus': [2549, 2676], '∼15-20': [2551], '2).': [2554], 'all': [2556, 2965, 3036, 3615], 'assays': [2558], 'carried': [2560, 4055], 'still': [2571], 'linear': [2574], 'range.': [2575], 'Length-dependence': [2577], 'Action': [2580], 'Cytidines—In': [2584], 'optimizing': [2588], 'assay,': [2590], 'wondered': [2592], 'whether': [2593], 'would': [2601, 3502, 3773, 4031, 4326], 'influence': [2602], 'single': [2609], 'imbedded': [2611], 'middle': [2614], 'Oligonucleotides': [2618], 'nucleotide,': [2625], 'differing': [2627], 'show': [2631, 3278], 'markedly': [2632], 'efficiencies': [2635], '3).': [2637], '20-mer': [2639], 'gave': [2640, 2982], 'minimal': [2642], '5.3%': [2643], 'conversion;': [2644], 'whereas': [2645], 'under': [2646], 'same': [2648, 2738, 2931], 'conditions,': [2650], '24-mer': [2652], 'resulted': [2653], '49%': [2655], 'conversion.': [2656], 'Increasing': [2657], '30': [2661, 3217], 'nt': [2662, 2679, 4325], 'enhanced': [2664], '62%.': [2668], 'Additional': [2669], '26': [2678, 2870], '3B).': [2681], 'Repositioning': [2682], 'residue': [2686, 3018, 3406], '(AGCA)': [2687], 'closer': [2688], '5′-': [2691], '3′-end': [2693], 'without': [2699], 'little': [2706], 'observed': [2715, 3177, 3508, 4301], 'conferred': [2721], 'cleaves': [2726], 'synthetic': [2728], 'uracil-containing': [2729], '(mimicking': [2731], 'products)': [2735], 'efficiency,': [2739, 3260], 'independent': [2740], '3C).': [2748], 'act': [2756, 3715], 'short': [2760], 'three': [2762], '(27Varshney': [2764], 'van': [2766], 'de': [2767], 'Sande': [2768], 'J.H.': [2769], 'Biochemistry.': [2770], '1991;': [2771], '30:': [2772], '4055-4061Crossref': [2773], '(96)': [2776], 'molecular': [2780], 'basis': [2781, 3886], 'known.': [2790], 'important': [2795, 3077, 3968], 'taken': [2799], 'into': [2800, 4230], 'consideration': [2801], 'when': [2802, 3832, 4052], 'designed': [2806], 'mechanism': [2810], 'considered': [2814], 'endogenous': [2816, 3378, 4216], 'sites.': [2818], 'Quantitation': [2819], 'Sequence': [2822], 'Preferences': [2823], 'Single-stranded': [2827], 'DNA—The': [2828], 'simple': [2829], 'configuration': [2831], 'chosen': [2832], 'permits': [2836], 'characterization': [2838], 'immediate': [2842], 'AID.': [2851, 4038, 4201], '27': [2854, 2910], 'preferred': [2859], '4A).': [2863, 2997], 'sufficient': [2872], 'maximal': [2874], 'Each': [2878], 'string': [2882], '11': [2884], 'Ts': [2885], 'sides': [2888], '5′NNCN3′': [2891], 'motif.': [2892, 3409, 3694, 3712, 4276], 'N': [2893], 'any': [2896], 'nucleotides,': [2900], 'G,': [2902], 'creates': [2906], 'total': [2908], 'possible': [2911], 'combinations.': [2912], 'excluded': [2915], 'creating': [2917], 'combination': [2919], 'avoid': [2921], 'complication': [2923], 'having': [2925], 'targets': [2928], 'Within': [2933], 'NNCN': [2935], 'sequence,': [2936, 3548], 'named': [2938], '-2,': [2942], '-1,': [2946, 3073], 'C,': [2948], '0,': [2949], '3′-most': [2951], '+1.': [2953], 'These': [2954, 3803], 'combinations': [2966], 'fit': [2968], 'WRCN': [2970], 'T,': [2976], 'than': [2984, 3066, 3099, 3148, 3880, 4354], '50%': [2985], 'conversion': [2986], 'assays,': [2989], 'contrast': [2991], 'non-WRCN': [2994], '+1': [2999, 3104, 3137, 3359], 'N-2N-1C0N+1': [3002], 'minor': [3005], 'T': [3017], 'confers': [3022], 'consistently': [3024], 'lower': [3025, 3879, 3889], 'compared': [3027], 'G.': [3031], 'true': [3034], '9': [3037], 'substrates,': [3040, 3193], 'whose': [3041], 'members': [3042], 'differ': [3043], 'position.': [3047, 3138, 3476], 'Hence,': [3048, 3955], 'indicates': [3058], 'WR': [3068], 'positions': [3069], '-2': [3071], 'note': [3079], 'full': [3082, 4338, 4341], 'range': [3083], 'sequences': [3085], 'deaminated,': [3088], 'despite': [3089], 'preferences': [3091], 'noted.': [3092], 'Next,': [3093], 'activity,': [3112], 'chose': [3114], 'vary': [3117], 'position;': [3122], 'hence,': [3123, 3681, 3997], 'seven': [3124, 3191], 'multiple': [3125], 'maintained': [3133], 'constant': [3134], 'caveat': [3140], 'analysis': [3143, 3376], '(and': [3154, 3498], 'therefore,': [3155], 'cleavage)': [3156], 'closest': [3160], '5′': [3163], 'label': [3164], 'will': [3165], 'mask': [3166], 'downstream': [3171], 'Cs.': [3172], 'Nevertheless,': [3173], 'rule': [3176], 'above': [3178], 'largely': [3180, 3340], 'preserved': [3181], '4B).': [3186, 3272], 'In': [3187, 3817, 3915, 4329], 'most': [3188, 3403], 'double-C': [3192], 'do': [3197], 'conform': [3199, 3266, 3525], 'generally': [3207, 3365], 'low': [3209], '(TGCC)': [3218], 'fits': [3219, 3237], 'very': [3225, 3936], 'efficiently.': [3226], '28': [3233], '(TACC),': [3234], 'moderately.': [3243], 'interesting': [3246, 3599, 3822, 4120], 'exception': [3247], '33': [3255], '(CGCT)': [3256], 'gives': [3257], 'moderate': [3258, 3532], 'even': [3261], 'though': [3262], 'Overall,': [3273], 'comparisons': [3276], 'clearly': [3277], 'prefers': [3281, 4273], 'context.': [3289], 'determined': [3291, 3487], 'comprehensive': [3298], 'set': [3299], 'comparable': [3302], 'substrates.': [3304], 'Our': [3305, 3347], 'others': [3310], 'suggest': [3328], '5′RGYW3′/5′WRCY3′': [3331], 'may': [3338, 3714, 3732, 3805, 3965, 4350], 'due': [3341], 'preference.': [3346, 3514], 'consensus': [3348], 'purines.': [3362], 'RGYW': [3363, 3430, 4126], 'regarded': [3366], 'based': [3373], 'genomic': [3379], 'genes': [3381], 'G': [3400, 3427], 'heavily': [3404], 'mutated': [3405], 'within': [3407], 'complementary': [3411, 3436, 3500], 'strand': [3412, 3631, 3684, 3703, 3741, 4022, 4051], '5′RGYW3′': [3415], '5′WRCY3′.': [3418], 'easy': [3421], 'understand': [3423], 'presence': [3425], 'WRCY.': [3439], 'Y': [3448], 'WRCY': [3451], '(corresponding': [3452], 'RGYW)': [3457], 'assays.': [3462], 'Instead,': [3463], 'slightly': [3469], 'favored': [3470], 'Considering': [3477], 'position,': [3483], 'best': [3492], 'described': [3493, 3562], '5′WRCr3′': [3496], '5′yGYW': [3504], '3′).': [3505], 'deviations': [3510], 'For': [3515], 'example,': [3516], 'CGCT,': [3521], 'shows': [3530], 'high': [3534], 'illustrates': [3538], 'influenced': [3544], 'local': [3549], 'structural': [3550, 4212], 'factors': [3551], 'probably': [3552], 'underlie': [3553], 'manner': [3557, 3975], 'sequence.': [3565], 'Although': [3566, 3695], 'surprising': [3575, 4347], 'hotspots,': [3578], 'what': [3579], 'might': [3580], 'relevance': [3583, 3808], 'recombination?': [3591], 'After': [3592], 'completing': [3593], 'study,': [3595], 'realized': [3597], 'several': [3598], 'features': [3601, 3779, 4213], 'relevant': [3602], 'point.': [3605], 'First,': [3606], 'vertebrates.': [3616], 'commonly': [3619], 'present': [3620, 3945], '5′-AGCT-3′': [3625, 3686], '5′-AGCA-3′': [3627], 'G-rich': [3630, 3830, 3929], '(non-template': [3632], 'strand).': [3633], 'case': [3637], 'vertebrates': [3639], 'distant': [3641], 'Xenopus': [3643], '(28Kitao': [3646], 'Arakawa': [3648], 'Kuma': [3650], 'Yamagishi': [3652], 'Nakamura': [3654], 'Furusawa': [3656], 'Yasuda': [3660], 'Ekino': [3662], 'Shimizu': [3664], 'Int.': [3666], '12:': [3669], '959-968Crossref': [3670], '(17)': [3673], 'Second,': [3676], 'AGCT': [3677], 'palindrome;': [3680], 'anti-parallel': [3683, 3702, 3953], 'reads': [3685], 'well,': [3688], 'conforming': [3690], 'AGCA': [3696], 'palindrome,': [3700], 'TGCT,': [3705], 'conforms': [3708], 'motifs': [3719, 3957], 'strands': [3723, 3964, 4191], 'concurrently,': [3724], 'edges': [3728], 'character': [3735], 'C-rich': [3738], '(template)': [3739], 'well': [3743], '(19Tian': [3744], 'If': [3764], 'case,': [3768], 'double-strand': [3771], 'break': [3772], 'result,': [3774], 'aspects': [3804], 'explain': [3806], 'recombination.': [3816], 'regard,': [3819], 'region,': [3831], 'substituted': [3833], 'Sγ1': [3836], 'able': [3840], 'R-loops': [3843], '(29Shinkura': [3846, 3893], 'Nature': [3858, 3905], '435-441Crossref': [3862, 3909], '(179)': [3865, 3912], 'undergo': [3872], 'about': [3877], '13-fold': [3878], 'normal': [3882], 'Sγ1,': [3883], 'unclear': [3892], 'observation': [3921], 'noted': [3922], 'above,': [3923], 'noteworthy': [3926], 'few': [3937, 3942], 'motifs,': [3939], 'nearby': [3950], 'strand.': [3954, 4014], 'close': [3958], 'together': [3959], 'quite': [3967], 'previously': [3980], 'considered.': [3981], 'Unlike': [3982], 'regions,': [3985], 'unlikely': [3989], 'transcription,': [3995], 'could': [4005], 'extensively': [4011], 'displaced': [4012], 'non-template': [4013, 4021, 4050], 'hypothesized': [4018], 'transiently': [4025], 'bubble,': [4029], 'Indeed,': [4039], 'acts': [4047], 'Escherichia': [4061], 'coli': [4062], '(16Sohail': [4063], '21Ramiro': [4084], '23Pham': [4101], 'note,': [4122], 'however,': [4123], 'hotspots': [4130], 'strand-specific': [4135], '(30Milstein': [4136], 'Staden': [4140], '1998;': [4149], '95:': [4150], '8791-8794Crossref': [4151], '(144)': [4154], '31Michael': [4157], 'Martin': [4159], 'Nicolae': [4161], 'D.': [4162], 'Kim': [4163], 'Padjen': [4165], 'Zhan': [4167], 'Nguyen': [4169], 'Pinkert': [4171], 'Storb': [4173], 'Immunity.': [4175], '16:': [4177], '123-134Abstract': [4178], '(69)': [4186], 'should': [4196], 'equally': [4198], 'accessible': [4199], 'Reconciliation': [4202], 'specificity': [4206], 'precise': [4211], 'awaits': [4218], 'investigation.': [4220], 'introduce': [4228], 'LacZα': [4233], 'reporter': [4235], 'otherwise': [4239], 'circular': [4241], 'That': [4260], 'reached': [4262], 'conclusion': [4265], 'regarding': [4266], 'preference,': [4269], 'namely': [4270], 'agreement': [4278], 'stronger': [4284], 'biological': [4289], 'purely': [4293], 'yielded': [4297], 'results.': [4299], 'dependence': [4306, 4349], 'size': [4316, 4357], '(24': [4319], 'kDa)': [4320], 'anticipated': [4322], '16-20': [4324], 'sufficient.': [4328], 'fact,': [4330], '≥': [4331], 'nts': [4333], 'necessary': [4335], 'reach': [4337], 'nearly': [4340], 'reflect': [4351], 'larger': [4353], 'expected': [4355], 'footprint': [4356], 'multimerization': [4361], 'another': [4365], 'possibility': [4366], '(14Chaudhuri': [4367], '32Ta': [4388], 'V.T.': [4389], 'Imai': [4398], 'Nonoyama': [4400], 'Tashiro': [4402], 'Ito': [4406], '945-946Crossref': [4418], '(5)': [4421]}, 'cited_by_api_url': 'https://api.openalex.org/works?filter=cites:W2025949960', 'counts_by_year': [{'year': 2024, 'cited_by_count': 7}, {'year': 2023, 'cited_by_count': 5}, {'year': 2022, 'cited_by_count': 6}, {'year': 2021, 'cited_by_count': 11}, {'year': 2020, 'cited_by_count': 5}, {'year': 2019, 'cited_by_count': 5}, {'year': 2018, 'cited_by_count': 5}, {'year': 2017, 'cited_by_count': 7}, {'year': 2016, 'cited_by_count': 4}, {'year': 2015, 'cited_by_count': 3}, {'year': 2014, 'cited_by_count': 4}, {'year': 2013, 'cited_by_count': 6}, {'year': 2012, 'cited_by_count': 13}], 'updated_date': '2025-01-16T06:33:37.064356', 'created_date': '2016-06-24'}
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