Structural evidence for Nap1‐dependent H2A–H2B deposition and nucleosome assembly

Name: Work Video:
Duration: 3 min 30 s
Carmen Aguilar‐Gurrieri; Amédé Larabi; Vinesh Vinayachandran; Nisha Patel; Kuangyu Yen; Rohit Reja; Ima‐O Ebong; Guy Schoehn; Carol V. Robinson; B. Franklin Pugh; Daniel Panne
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4400, 4408, 4420], 'editorial': [749, 753], 'decision': [750, 754], 'including': [752, 1222], 'letters,': [755], 'reviewer': [756], 'comments': [757], 'responses': [760], 'to': [761, 764, 798, 910, 1126, 1137, 1181, 1192, 1238, 1272, 1326, 1367, 1468, 1547, 1591, 1641, 1737, 1764, 1780, 1849, 1901, 1913, 1977, 1985, 2037, 2107, 2155, 2218, 2249, 2285, 2288, 2303, 2327, 2337, 2450, 2454, 2601, 2615, 2674, 2724, 2786, 2896, 2989, 3024, 3307, 3357, 3484, 3499, 3525, 3533, 3542, 3659, 3686, 3728, 3787, 3865, 3898, 3914, 4176, 4223, 4229, 4304], 'feedback.': [762], 'ToolsAdd': [763], 'favoritesDownload': [765], 'CitationsTrack': [766], 'CitationsPermissions': [767], 'ShareFacebookTwitterLinked': [768], 'InMendeleyWechatReddit': [769], 'Figures': [770], '&': [771, 1054, 1077, 1157, 1198, 1290, 1333, 1342, 2271, 2815, 4031], 'Info': [772], 'Abstract': [773], 'Nap1': [774, 796, 821, 858, 871, 912, 939, 946, 1384, 1405, 1436, 1450, 1462, 1533, 2235, 2246, 2771, 3496, 3753, 4002, 4054, 4077, 4188, 4250], 'is': [775, 859, 881, 920, 954, 969, 997, 1013, 1036, 1069, 1092, 1169, 1206, 1217, 1347, 1364, 1385, 1391, 1406, 1437, 1534, 1806, 1899, 1911, 1921, 1931, 1956, 1992, 2005, 2325, 2530, 2559, 2566, 2795, 2837, 2936, 3018, 3539, 3890, 3980, 4131, 4144, 4247, 4330, 4343], 'histone': [777, 913, 924, 1004, 1124, 1130, 1209, 1220, 1235, 1244, 1249, 1370, 1401, 1411, 1420, 1470, 1501, 1527, 2073, 2086, 2343, 2370, 2976, 3048, 3370, 3512, 3519, 3565, 3582, 3743, 3856, 3916], 'chaperone': [778, 885, 914, 973, 1402], 'involved': [779, 1218, 2502, 4132], 'in': [780, 802, 805, 841, 962, 1073, 1096, 1219, 1372, 1419, 1451, 1483, 1509, 1539, 1550, 1654, 1672, 1679, 1689, 1692, 1702, 1707, 1746, 1771, 1800, 1863, 1869, 1886, 1915, 1948, 1959, 2104, 2130, 2143, 2145, 2221, 2332, 2503, 2561, 2568, 2573, 2577, 2633, 2641, 2647, 2667, 2708, 2745, 2765, 2797, 2850, 2867, 2939, 3020, 3107, 3183, 3210, 3223, 3227, 3273, 3368, 3384, 3396, 3489, 3495, 3503, 3559, 3602, 3606, 3751, 3767, 3800, 3849, 3907, 4005, 4011, 4089, 4120, 4133, 4147, 4161, 4189, 4200, 4259, 4279, 4308, 4359, 4370, 4407], 'nuclear': [782], 'import': [783], 'assembly.': [788, 819, 899, 1531, 2521, 4373], 'Here,': [789], 'we': [790, 1433, 1552, 2022, 2068, 2098, 2242, 2282, 2754, 3361, 3466, 3748], 'report': [791], 'crystal': [793, 2265, 4116, 4134, 4245, 4361], 'structure': [794, 903, 929, 986, 1447, 2266, 2354, 2468, 2593, 2726, 2870, 2913, 3572, 4117, 4246], 'bound': [797, 1237, 2248, 3306, 3324], 'together': [800], 'with': [801, 870, 1275, 1374, 1453, 1577, 1705, 1753, 1778, 1809, 2000, 2048, 2174, 2256, 2360, 2393, 2589, 2665, 2955, 3152, 3179, 3201, 3426, 3567, 4091], 'vitro': [803, 1161, 3215, 4012, 4162], 'vivo': [806, 1540, 4006], 'functional': [807], 'studies': [808, 1162, 1233], 'that': [809, 857, 868, 879, 917, 1107, 1165, 1216, 1243, 1251, 1435, 1461, 1519, 1758, 1792, 1836, 1852, 1860, 1930, 1970, 2046, 2083, 2181, 2198, 2215, 2397, 2538, 2736, 2756, 2802, 2907, 3478, 3508, 3827, 3885, 3911, 4130], 'elucidate': [810], 'principles': [812], 'underlying': [813, 2063, 4216], 'Nap1-mediated': [814, 894], 'chaperoning': [816, 1421], 'dimer': [822, 940, 2331, 2565, 2681, 2739, 2794, 2813, 2910, 3538], 'provides': [823, 1496, 2721, 2920, 3929], 'an': [824, 1070, 1093, 1178, 1268, 1464, 1497, 1554, 1601, 1605, 1795, 1810, 2394, 2458, 2798, 4126], 'acidic': [825, 1269, 1465, 2923, 3181], 'binding': [826, 909, 950, 1176, 1187, 1270, 1466, 2482, 2492, 2608, 2654, 2767, 2828, 2924, 2942, 2951, 2977, 3009, 3032, 3037, 3049, 3127, 3156, 3371, 3376, 3404, 3450, 3470, 3485, 3520, 3583, 3754, 3790, 3806, 3839, 3857, 3899, 3918, 3969, 3979], 'surface': [827, 1467, 2857, 2925, 3157], 'asymmetrically': [829, 2938], 'engages': [830, 2945], 'single': [832, 943, 1474, 2759, 3428, 3763], 'heterodimer.': [834, 1476, 2658, 2833], 'Oligomerization': [835, 964, 1477, 3994, 3999, 4376], 'Nap1–H2A–H2B': [838, 932, 967, 1480], 'complex': [839, 933, 968, 1452, 2227, 2472, 2529, 2588, 2664, 2707, 2778, 3359, 3894, 3998, 4090, 4258], 'results': [840, 1482, 1508, 2849, 4369], 'burial': [842, 1484, 2852], 'surfaces': [844, 1486, 2952], 'required': [845, 860, 955, 1438, 1487, 1535], 'into': [850, 926, 982, 1015, 1493, 1954, 2060, 2208, 2240], 'nucleosomes.': [851, 927, 1609, 1648, 2191], 'Chromatin': [852, 1099], 'immunoprecipitation-exonuclease': [853], '(ChIP-exo)': [854], 'analysis': [855], 'shows': [856, 916, 4173], 'across': [864, 1515], 'genome.': [866], 'Mutants': [867], 'interfere': [869], 'oligomerization': [872, 880, 919, 1507, 2505, 2703, 3595, 3869, 3886, 4055, 4074, 4160, 4410, 4422], 'exhibit': [873], 'severe': [874], 'defects': [877, 1514], 'showing': [878, 3218, 3320], 'essential': [882, 1037, 3892], 'function.': [886], 'These': [887, 2080], 'findings': [888], 'establish': [889], 'molecular': [891, 1414, 2231, 2358], 'basis': [892, 2232, 4233], 'Synopsis': [900], 'co-crystal': [902], 'defines': [904], 'stoichiometry': [906, 4227], 'higher-order': [918, 985, 2504], 'needed': [921], 'proper': [923], 'incorporation': [925], 'Crystal': [928, 2467], 'at': [934, 1456, 2631, 3709, 3741], '6.7': [935, 1457], 'Å': [936, 1458, 2295, 4290], 'resolution.': [937], 'binds': [941, 2881], 'dimer.': [945, 2772], 'prevents': [947], 'non-specific': [948, 1276], 'DNA': [949, 1047, 1136, 1325, 1350, 1624, 1665, 1699, 1755, 1925, 1929, 2044, 2341, 2653, 2885, 2918, 2950, 3031, 3104, 3126, 3155], 'vivo.': [963, 1801, 2222], 'important': [970, 1094, 1366], 'function': [974], 'Nap1.': [976], 'Introduction': [977], 'genomes': [979], 'are': [980, 1521, 1830, 1907, 1941, 1975, 2279, 2499, 2506, 2539, 2650, 2806, 3100, 3112, 3333, 3382, 3493, 3562, 3574, 3600, 3617, 3958, 3985, 4282], 'organized': [981, 1014], 'chromatin,': [983, 1574, 2241], 'comprising': [987, 2628, 3185, 3204, 3440, 4399, 4419], 'histones': [988, 1240, 2311, 2392, 4124], 'DNA.': [990], 'basic': [992, 3154], 'repeating': [993], 'unit': [994, 2517, 4263], 'chromatin': [996, 1029, 1375, 1548, 1559, 1664, 1865, 2020, 2035, 2339], 'nucleosome,': [999, 1821, 2877, 3111], 'which': [1000, 1012, 2784, 2888, 2983, 3017, 3053, 3099], 'consists': [1001], 'octamer': [1005], 'enwrapped': [1006], '147': [1008], 'bp': [1009, 1630, 1846, 1885, 2152, 2157], 'DNA,': [1011, 1183], 'two': [1016, 1189, 1522, 2542, 2741, 2946, 4265, 4367, 4384], 'superhelical': [1017], 'turns': [1018, 2883], '(Luger': [1019, 2871], 'et': [1020, 1081, 1141, 1145, 1149, 1153, 1229, 1281, 1285, 1294, 1298, 1302, 1306, 1310, 1314, 1338, 2346, 2350, 2378, 2435, 2750, 2872, 3632, 3642, 4014, 4019, 4023, 4027, 4035, 4039, 4043, 4047, 4108, 4112, 4137, 4164, 4179, 4183, 4212], 'al,': [1021, 1082, 1142, 1146, 1150, 1154, 1230, 1282, 1286, 1295, 1299, 1303, 1307, 1311, 1315, 1339, 2347, 2351, 2379, 2436, 2751, 2873, 3633, 3643, 4015, 4020, 4024, 4028, 4036, 4040, 4044, 4048, 4109, 4113, 4138, 4165, 4180, 4184, 4213], '1997).': [1022, 2874], 'Spatial': [1023], 'temporal': [1025], 'regulation': [1026, 1052], 'specific': [1028], 'loci': [1030], 'dynamic': [1032, 1957, 2702], 'nucleosomes': [1035, 1091, 1328, 1494, 1955, 1969, 2184], 'control': [1040, 1359, 1381], 'DNA-templated': [1042], 'processes': [1043], 'such': [1044, 1813, 2801], 'as': [1045, 1060, 1128, 1717, 1814, 1896, 2334, 2336, 2646, 2865, 3558, 3591, 3593, 3612, 3614, 4094, 4206], 'replication,': [1046], 'damage': [1048], 'repair,': [1049], 'gene': [1051, 1074, 1097, 1361], '(Venkatesh': [1053], 'Workman,': [1055], '2015).': [1056, 1316], 'serves': [1059], 'general': [1062], 'transcriptional': [1063], 'repressor,': [1064], 'promoter': [1066], 'removal': [1068, 1134], 'early': [1071], 'step': [1072], 'activation': [1075], '(Becker': [1076], 'Horz,': [1078], '2002;': [1079, 1147, 4029, 4110], 'Bryant': [1080], '2008).': [1083, 1159, 2380, 4114, 4139, 4166], 'Thus,': [1084], 'ordered': [1086], 'disassembly': [1087], 'reassembly': [1089], 'paradigm': [1095], 'regulation.': [1098], 'remodeling': [1100], 'depends': [1101], 'recruitment': [1104], 'acetyltransferases': [1106], 'acetylate': [1108], 'four': [1110], 'core': [1111, 1623, 2320], 'histones,': [1112, 4171], 'activity': [1115], 'chromatin-remodeling': [1117], 'complexes': [1118], 'capacity': [1122], 'chaperones': [1125, 1236, 1245, 1319, 2236, 3513], 'act': [1127], 'acceptors,': [1131], 'facilitating': [1132], 'their': [1133, 1982, 2893], 'from': [1135, 1560, 1667, 1710, 2340, 2430, 2556, 3497, 3665], 'stimulate': [1138], 'transcription': [1139], '(Ito': [1140], '2000;': [1143], 'Asahara': [1144], 'Lorch': [1148], '2006;': [1151, 1283], 'Adkins': [1152], '2007;': [1155, 1340], 'Sharma': [1156], 'Nyborg,': [1158], 'In': [1160, 1201, 1428, 1988, 2110, 2161, 2263, 2875, 2964, 3214, 3409, 3811, 3938, 4082, 4167], 'have': [1163, 1241, 1425, 3514, 4079], 'revealed': [1164, 1242, 4125], 'two-step': [1171], 'process,': [1172], 'involving': [1173], 'initial': [1175], '(H3–H4)2': [1179], 'tetramer': [1180], 'followed': [1184, 2041], 'dimers': [1191, 2207, 4078], 'complete': [1193], 'octameric': [1195], '(Smith': [1197], 'Stillman,': [1199], '1991).': [1200], 'vivo,': [1202, 1551], 'catalyzed': [1207], 'chaperones,': [1210, 1371, 1412], 'diverse': [1212], 'class': [1213], 'proteins': [1215, 2259, 3298], 'turnover': [1221], 'transport,': [1223], 'transfer,': [1224], 'storage': [1226], '(De': [1227], 'Koning': [1228, 1337], '2007).': [1231], 'cognate': [1239], 'frequently': [1246, 1904], 'protect': [1247], 'hydrophobic': [1248], 'interfaces': [1250, 3226, 3356, 3372, 3459, 3481, 3492, 3851, 4377], 'become': [1252], 'solvent-exposed': [1253], 'outside': [1254], 'context': [1257, 3108], 'or': [1261, 1503, 2636, 3390, 3415, 3421, 3463, 3586, 3589, 3769, 3777, 3820, 4088, 4194], 'neutralize': [1262], 'excess': [1263], 'positive': [1264, 3087], 'charge': [1265, 3461], 'providing': [1267], 'pocket': [1271, 2768], 'directly': [1273], 'compete': [1274], 'electrostatic': [1277], 'histone–DNA': [1278], 'interactions': [1279, 4406, 4428], '(English': [1280], 'Zhou': [1284], '2008,': [1287], '2011;': [1288, 1292, 1296, 4045], 'Cho': [1289], 'Harrison,': [1291], 'Hu': [1293], 'Elsasser': [1297, 1341], '2012;': [1300, 1304], 'Liu': [1301], 'Hondele': [1305], '2013;': [1308], 'Obri': [1309], '2014;': [1312], 'Huang': [1313], 'However,': [1317, 1873, 3455, 3795], 'how': [1318, 1369, 2234], 'mediate': [1320, 1379], 'final': [1322], 'onto': [1324, 2679], 'assemble': [1327, 2338], 'remains': [1329], 'poorly': [1330], 'understood': [1331], '(Loyola': [1332], 'Almouzni,': [1334], '2004;': [1335, 4033], 'De': [1336], "D'Arcy,": [1343], '2012).': [1344, 4049, 4214], 'Nucleosome': [1345], 'central': [1348, 4294, 4317], 'replication': [1351], 'possibly': [1353], 'rate-limiting': [1355], 'factor': [1356], 'expression.': [1362], 'It': [1363], 'therefore': [1365, 3476, 4241], 'understand': [1368, 2229, 4230], 'conjunction': [1373], 'modifiers': [1376], 'remodelers,': [1378], 'process.': [1383], 'universally': [1386], 'conserved': [1387, 3494, 3569], 'among': [1388], 'eukaryotes': [1389], 'founding': [1393], 'member': [1394], 'large': [1397], 'NAP': [1398], 'family': [1399], 'proteins.': [1403], 'While': [1404, 3960], 'one': [1407], 'best-studied': [1410], 'determinants': [1415], 'its': [1417], 'role': [1418, 3220, 4052, 4236], 'remained': [1426, 4059], 'elusive.': [1427], 'work': [1430], 'reported': [1431], 'here,': [1432], 'find': [1434, 2906], 'genomic': [1444, 1659], 'scale.': [1445, 2029], 'yeast': [1449, 3498], 'H2A–H2B,': [1454, 3035], 'determined': [1455, 2356], 'resolution,': [1459], 'demonstrates': [1460], 'uses': [1463], 'engage': [1469, 3143], 'H2A': [1471, 2312, 2498, 2572, 2847, 2961, 2973, 3004, 3075, 3135, 3176, 3197, 3290, 3772, 3868, 3910, 3948], 'protomer': [1481, 2587, 4302, 4341], 'additional': [1498, 1936], 'function,': [1499], 'presumably': [1500], 'transport': [1502], 'storage.': [1504], 'Disruption': [1505, 3284], 'strong': [1511], 'genome': [1517], 'indicating': [1518, 1757, 1791, 1859, 3507, 3884], 'there': [1520, 2004], 'separable': [1523], 'functions': [1524], 'Nap1:': [1526], 'transport/storage': [1528], 'Results': [1532], 'To': [1541, 2012, 2058, 2228, 3349, 3735], 'determine': [1542], 'contribution': [1544, 3352, 3738], 'yNap1': [1546, 1567, 1653, 1793, 2018, 2199, 2216, 2269, 2302, 2488, 2491, 2564, 2680, 2738, 2793, 2824, 2841, 2909, 2944, 3063, 3144, 3151, 3184, 3537, 3599, 3662, 3679, 3702, 3908, 3940, 4086, 4159, 4172], 'performed': [1553, 3624], 'MNase': [1555, 1768, 1833, 1898, 2040], 'digestion': [1556], 'assay': [1557, 2031, 3217, 3380], 'wild-type': [1562, 1668, 1842, 3966], 'BY4741': [1563, 1738], '(WT)': [1564], 'deletion': [1568], 'strain': [1569, 1749, 1918, 1962, 2094, 2148], 'nap1Δ.': [1570], 'Gel': [1571], 'electrophoresis': [1572], 'partially': [1575, 1964], 'digested': [1576], 'MNase,': [1578], 'showed': [1579, 2082, 2386, 3836, 3853], 'nucleosomal': [1581, 1698, 1744, 1826, 1838, 1928, 2209, 2917], 'ladder': [1582], '(Fig': [1583, 1634, 1786, 2149, 2177, 2317, 2373, 2962, 2996, 3067, 3145, 3405, 3451, 3471, 3521, 3672, 3694, 3715, 3731, 3773, 3791, 3807, 3840, 3858, 3901, 3970, 3990, 4296, 4362], '1A).': [1584, 1635], 'distance': [1586, 1593, 1639], 'between': [1587, 1594, 1646, 2088, 2972, 3074], 'each': [1588, 1615, 3961, 3988, 4267, 4309], 'band': [1589, 1616, 3708], 'corresponds': [1590, 1640], 'most': [1596], 'distal': [1597], 'ends': [1599, 2810], 'within': [1600, 1972], 'MNase-cleaved': [1602], 'array': [1603, 1690], 'integral': [1606], 'number': [1607], 'For': [1610, 2522], 'oligonucleosomes,': [1611], 'size': [1613, 1700, 1774, 1805, 1894, 1946, 2144, 4204], 'includes': [1617], 'sum': [1619], 'lengths': [1625, 1628], 'plus': [1626, 1926], 'linker': [1627, 1759, 1924], '(147': [1629], '+': [1631, 3255, 3266, 3681, 3825, 3944, 3952], '20': [1632], 'bp)': [1633, 1777, 1785], 'Consequently,': [1636], 'interband': [1638, 1847], 'population': [1643, 1741, 2163], 'average': [1644], 'spacing': [1645, 1843, 1862, 1983, 1991, 2292], 'adjacent': [1647, 2123], 'Figure': [1649, 2465, 2605, 3147, 3342, 3529, 4374], '1.': [1650], 'Role': [1651], 'scale': [1660], 'Analysis': [1661], 'MNase-digested': [1663], 'fragments': [1666, 1769, 2045], '(WT,': [1669], 'sizes': [1670, 1677, 1745, 2116], 'indicated': [1671, 1678], 'black)': [1673], 'nap1Δ': [1675, 1693, 1706, 1748, 1871, 1888, 1917, 1961, 2093, 2147], '(N,': [1676], 'red)': [1680], 'cells': [1681], 'agarose': [1683], 'gel': [1684, 1857], 'electrophoresis.': [1685], 'Diagram': [1686], 'illustrating': [1687, 4379], 'reduction': [1688, 1895, 1947], 'length': [1691], 'cells.': [1694, 3668], 'Frequency': [1695], 'distribution': [1696, 1742], '(WT': [1701], 'gray': [1703], 'fill': [1704], 'blue': [1708], 'traces)': [1709], 'H3': [1711, 2050], 'ChIP-seq.': [1712], 'Calculation': [1713], 'fuzziness': [1716], 'standard': [1719, 2171], 'deviation': [1720, 2172], '(or': [1723, 1844], 'tag)': [1724], 'positions.': [1725], 'See': [1726, 2579, 3327], 'also': [1727, 2166, 2580, 3328, 3445, 3650, 3828], 'Appendix': [1728, 1788, 3385], 'Fig': [1729, 1789, 2078, 2581, 2616, 2648, 3329, 3534, 3560, 3975], 'S1.': [1730], 'Download': [1731, 1733, 2595, 2597, 2687, 2689, 3345, 3347, 3645, 3647], 'figure': [1732, 2596, 2688, 3346, 3636, 3646], 'PowerPoint': [1734, 2598, 2690, 3348, 3648], 'When': [1735], 'compared': [1736, 2154], '(WT),': [1739], 'enriched': [1752], 'smaller': [1754, 1773], 'fragments,': [1756], 'regions': [1760, 2278, 3755], 'were': [1761, 1879, 2052, 2095, 2119, 2140, 2185, 2254, 2283, 2677, 3312, 3912], 'accessible': [1763], 'MNase.': [1765], 'mononucleosome-sized': [1767], 'electrophoresed': [1770], 'range': [1775, 4205], '(~145': [1776], 'respect': [1779], 'wild': [1782, 2090, 2159, 3670], 'type': [1783, 2091, 3671], '(~170': [1784], '1A,': [1787], 'S1A),': [1790], 'has': [1794, 3270, 3829, 4056, 4219], 'impact': [1796, 2016, 3653], 'This': [1802, 2030, 2179, 2319, 2834], 'shorter': [1803, 1880], 'fragment': [1804], 'consistent': [1808], 'intermediate': [1812], 'hexasome': [1816], 'rather': [1817], 'than': [1818, 2189], 'full': [1820, 1979, 1998, 2190], 'although': [1822], 'other': [1823, 1989, 3989], 'types': [1824], 'subnucleosomal': [1828], 'structures': [1829, 2139, 2363, 2719], 'not': [1831, 3142, 3401, 3447, 3502, 3677, 3705, 3726, 3785, 3879, 3891, 4145], 'excluded.': [1832], 'digestions': [1834], 'indicate': [1835, 2214], 'arrays': [1839, 1878, 1974], 'maintained': [1840], 'approximate': [1841], '~165': [1845], 'distance)': [1848], 'extent': [1851], 'can': [1853, 2762], 'be': [1854, 1978, 1986, 2108, 2698, 2763], 'measured': [1855, 2070], 'electrophoresis,': [1858], 'bulk': [1864], 'generally': [1867, 3852], 'unaltered': [1868], 'strain.': [1872, 1889], 'di-': [1875], 'trinucleosome': [1877], 'constant': [1883], '~25': [1884], 'We': [1890, 2905, 3475, 3649, 4240], 'interpret': [1891], 'fixed': [1893, 1945], 'follows:': [1897], 'expected': [1900, 1912, 3711], 'cleave': [1902], 'where': [1905, 1919, 1939, 2003], 'linkers': [1906], 'longer,': [1908], 'occur': [1914, 2971, 3073], 'lost': [1922, 1942], '(i.e.,': [1923], 'vacated': [1932], 'H2A–H2B).': [1934], 'Having': [1935], 'cleavage': [1937, 2001], 'opportunities': [1938], 'produces': [1943], 'array.': [1950], 'If': [1951], 'even': [1958], '(but': [1963], 'shifted': [1965], 'toward': [1966, 2960, 3102], 'dissociation),': [1967], 'then': [1968, 2053], 'exist': [1971], 'cleaved': [1973], 'likely': [1976], 'nucleosomes,': [1980, 1999], 'since': [1981], 'appears': [1984], 'unchanged.': [1987], 'words,': [1990], 'set': [1993], 'predominance': [1996], 'occurring': [2002], 'relatively': [2007], 'infrequent': [2008], 'dissociation': [2009], 'H2A–H2B.': [2011, 2252, 3487], 'further': [2013, 3930], 'investigate': [2014], 'assembly,': [2021], 'mapped': [2023, 2678], 'positions': [2025], 'genomewide': [2028], 'involves': [2032], 'formaldehyde-cross-linking': [2033], 'fragmentation': [2036], 'mononucleosomes': [2038], 'using': [2039, 3377, 3625, 3639], 'ChIP.': [2043], 'immunoprecipitate': [2047], 'antibody': [2051], 'detected': [2054], 'deep': [2056], 'sequencing.': [2057], 'take': [2059], 'account': [2061], 'intrinsic': [2064], 'occupancy': [2066], 'levels,': [2067], 'first': [2069], 'overall': [2072, 2085, 2395, 2459], 'levels': [2074, 2087], 'immunoblotting': [2076], '(Appendix': [2077], 'S1B).': [2079], 'data': [2081, 2213, 3332], 'similar.': [2096], 'Therefore,': [2097], 'normalized': [2099], 'total': [2101], 'tag': [2102], 'counts': [2103], 'both': [2105, 2840, 3457, 3479, 3850], 'samples': [2106], 'equal.': [2109], 'these': [2111, 2138, 2194, 2212, 3509, 3983], 'single-read': [2112], 'sequencing': [2113], 'experiments,': [2114], '(including': [2117], 'subnucleosomes)': [2118], 'deduced': [2120], 'pairing': [2122], 'peaks': [2124], 'located': [2125, 3019, 4331, 4344], 'opposite': [2127, 2809], 'strands': [2128], '3′': [2132], 'direction.': [2133], 'Confirming': [2134], 'in-gel': [2136], 'observation,': [2137], 'approximately': [2141], 'hexasomal': [2142], '1B,': [2150], '~100–130': [2151], 'range,': [2153], '~150': [2156], 'type).': [2160], 'analysis,': [2164, 4066], 'they': [2165], 'had': [2167], 'fuzzier': [2168], 'locations': [2169], '(higher': [2170], 'associated': [2173], 'peak': [2175, 4097], 'calling)': [2176], '1C).': [2178], 'suggests': [2180], 'hexasomal-sized': [2183], 'positionally': [2186], 'dispersed': [2188], 'Accumulation': [2192], 'putative': [2195], 'hexasomes': [2196], 'indicates': [2197], 'preferentially': [2200], 'deposits': [2201, 2238], 'second': [2203, 3030, 3062], 'copy': [2204], 'arrays.': [2210], 'Together,': [2211, 3905], 'contributes': [2217, 3897], 'Structure': [2223], 'yNap1–H2A–H2B': [2226, 2471, 2586, 2613, 3358, 3997], 'crystallized': [2243], 'Saccharomyces': [2244], 'cerevisiae': [2245], '(yNap1)': [2247], 'Xenopus': [2250, 4186], 'laevis': [2251, 4187], 'Crystals': [2253], 'obtained': [2255], 'full-length': [2258, 2268, 4150], 'but': [2260, 3501, 3676, 3724, 3877, 3896, 4152, 4311], 'diffracted': [2261], 'poorly.': [2262], '(Park': [2270, 2377, 2814, 4136, 4163], 'Luger,': [2272, 2816], '2006),': [2273], 'N-': [2275, 2297], 'C-terminal': [2277, 2299, 3023], 'disordered': [2280, 3026], 'able': [2284, 3685], 'improve': [2286], 'diffraction': [2287, 2693], 'minimum': [2290], 'Bragg': [2291], '~6.7': [2294], 'truncation': [2300, 2308], 'residues': [2304, 3077, 3186, 3205, 3222, 3367, 3424, 3605, 3740, 3766, 3957], '75–365': [2305], 'N-terminal': [2307, 3000], '(14–130)': [2313], 'H2B': [2315, 2576, 3041, 3094, 3138], '(28–126)': [2316], '2A).': [2318], 'domain': [2321], 'yNAP1': [2323], '(yNap1c)': [2324], 'sufficient': [2326, 3786], 'bind': [2328, 3727], 'solution': [2333], 'well': [2335, 3592, 3613], 'components': [2344], '(Fujii-Nakata': [2345], '1992;': [2348, 4021], 'Park': [2349, 4038, 4111], '2005).': [2352], 'replacement': [2359, 2382, 3422], 'individual': [2362, 2445, 2715], 'yNap1c': [2366, 2716, 4119], 'homodimer': [2367, 2825], 'heterodimer': [2372, 2761, 2861, 2880, 2935, 3132, 3161], '2B': [2374], 'C)': [2376], 'without': [2383], 'unambiguously': [2385], 'presence': [2388, 2637, 4169, 4191], 'missing': [2391], 'fold': [2396], 'clearly': [2399], 'visible': [2400], '(Figs': [2401, 2901, 2928], '2': [2402, 2554, 2902, 3051, 3256, 3587, 3682, 3826, 3945, 4358], 'EV1A': [2404], 'B).': [2406], 'Recent': [2407], 'method': [2408, 4064], 'advances': [2409], 'allow': [2410], 'low-resolution': [2411, 2417, 2692, 2731], 'refinement': [2412, 2442], 'improvement': [2414], 'model': [2418], 'electron': [2420, 2622, 4209], 'density': [2421, 2623], 'map': [2422, 2624], 'deriving': [2424], 'deformable': [2425], 'elastic': [2426], 'network': [2427], '(DEN)': [2428], 'restraints': [2429], 'known': [2431], 'high-resolution': [2432], 'models': [2433], '(Schroder': [2434], '2010).': [2437], 'Parameter': [2438], 'optimization': [2439], 'DEN': [2441], 'covered': [2443], '510': [2444], 'computations': [2446], 'allowed': [2448], 'us': [2449], 'reduce': [2451], 'Rfree': [2453], '0.31': [2455], 'while': [2456], 'maintaining': [2457], 'good': [2460], 'coordinate': [2461], 'accuracy': [2462], '(Table': [2463, 2790], 'EV1).': [2464, 2791], '2.': [2466, 2617], 'Domain': [2473], 'architecture': [2474], 'yNap1,': [2476, 2982, 3016, 4151], 'H2A,': [2477, 3045, 3098], 'H2B.': [2479], 'Histone': [2481], 'region': [2483, 2493, 2627, 2978, 3022, 3050, 3443, 3584, 3782], '(HBR1': [2484, 3588], 'HBR2)': [2486, 3590], '(NBR1': [2494], 'NBR2)': [2496], 'indicated.': [2500, 3618], 'Regions': [2501], 'shown': [2507, 2560, 2567, 3575], '(IF1': [2508], 'IF2).': [2510], 'Ribbon': [2511, 4412], 'view': [2512, 2548, 4392, 4404, 4413, 4426], 'asymmetric': [2515, 2781, 4262], 'crystallographic': [2516, 2782, 4261], 'containing': [2518, 3036, 3133, 3797, 3845, 4268], '(yNap1c2–H2AΔ14–H2BΔ28)6': [2520], 'clarity,': [2523], 'only': [2524, 2757], 'layer': [2525, 2553, 4280], '1': [2526, 2533, 2979, 3585, 4356], 'shown.': [2531, 2651, 3563], 'Layer': [2532], 'contains': [2534, 3235, 3259], 'three': [2535, 2949, 4269], 'protomers': [2536, 4270, 4319, 4336, 4395, 4415], 'A–C': [2537], 'related': [2540, 3511, 4283], 'perpendicular': [2543], 'non-crystallographic': [2544, 4299], 'dyads': [2545, 4300], '().': [2546], 'Side': [2547], 'complex.': [2551, 2729, 3166], 'omitted': [2555], 'panel': [2557, 3303], '(B)': [2558, 2638], 'gray.': [2562], 'green': [2569], 'yellow,': [2571], 'red,': [2574], 'blue.': [2578], 'EV1.': [2582, 2606], 'View': [2583, 2660], 'labeling': [2590], 'secondary': [2592], 'elements.': [2594], 'Click': [2599, 3523], 'here': [2600, 3524], 'expand': [2602, 3526], 'figure.': [2604, 3338, 3528], 'DNA–H2A–H2B': [2607], 'electrostatics': [2610, 2671, 2915], 'complexRelated': [2614], 'A,': [2618], 'B.': [2619], '2F0–Fc': [2620], 'omit': [2621], 'contoured': [2630], '1σ': [2632], 'absence': [2634, 4122], '(A)': [2635], 'H2A/H2B': [2640], 'ribbon': [2642, 2668, 4391], 'representation.': [2643, 2669], 'Similar': [2644, 3556], 'views': [2645, 3557], '2A–C': [2649], 'C–E.': [2652], 'F.': [2659], 'ternary': [2663], 'APBS-calculated': [2670], '(−7': [2672], 'kT': [2673], '+7': [2675], 'kT)': [2676], 'surface.': [2682], 'G.': [2683], 'HBR1.': [2684, 3547], 'H.': [2685], 'HBR2.': [2686, 3546], 'crystals': [2696, 4148], 'may': [2697], 'reflective': [2699], 'yNap1c2–H2A–H2B': [2706, 2777, 4257, 4388], 'solution;': [2709], 'however,': [2710], 'availability': [2712], 'effectively': [2720], 'atomic-resolution': [2722], 'details': [2723], 'Previous': [2730], 'hydrogen–deuterium': [2732], 'exchange': [2733], 'experiments': [2734], 'suggested': [2735], 'accommodates': [2740], 'copies': [2742, 2774, 4254], 'tetrameric': [2747], 'conformation': [2748], "(D'Arcy": [2749], '2013).': [2752], 'Instead,': [2753], 'found': [2755], 'accommodated': [2764], 'Six': [2773], 'form': [2779, 4264], 'unit,': [2783], 'belong': [2785], 'space': [2787], 'group': [2788], 'P21': [2789], 'arranged': [2796], 'antiparallel': [2799], 'fashion': [2800], 'globular': [2804], 'domains': [2805], 'positioned': [2807, 2937], '2006).': [2817], 'concave': [2819, 2922], 'face': [2820], 'dome-shaped': [2823], 'constitutes': [2826], 'site': [2829], 'protein–protein': [2835], 'interface': [2836, 3010, 3033, 3128, 3399, 3596, 3870, 3889, 4143, 4157, 4423], 'mediated': [2838], 'subunits': [2842], 'almost': [2844], 'exclusively': [2845], '~761': [2854], 'Å2': [2855], 'area.': [2858], 'retains': [2862], 'configuration': [2864], 'seen': [2866], '2.5': [2882], 'double': [2886], 'helix,': [2887], 'arcs': [2889], 'around': [2890], 'them': [2891], 'along': [2892, 4292, 4315], 'long': [2894], 'axes': [2895], 'generate': [2897], '~140°': [2899], 'bend': [2900], 'EV1C–E).': [2904], 'mimics': [2911], '2D': [2929], 'EV1F–H).': [2931], 'As': [2932, 3698], 'electronegative': [2941], 'cavity,': [2943], 'majority': [2957, 3070], 'contacts': [2959, 2970, 3072, 3178, 3200], '3A).': [2963, 3146], 'center': [2966], 'heterodimer,': [2969], 'α1': [2974], '(HBR1)': [2980], 'spans': [2984], 'C-terminus': [2986], 'α4': [2988], 'N-terminus': [2991, 3056], 'α6': [2993], '(residues': [2994, 3005, 3065], '194–205)': [2995], '3B).': [2997], 'unique': [2999], 'helix': [3001, 3058, 3082, 3091, 3120], 'αN': [3002], '16–21)': [3006], 'complements': [3007], 'packing': [3012, 4135, 4142, 4156, 4364], 'against': [3013, 3047, 3964, 3987], 'E310': [3014], 'β-hairpin': [3027], '(β5–β6).': [3028], 'loops': [3038, 3140], 'L1': [3039, 3136], 'L2': [3043, 3076, 3139], 'packs': [3046], '(HBR2),': [3052], 'comprises': [3054], 'α8': [3059, 3083, 3121, 3211, 3439], 'monomer': [3064], '328–336)': [3066], '3C).': [3068], 'K75–R81': [3078], 'E328–E336': [3080], 'yNap1.': [3085, 3123, 3213], 'dipole': [3088], 'moments': [3089], 'α2': [3092], 'α3': [3096], 'directed': [3101], 'phosphodiester': [3105], 'backbone': [3106], 'capped': [3113], 'negatively': [3116], 'charged': [3117, 3955], 'patch': [3118], 'third': [3125], 'does': [3141], '3.': [3148, 3535], 'Interactions': [3149], 'Overview': [3162], 'yNap1c2–H2AΔ14–H2BΔ28': [3165], 'Residues': [3167, 3191, 3488], 'R17,': [3168], 'R20,': [3169], 'R29,': [3170], 'R32,': [3171], 'R35,': [3172], 'K36': [3174], 'make': [3177, 3198], 'HBR1': [3182, 3232, 3254, 3265, 3398, 3608, 3680, 3943], 'D201,': [3187], 'D205,': [3188], 'E310.': [3190], 'K75,': [3192], 'R77,': [3193], 'R81': [3195], 'polar': [3199], 'HBR2': [3203, 3244, 3411, 3442, 3610], 'E332,': [3206, 3250], 'D333,': [3207, 3251, 3418], 'E339': [3209], 'GST-pulldown': [3216, 3379], 'HBR': [3225, 3276, 3355, 3458, 3480, 3491], 'binding.': [3229], 'mutant-labeled': [3231, 3264], '(lane': [3233, 3245, 3257, 3268], '6)': [3234], 'triple': [3237, 3248, 3391, 3416, 3814], 'mutation': [3238, 3420, 3778, 4153], 'D201R,': [3239], 'D205R,': [3240, 3393], 'E310R,': [3242], '12),': [3246], 'mutations': [3249, 3395, 3655, 3750, 3799, 3832, 3848, 3906], 'E336.': [3253], '13)': [3258], 'all': [3260], 'six': [3261, 3275], 'mutations.': [3262], '2A': [3267], '14)': [3269], 'alanine': [3271, 3464], 'replacements': [3272], 'residues.': [3277, 3570], 'Top': [3278], 'panel:': [3279, 3282, 3293], 'Bound.': [3280], 'Bottom': [3281, 3292], 'Input.': [3283], 'Nap1–histone': [3287, 4238], 'interaction': [3288], 'mutation.': [3291], 'Inputs': [3294], 'coexpressed': [3297], '(soluble': [3299], 'extract)': [3300], 'top': [3302], 'material': [3305], 'glutathione': [3309, 3691], 'affinity': [3310, 3692], 'column': [3311], 'analyzed': [3313], 'SDS–PAGE': [3315], 'Coomassie': [3317], 'staining.': [3318], 'Controls': [3319], 'input': [3321], '(bottom)': [3322], '(top)': [3325], 'fractions.': [3326], 'EV2.': [3330, 3530], 'available': [3334, 4146], 'Data': [3340], '3': [3343], '[embj201694105-sup-0005-SDataFig3.pdf]': [3344], 'assess': [3350, 3736], 'formation,': [3360], 'created': [3362], 'mutants': [3363, 3984], 'targeting': [3364], 'conserved,': [3365], 'surface-exposed': [3366], 'tested': [3374, 3651, 3963, 3986], '(data': [3381], 'summarized': [3383], 'Table': [3386], 'S2).': [3387], 'Single,': [3388], 'double,': [3389, 3414], '(D201R,': [3392], 'E310R)': [3394], 'did': [3400, 3446, 3704, 3725, 3878], 'abolish': [3402, 3448, 3789, 3881], '3D,': [3406, 3452, 3472, 3971], 'lanes': [3407, 3453, 3473, 3775, 3809, 3842], '1–6).': [3408], 'interface,': [3412, 3747], 'single,': [3413], '(E332,': [3417], 'E336)': [3419], '319–337': [3425], 'Gly': [3429], 'amino': [3430, 3578, 3764], 'acid': [3431, 3579, 3765], 'residue,': [3432], 'modification': [3434], 'ablating': [3435], 'segment': [3437], '(ΔHBR2),': [3444], '7–12).': [3454], 'when': [3456, 3982], 'contained': [3460], 'reversal': [3462], 'mutations,': [3465], 'observed': [3467], 'reduced': [3468, 3804, 3838, 3855, 3876], '13–15).': [3474], 'conclude': [3477], 'contribute': [3482], 'synergistically': [3483], 'humans': [3500], 'Vps75': [3504], 'SET': [3506], 'structurally': [3510], 'evolved': [3515], 'different': [3516, 4073], 'modes': [3517], 'EV2A–D).': [3522], 'Sequence': [3531], 'conservationRelated': [3532], 'color-coded': [3540], 'according': [3541], 'sequence': [3544, 3621], 'conservation.': [3545], 'higher': [3549], 'conservation,': [3551], 'darker': [3553], 'color.': [3555], '3A–C': [3561], 'Nap1-like': [3564], 'chaperons': [3566], 'highlighted': [3568, 3601], 'Secondary': [3571], 'elements': [3573], 'above': [3576, 4345], 'sequences.': [3580], '(IF1)': [3597], 'green.': [3603], 'Key': [3604], '(●)': [3611], 'IF1': [3615, 4401, 4409], '(▵)': [3616], 'structure-based': [3620], 'alignment': [3622], 'Pymol': [3626], '(Schrodinger,': [3627], '2010)': [3628], 'ClustalW': [3630], '(Thompson': [3631], '1994).': [3634], 'generated': [3638], 'Espript': [3640], '(Gouet': [3641], '2003).': [3644], 'ability': [3658], 'copurify': [3660, 3687], 'overexpressed': [3661], 'E.': [3666], 'coli': [3667], 'GST-yNap1': [3669], '3E,': [3673, 3732, 3774, 3792, 3808, 3841, 3859, 3902, 3976], 'lane': [3674, 3696, 3717, 3733, 3793, 3860, 3903, 3972, 3977, 3992], '1)': [3675, 3718], 'mutant': [3683, 3816, 3823, 3863, 3942, 3950, 3962], 'resin': [3693, 3730], '3F,': [3695, 3716, 3991], '2).': [3697], 'expected,': [3699], 'expression': [3700], 'alone': [3703, 3721, 3783, 4087], 'show': [3706], 'position': [3712], 'expressed': [3723], '14).': [3734], 'side': [3744], 'introduced': [3749], 'NBR1': [3756, 3768, 3801, 3815, 3824, 3951], 'NBR2': [3758, 3770, 3781, 3803, 3831], 'H2A.': [3760], 'Mutation': [3761], '2–6)': [3776], 'fully': [3788, 3880], '11).': [3794], 'variants': [3796], 'several': [3798], '7–13).': [3810], 'particular,': [3812], '(R30E,': [3817], 'R33E,': [3818], 'K37E)': [3819], 'sextuple': [3822, 3941, 3949], 'K75E,': [3833], 'R78E,': [3834], 'R82E': [3835], 'drastically': [3837], '12–13).': [3843], 'Variants': [3844], 'combinations': [3846], 'greatly': [3854], '7–9).': [3861], 'designed': [3864, 3913], 'disrupt': [3866], 'IF2': [3871], '(N94E,': [3872], 'G98D,': [3873], 'R99D,': [3874], 'T101D)': [3875], 'binding,': [3883], 'through': [3887, 4324], 'formation': [3895], 'avidity': [3900], '10).': [3904], 'decrease': [3915], 'do': [3919], 'indeed': [3920], 'weaken': [3921], 'yNap1–histone': [3923], 'interaction.': [3925], 'charge-swap': [3927], 'experiment': [3928], 'proof': [3931], 'validity': [3934], 'interface:': [3937], '2,': [3953], 'interfacial': [3956], 'swapped.': [3959], 'counterpart': [3967], 'loses': [3968], '10': [3973], '13),': [3978], 'restored,': [3981], '3).': [3993], 'various': [4001, 4104], 'orthologs': [4003], 'occurs': [4004], 'under': [4008], 'physiological': [4009], 'conditions': [4010], '(Ishimi': [4013], '1983,': [4016], '1984;': [4017], 'Fujii-Nakata': [4018], 'Chang': [4022], '1997;': [4025], 'Mosammaparast': [4026], 'McBryant': [4030], 'Peersen,': [4032], 'Toth': [4034], '2005;': [4037, 4181], '2008;': [4041], 'Noda': [4042, 4182], 'Newman': [4046], 'biological': [4051, 4235], 'so': [4057], 'far': [4058], 'unclear.': [4060], 'Depending': [4061], 'ionic': [4068], 'strength,': [4069], 'concentration': [4071], 'used,': [4072], 'states': [4075], 'been': [4080], 'reported.': [4081], 'size-exclusion': [4083], 'chromatography,': [4084], 'purified': [4085], 'elutes': [4093], 'broad': [4096], 'indicative': [4098], 'heterogeneous': [4101, 4197], 'mixtures': [4102], 'oligomeric': [4105], 'species': [4106], '(Mosammaparast': [4107], 'extended': [4127], 'β5–β6': [4128], 'hairpin': [4129], 'same': [4141], 'reduces': [4158], 'similar': [4174], 'propensities': [4175], 'oligomerize': [4177], '(Toth': [4178], '2011).': [4185], 'H3–H4': [4195], 'forms': [4196], 'ring-like': [4198], 'particles': [4199], '0.5–1.0': [4202], 'MDa': [4203], 'visualized': [4207], 'microscopy': [4210], '(Newman': [4211], 'compositional': [4217], 'heterogeneity': [4218], 'made': [4220], 'it': [4221], 'difficult': [4222], 'ascertain': [4224], 'exact': [4226], 'structural': [4232], 'oligomerization.': [4239, 4251], 'asked': [4242], 'whether': [4243], 'our': [4244], 'relevant': [4248], '6': [4253], 'layers,': 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