Publication Information

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711, 723, 761, 796, 807, 820, 979], 'report': [245], 'ChIP-SICAP,': [246], 'a': [247, 358, 420, 511, 515, 525, 649, 672, 741, 863, 935, 1097, 1144, 1191, 1261, 1319, 1359, 1397, 1459, 1482, 1558, 1612, 1865], 'powerful': [248], 'tool': [249], 'proteome': [254, 1697, 1736], 'combining': [256, 1552], 'immunoprecipitation,': [258, 595], 'selective': [259, 868, 1047, 1493, 1517, 1928], 'isolation': [260, 869, 894, 1048, 1520, 1929], 'chromatin-associated': [262, 377, 440, 507, 871, 1050, 1522, 1770, 1804, 1931], 'proteins': [263, 388, 508, 581, 635, 690, 816, 872, 897, 1051, 1087, 1141, 1257, 1899], 'mass': [265, 423, 812, 1342, 1674, 1895, 1951], 'spectrometry.': [266, 1675], 'Chromatin': [267, 343], 'dynamic': [270, 347, 1352], 'macromolecular': [271], 'complex': [272, 1431], 'DNA,': [274, 889], 'histones': [275], 'regulatory': [277, 335, 1581, 1665], 'proteins,': [278, 449, 735, 1272, 1523], 'its': [280, 754, 1617, 1738], 'structure': [281, 302, 344], 'critical': [285], 'all': [287, 549, 824], 'DNA-dependent': [288], 'processes,': [289], 'including': [290, 1210], 'transcription,': [291], 'DNA': [292, 295, 307, 332, 363, 447, 605, 834, 1053, 1236, 1259, 1529], 'replication': [293, 1237], 'repair.': [296], 'The': [297, 685, 877, 908, 1150, 1373, 1507, 1732, 1863, 1945], 'fundamental': [298], 'feature': [299, 1076], 'involves': [303, 879], 'wrapping': [305], 'around': [308], 'nucleosomes,': [309], 'compacted': [310], 'varying': [312], 'degrees': [313], 'folding': [315], 'into': [316], 'higher': [317, 1384, 1435], 'order': [318, 1367], 'structures': [320], 'degree': [323], 'compaction': [325], 'in': [326, 352, 362, 396, 503, 546, 564, 624, 648, 704, 716, 753, 835, 951, 1001, 1032, 1176, 1182, 1260, 1265, 1300, 1337, 1366, 1388, 1429, 1486, 1557, 1572, 1584, 1619, 1994], 'turn': [327], 'affects': [328], 'accessibility': [330], 'hence': [339], 'modulates': [340], 'gene': [341, 393, 516, 1580, 1989], 'expression.': [342], 'highly': [346, 602], 'can': [349, 468, 494, 557, 1117, 1283, 1423], 'be': [350, 662, 1284, 1364, 1425, 1569], 'remodelled': [351], 'response': [353], 'diverse': [355, 1579], 'stimuli': [356], 'through': [357], 'combination': [359, 625, 936], 'changes': [361, 502], 'methylation': [364], 'histone': [366, 463, 1669], 'post-translational': [367, 464], 'modifications,': [368], 'as': [369, 371, 451, 470, 764, 791, 1190, 1454], 'well': [370], 'via': [372], 'recruitment': [374], 'complexes.': [379, 1809, 1905], 'Understanding': [380], 'molecular': [382], 'between': [384, 1307, 1538], 'chromatin-interacting': [387, 734], 'key': [390], 'regulation,': [394], 'both': [395, 1256, 1583], 'physiological': [397], 'disease': [399], 'contexts': [400], 'depends,': [402], 'inter': [403], 'alia,': [404], 'upon': [405], 'having': [406], 'sensitive': [407], 'methods': [408, 427, 478, 697, 823, 1449], 'accurate': [411], 'measurement': [412, 461], 'proteome.': [416], 'years,': [419], 'number': [421], 'spectrometry': [424, 813, 1871, 1896, 1952], '(MS)-based': [425], 'proteomic': [426, 1395, 1956], 'have': [428, 587, 598, 698, 779, 1334], 'been': [429, 699, 780], 'developed': [430, 781, 972], 'allow': [432, 891], 'unbiased': [433], 'comprehensive': [435], 'characterization': [436], 'proteins.': [441, 645, 1932], 'This': [442, 491, 618, 961, 1105, 1180, 1405, 1979], 'includes': [443], 'detection': [445, 1382, 1416], 'binding': [448, 522, 1275], 'such': [450, 790, 1453], 'transcription': [452, 656, 1807], 'factors,': [453, 1169], 'regulators': [455], 'epigenetic': [457], 'modifiers': [458], 'modification': [465, 1670], 'patterns,': [466], 'which': [467, 845, 874, 1002, 1029, 1143], 'act': [469], 'determinants': [471], 'binding.': [474], 'Most': [475], 'these': [477], 'rely': [479], 'on': [480, 747, 898, 1014, 1107, 1126, 1544], 'initial': [482], 'enrichment': [483, 784], 'components': [486], 'immunoprecipitation': [489, 550, 811, 1040, 1894], '(ChIP).': [490], 'pre-enrichment': [492], 'step': [493, 828, 1465], 'provide': [495], 'sensitivity': [497], 'required,': [498], 'either': [499, 586, 752, 1008, 1311], 'identify': [501], 'levels': [505, 687, 850, 1357], 'present': [509, 613, 1428], 'at': [510, 614, 1207], 'specific': [512, 526, 893, 1512, 1624], 'locus': [513], '(e.g.': [514], 'promoter),': [517], 'or': [518, 528, 596, 607, 756, 1012, 1313, 1545], 'determine': [520], 'sites': [523, 1276], 'protein,': [527], 'complex,': [530], 'over': [531], 'entire': [533], 'genome': [534], 'compare': [537], 'how': [538], 'may': [540, 744], 'vary': [541], 'under': [542, 841], 'conditions.': [544], 'However,': [545, 1125], 'common': [547], 'with': [548, 626, 643, 885, 998, 1031, 1203, 1346, 1403, 1433, 1466, 1505, 1525], 'related': [552, 1339], '“pull-down”': [553], 'methods,': [554], 'ChIP-based': [555], 'assays': [556], 'suffer': [558], 'from': [559, 578, 1119, 1286], 'lack': [560], 'selectivity,': [562], 'resulting': [563, 1380], 'low': [565, 610], 'signal': [566], 'background': [568, 574, 620, 689, 849], 'noise.': [569], 'case,': [572], 'noise': [575], 'results': [576], 'predominantly': [577], 'contaminating': [580], 'routinely': [582], 'detected': [583], 'because': [584], 'they': [585], 'high': [588, 616, 619, 686], 'affinity': [589, 599, 611, 783, 1869], 'reagents': [592], 'used': [593, 926], 'else': [597], 'negatively': [603], 'charged': [604], 'backbone,': [606], 'are': [608, 692, 1007, 2035], 'simply': [609], 'binders': [612], 'very': [615, 1320, 1483], 'abundance.': [617], 'particularly': [622], 'problematic': [623], 'fact': [628], 'that': [629, 691, 737, 1080, 1116, 1170, 1218, 1249, 1309, 1361, 1422, 1564, 1663], 'abundance': [631, 653, 670, 1356, 1385], 'many': [633, 637], 'chromatin-binding': [634], 'orders': [638], 'magnitude': [640], 'lower': [641], 'compared': [642, 997], 'other': [644, 999, 1128, 1392], 'For': [646, 1456], 'example,': [647, 1457], 'factor': [657, 1808], 'c-Myc': [658], 'was': [659, 675, 962, 1156, 1199], 'estimated': [660], '~2,000': [663], 'copies': [664, 678], 'per': [665, 679], 'cell,': [666], 'while': [667], 'average': [669], 'ribosomal': [673], '~3': [676], 'million': [677], 'cell': [680, 1234, 1735], '(Hukelmann': [681], '2016).': [684, 821], 'consistently': [693], 'identified': [694, 1667, 2025], 'immunoprecipitation-based': [696], 'previously': [700], 'documented,': [701], 'example': [703], '“protein': [706], 'frequency': [707, 1614], 'library”': [708], '(Boulon': [709], '2010)': [712], 'and,': [713], 'recently,': [715], 'so': [718], 'called': [719], '“CRAPome”': [720], '(Mellacheruvu': [721], '2013).': [724], 'Another': [725], 'limitation': [726, 1377], 'existing': [728], 'approaches,': [729, 1349], 'especially': [730], 'relevant': [731], 'when': [732, 1427], 'analysing': [733, 1160, 1325], 'interactors': [739, 1295], 'given': [742], 'differ,': [745], 'depending': [746], 'whether': [748], 'chromatin-bound': [755], 'soluble': [757, 1806], 'state': [758, 1303], '(Li': [759], '2015).': [762], 'While': [763, 1316], 'yet': [765], 'there': [766], 'no': [768], 'accepted': [769], 'gold': [770], 'standard': [771], 'established': [772], 'proteomes,': [775], 'several': [776, 1511], 'useful': [777, 1321, 1484], 'methodologies': [778], 'analysis': [786, 989, 1139, 1554, 1577, 1698, 1902], 'complexes,': [789, 883, 950], 'modified': [792], 'ChIP': [793, 880, 1949], '(Lambert': [794], '2009),': [797], 'proteomics': [799, 995, 1553, 1764], '(ChroP)(Soldi': [800], 'Bonaldi,': [802], '2014),': [803, 980], 'ChIP-MS': [804], '(Engelen': [805], '2015)': [808], 'rapid': [810], 'endogenous': [815, 1086, 1898], '(RIME)': [817, 1900], '(Mohammed': [818], 'These': [822], 'share': [825], 'starting': [827], 'crosslinking': [830, 914], 'cellulo': [836, 1033], 'facilitate': [838], 'recovery': [840, 1254], 'harsh': [842], 'extraction': [843], 'conditions,': [844], 'helps': [846, 1406], 'reduce': [848, 920, 1408], 'co-isolated': [852], 'contaminants.': [853], 'work,': [857], '(2016)': [861, 1480, 1731, 1892, 1921], 'describe': [862], 'new': [864, 1192], 'method': [865, 878, 1155, 1247, 1509], '(SICAP),': [873], 'improves': [875, 993], 'selectivity.': [876], 'DNA-protein': [882], 'combined': [884, 1402], 'biotin': [886], 'tagging': [887], 'DNA-bound': [896, 949, 1004, 1302], 'streptavidin': [899, 946, 959], 'beads,': [900, 1016], 'followed': [901, 1036], 'MS-based': [903, 1348], 'identification': [905, 1084, 1184, 1269, 1496, 1622], '(Fig': [906], '1).': [907], 'use': [909], 'formaldehyde': [911, 1034], 'allows': [915, 1055, 1082, 1305, 1516], 'stringent': [916, 954], 'purification': [917, 1494], 'conditions': [918], 'non-specific': [921], 'background.': [922], 'Importantly,': [923], 'antibody': [925, 983, 1060, 1147], 'target': [928], 'bait': [930, 1298], 'removed': [933], 'using': [934, 968, 1215, 1458, 1699], 'reducing': [938], 'agents': [939], 'ionic': [941], 'detergents': [942], '(SDS),': [943], 'prior': [944, 1017, 1061, 1470], 'capture': [947], 'addition': [952, 1266], 'denaturing/high': [955], 'salt': [956], 'washes': [957], 'after': [958], 'purification.': [960], 'facilitated': [963], 'processing': [965, 1064], 'samples': [967], 'SP3': [970, 1063], 'protocol': [971], 'same': [975, 1288], 'laboratory': [976], '(Hughes': [977], 'thus': [981, 1413], 'avoiding': [982], 'contamination': [984], 'during': [985, 2040], 'subsequent': [987], 'MS': [988], 'step.': [990], 'Consequently,': [991], 'readout': [996], 'protocols': [1000], 'resolved': [1009], 'SDS–PAGE,': [1011], 'digested': [1013], 'LC-MS.': [1019], 'Figure': [1020], '1.': [1021], 'SICAP': [1022, 1331], 'methodSchematic': [1023], 'representation': [1024], 'ChIP-SICAP': [1027, 1078, 1154, 1246, 1508, 1566], 'workflow,': [1028], 'starts': [1030], 'crosslinking,': [1035], 'sonication': [1038], '(ChIP),': [1043], 'then': [1044], '(SICAP).': [1052], 'biotinylation': [1054], 'removal': [1057], 'LC-MS/MS': [1066], 'ChIP-seq': [1068, 1556], 'analyses.': [1069], 'Download': [1070, 1072], 'figure': [1071], 'PowerPoint': [1073], 'An': [1074, 2013], 'important': [1075], 'it': [1081, 1130, 1250, 1317, 1515, 1532, 1550], 'native': [1090], 'chromatin,': [1091, 1547], 'without': [1092], 'need': [1094], 'over-express': [1096], 'tagged': [1098, 1122], 'version': [1099], 'interest.': [1104], 'prevents,': [1106], 'one': [1109, 1441], 'hand,': [1110, 1129], 'some': [1111, 1335], 'potential': [1114], 'artefacts': [1115], 'arise': [1118], 'over-expression': [1120], 'baits.': [1124], 'limits': [1131], 'applicability': [1133], 'technique': [1136, 1332], 'high-quality,': [1145], '“ChIP-grade”,': [1146], 'available.': [1149], 'efficacy': [1151], 'elegantly': [1157], 'demonstrated': [1158], 'interaction': [1163, 1386, 1502, 1626], 'network': [1164], 'canonical': [1167], 'pluripotency': [1168, 1196, 1205, 1926], 'Oct4,': [1172], 'Sox2': [1173], 'Nanog,': [1175], 'mouse': [1177], 'ES': [1178], 'cells.': [1179], 'resulted': [1181], 'E3-ubiquitin': [1187], 'ligase,': [1188], 'Trim24,': [1189], 'component': [1193], 'network.': [1197], 'Trim24': [1198, 1220], 'shown': [1200], 'co-localize': [1202], 'markers': [1206], '813': [1208], 'enhancers,': [1209], '88': [1211], 'super-enhancers.': [1212], 'Knockdown': [1213], 'experiments': [1214], 'shRNA': [1216], 'showed': [1217], 'required': [1223], 'suppress': [1225], 'developmental': [1226], 'genes': [1227], 'maintain': [1230], 'expression': [1232, 1990, 2020], 'cycle,': [1235], 'Polycomb': [1239], 'components.': [1240], 'A': [1241, 1762, 2007], 'notable': [1242], 'advantage': [1243], 'permits': [1251], 'simultaneous': [1253], 'single': [1262, 1559], 'experiment.': [1263, 1560], 'Therefore,': [1264], 'co-localizing': [1271], 'interest': [1281], 'also': [1282, 1447], 'identified,': [1285], 'sample,': [1289, 1469], 'sequencing.': [1291, 2028], 'Moreover,': [1292], 'capturing': [1293], 'potentially': [1304], 'distinguishing': [1306], 'occur': [1310], 'on,': [1312], 'off,': [1314, 1546], 'chromatin.': [1315, 1506, 1959], 'represents': [1318], 'technical': [1322], 'advance': [1323], 'proteome,': [1328], 'inevitably,': [1329], 'does': [1333], 'limitations,': [1336], 'particular': [1338], 'spectrometric': [1343], 'readout.': [1344], 'As': [1345], 'most': [1347], 'wide': [1351], 'range': [1353], 'remains': [1358], 'problem': [1360], 'has': [1362], 'overcome': [1365], 'reliably': [1369], 'measure': [1370], 'low-abundance': [1371, 1420], 'species.': [1372], 'authors': [1374], 'recognize': [1375], 'preferential': [1381], 'partners': [1387], 'experiments.': [1390], 'types': [1393], 'analyses,': [1396], 'pre-fractionation': [1398, 1464], 'strategy': [1399, 1446], 'often': [1401], 'LC-MS/MS.': [1404], 'overall': [1409], 'sample': [1410], 'complexity': [1411], 'enhances': [1414], 'quantitation': [1418], 'species': [1421], 'otherwise': [1424], 'missed': [1426], 'extracts': [1432], 'much': [1434], 'abundant': [1436], 'peptides.': [1437], 'principle,': [1439], 'therefore,': [1440], 'could': [1442], 'envisage': [1443], 'applying': [1444], 'proteomics,': [1452], 'SICAP.': [1455], 'form': [1460], 'miniaturized,': [1462], 'on-tip': [1463], 'immunoprecipitated': [1468], 'LC–MS/MS.': [1472], 'Overall,': [1473], 'study': [1475], 'presents': [1481], 'improvement': [1485], 'methodological': [1488], 'toolbox': [1489], 'available': [1490], 'networks': [1503], 'associated': [1504], 'offers': [1510, 1533], 'advantages:': [1513], '(i)': [1514], 'reproducible': [1519], 'together': [1524], 'cognate,': [1527], 'element,': [1530], '(ii)': [1531], 'possibility': [1535], 'distinguish': [1537], 'taking': [1541], 'place': [1542], 'either,': [1543], '(iii)': [1549], 'facilitates': [1551], 'We': [1561], 'therefore': [1562], 'anticipate': [1563], 'approach': [1567, 1765, 1947, 2014], 'will': [1568], 'widely': [1570], 'adopted': [1571], 'future': [1573], 'studies': [1574], 'networks,': [1582], 'human': [1585], 'cells': [1586], 'model': [1588], 'organisms.': [1589], 'References': [1590], 'Boulon': [1591], 'S,': [1592, 1686, 1835], 'Ahmad': [1593], 'Y,': [1594, 1788], 'Trinkle-Mulcahy': [1595], 'L,': [1596, 1643, 1754], 'Verheggen': [1597], 'C,': [1598, 1883, 1916], 'Cobley': [1599], 'A,': [1600, 1756, 1786, 1847, 1849], 'Gregor': [1601], 'P,': [1602], 'Bertrand': [1603], 'E,': [1604, 1637], 'Whitehorn': [1605], 'M,': [1606, 1857, 1941], 'AI': [1608], '(2010)': [1609], 'Establishment': [1610], 'library': [1615], 'application': [1618], 'reliable': [1621], 'partners.': [1627], 'Mol': [1628, 1703, 1773, 1810, 1933], 'Cell': [1629, 1774, 1934], 'Proteomics': [1630, 1775], '9:': [1631], '861–879CrossrefCASPubMedWeb': [1632], 'Science®Google': [1634, 1681, 1711, 1749, 1818, 1878, 1911, 1938], 'Scholar': [1635, 1682, 1712, 1750, 1778, 1819, 1879, 1912, 1939, 1965], 'Engelen': [1636], 'Brandsma': [1638], 'JH,': [1639], 'Moen': [1640], 'MJ,': [1641], 'Signorile': [1642], 'Dekkers': [1644], 'DHW,': [1645], 'Demmers': [1646], 'J,': [1647, 1784, 1796], 'Kockx': [1648], 'CEM,': [1649], 'Ozgur': [1650], 'Z,': [1651, 1823], 'van': [1652, 1655], 'Ijcken': [1653], 'WFJ,': [1654], 'den': [1656], 'Berg': [1657], 'DLC,': [1658], 'Poot': [1659], 'RA': [1660], '(2015)': [1661, 1799], 'Proteins': [1662], 'bind': [1664], 'regions': [1666], 'immunoprecipitations': [1672], 'Nat': [1676, 1744, 1873, 1906], 'Commun': [1677], '6:': [1678], '7155CrossrefPubMedWeb': [1679], 'Hughes': [1683], 'CS,': [1684], 'Foehr': [1685], 'Garfield': [1687], 'DA,': [1688], 'Furlong': [1689], 'EE,': [1690], 'Steinmetz': [1691], 'LM,': [1692], 'J': [1694, 1798, 1920, 1960], '(2014)': [1695, 1944], 'Ultrasensitive': [1696], 'paramagnetic': [1700], 'bead': [1701], 'technology.': [1702], 'Syst': [1704, 1811], 'Biol': [1705, 1812], '10:': [1706, 1875], '757Wiley': [1707], 'Online': [1708, 1815], 'LibraryPubMedWeb': [1709, 1816], 'Hukelmann': [1713], 'JL,': [1714], 'Anderson': [1715], 'KE,': [1716], 'Sinclair': [1717], 'LV,': [1718], 'Grzes': [1719], 'KM,': [1720], 'Murillo': [1721], 'AB,': [1722], 'Hawkins': [1723], 'PT,': [1724], 'Stephens': [1725], 'LR,': [1726], 'AI,': [1728], 'Cantrell': [1729], 'DA': [1730], 'cytotoxic': [1733], 'T': [1734, 1943], 'shaping': [1739], 'kinase': [1742], 'mTOR.': [1743], 'Immunol': [1745], '17:': [1746], '104–112CrossrefCASPubMedWeb': [1747], 'Lambert': [1751, 1826], 'J-P,': [1752, 1827], 'Mitchell': [1753], 'Rudner': [1755], 'Baetz': [1757], 'K,': [1758], 'Figeys': [1759], 'D': [1760], '(2009)': [1761], 'novel': [1763], 'discovery': [1768], 'networks.': [1772], '8:': [1776], '870–882CrossrefCASPubMedGoogle': [1777], 'Li': [1779, 1789, 1830], 'X,': [1780], 'Wang': [1781, 1783], 'W,': [1782, 1790], 'Malovannaya': [1785], 'Xi': [1787], 'Guerra': [1791], 'R,': [1792], 'Hawke': [1793], 'DH,': [1794], 'Qin': [1795], 'Chen': [1797], 'Proteomic': [1800], 'analyses': [1801], 'reveal': [1802], 'distinct': [1803], '11:': [1813, 1908], '775Wiley': [1814], 'Mellacheruvu': [1820], 'D,': [1821, 1851, 1853], 'Wright': [1822], 'Couzens': [1824], 'AL,': [1825], 'St-Denis': [1828], 'NA,': [1829], 'T,': [1831], 'Miteva': [1832], 'YV,': [1833], 'Hauri': [1834], 'Sardiu': [1836], 'ME,': [1837], 'Low': [1838], 'TY,': [1839], 'Halim': [1840], 'VA,': [1841], 'Bagshaw': [1842], 'RD,': [1843], 'Hubner': [1844], 'NC,': [1845], 'al-Hakim': [1846], 'Bouchard': [1848], 'Faubert': [1850], 'Fermin': [1852], 'Dunham': [1854], 'WH,': [1855], 'Goudreault': [1856], 'Lin': [1858], 'Z-Y': [1859], '(2013)': [1862], 'CRAPome:': [1864], 'contaminant': [1866], 'repository': [1867], 'purification-mass': [1870], 'data.': [1872], 'Meth': [1874], '730–736CrossrefCASPubMedWeb': [1876], 'Mohammed': [1880], 'H,': [1881], 'Taylor': [1882], 'Brown': [1884], 'GD,': [1885], 'Papachristou': [1886], 'EK,': [1887], 'Carroll': [1888], 'JS,': [1889], "D'Santos": [1890], 'CS': [1891], 'Rapid': [1893], 'Protocols': [1907], '316–326CrossrefCASPubMedWeb': [1909], 'MR,': [1914], 'Girardot': [1915], 'Sigismondo': [1917], 'G,': [1918], 'Expanding': [1922], 'circuitry': [1924], '64:': [1935], '624–635CrossrefCASPubMedWeb': [1936], 'Soldi': [1940], 'Bonaldi': [1942], 'ChroP': [1946], 'combines': [1948], 'dissect': [1954], 'locus-specific': [1955], 'landscapes': [1957], 'Vis': [1961], 'Exp': [1962], '86:': [1963], 'e51220Google': [1964], 'Previous': [1966], 'ArticleNext': [1967], 'Article': [1968, 1984], 'Read': [1969], 'MoreAbout': [1970], 'coverClose': [1972], 'modalView': [1973], 'large': [1974], 'imageVolume': [1975], '12,Issue': [1976], '11,November': [1977], '2016Cover:': [1978], "month's": [1980], 'cover': [1981], 'highlights': [1982], '“': [1985], 'Single‐cell': [1986], 'sequencing': [1987], 'maps': [1988], 'mutational': [1992], 'phylogenies': [1993], 'PDGF': [1995], 'EGF': [1997], 'driven': [1998], 'gliomas”': [1999], 'Sören': [2001], 'Müller,': [2002], 'S': [2003], 'John': [2004], 'Liu,': [2005], 'Daniel': [2006], 'Lim,': [2008], 'Aaron': [2009], 'Diaz': [2010], 'colleagues.': [2012], 'presented': [2016], 'mapping': [2018], 'single-cell': [2019], 'profiles': [2021], 'sequentially-acquired': [2023], 'mutations': [2024], 'exome': [2027], 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