A new class of disordered elements controls DNA replication through initiator self-assembly

Abstract

The initiation of DNA replication in metazoans occurs at thousands of chromosomal sites known as origins. At each origin, the Origin Recognition Complex (ORC), Cdc6, and Cdt1 co-assemble to load the Mcm2-7 replicative helicase onto chromatin. Current replication models envisage a linear arrangement of isolated origins functioning autonomously; the extent of inter-origin organization and communication is unknown. Here, we report that the replication initiation machinery of D. melanogaster unexpectedly undergoes liquid-liquid phase separation (LLPS) upon binding DNA in vitro. We find that ORC, Cdc6, and Cdt1 contain intrinsically disordered regions (IDRs) that drive LLPS and constitute a new class of phase separating elements. Initiator IDRs are shown to regulate multiple functions, including chromosome recruitment, initiator-specific co-assembly, and Mcm2-7 loading. These data help explain how CDK activity controls replication initiation and suggest that replication programs are subject to higher-order levels of inter-origin organization.

References 122

1. 1.

   Arias EE, Walter JC. PCNA functions as a molecular platform to trigger Cdt1 destruction and prevent re-replication. Nature Cell Biology. 2006;8:84-90.

   Not in our library10.1038/ncb1346

2. 2.

   Aumiller WM, Keating CD. Phosphorylation-mediated RNA/peptide complex coacervation as a model for intracellular liquid organelles. Nature Chemistry. 2016;8:129-137.

   Not in our library10.1038/nchem.2414

3. 3.

   Austin RJ, Orr-Weaver TL, Bell SP. Drosophila ORC specifically binds to ACE3, an origin of DNA replication control element. Genes & Development. 1999;13:2639-2649.

   Not in our library10.1101/gad.13.20.2639

4. 4.

   Balasov M, Huijbregts RP, Chesnokov I. Role of the Orc6 protein in origin recognition complex-dependent DNA binding and replication in Drosophila Melanogaster. Molecular and Cellular Biology. 2007;27:3143-3153.

   Not in our library10.1128/mcb.02382-06

5. 5.

   Baldinger T, Gossen M. Binding of Drosophila ORC proteins to anaphase chromosomes requires cessation of mitotic cyclin-dependent kinase activity. Molecular and Cellular Biology. 2009;29:140-149.

   Not in our library10.1128/mcb.00981-08

6. 6.

   Bell SP, Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature. 1992;357:128-134.

   Not in our library10.1038/357128a0

7. 7.

   Bleichert F, Botchan MR, Berger JM. Mechanisms for initiating cellular DNA replication. Science. 2017;355:eaah6317.

   Not in our library10.1126/science.aah6317

8. 8.

   Bleichert F, Leitner A, Aebersold R, Botchan MR, Berger JM. Conformational control and DNA-binding mechanism of the metazoan origin recognition complex. PNAS. 2018;115:E5906-E5915.

   Not in our library10.1073/pnas.1806315115

9. 9.

   Boeynaems S, Alberti S, Fawzi NL, Mittag T, Polymenidou M, Rousseau F, Schymkowitz J, Shorter J, Wolozin B, Van Den Bosch L, Tompa P, Fuxreiter M. Protein phase separation: a new phase in cell biology. Trends in Cell Biology. 2018;28:420-435.

   Not in our library10.1016/j.tcb.2018.02.004

10. 10.

    Bowers JL, Randell JC, Chen S, Bell SP. ATP hydrolysis by ORC catalyzes reiterative Mcm2-7 assembly at a defined origin of replication. Molecular Cell. 2004;16:967-978.

    Not in our library10.1016/j.molcel.2004.11.038

11. 11.

    Brangwynne CP, Eckmann CR, Courson DS, Rybarska A, Hoege C, Gharakhani J, Jülicher F, Hyman AA. Germline P granules are liquid droplets that localize by controlled dissolution/condensation. Science. 2009;324:1729-1732.

    Not in our library10.1126/science.1172046

12. 12.

    Brüne D, Andrade-Navarro MA, Mier P. Proteome-wide comparison between the amino acid composition of domains and linkers. BMC Research Notes. 2018;11:117.

    Not in our library10.1186/s13104-018-3221-0

13. 13.

    Cayrou C, Coulombe P, Vigneron A, Stanojcic S, Ganier O, Peiffer I, Rivals E, Puy A, Laurent-Chabalier S, Desprat R, Méchali M. Genome-scale analysis of metazoan replication origins reveals their organization in specific but flexible sites defined by conserved features. Genome Research. 2011;21:1438-1449.

    Not in our library10.1101/gr.121830.111

14. 14.

    Cayrou C, Coulombe P, Puy A, Rialle S, Kaplan N, Segal E, Méchali M. New insights into replication origin characteristics in metazoans. Cell Cycle. 2012;11:658-667.

    Not in our library10.4161/cc.11.4.19097

15. 15.

    Cayrou C, Ballester B, Peiffer I, Fenouil R, Coulombe P, Andrau JC, van Helden J, Méchali M. The chromatin environment shapes DNA replication origin organization and defines origin classes. Genome Research. 2015;25:1873-1885.

    Not in our library10.1101/gr.192799.115

16. 16.
    4D Visualization of replication foci in mammalian cells corresponding to individual replicons · 2016

    No notice
17. 17.

    Chen BC, Legant WR, Wang K, Shao L, Milkie DE, Davidson MW, Janetopoulos C, Wu XS, Hammer JA, Liu Z, English BP, Mimori-Kiyosue Y, Romero DP, Ritter AT, Lippincott-Schwartz J, Fritz-Laylin L, Mullins RD, Mitchell DM, Bembenek JN, Reymann AC, Böhme R, Grill SW, Wang JT, Seydoux G, Tulu US, Kiehart DP, Betzig E. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science. 2014;346:1257998.

    Not in our library10.1126/science.1257998

18. 18.

    Chesnokov I, Remus D, Botchan M. Functional analysis of mutant and wild-type Drosophila origin recognition complex. PNAS. 2001;98:11997-12002.

    Not in our library10.1073/pnas.211342798

19. 19.

    Chong PA, Vernon RM, Forman-Kay JD. RGG/RG motif regions in RNA binding and phase separation. Journal of Molecular Biology. 2018a;430:4650-4665.

    Not in our library10.1016/j.jmb.2018.06.014

20. 20.

    Chong S, Dugast-Darzacq C, Liu Z, Dong P, Dailey GM, Cattoglio C, Heckert A, Banala S, Lavis L, Darzacq X, Tjian R. Imaging dynamic and selective low-complexity domain interactions that control gene transcription. Science. 2018b;361:eaar2555.

    Not in our library10.1126/science.aar2555

21. 21.
    The fission yeast homologue of Orc4p binds to replication origin DNA via multiple AT-hooks · 1999

    Not checked
22. 22.

    Cook PR. The organization of replication and transcription. Science. 1999;284:1790-1795.

    Not in our library10.1126/science.284.5421.1790

23. 23.

    Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nature Reviews Genetics. 2001;2:292-301.

    Not in our library10.1038/35066075

24. 24.

    Davey NE, Van Roey K, Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ. Attributes of short linear motifs. Mol. BioSyst. 2012;8:268-281.

    Not in our library10.1039/c1mb05231d

25. 25.

    Drosophila 12 Genomes Consortium, Clark AG, Eisen MB, Smith DR, Bergman CM, Oliver B, Markow TA, Kaufman TC, Kellis M, Gelbart W, Iyer VN, Pollard DA, Sackton TB, Larracuente AM, Singh ND, Abad JP, Abt DN, Adryan B, Aguade M, Akashi H, Anderson WW, Aquadro CF, Ardell DH, Arguello R, Artieri CG, Barbash DA, Barker D, Barsanti P, Batterham P, Batzoglou S, Begun D, Bhutkar A, Blanco E, Bosak SA, Bradley RK, Brand AD, Brent MR, Brooks AN, Brown RH, Butlin RK, Caggese C, Calvi BR, Bernardo de Carvalho A, Caspi A, Castrezana S, Celniker SE, Chang JL, Chapple C, Chatterji S, Chinwalla A, Civetta A, Clifton SW, Comeron JM, Costello JC, Coyne JA, Daub J, David RG, Delcher AL, Delehaunty K, Do CB, Ebling H, Edwards K, Eickbush T, Evans JD, Filipski A, Findeiss S, Freyhult E, Fulton L, Fulton R, Garcia AC, Gardiner A, Garfield DA, Garvin BE, Gibson G, Gilbert D, Gnerre S, Godfrey J, Good R, Gotea V, Gravely B, Greenberg AJ, Griffiths-Jones S, Gross S, Guigo R, Gustafson EA, Haerty W, Hahn MW, Halligan DL, Halpern AL, Halter GM, Han MV, Heger A, Hillier L, Hinrichs AS, Holmes I, Hoskins RA, Hubisz MJ, Hultmark D, Huntley MA, Jaffe DB, Jagadeeshan S, Jeck WR, Johnson J, Jones CD, Jordan WC, Karpen GH, Kataoka E, Keightley PD, Kheradpour P, Kirkness EF, Koerich LB, Kristiansen K, Kudrna D, Kulathinal RJ, Kumar S, Kwok R, Lander E, Langley CH, Lapoint R, Lazzaro BP, Lee SJ, Levesque L, Li R, Lin CF, Lin MF, Lindblad-Toh K, Llopart A, Long M, Low L, Lozovsky E, Lu J, Luo M, Machado CA, Makalowski W, Marzo M, Matsuda M, Matzkin L, McAllister B, McBride CS, McKernan B, McKernan K, Mendez-Lago M, Minx P, Mollenhauer MU, Montooth K, Mount SM, Mu X, Myers E, Negre B, Newfeld S, Nielsen R, Noor MA, O'Grady P, Pachter L, Papaceit M, Parisi MJ, Parisi M, Parts L, Pedersen JS, Pesole G, Phillippy AM, Ponting CP, Pop M, Porcelli D, Powell JR, Prohaska S, Pruitt K, Puig M, Quesneville H, Ram KR, Rand D, Rasmussen MD, Reed LK, Reenan R, Reily A, Remington KA, Rieger TT, Ritchie MG, Robin C, Rogers YH, Rohde C, Rozas J, Rubenfield MJ, Ruiz A, Russo S, Salzberg SL, Sanchez-Gracia A, Saranga DJ, Sato H, Schaeffer SW, Schatz MC, Schlenke T, Schwartz R, Segarra C, Singh RS, Sirot L, Sirota M, Sisneros NB, Smith CD, Smith TF, Spieth J, Stage DE, Stark A, Stephan W, Strausberg RL, Strempel S, Sturgill D, Sutton G, Sutton GG, Tao W, Teichmann S, Tobari YN, Tomimura Y, Tsolas JM, Valente VL, Venter E, Venter JC, Vicario S, Vieira FG, Vilella AJ, Villasante A, Walenz B, Wang J, Wasserman M, Watts T, Wilson D, Wilson RK, Wing RA, Wolfner MF, Wong A, Wong GK, Wu CI, Wu G, Yamamoto D, Yang HP, Yang SP, Yorke JA, Yoshida K, Zdobnov E, Zhang P, Zhang Y, Zimin AV, Baldwin J, Abdouelleil A, Abdulkadir J, Abebe A, Abera B, Abreu J, Acer SC, Aftuck L, Alexander A, An P, Anderson E, Anderson S, Arachi H, Azer M, Bachantsang P, Barry A, Bayul T, Berlin A, Bessette D, Bloom T, Blye J, Boguslavskiy L, Bonnet C, Boukhgalter B, Bourzgui I, Brown A, Cahill P, Channer S, Cheshatsang Y, Chuda L, Citroen M, Collymore A, Cooke P, Costello M, D'Aco K, Daza R, De Haan G, DeGray S, DeMaso C, Dhargay N, Dooley K, Dooley E, Doricent M, Dorje P, Dorjee K, Dupes A, Elong R, Falk J, Farina A, Faro S, Ferguson D, Fisher S, Foley CD, Franke A, Friedrich D, Gadbois L, Gearin G, Gearin CR, Giannoukos G, Goode T, Graham J, Grandbois E, Grewal S, Gyaltsen K, Hafez N, Hagos B, Hall J, Henson C, Hollinger A, Honan T, Huard MD, Hughes L, Hurhula B, Husby ME, Kamat A, Kanga B, Kashin S, Khazanovich D, Kisner P, Lance K, Lara M, Lee W, Lennon N, Letendre F, LeVine R, Lipovsky A, Liu X, Liu J, Liu S, Lokyitsang T, Lokyitsang Y, Lubonja R, Lui A, MacDonald P, Magnisalis V, Maru K, Matthews C, McCusker W, McDonough S, Mehta T, Meldrim J, Meneus L, Mihai O, Mihalev A, Mihova T, Mittelman R, Mlenga V, Montmayeur A, Mulrain L, Navidi A, Naylor J, Negash T, Nguyen T, Nguyen N, Nicol R, Norbu C, Norbu N, Novod N, O'Neill B, Osman S, Markiewicz E, Oyono OL, Patti C, Phunkhang P, Pierre F, Priest M, Raghuraman S

    Not in our library10.1038/nature06341

26. 26.

    Duzdevich D, Warner MD, Ticau S, Ivica NA, Bell SP, Greene EC. The dynamics of eukaryotic replication initiation: origin specificity, licensing, and firing at the single-molecule level. Molecular Cell. 2015;58:483-494.

    Not in our library10.1016/j.molcel.2015.03.017

27. 27.

    Elbaum-Garfinkle S, Kim Y, Szczepaniak K, Chen CC, Eckmann CR, Myong S, Brangwynne CP. The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics. PNAS. 2015;112:7189-7194.

    Not in our library10.1073/pnas.1504822112

28. 28.

    Evrin C, Clarke P, Zech J, Lurz R, Sun J, Uhle S, Li H, Stillman B, Speck C. A double-hexameric MCM2-7 complex is loaded onto origin DNA during licensing of eukaryotic DNA replication. PNAS. 2009;106:20240-20245.

    Not in our library10.1073/pnas.0911500106

29. 29.

    Evrin C, Fernandez-Cid A, Zech J, Herrera MC, Riera A, Clarke P, Brill S, Lurz R, Speck C. In the absence of ATPase activity, pre-RC formation is blocked prior to MCM2-7 hexamer dimerization. Nucleic Acids Research. 2013;41:3162-3172.

    Not in our library10.1093/nar/gkt043

30. 30.
    Identification and Characterization of Saccharomyces cerevisiae Cdc6 DNA-binding Properties · 2000

    Not checked
31. 31.

    Feric M, Vaidya N, Harmon TS, Mitrea DM, Zhu L, Richardson TM, Kriwacki RW, Pappu RV, Brangwynne CP. Coexisting liquid phases underlie nucleolar subcompartments. Cell. 2016;165:1686-1697.

    Not in our library10.1016/j.cell.2016.04.047

32. 32.

    Findeisen M, El-Denary M, Kapitza T, Graf R, Strausfeld U. Cyclin A-dependent kinase activity affects chromatin binding of ORC, Cdc6, and MCM in egg extracts of xenopus laevis. European Journal of Biochemistry. 1999;264:415-426.

    Not in our library10.1046/j.1432-1327.1999.00613.x

33. 33.

    Frigola J, He J, Kinkelin K, Pye VE, Renault L, Douglas ME, Remus D, Cherepanov P, Costa A, Diffley JFX. Cdt1 stabilizes an open MCM ring for helicase loading. Nature Communications. 2017;8:15720.

    Not in our library10.1038/ncomms15720

34. 34.

    Gilbert N, Gilchrist S, Bickmore WA. Chromatin organization in the mammalian nucleus. International Review of Cytology. 2005;242:283-336.

    Not in our library10.1016/s0074-7696(04)42007-5

35. 35.

    Giordano-Coltart J, Ying CY, Gautier J, Hurwitz J. Studies of the properties of human origin recognition complex and its walker A motif mutants. PNAS. 2005;102:69-74.

    Not in our library10.1073/pnas.0408690102

36. 36.

    Heinzel SS, Krysan PJ, Tran CT, Calos MP. Autonomous DNA replication in human cells is affected by the size and the source of the DNA. Molecular and Cellular Biology. 1991;11:2263-2272.

    Not in our library10.1128/mcb.11.4.2263

37. 37.

    Hemerly AS, Prasanth SG, Siddiqui K, Stillman B. Orc1 controls centriole and centrosome copy number in human cells. Science. 2009;323:789-793.

    Not in our library10.1126/science.1166745

38. 38.

    Hennig S, Kong G, Mannen T, Sadowska A, Kobelke S, Blythe A, Knott GJ, Iyer KS, Ho D, Newcombe EA, Hosoki K, Goshima N, Kawaguchi T, Hatters D, Trinkle-Mulcahy L, Hirose T, Bond CS, Fox AH. Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. The Journal of Cell Biology. 2015;210:529-539.

    Not in our library10.1083/jcb.201504117

39. 39.

    Hossain M, Bhalla K, Stillman B. Cyclin binding cy motifs have multiple activities in the initiation of DNA replication. bioRxiv. 2019.

    Not in our library10.1101/681668

40. 40.

    Houchens CR, Lu W, Chuang RY, Frattini MG, Fuller A, Simancek P, Kelly TJ. Multiple mechanisms contribute to Schizosaccharomyces pombe origin recognition complex-DNA interactions. Journal of Biological Chemistry. 2008;283:30216-30224.

    Not in our library10.1074/jbc.m802649200

41. 41.

    Huang DW, Fanti L, Pak DT, Botchan MR, Pimpinelli S, Kellum R. Distinct cytoplasmic and nuclear fractions of Drosophila heterochromatin protein 1: their phosphorylation levels and associations with origin recognition complex proteins. The Journal of Cell Biology. 1998;142:307-318.

    Not in our library10.1083/jcb.142.2.307

42. 42.

    Hug CB, Grimaldi AG, Kruse K, Vaquerizas JM. Chromatin architecture emerges during zygotic genome activation independent of transcription. Cell. 2017;169:216-228.

    Not in our library10.1016/j.cell.2017.03.024

43. 43.

    Hyrien O, Méchali M. Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of xenopus early embryos. The EMBO Journal. 1993;12:4511-4520.

    Not in our library10.1002/j.1460-2075.1993.tb06140.x

44. 44.

    Jiang H, Wang S, Huang Y, He X, Cui H, Zhu X, Zheng Y. Phase transition of spindle-associated protein regulate spindle apparatus assembly. Cell. 2015;163:108-122.

    Not in our library10.1016/j.cell.2015.08.010

45. 45.
    DISOPRED3: precise disordered region predictions with annotated protein-binding activity · 2014

    No notice
46. 46.

    Kang S, Warner MD, Bell SP. Multiple functions for Mcm2-7 ATPase motifs during replication initiation. Molecular Cell. 2014;55:655-665.

    Not in our library10.1016/j.molcel.2014.06.033

47. 47.

    Kara N, Hossain M, Prasanth SG, Stillman B. Orc1 binding to mitotic chromosomes precedes spatial patterning during G1 phase and assembly of the origin recognition complex in human cells. Journal of Biological Chemistry. 2015;290:12355-12369.

    Not in our library10.1074/jbc.m114.625012

48. 48.

    Kato M, Han TW, Xie S, Shi K, Du X, Wu LC, Mirzaei H, Goldsmith EJ, Longgood J, Pei J, Grishin NV, Frantz DE, Schneider JW, Chen S, Li L, Sawaya MR, Eisenberg D, Tycko R, McKnight SL. Cell-free formation of RNA granules: low complexity sequence domains form dynamic fibers within hydrogels. Cell. 2012;149:753-767.

    Not in our library10.1016/j.cell.2012.04.017

49. 49.

    Kawakami H, Ohashi E, Kanamoto S, Tsurimoto T, Katayama T. Specific binding of eukaryotic ORC to DNA replication origins depends on highly conserved basic residues. Scientific Reports. 2015;5:14929.

    Not in our library10.1038/srep14929

50. 50.

    Kennedy BK, Barbie DA, Classon M, Dyson N, Harlow E. Nuclear organization of DNA replication in primary mammalian cells. Genes & Development. 2000;14:2855-2868.

    Not in our library10.1101/gad.842600

51. 51.

    Kim GS, Kang J, Bang SW, Hwang DS. Cdc6 localizes to S- and G2-phase centrosomes in a cell cycle-dependent manner. Biochemical and Biophysical Research Communications. 2015;456:763-767.

    Not in our library10.1016/j.bbrc.2014.12.018

52. 52.

    Klemm RD, Austin RJ, Bell SP. Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex. Cell. 1997;88:493-502.

    Not in our library10.1016/s0092-8674(00)81889-9

53. 53.

    Klemm RD, Bell SP. ATP bound to the origin recognition complex is important for preRC formation. PNAS. 2001;98:8361-8367.

    Not in our library10.1073/pnas.131006898

54. 54.

    Kuo AJ, Song J, Cheung P, Ishibe-Murakami S, Yamazoe S, Chen JK, Patel DJ, Gozani O. The BAH domain of ORC1 links H4K20me2 to DNA replication licensing and Meier-Gorlin syndrome. Nature. 2012;484:115-119.

    Not in our library10.1038/nature10956

55. 55.

    Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB, Burlingame AL, Agard DA, Redding S, Narlikar GJ. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature. 2017;547:236-240.

    Not in our library10.1038/nature22822

56. 56.

    Lee JK, Moon KY, Jiang Y, Hurwitz J. The Schizosaccharomyces pombe origin recognition complex interacts with multiple AT-rich regions of the replication origin DNA by means of the AT-hook domains of the spOrc4 protein. PNAS. 2001;98:13589-13594.

    Not in our library10.1073/pnas.251530398

57. 57.

    Lee KY, Bang SW, Yoon SW, Lee SH, Yoon JB, Hwang DS. Phosphorylation of ORC2 protein dissociates origin recognition complex from chromatin and replication origins. Journal of Biological Chemistry. 2012;287:11891-11898.

    Not in our library10.1074/jbc.m111.338467

58. 58.

    Li CJ, Vassilev A, DePamphilis ML. Role for Cdk1 (Cdc2)/cyclin A in preventing the mammalian origin recognition complex’s largest subunit (Orc1) from binding to chromatin during mitosis. Molecular and Cellular Biology. 2004;24:5875-5886.

    Not in our library10.1128/mcb.24.13.5875-5886.2004

59. 59.

    Li P, Banjade S, Cheng HC, Kim S, Chen B, Guo L, Llaguno M, Hollingsworth JV, King DS, Banani SF, Russo PS, Jiang QX, Nixon BT, Rosen MK. Phase transitions in the assembly of multivalent signalling proteins. Nature. 2012;483:336-340.

    Not in our library10.1038/nature10879

60. 60.
    Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition · 2014

    No notice
61. 61.

    Li N, Lam WH, Zhai Y, Cheng J, Cheng E, Zhao Y, Gao N, Tye BK. Structure of the origin recognition complex bound to DNA replication origin. Nature. 2018;559:217-222.

    Not in our library10.1038/s41586-018-0293-x

62. 62.

    Lidonnici MR, Rossi R, Paixão S, Mendoza-Maldonado R, Paolinelli R, Arcangeli C, Giacca M, Biamonti G, Montecucco A. Subnuclear distribution of the largest subunit of the human origin recognition complex during the cell cycle. Journal of Cell Science. 2004;117:5221-5231.

    Not in our library10.1242/jcs.01405

63. 63.
    Intrinsically disordered sequences enable modulation of protein phase separation through distributed tyrosine motifs · 2017

    No notice
64. 64.

    Liu S, Balasov M, Wang H, Wu L, Chesnokov IN, Liu Y. Structural analysis of human Orc6 protein reveals a homology with transcription factor TFIIB. PNAS. 2011;108:7373-7378.

    Not in our library10.1073/pnas.1013676108

65. 65.

    MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Research. 2010;20:201-211.

    Not in our library10.1101/gr.097873.109

66. 66.

    Maeshima K, Ide S, Hibino K, Sasai M. Liquid-like behavior of chromatin. Current Opinion in Genetics & Development. 2016;37:36-45.

    Not in our library10.1016/j.gde.2015.11.006

67. 67.

    Markow TA, Beall S, Matzkin LM. Egg size, embryonic development time and ovoviviparity in Drosophila species. Journal of Evolutionary Biology. 2009;22:430-434.

    Not in our library10.1111/j.1420-9101.2008.01649.x

68. 68.

    Matson JP, Dumitru R, Coryell P, Baxley RM, Chen W, Twaroski K, Webber BR, Tolar J, Bielinsky AK, Purvis JE, Cook JG. Rapid DNA replication origin licensing protects stem cell pluripotency. eLife. 2017;6:e30473.

    Not in our library10.7554/elife.30473

69. 69.

    McNairn AJ, Okuno Y, Misteli T, Gilbert DM. Chinese hamster ORC subunits dynamically associate with chromatin throughout the cell-cycle. Experimental Cell Research. 2005;308:345-356.

    Not in our library10.1016/j.yexcr.2005.05.009

70. 70.

    Méchali M, Kearsey S. Lack of specific sequence requirement for DNA replication in xenopus eggs compared with high sequence specificity in yeast. Cell. 1984;38:55-64.

    Not in our library10.1016/0092-8674(84)90526-9

71. 71.

    Méndez J, Zou-Yang XH, Kim SY, Hidaka M, Tansey WP, Stillman B. Human origin recognition complex large subunit is degraded by ubiquitin-mediated proteolysis after initiation of DNA replication. Molecular Cell. 2002;9:481-491.

    Not in our library10.1016/s1097-2765(02)00467-7

72. 72.

    Miotto B, Ji Z, Struhl K. Selectivity of ORC binding sites and the relation to replication timing, fragile sites, and deletions in cancers. PNAS. 2016;113:E4810-E4819.

    Not in our library10.1073/pnas.1609060113

73. 73.
    Dense Bicoid hubs accentuate binding along the morphogen gradient · 2017

    No notice
74. 74.

    Mir M, Reimer A, Stadler M, Tangara A, Hansen AS, Hockemeyer D, Eisen MB, Garcia H, Darzacq X. Single molecule imaging in live embryos using lattice Light-Sheet microscopy. Methods in Molecular Biology. 2018;1814:541-559.

    Not in our library10.1007/978-1-4939-8591-3_32

75. 75.

    Mir M. GitHub. 2019.

    Not in our library

76. 76.
    Phase separation in biology; functional organization of a higher order · 2016

    No notice
77. 77.

    Natale DA. Selective instability of Orc1 protein accounts for the absence of functional origin recognition complexes during the M-G1 transition in mammals. The EMBO Journal. 2000;19:2728-2738.

    Not in our library10.1093/emboj/19.11.2728

78. 78.

    Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, Dekker J. Organization of the mitotic chromosome. Science. 2013;342:948-953.

    Not in our library10.1126/science.1236083

79. 79.

    Nguyen VQ, Co C, Li JJ. Cyclin-dependent kinases prevent DNA re-replication through multiple mechanisms. Nature. 2001;411:1068-1073.

    Not in our library10.1038/35082600

80. 80.

    Noguchi K, Vassilev A, Ghosh S, Yates JL, DePamphilis ML. The BAH domain facilitates the ability of human Orc1 protein to activate replication origins in vivo. The EMBO Journal. 2006;25:5372-5382.

    Not in our library10.1038/sj.emboj.7601396

81. 81.
    Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles · 2015

    No notice
82. 82.

    Nuebler J, Fudenberg G, Imakaev M, Abdennur N, Mirny LA. Chromatin organization by an interplay of loop extrusion and compartmental segregation. PNAS. 2018;115:E6697-E6706.

    Not in our library10.1073/pnas.1717730115

83. 83.

    Oomen ME, Dekker J. Epigenetic characteristics of the mitotic chromosome in 1D and 3D. Critical Reviews in Biochemistry and Molecular Biology. 2017;52:185-204.

    Not in our library10.1080/10409238.2017.1287160

84. 84.

    Pak DT, Pflumm M, Chesnokov I, Huang DW, Kellum R, Marr J, Romanowski P, Botchan MR. Association of the origin recognition complex with heterochromatin and HP1 in higher eukaryotes. Cell. 1997;91:311-323.

    Not in our library10.1016/s0092-8674(00)80415-8

85. 85.

    Pak CW, Kosno M, Holehouse AS, Padrick SB, Mittal A, Ali R, Yunus AA, Liu DR, Pappu RV, Rosen MK. Sequence determinants of intracellular phase separation by complex coacervation of a disordered protein. Molecular Cell. 2016;63:72-85.

    Not in our library10.1016/j.molcel.2016.05.042

86. 86.

    Park SY, Asano M. The origin recognition complex is dispensable for endoreplication in Drosophila. PNAS. 2008;105:12343-12348.

    Not in our library10.1073/pnas.0805189105

87. 87.

    Parker MW, Botchan MR, Berger JM. Mechanisms and regulation of DNA replication initiation in eukaryotes. Critical Reviews in Biochemistry and Molecular Biology. 2017;52:107-144.

    Not in our library10.1080/10409238.2016.1274717

88. 88.

    Patel A, Malinovska L, Saha S, Wang J, Alberti S, Krishnan Y, Hyman AA. ATP as a biological hydrotrope. Science. 2017;356:753-756.

    Not in our library10.1126/science.aaf6846

89. 89.
    Replication landscape of the human genome · 2016

    No notice
90. 90.

    Pflumm MF, Botchan MR. Orc mutants arrest in metaphase with abnormally condensed chromosomes. Development. 2001;128:1697-1707.

    Not in our library10.1242/dev.128.9.1697

91. 91.

    Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, Vera DL, Wang Y, Hansen RS, Canfield TK, Thurman RE, Cheng Y, Gülsoy G, Dennis JH, Snyder MP, Stamatoyannopoulos JA, Taylor J, Hardison RC, Kahveci T, Ren B, Gilbert DM. Topologically associating domains are stable units of replication-timing regulation. Nature. 2014;515:402-405.

    Not in our library10.1038/nature13986

92. 92.

    Pozo P, Cook J. Regulation and function of Cdt1; A key factor in cell proliferation and genome stability. Genes. 2016;8:2.

    Not in our library10.3390/genes8010002

93. 93.

    Prasanth SG, Prasanth KV, Siddiqui K, Spector DL, Stillman B. Human Orc2 localizes to Centrosomes, centromeres and heterochromatin during chromosome inheritance. The EMBO Journal. 2004;23:2651-2663.

    Not in our library10.1038/sj.emboj.7600255

94. 94.

    Prasanth SG, Shen Z, Prasanth KV, Stillman B. Human origin recognition complex is essential for HP1 binding to chromatin and heterochromatin organization. PNAS. 2010;107:15093-15098.

    Not in our library10.1073/pnas.1009945107

95. 95.
    FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions · 2018

    No notice
96. 96.

    Remus D, Beall EL, Botchan MR. DNA topology, not DNA sequence, is a critical determinant for Drosophila ORC-DNA binding. The EMBO Journal. 2004;23:897-907.

    Not in our library10.1038/sj.emboj.7600077

97. 97.

    Remus D, Blanchette M, Rio DC, Botchan MR. CDK phosphorylation inhibits the DNA-binding and ATP-hydrolysis activities of the Drosophila origin recognition complex. Journal of Biological Chemistry. 2005;280:39740-39751.

    Not in our library10.1074/jbc.m508515200

98. 98.

    Remus D, Beuron F, Tolun G, Griffith JD, Morris EP, Diffley JF. Concerted loading of Mcm2-7 double hexamers around DNA during DNA replication origin licensing. Cell. 2009;139:719-730.

    Not in our library10.1016/j.cell.2009.10.015

99. 99.

    Rowles A, Tada S, Blow JJ. Changes in association of the xenopus origin recognition complex with chromatin on licensing of replication origins. Journal of Cell Science. 1999;112:2011-2018.

    Not in our library10.1242/jcs.112.12.2011

100. 100.

     Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A. Fiji: an open-source platform for biological-image analysis. Nature Methods. 2012;9:676-682.

     Not in our library10.1038/nmeth.2019

101. 101.

     Shen Z, Sathyan KM, Geng Y, Zheng R, Chakraborty A, Freeman B, Wang F, Prasanth KV, Prasanth SG. A WD-repeat protein stabilizes ORC binding to chromatin. Molecular Cell. 2010;40:99-111.

     Not in our library10.1016/j.molcel.2010.09.021

102. 102.

     Shin Y, Brangwynne CP. Liquid phase condensation in cell physiology and disease. Science. 2017;357:eaaf4382.

     Not in our library10.1126/science.aaf4382

103. 103.

     Sonneville R, Querenet M, Craig A, Gartner A, Blow JJ. The dynamics of replication licensing in live Caenorhabditis elegans embryos. The Journal of Cell Biology. 2012;196:233-246.

     Not in our library10.1083/jcb.201110080

104. 104.

     Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH. Phase separation drives heterochromatin domain formation. Nature. 2017;547:241-245.

     Not in our library10.1038/nature22989

105. 105.

     Su X, Ditlev JA, Hui E, Xing W, Banjade S, Okrut J, King DS, Taunton J, Rosen MK, Vale RD. Phase separation of signaling molecules promotes T cell receptor signal transduction. Science. 2016;352:595-599.

     Not in our library10.1126/science.aad9964

106. 106.

     Sun WH, Coleman TR, DePamphilis ML. Cell cycle-dependent regulation of the association between origin recognition proteins and somatic cell chromatin. The EMBO Journal. 2002;21:1437-1446.

     Not in our library10.1093/emboj/21.6.1437

107. 107.

     Sun J, Evrin C, Samel SA, Fernández-Cid A, Riera A, Kawakami H, Stillman B, Speck C, Li H. Cryo-EM structure of a helicase loading intermediate containing ORC-Cdc6-Cdt1-MCM2-7 bound to DNA. Nature Structural & Molecular Biology. 2013;20:944-951.

     Not in our library10.1038/nsmb.2629

108. 108.

     Takara TJ, Bell SP. Multiple Cdt1 molecules act at each origin to load replication-competent Mcm2-7 helicases. The EMBO Journal. 2011;30:4885-4896.

     Not in our library10.1038/emboj.2011.394

109. 109.

     Ticau S, Friedman LJ, Ivica NA, Gelles J, Bell SP. Single-molecule studies of origin licensing reveal mechanisms ensuring bidirectional helicase loading. Cell. 2015;161:513-525.

     Not in our library10.1016/j.cell.2015.03.012

110. 110.

     Vashee S, Cvetic C, Lu W, Simancek P, Kelly TJ, Walter JC. Sequence-independent DNA binding and replication initiation by the human origin recognition complex. Genes & Development. 2003;17:1894-1908.

     Not in our library10.1101/gad.1084203

111. 111.

     Vaughn JP, Dijkwel PA, Hamlin JL. Replication initiates in a broad zone in the amplified CHO dihydrofolate reductase domain. Cell. 1990;61:1075-1087.

     Not in our library10.1016/0092-8674(90)90071-l

112. 112.
     Pi-Pi contacts are an overlooked protein feature relevant to phase separation · 2018

     No notice
113. 113.

     Wang J, Choi J-M, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D, Poser I, Pappu RV, Alberti S, Hyman AA. A molecular grammar governing the driving forces for phase separation of Prion-like RNA binding proteins. Cell. 2018;174:688-699.

     Not in our library10.1016/j.cell.2018.06.006

114. 114.

     Wegmann S, Eftekharzadeh B, Tepper K, Zoltowska KM, Bennett RE, Dujardin S, Laskowski PR, MacKenzie D, Kamath T, Commins C, Vanderburg C, Roe AD, Fan Z, Molliex AM, Hernandez-Vega A, Muller D, Hyman AA, Mandelkow E, Taylor JP, Hyman BT. Tau protein liquid-liquid phase separation can initiate tau aggregation. The EMBO Journal. 2018;37:e98049.

     Not in our library10.15252/embj.201798049

115. 115.

     Woodruff JB, Wueseke O, Viscardi V, Mahamid J, Ochoa SD, Bunkenborg J, Widlund PO, Pozniakovsky A, Zanin E, Bahmanyar S, Zinke A, Hong SH, Decker M, Baumeister W, Andersen JS, Oegema K, Hyman AA. Regulated assembly of a supramolecular centrosome scaffold in vitro. Science. 2015;348:808-812.

     Not in our library10.1126/science.aaa3923

116. 116.

     Woodruff JB, Ferreira Gomes B, Widlund PO, Mahamid J, Honigmann A, Hyman AA. The centrosome is a selective condensate that nucleates microtubules by concentrating tubulin. Cell. 2017;169:1066-1077.

     Not in our library10.1016/j.cell.2017.05.028

117. 117.

     Wootton JC, Federhen S. Statistics of local complexity in amino acid sequences and sequence databases. Computers & Chemistry. 1993;17:149-163.

     Not in our library10.1016/0097-8485(93)85006-x

118. 118.

     Wu M, Lu W, Santos RE, Frattini MG, Kelly TJ. Geminin inhibits a late step in the formation of human pre-replicative complexes. Journal of Biological Chemistry. 2014;289:30810-30821.

     Not in our library10.1074/jbc.m114.552935

119. 119.

     Xiang W, Roberti MJ, Hériché JK, Huet S, Alexander S, Ellenberg J. Correlative live and super-resolution imaging reveals the dynamic structure of replication domains. The Journal of Cell Biology. 2018;217:1973-1984.

     Not in our library10.1083/jcb.201709074

120. 120.

     Yanagi K, Mizuno T, You Z, Hanaoka F. Mouse geminin inhibits not only Cdt1-MCM6 interactions but also a novel intrinsic Cdt1 DNA binding activity. The Journal of Biological Chemistry. 2002;277:40871-40880.

     Not in our library10.1074/jbc.m206202200

121. 121.

     Yuan Z, Riera A, Bai L, Sun J, Nandi S, Spanos C, Chen ZA, Barbon M, Rappsilber J, Stillman B, Speck C, Li H. Structural basis of Mcm2-7 replicative helicase loading by ORC-Cdc6 and Cdt1. Nature Structural & Molecular Biology. 2017;24:316-324.

     Not in our library10.1038/nsmb.3372

122. 122.
     RNA stores tau reversibly in complex coacervates · 2017

     No notice

Cited by papers we hold 2

• Structural mechanism for replication origin binding and remodeling by a metazoan origin recognition complex and its co-loader Cdc6 · 2020
  Not checked
• Biological phase separation: cell biology meets biophysics · 2020
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.