Spatial and Temporal Organization of Chromatin at Small and Large Scales

Literature Cited

1. 1.

   Schiessel H. 2003. J. Phys. Condens. Matter 15:R699–774
2. 2.

   Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Nature 389:251–60
3. 3.

   Ngo TTM, Zhang Q, Zhou R, Yodh JG, Ha T. 2015. Cell 160:1135–44
4. 4.

   Eslami-Mossallam B, Schram RD, Tompitak M, van Noort J, Schiessel H. 2016. PLOS ONE 11:e0156905
5. 5.

   Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT, Wang MD. 2009. Nat. Struct. Mol. Biol. 16:124–29
6. 6.

   Bustamante C, Marko JF, Siggia ED, Smith S. 1994. Science 265:1599–600
7. 7.

   Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D et al. 2009. Nature 458:362–66
8. 8.

   Lowary PT, Widom J. 1997. PNAS 94:1183–88
9. 9.

   Satchwell SC, Drew HR, Travers AA. 1986. J. Mol. Biol. 191:659–75
10. 10.

    Segal E, Fondufe-Mittendorf Y, Chen L, Thåström A, Field Y et al. 2006. Nature 442:772–78
11. 11.

    Jin H, Rube HT, Song JS 2016. Nucl. Acids Res. 44:2047–57
12. 12.

    Tillo D, Hughes TR 2009. BMC Bioinform. 10:442
13. 13.

    Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV. 2010. PNAS 107:20998–1003
14. 14.

    Struhl K, Segal E. 2013. Nat. Struct. Mol. Biol. 20:267–73
15. 15.

    Drillon G, Audit B, Argoul F, Arneodo A 2016. BMC Genom. 17:526
16. 16.

    Tompitak M, Vaillant C, Schiessel H. 2017. Biophys. J. 112:505–11
17. 17.

    Olson WK, Gorin AA, Lu X-J, Hock LM, Zhurkin VB. 1998. PNAS 95:11163–68
18. 18.

    Hinckley DM, Freeman GS, Whitmer JK, de Pablo JJ. 2013. J. Phys. Chem. 139:144903
19. 19.

    Lankaš F, Šponer J, Langowski J, Cheatham TE III 2003. Biophys. J. 85:2872–83
20. 20.

    Morozov AV, Fortney K, Gaykalova DA, Studitsky VM, Widom J, Siggia ED. 2009. Nucl. Acids Res. 37:4707–22
21. 21.

    Freeman GS, Lequieu JP, Hinckley DM, Whitmer JK, de Pablo JJ. 2014. Phys. Rev. Lett. 113:168101
22. 22.

    Zuiddam M, Everaers R, Schiessel H. 2017. Phys. Rev. E 96:052412
23. 23.

    Neipel J, Brandani G, Schiessel H. 2020. Phys. Rev. E 101:022405
24. 24.

    Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. 2013. Nat. Methods 10:1213–18
25. 25.

    Brogaard K, Xi L, Wang JP, Widom J. 2012. Nature 486:496–501
26. 26.

    Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA. 2012. Genome Res. 22:2497–506
27. 27.

    Kornberg RD, Stryer L. 1988. Nucl. Acids Res. 16:6677–90
28. 28.

    Chevereau G, Palmeira L, Thermes C, Arneodo A, Vaillant C. 2009. Phys. Rev. Lett. 103:188103
29. 29.

    Tillo D, Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ et al. 2010. PLOS ONE 5:e9129
30. 30.

    Vavouri T, Lehner B. 2011. PLOS Genet. 7:e1002036
31. 31.

    Hammoud SS, Nix DA, Zhang H, Purwar J, Carrell DT, Cairns BR. 2009. Nature 460:473–78
32. 32.

    Eslami-Mossallam B, Schiessel H, van Noort J. 2016. Adv. Colloid Interface Sci. 232:101–13
33. 33.

    Fierz B, Poirier MG. 2019. Annu. Rev. Biophys. 48:321–45
34. 34.

    Polach KJ, Widom J. 1995. J. Mol. Biol. 254:130–49
35. 35.

    Anderson JD, Lowary PT, Widom J. 2001. J. Mol. Biol. 307:977–85
36. 36.

    Li G, Widom J. 2004. Nat. Struct. Mol. Biol. 11:763–69
37. 37.

    Li G, Levitus M, Bustamante C, Widom J. 2005. Nat. Struct. Mol. Biol. 12:46–53
38. 38.

    Kelbauskas L, Chan N, Bash R, Yodh J, Woodbury N, Lohr D. 2007. Biochemistry 46:2239–48
39. 39.

    Koopmans WJA, Brehm A, Logie C, Schmidt T, van Noort J. 2007. J. Fluoresc. 17:785–95
40. 40.

    Moyle-Heyrman G, Tims HS, Widom J. 2011. J. Mol. Biol. 412:634–46
41. 41.

    Tims HS, Gurunathan K, Levitus M, Widom J. 2011. J. Mol. Biol. 411:430–48
42. 42.

    Gansen A, Felekyan S, Kühnemuth R, Lehmann K, Tóth K et al. 2018. Nat. Commun. 9:4628
43. 43.

    Konrad SF, Vanderlinden W, Frederickx W, Brouns T, Menze BH et al. 2021. Nanoscale 13:5435–47
44. 44.

    Konrad SF, Vanderlinden W, Lipfert J. 2022. Biophys. J. 121:841–51
45. 45.

    Prinsen P, Schiessel H. 2010. Biochimie 92:1722–28
46. 46.

    Anderson JD, Widom J. 2001. Mol. Cell. Biol. 21:3830–39
47. 47.

    Kelbauskis L, Woodbury N, Lohr D. 2009. Biochem. Cell Biol. 87:323–35
48. 48.

    Gansen A, Tóth, Schwarz N, Langowski J 2009. J. Phys. Chem. B 113:2604–13
49. 49.

    Tóth K, Böhm V, Sellmann C, Danner M, Hanne J et al. 2013. Cytometry A 83:839–46
50. 50.

    Lowary PT, Widom J. 1998. J. Mol. Biol. 276:19–42
51. 51.

    Mauney AW, Tokuda JM, Gloss LM, Gonzalez O, Pollack M. 2018. Biophys. J. 115:773–81
52. 52.

    van Deelen K, Schiessel H, de Bruin L. 2020. Biophys. J. 118:2297–308
53. 53.

    Polach KJ, Widom J. 1996. J. Mol. Biol. 258:800–12
54. 54.

    Culkin J, de Bruin L, Tompitak M, Phillips R, Schiessel H. 2017. Eur. Phys. J. E 40:106
55. 55.

    Winogradoff D, Aksimentiev A. 2019. J. Mol. Biol. 431:323–35
56. 56.

    Armeev GA, Kniazeva AS, Komarova GA, Kirpichnikov MP, Shaytan AK. 2021. Nat. Commun. 12:2387
57. 57.

    Brower-Toland BD, Smith CL, Yeh RC, Lis JT, Peterson CL, Wang MD. 2002. PNAS 99:1960–65
58. 58.

    Kulić IM, Schiessel H. 2004. Phys. Rev. Lett. 92:228101
59. 59.

    Wocjan T, Klenin K, Langowski J. 2009. J. Phys. Chem. B 113:2639–46
60. 60.

    Sudhanshu B, Mihardja S, Koslover EF, Mehraeen S, Bustamante C, Spakowitz AJ. 2011. PNAS 108:1885–90
61. 61.

    Ettig R, Kepper N, Stehr R, Wedemann G, Rippe K. 2011. Biophys. J. 101:1999–2008
62. 62.

    Mollazadeh-Beidokhti L, Mohammad-Rafiee F, Schiessel H. 2012. Biophys. J. 102:2235–40
63. 63.

    Lanzani G, Schiessel H. 2012. Europhys. Lett. 100:48001
64. 64.

    Mochrie SGJ, Mack AH, Schlingwein DJ, Collins R, Kamenetska M, Regan L 2013. Phys. Rev. E 87:012710
65. 65.

    Mack AH, Schlingman DJ, Salinas RD, Regan L, Mochrie SGJ 2015. J. Phys. Condens. Matter 27:064106
66. 66.

    Lequieu J, Córdoba A, Schwartz DC, de Pablo JJ. 2016. ACS Cent. Sci. 2:660–66
67. 67.

    Khodabandeh F, Fatemi H, Mohammad-Rafiee F. 2020. Soft Matter 16:4806–13
68. 68.

    Reddy G, Thirumalai D. 2021. Nucl. Acids Res. 49:4907–18
69. 69.

    de Bruin L, Tompitak M, Eslami-Mossallam B, Schiessel H. 2016. J. Phys. Chem. B 120:5855–63
70. 70.

    Tompitak M, de Bruin L, Eslami-Mossallam B, Schiessel H. 2017. Phys. Rev. E 95:052402
71. 71.

    Durkin SG, Glover TW. 2007. Annu. Rev. Genet. 41:169–92
72. 72.

    Chan KL, Palmai-Pallag T, Ying S, Hickson ID 2009. Nat. Cell Biol. 11:753–60
73. 73.

    Biebricher A, Hirano S, Enzlin JH, Wiechens N, Streicher WW et al. 2013. Mol. Cell 51:691–701
74. 74.

    Meersseman G, Pennings S, Bradbury EM. 1992. EMBO J. 11:2951–59
75. 75.

    Kulić IM, Schiessel H. 2003. Phys. Rev. Lett. 91:148103
76. 76.

    Mohammad-Rafiee F, Kulić IM, Schiessel H. 2004. J. Mol. Biol. 344:47–58
77. 77.

    Brandani GB, Niina T, Tan C, Takada S. 2018. Nucl. Acids Res. 46:2788–801
78. 78.

    Schiessel H, Widom J, Bruinsma RF, Gelbart WM. 2001. Phys. Rev. Lett. 86:4414–17
79. 79.

    Kulić IM, Schiessel H. 2003. Biophys. J. 84:3197–211
80. 80.

    Lequieu J, Schwartz DC, de Pablo JJ. 2017. PNAS 114:E9197–205
81. 81.

    Niina T, Brandani GB, Tan C, Takada S. 2017. PLOS Comput. Biol. 13:e1005880
82. 82.

    Rudnizky S, Khamis H, Malik O, Melamed P, Kaplan A. 2019. PNAS 116:12161–66
83. 83.

    Winger J, Nodelman IM, Levendosky RF, Bowman GD 2018. eLife 7:e34100
84. 84.

    Li M, Xia X, Tian Y, Jia Q, Liu X et al. 2019. Nature 567:409–13
85. 85.

    Sabantsev A, Levendosky RF, Zhuang X, Bowman GD, Deindl S. 2019. Nat. Commun. 10:1720
86. 86.

    Brandani GB, Takada S. 2018. PLOS Comput. Biol. 14:e1006512
87. 87.

    Segal E, Widom J. 2009. Trend Genet. 25:335–43
88. 88.

    Nodelman IM, Das S, Faustino AM, Fried SD, Bowman GD, Armache JP. 2022. Nat. Struct. Mol. Biol. 29:121–29
89. 89.

    Narlikar GJ. 2010. Curr. Opin. Chem. Biol. 14:660–65
90. 90.

    Schiessel H, Blossey R. 2020. Phys. Rev. E 101:040401(R)
91. 91.

    Eltsov M, MacLellan KM, Maeshima K, Frangakis AS, Dubochet J. 2008. PNAS 105:19732–37
92. 92.

    Joti Y, Hikima T, Nishino Y, Kamada F, Hihara S et al. 2012. Nucleus 3:404–10
93. 93.

    Ricci MA, Manzo C, García-Parajo MF, Lakadamyali M, Cosma MP. 2015. Cell 160:1145–58
94. 94.

    Portillo-Ledesma S, Tsao LH, Wagley M, Lakadamyali M, Cosma MP, Schlick T. 2021. J. Mol. Biol. 433:166701
95. 95.

    Sazer S, Schiessel H. 2018. Traffic 19:87–104
96. 96.

    de Gennes PG. 1979. Scaling Concepts in Polymer Physics Ithaka, NY: Cornell Univ. Press
97. 97.

    van den Engh G, Sachs R, Trask BJ. 1992. Science 257:1410–12
98. 98.

    Bolzer A, Kreth G, Solovei I, Koehler D, Saracoglu K et al. 2005. PLOS Biol. 3:e157
99. 99.

    Emanuel M, Radja NH, Henriksson A, Schiessel H. 2009. Phys. Biol. 6:025008
100. 100.

     Mateos-Langerak J, Bohn M, de Leeuw W, Giromus O, Manders EMM et al. 2009. PNAS 106:3812–17
101. 101.

     Maeshima K, Rogge R, Tamura S, Joti Y, Hikima T et al. 2016. EMBO J. 35:1115–32
102. 102.

     Gibson BA, Doolittle LK, Schneider MWG, Jensen LE, Gamarra N et al. 2019. Cell 179:470–84
103. 103.

     Strickfaden H, Tolsma TO, Sharma A, Underhill DA, Hansen JC, Hendzel MJ. 2020. Cell 183:1772–84
104. 104.

     Bajpai G, Pavlov DA, Lorber D, Volk T, Safran S 2021. eLife 10:e63976
105. 105.

     Amiad-Pavlov D, Lorber D, Bajpai G, Reuveny A, Roncato F et al. 2021. Sci. Adv. 7:eabf6251
106. 106.

     Farr SE, Woods EJ, Joseph JA, Garaizar A, Collepardo-Guevara R. 2021. Nat. Commun. 12:2883
107. 107.

     Lua R, Borovinskiy AL, Grosberg AY. 2004. Polymer 45:717–31
108. 108.

     Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T et al. 2009. Science 326:289–93
109. 109.

     Grosberg A, Rabin R, Havlin S, Neer A. 1993. Europhys. Lett. 23:373–78
110. 110.

     Smrek J, Grosberg AY. 2013. Physica A 392:6375–88
111. 111.

     Schram RD, Barkema GT, Schiessel H. 2013. J. Chem. Phys. 138:224901
112. 112.

     Sikorav JL, Jannink G. 1994. Biophys. J. 66:827–37
113. 113.

     Rosa A, Everaers R. 2008. PLOS Comput. Biol. 4:e1000153
114. 114.

     Schiessel H. 2022. Biophysics for Beginners: A Journey Through the Cell Nucleus Singapore: Jenny Stanford Publ. , 2nd ed..
115. 115.

     Halverson JD, Lee WB, Grest GS, Grosberg AY, Kremer K. 2011. J. Chem. Phys. 134:204904
116. 116.

     Rosa A, Everaers R. 2014. Phys. Rev. Lett. 112:118302
117. 117.

     Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID et al. 2014. Cell 159:1665–80
118. 118.

     Golfier S, Quail T, Kimura H, Brugués 2020. eLife 9:e53885
119. 119.

     Fudenberg G, Imakaev M, Lu C, Goloborodko A, Mirny LA. 2016. Cell Rep. 15:2038–49
120. 120.

     Banigan EJ, van den Berg AA, Brandão HB, Marko JF, Mirny LA 2020. eLife 9:e53558
121. 121.

     Banigan EJ, Mirny LA 2020. eLife 9:e63528
122. 122.

     Sanborn AL, Rao SSP, Huang SC, Durand NC, Huntley MH et al. 2015. PNAS 112:E6456–65
123. 123.

     Grosberg AY, Khalatur PG, Khokhlov AR. 1982. Makromol. Chem. Rapid Commun. 3:709–13
124. 124.

     Terakawa T, Bisht S, Eeftens JM, Dekker C, Haering CH, Greene EC. 2017. Science 358:672–76
125. 125.

     Ganji M, Shaltiel IA, Bisht S, Kim E, Kalichava A et al. 2018. Science 360:102–5
126. 126.

     Gibcus JH, Samejima K, Goloborodko A, Samejima I, Naumova N et al. 2018. Science 359:eaao6135
127. 127.

     Goloborodko A, Imakaev MV, Marko JF, Mirny L 2016. eLife 5:e14864
128. 128.

     Shintomi K, Inoue F, Watanabe H, Ohsumi K, Ohsugi M, Hirano T. 2017. Science 356:1284–87
129. 129.

     Shintomi K, Hirano T. 2021. Nat. Commun. 12:2917
130. 130.

     Yamamoto T, Schiessel H. 2022. Biophys. J. 121:142742–50
131. 131.

     Cortini R, Barbi M, Caré BR, Lavelle C, Lesne A et al. 2016. Rev. Mod. Phys. 88:025002
132. 132.

     Yu C, Gan H, Serra-Cardona A, Zhang L, Gan S et al. 2018. Science 361:1386–89
133. 133.

     Barkess G, West AG 2012. Epigenomics 4:67–80
134. 134.

     Gazner M, Felsenfeld G. 2006. Nat. Rev. 7:703–13
135. 135.

     Larson AG, Elnatan D, Keenen MM, Trnka MJ, Johnston JB et al. 2017. Nature 547:236–40
136. 136.

     Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH. 2017. Nature 547:241–45
137. 137.

     Bannister AJ, Zegerman P, Partridge JF, Miska EA, Thomas JO et al. 2001. Nature 410:120–24
138. 138.

     Lachner M, O'Carroll D, Rea S, Mechtler K, Jenuwein T. 2001. Nature 410:116–20
139. 139.

     Nakayama J, Rice JC, Strahl BD, Allis CD, Grewal SIS. 2001. Science 292:110–13
140. 140.

     Banani SF, Lee HO, Hyman AA, Rosen MK. 2017. Nat. Rev. Mol. Cell Biol. 18:285–98
141. 141.

     Sommer J-U, Daoud M. 1996. Phys. Rev. E 53:905–20
142. 142.

     Aagaard L, Laible G, Selenko P, Schmid M, Dorn R et al. 1999. EMBO J. 18:1923–38
143. 143.

     Raurell-Vila H, Bosch-Presegue L, Gonzalez J, Kane-Goldsmith N, Casal C et al. 2017. Epigenetics 12:166–75
144. 144.

     Sommer J-U, Merlitz H, Schiessel H. 2022. Macromolecules 55:114841–51
145. 145.

     Sandholtz SH, MacPherson Q, Spakowitz AJ. 2020. PNAS 117:20423–29
146. 146.

     Eeftens JM, Kapoor M, Michieletto D, Brangwynne CP. 2021. Nat. Commun. 12:5888
147. 147.

     Kireeva ML, Walter W, Tchernajenko V, Bondarenko V, Kashlev M, Studitsky VM. 2002. Mol. Cell 9:541–52
148. 148.

     Zidovska A, Weitz DA, Mitchison TJ. 2013. PNAS 110:15555–60
149. 149.

     Shaban HA, Barth R, Bystricky K. 2018. Nucl. Acids Res. 46:e77
150. 150.

     Eshghi I, Eaton JA, Zidovska A. 2021. Phys. Rev. Lett. 126:228101