Allahverdi A, Yang R, Korolev N, Fan Y, Davey CA, Liu CF, Nordenskiold L (2011) The effects of histone H4 tail acetylations on cation-induced chromatin folding and self-association. Nucleic Acids Res 39(5):1680–1691. https://doi.org/10.1093/nar/gkq900

Article  CAS  PubMed  Google Scholar 

Amitai A, Seeber A, Gasser SM, Holcman D (2017) Visualization of chromatin decompaction and break site extrusion as predicted by statistical polymer modeling of single-locus trajectories. Cell Rep 18(5):1200–1214. https://doi.org/10.1016/j.celrep.2017.01.018

Article  CAS  PubMed  Google Scholar 

Ashwin SS, Nozaki T, Maeshima K, Sasai M (2019) Organization of fast and slow chromatin revealed by single-nucleosome dynamics. Proc Natl Acad Sci U S A 116(40):19939–19944. https://doi.org/10.1073/pnas.1907342116

Article  CAS  PubMed  PubMed Central  Google Scholar 

Benedum J, Meusch M (1999) Robert Fuelgen (1884–1955) - some biographical thoughts. Histochem Cell Biol 111(5):337–343. https://doi.org/10.1007/s004180050366

Article  CAS  PubMed  Google Scholar 

Bennett RL, Bele A, Small EC, Will CM, Nabet B, Oyer JA, Huang X, Ghosh RP, Grzybowski AT, Yu T, Zhang Q, Riva A, Lele TP, Schatz GC, Kelleher NL, Ruthenburg AJ, Liphardt J, Licht JD (2019) A mutation in histone H2B represents a new class of oncogenic driver. Cancer Discov 9(10):1438–1451. https://doi.org/10.1158/2159-8290.CD-19-0393

Article  CAS  PubMed  PubMed Central  Google Scholar 

Betzig E, Patterson GH, Sougrat R, Lindwasser OW, Olenych S, Bonifacino JS, Davidson MW, Lippincott-Schwartz J, Hess HF (2006) Imaging intracellular fluorescent proteins at nanometer resolution. Science 313(5793):1642–1645. https://doi.org/10.1126/science.1127344

Article  PubMed  Google Scholar 

Bone JR, Lavender J, Richman R, Palmer MJ, Turner BM, Kuroda MI (1994) Acetylated histone H4 on the male X chromosome is associated with dosage compensation in Drosophila. Genes Dev 8(1):96–104. https://doi.org/10.1101/gad.8.1.96

Article  CAS  PubMed  Google Scholar 

Consortium EP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74. https://doi.org/10.1038/nature11247

Article  CAS  Google Scholar 

Cremer T, Cremer M, Hubner B, Silahtaroglu A, Hendzel M, Lanctot C, Strickfaden H, Cremer C (2020) The interchromatin compartment participates in the structural and functional organization of the cell nucleus. BioEssays 42(2):e1900132. https://doi.org/10.1002/bies.201900132

Article  PubMed  Google Scholar 

Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J Mol Biol 319(5):1097–1113. https://doi.org/10.1016/S0022-2836(02)00386-8

Article  CAS  PubMed  Google Scholar 

Davis CA, Hitz BC, Sloan CA, Chan ET, Davidson JM, Gabdank I, Hilton JA, Jain K, Baymuradov UK, Narayanan AK, Onate KC, Graham K, Miyasato SR, Dreszer TR, Strattan JS, Jolanki O, Tanaka FY, Cherry JM (2018) The encyclopedia of DNA elements (ENCODE): data portal update. Nucleic Acids Res 46(D1):D794–D801. https://doi.org/10.1093/nar/gkx1081

Article  CAS  PubMed  Google Scholar 

Dion V, Gasser SM (2013) Chromatin movement in the maintenance of genome stability. Cell 152(6):1355–1364. https://doi.org/10.1016/j.cell.2013.02.010

Article  CAS  PubMed  Google Scholar 

Dion MF, Altschuler SJ, Wu LF, Rando OJ (2005) Genomic characterization reveals a simple histone H4 acetylation code. Proc Natl Acad Sci U S A 102(15):5501–5506. https://doi.org/10.1073/pnas.0500136102

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dorigo B, Schalch T, Bystricky K, Richmond TJ (2003) Chromatin fiber folding: requirement for the histone H4 N-terminal tail. J Mol Biol 327(1):85–96. https://doi.org/10.1016/s0022-2836(03)00025-1

Article  CAS  PubMed  Google Scholar 

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S (2020) The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol 38(3):276–278. https://doi.org/10.1038/s41587-020-0439-x

Article  CAS  PubMed  Google Scholar 

Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S (2022) The nf-core framework for community-curated bioinformatics pipelines. Zenodo. https://doi.org/10.5281/zenodo.7139814

Gatto A, Forest A, Quivy JP, Almouzni G (2022) HIRA-dependent boundaries between H3 variants shape early replication in mammals. Mol Cell 82(10):1909-1923.e1905. https://doi.org/10.1016/j.molcel.2022.03.017

Article  CAS  PubMed  Google Scholar 

Gorisch SM, Wachsmuth M, Toth KF, Lichter P, Rippe K (2005) Histone acetylation increases chromatin accessibility. J Cell Sci 118(Pt 24):5825–5834. https://doi.org/10.1242/jcs.02689

Article  CAS  PubMed  Google Scholar 

Grunstein M (1997) Histone acetylation in chromatin structure and transcription. Nature 389(6649):349–352. https://doi.org/10.1038/38664

Article  CAS  PubMed  Google Scholar 

Hansen AS, Woringer M, Grimm JB, Lavis LD, Tjian R, Darzacq X (2018) Robust model-based analysis of single-particle tracking experiments with spot-on. Elife. https://doi.org/10.7554/eLife.33125

Article  PubMed  PubMed Central  Google Scholar 

Hansen JC, Maeshima K, Hendzel MJ (2021) The solid and liquid states of chromatin. Epigenetics Chromatin 14(1):50. https://doi.org/10.1186/s13072-021-00424-5

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hihara S, Pack CG, Kaizu K, Tani T, Hanafusa T, Nozaki T, Takemoto S, Yoshimi T, Yokota H, Imamoto N, Sako Y, Kinjo M, Takahashi K, Nagai T, Maeshima K (2012) Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells. Cell Rep 2(6):1645–1656. https://doi.org/10.1016/j.celrep.2012.11.008

Article  CAS  PubMed  Google Scholar 

Ide S, Sasaki A, Kawamoto Y, Bando T, Sugiyama H, Maeshima K (2021) Telomere-specific chromatin capture using a pyrrole-imidazole polyamide probe for the identification of proteins and non-coding RNAs. Epigenetics Chromatin 14(1):46. https://doi.org/10.1186/s13072-021-00421-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ide S, Tamura S, Maeshima K (2022) Chromatin behavior in living cells: lessons from single-nucleosome imaging and tracking. BioEssays 44(7):e2200043. https://doi.org/10.1002/bies.202200043

Article  CAS  PubMed  Google Scholar 

Iida S, Shinkai S, Itoh Y, Tamura S, Kanemaki MT, Onami S, Maeshima K (2022) Single-nucleosome imaging reveals steady-state motion of interphase chromatin in living human cells. Sci Adv 8(22):eabn5626. https://doi.org/10.1126/sciadv.abn5626

Article  CAS  PubMed  PubMed Central  Google Scholar 

Iida S, Ide S, Tamura S, Tani T, Goto T, Shribak M, Maeshima K (2023) Orientation-Independent-DIC imaging reveals that a transient rise in depletion force contributes to mitotic chromosome condensation. bioRxiv. https://doi.org/10.1101/2023.11.11.566679

Article  PubMed  PubMed Central  Google Scholar 

Izeddin I, Recamier V, Bosanac L, Cisse II, Boudarene L, Dugast-Darzacq C, Proux F, Benichou O, Voituriez R, Bensaude O, Dahan M, Darzacq X (2014) Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus. Elife. https://doi.org/10.7554/eLife.02230

Article  PubMed  PubMed Central  Google Scholar 

Jaqaman K, Loerke D, Mettlen M, Kuwata H, Grinstein S, Schmid SL, Danuser G (2008) Robust single-particle tracking in live-cell time-lapse sequences. Nat Methods 5(8):695–702. https://doi.org/10.1038/nmeth.1237

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kimura H, Cook PR (2001) Kinetics of core histones in living human cells: little exchange of H3 and H4 and some rapid exchange of H2B. J Cell Biol 153(7):1341–1353. https://doi.org/10.1083/jcb.153.7.1341

Article  CAS  PubMed  PubMed Central  Google Scholar 

Koyama M, Kurumizaka H (2018) Structural diversity of the nucleosome. J Biochem 163(2):85–95. https://doi.org/10.1093/jb/mvx081

Article  CAS  PubMed  Google Scholar 

Kwiatkowski N, Zhang T, Rahl PB, Abraham BJ, Reddy J, Ficarro SB, Dastur A, Amzallag A, Ramaswamy S, Tesar B, Jenkins CE, Hannett NM, McMillin D, Sanda T, Sim T, Kim ND, Look T, Mitsiades CS, Weng AP, Brown JR, Benes CH, Marto JA, Young RA, Gray NS (2014) Targeting transcription regulation in cancer with a covalent CDK7 inhibitor. Nature 511(7511):616–620. https://doi.org/10.1038/nature13393

Article  CAS  PubMed  PubMed Central  Google Scholar 

Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227(5259):680–685. https://doi.org/10.1038/227680a0

Article  CAS  PubMed  Google Scholar 

Lakadamyali M (2022) Single nucleosome tracking to study chromatin plasticity. Curr Opin Cell Biol 74:23–28. https://doi.org/10.1016/j.ceb.2021.12.005