Abdennur N, Mirny LA (2020) Cooler: scalable storage for Hi-C data and other genomically labeled arrays. Bioinformatics 36:311–316. https://doi.org/10.1093/bioinformatics/btz540
Article CAS PubMed Google Scholar
Allshire RC, Madhani HD (2018) Ten principles of heterochromatin formation and function. Nat Rev Mol Cell Biol 19:229–244. https://doi.org/10.1038/nrm.2017.119
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 116:19939–19944. https://doi.org/10.1073/pnas.1907342116
Article ADS CAS PubMed 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 313:1642–1645. https://doi.org/10.1126/science.1127344
Article ADS PubMed Google Scholar
Bustin M, Misteli T (2016) Nongenetic functions of the genome. Science 352:aad6933. https://doi.org/10.1126/science.aad6933
Article CAS PubMed PubMed Central Google Scholar
Dekker J, Heard E (2015) Structural and functional diversity of Topologically Associating Domains. FEBS Lett 589:2877–2884. https://doi.org/10.1016/j.febslet.2015.08.044
Article CAS PubMed Google Scholar
Dekker J, Marti-Renom MA, Mirny LA (2013) Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet 14:390–403. https://doi.org/10.1038/nrg3454
Article CAS PubMed PubMed Central Google Scholar
Dunn KL, He S, Wark L, Delcuve GP, Sun JM, Yu Chen H, Mai S, Davie JR (2009) Increased genomic instability and altered chromosomal protein phosphorylation timing in HRAS-transformed mouse fibroblasts. Genes Chromosomes Cancer 48:397–409. https://doi.org/10.1002/gcc.20649
Article CAS PubMed Google Scholar
Egan SE, McClarty GA, Jarolim L, Wright JA, Spiro I, Hager G, Greenberg AH (1987) Expression of H-ras correlates with metastatic potential: evidence for direct regulation of the metastatic phenotype in 10T1/2 and NIH 3T3 cells. Mol Cell Biol 7:830–837. https://doi.org/10.1128/mcb.7.2.830-837.1987
Article CAS PubMed PubMed Central 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 38:276–278. https://doi.org/10.1038/s41587-020-0439-x
Article CAS PubMed Google Scholar
Furusawa T, Rochman M, Taher L, Dimitriadis EK, Nagashima K, Anderson S, Bustin M (2015) Chromatin decompaction by the nucleosomal binding protein HMGN5 impairs nuclear sturdiness. Nat Commun 6:6138. https://doi.org/10.1038/ncomms7138
Article ADS CAS PubMed Google Scholar
Gerlitz G (2020) The Emerging Roles of Heterochromatin in Cell Migration. Front Cell Dev Biol 8:394. https://doi.org/10.3389/fcell.2020.00394
Article PubMed PubMed Central Google Scholar
Germier T, Kocanova S, Walther N, Bancaud A, Shaban HA, Sellou H, Politi AZ, Ellenberg J, Gallardo F, Bystricky K (2017) Real-Time Imaging of a Single Gene Reveals Transcription-Initiated Local Confinement. Biophys J 113:1383–1394. https://doi.org/10.1016/j.bpj.2017.08.014
Article CAS PubMed PubMed Central Google Scholar
Grewal SI, Jia S (2007) Heterochromatin revisited. Nat Rev Genet 8:35–46. https://doi.org/10.1038/nrg2008
Article CAS PubMed Google Scholar
Hihara S, Pack CG, Kaizu K, Tani T, Hanafusa T, Nozaki T, Takemoto S, Yoshimi T, Yokota H, Imamoto N et al (2012) Local nucleosome dynamics facilitate chromatin accessibility in living mammalian cells. Cell Rep 2:1645–1656. https://doi.org/10.1016/j.celrep.2012.11.008
Article CAS PubMed Google Scholar
Hsia CR, McAllister J, Hasan O, Judd J, Lee S, Agrawal R, Chang CY, Soloway P, Lammerding J (2022) Confined migration induces heterochromatin formation and alters chromatin accessibility. iScience 25:104978. https://doi.org/10.1016/j.isci.2022.104978
Article ADS 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: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:eabn5626. https://doi.org/10.1126/sciadv.abn5626
Izeddin I, Recamier V, Bosanac L, Cisse II, Boudarene L, Dugast-Darzacq C, Proux F, Benichou O, Voituriez R, Bensaude O et al (2014) Single-molecule tracking in live cells reveals distinct target-search strategies of transcription factors in the nucleus. eLife 3. https://doi.org/10.7554/eLife.02230
Janssen A, Colmenares SU, Karpen GH (2018) Heterochromatin: Guardian of the Genome. Annu Rev Cell Dev Biol 34:265–288. https://doi.org/10.1146/annurev-cellbio-100617-062653
Article CAS PubMed 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 5:695–702. https://doi.org/10.1038/nmeth.1237
Article CAS PubMed PubMed Central Google Scholar
Jinesh GG, Sambandam V, Vijayaraghavan S, Balaji K, Mukherjee S (2018) Molecular genetics and cellular events of K-Ras-driven tumorigenesis. Oncogene 37:839–846. https://doi.org/10.1038/onc.2017.377
Article CAS PubMed Google Scholar
Kawaguchi A, Tanaka EM (2023) Chromosome Conformation Capture for Large Genomes. Methods Mol Biol 2562:291–318. https://doi.org/10.1007/978-1-0716-2659-7_20
Article CAS PubMed 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 153:1341–1353. 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 163:85–95. https://doi.org/10.1093/jb/mvx081
Article CAS PubMed Google Scholar
Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685. https://doi.org/10.1038/227680a0
Article ADS 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
Article CAS PubMed PubMed Central Google Scholar
Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. https://doi.org/10.1038/nmeth.1923
Article CAS PubMed PubMed Central Google Scholar
Lerner J, Gomez-Garcia PA, McCarthy RL, Liu Z, Lakadamyali M, Zaret KS (2020) Two-Parameter Mobility Assessments Discriminate Diverse Regulatory Factor Behaviors in Chromatin. Mol Cell 79(677–688):e676. https://doi.org/10.1016/j.molcel.2020.05.036
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293. https://doi.org/10.1126/science.1181369
Article ADS CAS PubMed PubMed Central Google Scholar
Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260. https://doi.org/10.1038/38444
Article ADS CAS PubMed Google Scholar
Maeshima K, Tamura S, Shimamoto Y (2018) Chromatin as a nuclear spring. Biophys Physicobiol 15:189–195. https://doi.org/10.2142/biophysico.15.0_189
Article CAS PubMed Google Scholar
Maeshima K, Iida S, Shimazoe MA, Tamura S, Ide S (2024) Is euchromatin really open in the cell? Trends Cell Biol 34:7–17 https://doi.org/10.1016/j.tcb.2023.05.007
Maeshima K, Iida S, Tamura S (2021) Physical Nature of Chromatin in the Nucleus. Cold Spring Harb Perspect Biol 13. https://doi.org/10.1101/cshperspect.a040675
Maizels Y, Elbaz A, Hernandez-Vicens R, Sandrusy O, Rosenberg A, Gerlitz G (2017) Increased chromatin plasticity supports enhanced metastatic potential of mouse melanoma cells. Exp Cell Res 357:282–290. https://doi.org/10.1016/j.yexcr.2017.05.025
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