Kinetics of Core Histones in Living Human Cells
Open accessAbstract
Histones H2A and H2B form part of the same nucleosomal structure as H3 and H4. Stable HeLa cell lines expressing histones H2B, H3, and H4 tagged with green fluorescent protein (GFP) were established; the tagged molecules were assembled into nucleosomes. Although H2B-GFP was distributed like DNA, H3-GFP and H4-GFP were concentrated in euchromatin during interphase and in R-bands in mitotic chromosomes. These differences probably result from an unregulated production of tagged histones and differences in exchange. In both single cells and heterokaryons, photobleaching revealed that H2B-GFP exchanged more rapidly than H3-GFP and H4-GFP. About 3% of H2B exchanged within minutes, whereas approximately 40% did so slowly (t(1/2) approximately 130 min). The rapidly exchanging fraction disappeared in 5,6-dichloro-1-beta-d-ribofuranosylbenzimidazole and so may represent H2B in transcriptionally active chromatin. The slowly exchanging fraction was probably associated with chromatin domains surrounding active units. H3-GFP and H4-GFP were assembled into chromatin when DNA was replicated, and then >80% remained bound permanently. These results reveal that the inner core of the nucleosome is very stable, whereas H2B on the surface of active nucleosomes exchanges continually.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The mobility of Stat1 is much faster than core histones and similar to other inducible transcriptional regulators.
“Compared with other studies, the mobility of Stat1 was much faster than the core histones and similar to other inducible transcriptional regulators (McNally et al. 2000; Kimura and Cook 2001; Lillemeier et al. 2001).”
From DNA binding controls inactivation and nuclear accumulation of the transcription factor Stat1 (2003) · cites this paper as Kimura and Cook 2001
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Kimura, H., Tao, Y., Roeder, R. G., & Cook, P. R. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.8.5383 · Cited by 164 · see citing works
Self-citation
Flagged first, then by citations
Research works printed but not linked: 49
- Bednar J. Studitsky V.M. Grigoryev S.A. Felsenfeld G. Woodcock C.L. The nature of the nucleosomal barrier to transcriptiondirect observation of paused intermediates by electron cryomicroscopy Mol. Cell. 4 1999 377 386 10518218
- Bell A.C. Felsenfeld G. Stopped at the borderboundaries and insulators Curr. Opin. Genet. Dev. 9 1999 191 198 10322134
- Belmont A.S. Dietzel S. Nye A.C. Strukov Y.G. Tumbar T. Large-scale chromatin structure and function Curr. Opin. Cell Biol. 11 1999 307 311 10395564
- Bonner W.M. Wu R.S. Panusz H.T. Muneses C. Kinetics of accumulation and depletion of soluble newly synthesized histone in the reciprocal regulation of histone and DNA synthesis Biochemistry 27 1988 6542 6550 3146349
- Dey A. Ellenberg J. Farina A. Coleman A.E. Maruyama T. Sciortino S. Lippincott-Schwartz J. Ozato K. A bromodomain protein, MCAP, associates with mitotic chromosomes and affects G(2)-to-M transition Mol. Cell. Biol. 20 2000 6537 6549 10938129 PMC86127
- Ellenberg J. Lippincott-Schwartz J. Dynamics and mobility of nuclear envelope proteins in interphase and mitotic cells revealed by green fluorescent protein chimeras Methods. 19 1999 362 372 10579931
- Haraguchi T. Kaneda T. Hiraoka Y. Dynamics of chromosomes and microtubules visualized by multiple-wavelength fluorescence imaging in living mammalian cellseffects of mitotic inhibitors on cell cycle progression Genes Cells. 2 1997 369 380 9286855
- Hebbes T.R. Clayton A.L. Thorne A.W. Crane-Robinson C. Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken b-globin chromosomal domain EMBO J. 13 1994 1823 1830 8168481 PMC395022
- Hendzel M.J. Davie J.R. Nucleosomal histones of transcriptionally active/competent chromatin preferentially exchange with newly synthesized histones in quiescent chicken erythrocytes Biochem. J. 271 1990 67 73 2171504 PMC1149514
- Ishimi Y. Komamura Y. You Z. Kimura H. Biochemical function of mouse minichromosome maintenance 2 protein J. Biol. Chem. 273 1998 8369 8375 9525946
- Ito T. Ikehara T. Nakagawa T. Kraus W.L. Muramatsu M. p300-mediated acetylation facilitates the transfer of histone H2A-H2B dimers from nucleosomes to a histone chaperone Genes Dev. 14 2000 1899 1907 10921904 PMC316828
- Izumi M. Miyazawa H. Kamakura T. Yamaguchi I. Endo T. Hanaoka F. Blasticidin S-resistance gene (bsr)a novel selectable marker for mammalian cells Exp. Cell Res. 197 1991 229 233 1720391
- Jackson V. Chalkley R. Histone synthesis and deposition in the G1 and S phases of hepatoma tissue culture cells Biochemistry. 24 1985 6921 6930 3935167
- Jackson V. In vivo studies on the dynamics of histone-DNA interactionevidence for nucleosome dissolution during replication and transcription and a low level of dissolution independent of both Biochemistry. 29 1990 719 731 1692479
- Kanda T. Sullivan K.F. Wahl G.M. Histone-GFP fusion protein enables sensitive analysis of chromosome dynamics in living mammalian cells Curr. Biol. 8 1998 377 385 9545195
- Kimura H. Takizawa N. Nozaki N. Sugimoto K. Molecular cloning of cDNA encoding mouse Cdc21 and CDC46 homologs and characterization of the productsphysical interaction between P1(MCM3) and CDC46 proteins Nucl. Acids Res. 23 1995 2097 2104 7610039 PMC306996
- Kruhlak M.J. Lever M.A. Fischle W. Verdin E. Bazett-Jones D.P. Hendzel M.J. Reduced mobility of the alternate splicing factor (ASF) through the nucleoplasm and steady state speckle compartments J. Cell Biol. 150 2000 41 51 10893255 PMC2185567
- Lever M.A. Th'ng J.P.H. Sun X. Hendzel M.J. Rapid exchange of histone H1.1 on chromatin in living human cells Nature 408 2000 873 876 11130728
- Li W. Nagaraja S. Delcuve G.P. Hendzel M.J. Davie J.R. Effects of histone acetylation, ubiquitination and variants on nucleosome stability Biochem. J. 296 1993 737 744 8280071 PMC1137757
- Louters L. Chalkley R. Exchange of histones H1, H2A, and H2B in vivo Biochemistry. 4 1985 3080 3085 4027229
- Luger K. Mäder A.W. Richmond R.K. Sargent D.F. Richmond T.J. Crystal structure of the nucleosome core particle at 2.8 Å resolution Nature. 389 1997 251 260 9305837
- Manders E.M.M. Kimura H. Cook P.R. Direct imaging of DNA in living cells reveals the dynamics of chromosome formation J. Cell Biol. 144 1999 813 821 10085283 PMC2148202
- Misteli T. Protein dynamicsimplications for nuclear architecture and gene expression Science. 291 2001 843 847 11225636
- Misteli T. Gunjan A. Hock R. Bustin M. Brown D.T. Dynamic binding of histone H1 to chromatin in living cells Nature. 408 2000 877 881 11130729
- Mizushima S. Nagata S. pEF-BOS, a powerful mammalian expression vector Nucleic Acids Res. 18 1990 5322 1698283 PMC332193
- Nguyen V.T. Giannoni F. Dubois M.F. Seo S.J. Vigneron M. Kedinger C. Bensaude O. In vivo degradation of RNA polymerase II largest subunit triggered by alpha-amanitin Nucl. Acids Res. 24 1996 2924 2929 8760875 PMC146057
- O'Keefe R.T. Henderson S.C. Spector D.L. Dynamic organization of DNA replication in mammalian cell nucleispatially and temporally defined replication of chromosome-specific alpha-satellite DNA sequences J. Cell Biol. 116 1992 1095 1110 1740468 PMC2289349
- O'Neill L.P. Keohane A.M. Lavender J.S. McCabe V. Heard E. Avner P. Brockdorff N. Turner B.M. A developmental switch in H4 acetylation upstream of Xist plays a role in X chromosome inactivation EMBO J. 18 1999 2897 2907 10329635 PMC1171370
- Orphanides G. Reinberg D. RNA polymerase II elongation through chromatin Nature. 407 2000 471 475 11028991
- Osley M.A. The regulation of histone synthesis in the cell cycle Annu. Rev. Biochem. 60 1991 827 861 1883210
- Perche P.-Y. Vourc'h C. Konecny L. Souchier C. Robert-Nicoud M. Dimitrov S. Khochbin S. Higher concentrations of histone macroH2A in the Barr body are correlated with higher nucleosome density Curr. Biol. 10 2000 1531 1534 11114523
- Perry M. Chalkley R. Histone acetylation increases the solubility of chromatin and occurs sequentially over most of the chromatin. A novel model for the biological role of histone acetylation J. Biol. Chem. 257 1982 7336 7347 7085629
- Perry C.A. Dadd C.A. Allis C.D. Annunziato A.T. Analysis of nucleosome assembly and histone exchange using antibodies specific for acetylated H4 Biochemistry. 32 1993 13605 13614 7504954
- Peterson C.L. Workman J.L. Promoter targeting and chromatin remodeling by the SWI/SNF complex Curr. Opin. Genet. Dev. 10 2000 187 192 10753786
- Phair R.D. Misteli T. High mobility of proteins in the mammalian cell nucleus Nature. 404 2000 604 609 10766243
- Ridgway P. Almouzni G. CAF-1 and the inheritance of chromatin statesat the crossroads of DNA replication and repair J. Cell Sci. 133 2000 2647 2658 10893180
- Sathyanarayana U.G. Freeman L.A. Lee M.-S. Garrard W.T. RNA polymerase-specific nucleosome disruption by transcription in vivo J. Biol. Chem. 274 1999 16431 16436 10347204
- Schmidt-Zachmann M.S. Dargemont C. Kuhn L.C. Nigg E.A. Nuclear export of proteinsthe role of nuclear retention Cell 74 1993 493 504 8348616
- Sehgal P.B. Darnell J.E. Tamm I. The inhibition by DRB (5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole) of hnRNA and mRNA production in HeLa cells Cell. 9 1976 473 480 1086720
- Stemmer C. Briand J.-P. Muller S. Mapping of linear histone regions exposed at the surface of the nucleosome in solution J. Mol. Biol. 273 1997 52 60 9367745
- Turner B.M. Histone acetylation and control of gene expression J. Cell Sci. 99 1991 13 20 1757496
- Turner B.M. Histone acetylation and epigenetic code BioEssays. 22 2000 836 845 10944586
- van-Holde K.E. Lohr D.E. Robert C. What happens to nucleosomes during transcription? J. Biol. Chem. 267 1992 2837 2840 1310672
- Verreault A. De novo nucleosome assemblynew pieces in old puzzle Genes Dev. 14 2000 1430 1438 10859162
- Wang T.S. Eukaryotic DNA polymerases Annu. Rev. Biochem. 60 1991 513 552 1883203
- White J. Stelzer E. Photobleaching GFP reveals protein dynamics inside live cells Trends Cell Biol. 9 1999 61 65 10087620
- Wolffe A.P. Hayes J.J. Chromatin disruption and modification Nucl. Acids Res. 27 1999 711 720 9889264 PMC148238
- Workman J.L. Kingston R.E. Alteration of nucleosome structure as a mechanism of transcriptional regulation Ann. Rev. Biochem. 67 1998 545 579 9759497
- Wyrick J.J. Hostege F.C.P. Jennings E.G. Causton H.C. Shore D. Grunstein M. Lander E.S. Young R.A. Chromosomal landscape of nucleosome-dependent gene expression and silencing in yeast Nature 402 1999 418 421 10586882
Cited by
Sorted by citations
From Silencing to Gene Expression
Janicki, S. M., Tsukamoto, T., Salghetti, S. E., Tansey, W. P., Sachidanandam, R., Prasanth, K. V., Ried, T., Shav-Tal, Y., Bertrand, E., Singer, R. H., et al. (2004) · Cell · doi:10.1016/s0092-8674(04)00171-0 · Cited by 704 · see citing works
Identification of long-lived proteins reveals exceptional stability of essential cellular structures
Toyama, B. H., Savas, J. N., Park, S. K., Harris, M. S., Ingolia, N. T., Yates, J. R., & Hetzer, M. W. (2013) · Cell · doi:10.1016/j.cell.2013.07.037 · Cited by 572 · see citing works
Changes in chromatin structure and mobility in living cells at sites of DNA double-strand breaks
Kruhlak, M. J., Celeste, A., Dellaire, G., Fernandez-Capetillo, O., Müller, W. G., McNally, J. G., Bazett-Jones, D. P., & Nussenzweig, A. (2006) · The Journal of Cell Biology · doi:10.1083/jcb.200510015 · Cited by 518 · see citing works
Prime, Repair, Restore: The Active Role of Chromatin in the DNA Damage Response
Soria, G., Polo, S. E., & Almouzni, G. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.06.002 · Cited by 342 · see citing works
Chromatin and Transcription in Yeast
Rando, O. J., & Winston, F. (2012) · Genetics · doi:10.1534/genetics.111.132266 · Cited by 269 · see citing works
Transcription in Living Cells: Molecular Mechanisms of Bursting
Rodriguez, J., & Larson, D. R. (2020) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-011520-105250 · Cited by 224 · see citing works
HP1α recruitment to DNA damage by p150CAF-1 promotes homologous recombination repair
Baldeyron, C., Soria, G., Roche, D., Cook, A. J. L., & Almouzni, G. (2011) · Journal of Cell Biology · doi:10.1083/jcb.201101030 · Cited by 200 · see citing works
The p400 ATPase regulates nucleosome stability and chromatin ubiquitination during DNA repair
Xu, Y., Sun, Y., Jiang, X., Ayrapetov, M. K., Moskwa, P., Yang, S., Weinstock, D. M., & Price, B. D. (2010) · Journal of Cell Biology · doi:10.1083/jcb.201001160 · Cited by 194 · see citing works
DNA binding controls inactivation and nuclear accumulation of the transcription factor Stat1
Meyer, T., Marg, A., Lemke, P., Wiesner, B., & Vinkemeier, U. (2003) · Genes & Development · doi:10.1101/gad.268003 · Cited by 161 · see citing works
Luijsterburg, M. S., von Bornstaedt, G., Gourdin, A. M., Politi, A. Z., Moné, M. J., Warmerdam, D. O., Goedhart, J., Vermeulen, W., van Driel, R., & Höfer, T. (2010) · Journal of Cell Biology · doi:10.1083/jcb.200909175 · Cited by 121 · see citing works
Histone dynamics in living cells revealed by photobleaching
Kimura, H. (2005) · DNA Repair · doi:10.1016/j.dnarep.2005.04.012 · Cited by 109 · see citing works
Self-citationLuijsterburg, M. S., Goedhart, J., Moser, J., Kool, H., Geverts, B., Houtsmuller, A. B., Mullenders, L. H. F., Vermeulen, W., & van Driel, R. (2007) · Journal of Cell Science · doi:10.1242/jcs.008367 · Cited by 105 · see citing works
A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting
Lammers, N. C., Kim, Y. J., Zhao, J., & Garcia, H. G. (2020) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2020.08.001 · Cited by 99 · see citing works
“cleosome Turnover Histone H3.3 Drosophila cell Genome-wide proling 1-1.5h [70] Histone H3 Yeast Genomic tiling arrays ˘1h [71] Histone H2B, H3, and H4 tagged with GFP Human cell FRAP several minutes [74] Histone H1 tagged with GFP Human cell FRAP several minutes [73] Histone H3 Plant cell (Alfalfa) Isotope labeling se…”
MethodChromatin structure and dynamics: Functional implications
Morales, V., Giamarchi, C., Chailleux, C., Moro, F., Marsaud, V., Le Ricousse, S., & Richard-Foy, H. (2001) · Biochimie · doi:10.1016/s0300-9084(01)01347-5 · Cited by 65 · see citing works
Dang, X., Singh, A., Spetman, B. D., Nolan, K. D., Isaacs, J. S., Dennis, J. H., Dalton, S., Marshall, A. G., & Young, N. L. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00414 · Cited by 41 · see citing works
- Authors
- Kimura, H., & Cook, P. R.
- Affiliations
- aSir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
- University of Oxford (GB)
- ORCID
- Cook, Peter R.
- Venue
- The Journal of Cell Biology
- Publisher
- Rockefeller University Press
- Published
- 2001-06-18
- Volume
- 153
- Issue
- 7
- Pages
- 1341-1354
- ISSN
- 0021-9525 (ISSN-L)
- 1540-8140
- PMC
- PMC2150718
- OpenAlex
- W2143351999
- Cited by
- 675
- References
- 1
- Citations by year
- 2026: 14 · 2025: 11 · 2024: 21 · 2023: 25 · 2022: 12 · 2021: 32 · 2020: 29 · 2019: 23 · 2018: 17 · 2017: 17 · 2016: 30 · 2015: 28 · 2014: 20 · 2013: 27 · 2012: 19
- FWCI
- 12.36
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- cc-by-nc-sa
- Locations
- The Journal of Cell Biology (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- histone H2B, histone H3, histone H4, nucleosome, euchromatin, R-band, metaphase chromosomes, heterokaryons, photobleaching, 5,6-dichloro-1-beta-D-ribofuranosylbenzimidazole, chromatin replication, transcriptionally active chromatin, nucleosome stability
- MeSH terms
- Cell Line, Cell Nucleus, Chromatin, Chromosomes, Dichlororibofuranosylbenzimidazole, DNA, HeLa Cells, Histones, Humans, Kinetics, Luminescent Proteins, Microscopy, Fluorescence, Nucleosomes, Photochemistry, Protein Binding, Recombinant Fusion Proteins, Transfection, S Phase, Macromolecular Substances, Green Fluorescent Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review