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Regulation of nucleosome dynamics by histone modifications
Abstract
Chromatin is a dynamic structure that must respond to myriad stimuli to regulate access to DNA, and chemical modification of histones is a major means by which the cell modulates nucleosome mobility and turnover. Histone modifications are linked to essentially every cellular process requiring DNA access, including transcription, replication and repair. Here we consider properties of the major types of histone modification in the context of their associated biological processes to view them in light of the cellular mechanisms that regulate nucleosome dynamics.
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“histones enter in nucleosome formation and proper DNA wrapping after the S phase of cell cycle [65]”
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Cites
Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
Mikkelsen, T. S., Ku, M., Jaffe, D. B., Issac, B., Lieberman, E., Giannoukos, G., Alvarez, P., Brockman, W., Kim, T.-K., Koche, R. P., et al. (2007) · Nature · doi:10.1038/nature06008 · Cited by 4,129
Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain
Bannister, A. J., Zegerman, P., Partridge, J. F., Miska, E. A., Thomas, J. O., Allshire, R. C., & Kouzarides, T. (2001) · Nature · doi:10.1038/35065138 · Cited by 2,903
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898
ACETYLATION AND METHYLATION OF HISTONES AND THEIR POSSIBLE ROLE IN THE REGULATION OF RNA SYNTHESIS
Allfrey, V. G., Faulkner, R. D., & Mirsky, A. E. (1964) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.51.5.786 · Cited by 2,788
Combinatorial patterns of histone acetylations and methylations in the human genome
Wang, Z., Zang, C., Rosenfeld, J. A., Schones, D. E., Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Peng, W., Zhang, M. Q., et al. (2008) · Nature Genetics · doi:10.1038/ng.154 · Cited by 2,331
A unique chromatin signature uncovers early developmental enhancers in humans
Rada-Iglesias, A., Bajpai, R., Swigut, T., Brugmann, S. A., Flynn, R. A., & Wysocka, J. (2011) · Nature · doi:10.1038/nature09692 · Cited by 2,233
A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage
Paull, T. T., Rogakou, E. P., Yamazaki, V., Kirchgessner, C. U., Gellert, M., & Bonner, W. M. (2000) · Current Biology · doi:10.1016/s0960-9822(00)00610-2 · Cited by 2,098
DNA Replication in Eukaryotic Cells
Bell, S. P., & Dutta, A. (2002) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.71.110601.135425 · Cited by 2,065
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
Wang, K., Yang, Y. W., Liu, B., Sanyal, A., Corces, M. R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., et al. (2011) · Nature · doi:10.1038/nature09819 · Cited by 2,005
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Items 101–200 of 925
Role of chromatin in water stress responses in plants
Han, S., & Wagner, D. (2013) · Journal of Experimental Botany · doi:10.1093/jxb/ert403 · Cited by 99
“The functional outcome of these changes in histone modifications is either alteration of the strength of the DNA histone interaction or recruitment of non-histone proteins, the so-called ‘readers’, to the chromatin (reviewed by Bannister and Kouzarides, 2011; Patel and Wang, 2013; Zentner and Henikoff, 2013).”
BackgroundInfluentialFenley, A. T., Anandakrishnan, R., Kidane, Y. H., & Onufriev, A. V. (2018) · Epigenetics & Chromatin · doi:10.1186/s13072-018-0181-5 · Cited by 100
Histone Core Phosphorylation Regulates DNA Accessibility
Brehove, M., Wang, T., North, J., Luo, Y., Dreher, S. J., Shimko, J. C., Ottesen, J. J., Luger, K., & Poirier, M. G. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m115.661363 · Cited by 93
“Peptides H3(47-90)A47Thz with or without K56ac and H3(1-46) with or without pY41 were prepared on Fmoc-Dbz(Alloc)-derivitized resin as described in (42) and cleaved and purified as the C-terminal N-acylurea derivatives.”
MethodChromatin remodelling during male gametophyte development
Borg, M., & Berger, F. (2015) · The Plant Journal · doi:10.1111/tpj.12856 · Cited by 88
Michieletto, D., Orlandini, E., & Marenduzzo, D. (2016) · Physical Review X · doi:10.1103/physrevx.6.041047 · Cited by 100
Dehennaut, V., Leprince, D., & Lefebvre, T. (2014) · Frontiers in Endocrinology · doi:10.3389/fendo.2014.00155 · Cited by 91
“The chromatin organization is managed in part by a complex network of PTMs of histones called the “histone code” (15).”
BackgroundAn Overview of Chromatin-Regulating Proteins in Cells
Zhang, P., Torres, K. E., Liu, X., Liu, C.-G., & Pollock, R. E. (2016) · Current Protein and Peptide Science · doi:10.2174/1389203717666160122120310 · Cited by 91
“The status of histone acetylation on nucleosomes is very dynamic and is regulated by two groups of enzymes that have opposite functions: 1) histone acetyl-transferases (HATs), which cause histone acetylation, and 2) histone deacetylases (HDACs), which cause histone deacetylation.”
BackgroundInfluentialA phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution
Grau‐Bové, X., Navarrete, C., Chiva, C., Pribasnig, T., Antó, M., Torruella, G., Galindo, L. J., Lang, B. F., Moreira, D., López‐García, P., et al. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01771-6 · Cited by 87
“Histone chemical modifications, including acetylations and methylations play a central role in genome regulation and transgenerational epigenetic inheritance 3,18–21 .”
BackgroundWang, Z., Mao, Y., Guo, Y., Gao, J., Liu, X., Li, S., Lin, Y. J., Chen, H., Wang, J. P., Chiang, V. L., et al. (2020) · PLANT PHYSIOLOGY · doi:10.1104/pp.20.01033 · Cited by 87
“326 There is growing evidence that transcriptional repression events may result from histone 327 deacetylation (Shahbazian and Grunstein, 2007; Zentner and Henikoff, 2013; Liu et al., 2014; 328 Gao et al., 2015; Han et al., 2016; Li et al., 2017; Zhang et al., 2018; Park et al., 2019; Ueda and…”
BackgroundOxygen‐sensing mechanisms in cells
Wilson, J. W., Shakir, D., Batie, M., Frost, M., & Rocha, S. (2020) · The FEBS Journal · doi:10.1111/febs.15374 · Cited by 86
Chromosome boundary elements and regulation of heterochromatin spreading
Wang, J., Lawry, S. T., Cohen, A. L., & Jia, S. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1725-x · Cited by 96
“It is well established that chromatin structure is regulated by both chromatin remodeling activities and the modification of histones and DNA [10].”
BackgroundHistone ubiquitylation and its roles in transcription and DNA damage response
Meas, R., & Mao, P. (2015) · DNA repair · doi:10.1016/j.dnarep.2015.09.016 · Cited by 90
“Various post-translational modifications (PTMs), such as methylation, acetylation, ubiquitylation, and phosphorylation on histones, have emerged as major regulators of chromatin structure, reviewed in Suganuma and Workman, and Zentner and Henikoff [4,5].”
Early secure attachment as a protective factor against later cognitive decline and dementia
Walsh, E., Blake, Y., Donati, A., Stoop, R., & von Gunten, A. (2019) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2019.00161 · Cited by 84
“Acetylation of histones, on the other hand, leads to greater levels of gene transcription (Zentner and Henikoff, 2013).”
BackgroundUnderstanding Epigenetics in the Neurodegeneration of Alzheimer’s Disease: SAMP8 Mouse Model
Griñán‐Ferré, C., Corpas, R., Puigoriol‐Illamola, D., Palomera‐Ávalos, V., Sanfeliu, C., & Pallàs, M. (2018) · Journal of Alzheimer s Disease · doi:10.3233/jad-170664 · Cited by 86
“has an opposite effect to that of methylation [46].”
BackgroundDNA binding drives the association of BRG1/hBRM bromodomains with nucleosomes
Morrison, E. A., Sanchez, J. C., Ronan, J. L., Farrell, D. P., Varzavand, K., Johnson, J. K., Gu, B. X., Crabtree, G. R., & Musselman, C. A. (2017) · Nature Communications · doi:10.1038/ncomms16080 · Cited by 81
“Comparison of 1H-15N HSQC spectra for BRD or AT-BRD in the (1) apo state, (2) presence of DNA alone, (3) presence of peptide alone or (4) presence of both DNA and peptide provides insight into possible ternary complex formation and communication between binding pockets.”
BackgroundMethodPoliner, E., Panchy, N. L., Newton, L. A., Wu, G., Lapinsky, A., Bullard, B. A., Zienkiewicz, A., Benning, C., Shiu, S., & Farré, E. M. (2015) · The Plant Journal · doi:10.1111/tpj.12944 · Cited by 80
Hardeland, R. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms151018221 · Cited by 84
“, utilisation of exons or regulatory sections of introns wherever CpG islands are found [7–10], chromatin remodeling via histone modification [11–14], and the previously enigmatic imprinting of alleles [15].”
BackgroundLysine-specific modifications of p53: a matter of life and death?
Marouco, D. M., Garabadgiu, A. V., Melino, G., & Barlev, N. A. (2013) · Oncotarget · doi:10.18632/oncotarget.1436 · Cited by 84
“In a similar way, lysine acetylation of histone proteins is known to decrease the interaction between the histones and the DNA, leading to a more relaxed chromatin state, and thus facilitating the access of the transcriptional machinery to the DNA [107] (Table 1).”
BackgroundBerr, A., Shafiq, S., Pinon, V., Dong, A., & Shen, W. (2014) · The Plant Journal · doi:10.1111/tpj.12729 · Cited by 81
“Covalent modifications of histone tails are crucial for regulation of gene transcription within the chromatin context (Berr et al., 2011; Zentner and Henikoff, 2013).”
BackgroundHistone target selection within chromatin: an exemplary case of teamworkPreprint
Lalonde, M., Cheng, X., & Côté, J. (2014) · Genes & Development · doi:10.1101/gad.236331.113 · Cited by 85
“More recently, new PTMs, including lysine acylation or crotonylation and serine glycosylation, have begun to emerge, but little is known about how they influence chromatin dynamics (Tan et al. 2011; Zentner and Henikoff 2013).”
BackgroundZhang, W., Huang, J. T., & Cook, D. E. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009376 · Cited by 79
“In eukaryotes, nuclear DNA is packaged around histone proteins to form nucleosomes [5].”
BackgroundWoods, R. M., Lorusso, J. M., Fletcher, J., ElTaher, H., McEwan, F., Harris, I., Kowash, H. M., D'Souza, S. W., Harte, M., Hager, R., et al. (2023) · Neuronal Signaling · doi:10.1042/ns20220064 · Cited by 87
Evidence for the implication of the histone code in building the genome structure
Prakash, K., & Fournier, D. (2017) · Biosystems · doi:10.1016/j.biosystems.2017.11.005 · Cited by 82
Histone N-alpha terminal modifications: genome regulation at the tip of the tail
Demetriadou, C., Koufaris, C., & Kirmizis, A. (2020) · Epigenetics & Chromatin · doi:10.1186/s13072-020-00352-w · Cited by 81
Fujioka, N., Fritz, V. A., Upadhyaya, P., Kassie, F., & Hecht, S. S. (2016) · Molecular Nutrition & Food Research · doi:10.1002/mnfr.201500889 · Cited by 84
“Although reduced DNMT expression is expected to result in an overall decrease in promoter methylation, the authors postulated that DNA methylation patterns induced by DIM could not simply be explained by its DNMT inhibitory activities, and additional factors such as the presence or absence of other chromatin-associate…”
Ferioli, M., Zauli, G., Maiorano, P., Milani, D., Mirandola, P., & Neri, L. M. (2019) · Journal of Cellular Physiology · doi:10.1002/jcp.28304 · Cited by 85
“Consequently, acetylation facilitates gene transcription whereas deacetylation inhibits gene transcription (Jahan, Sun, He, & Davie, 2018; Zentner & Henikoff, 2013).”
BackgroundNiederberger, E., Resch, E., Parnham, M. J., & Geißlinger, G. (2017) · Nature Reviews Neurology · doi:10.1038/nrneurol.2017.68 · Cited by 77
Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation
Nalabothula, N., Al-jumaily, T., Eteleeb, A. M., Flight, R. M., Shao, X., Moseley, H., Rouchka, E. C., & Fondufe‐Mittendorf, Y. N. (2015) · PLoS ONE · doi:10.1371/journal.pone.0135410 · Cited by 80
“H3K36me3, H3K4me3, and H3K27ac are considered “active”marks, whereas H3K9me3 and H3K27me3 are considered “repressive”marks [63].”
Epigenomics and the concept of degeneracy in biological systems
Maleszka, R., Mason, P. H., & Barron, A. B. (2013) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt050 · Cited by 78
Histone Acetylation Changes in Plant Response to Drought Stress
Li, S., He, X. J., Gao, Y., Zhou, C., Chiang, V. L., & Li, W. (2021) · Genes · doi:10.3390/genes12091409 · Cited by 77
How is epigenetic information maintained through DNA replication?
Budhavarapu, V. N., Chavez-Tomar, M., & Tyler, J. K. (2013) · Epigenetics & Chromatin · doi:10.1186/1756-8935-6-32 · Cited by 77
“As such, there are clear examples of specific histone modifier enzymes, particularly those that generate repressive histone post-translational modifications, being physically recruited to the site of DNA replication to re-establish the histone post-translational modifications [37,38].”
BackgroundPharmacological intervention of histone deacetylase enzymes in the neurodegenerative disorders
Gupta, R. V., Ambasta, R. K., & Kumar, P. (2020) · Life Sciences · doi:10.1016/j.lfs.2020.117278 · Cited by 85
Wang, L., Xu, Z., Khawar, M. B., Liu, C., & Li, W. (2017) · Reproduction · doi:10.1530/rep-17-0153 · Cited by 78
“More than 50 histone PTMs have been identified, and this number is growing rapidly (Grunstein 1997, Jenuwein & Allis 2001, Eberharter & Becker 2002, Iizuka & Smith 2003, Zentner & Henikoff 2013).”
BackgroundZhang, Z., Yang, H., & Wang, H. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.599605 · Cited by 79
“Covalent modifications of histones, including acetylation, methylation, phosphorylation, and ubiquitination, are important regulators of chromatin-based nuclear processes including transcription and DNA damage repair (1, 2).”
Clouaire, T., Webb, S., & Bird, A. P. (2014) · Genome biology · doi:10.1186/s13059-014-0451-x · Cited by 76
“Our data could also fit with the idea that histone modifications mainly modulate nucleosome dynamics [58,59].”
The effects of superovulation and reproductive aging on the epigenome of the oocyte and embryo
Marshall, K. L., & Rivera, R. M. (2017) · Molecular Reproduction and Development · doi:10.1002/mrd.22951 · Cited by 83
“…of lysine residues of histone tails (Phillips, 1963) neutralizes their positive charge, interrupting histone interaction with DNA and creating a transcriptionally permissive chromatin structure (Allfrey, Faulkner, & Mirsky, 1964; Brownell et al., 1996; reviewed by Zentner & Henikoff, 2013).”
BackgroundCan changes in histone acetylation contribute to memory formation?
López‐Atalaya, J. P., & Barco, Á. (2014) · Trends in Genetics · doi:10.1016/j.tig.2014.09.003 · Cited by 79
Song, Y., Li, Z., Liu, X., Wang, R., Li, L.-W., & Zhang, Q. (2017) · Tumor Biology · doi:10.1177/1010428317712617 · Cited by 73
Metabolic Mechanisms of Epigenetic Regulation
Meier, J. L. (2013) · ACS Chemical Biology · doi:10.1021/cb400689r · Cited by 75
Epigenetic Modification Mechanisms Involved in Inflammation and Fibrosis in Renal Pathology
Morgado‐Pascual, J. L., Marchant, V. A., Rodrigues-Díez, R. R., Doladé, N. G., Suárez-Álvarez, B., Kerr, B., Valdivielso, J. M., Ruiz‐Ortega, M., & Rayego‐Mateos, S. (2018) · Mediators of Inflammation · doi:10.1155/2018/2931049 · Cited by 73
“Histone modifications can occur within the folded domain of the histones or in the N- and C-terminal domains that extend beyond the nucleosome [56, 57].”
BackgroundWalker, M., Billings, T., Baker, C. L., Powers, N. R., Tian, H., Saxl, R. L., Choi, K., Hibbs, M., Carter, G. W., Handel, M. A., et al. (2015) · Epigenetics & Chromatin · doi:10.1186/s13072-015-0024-6 · Cited by 70
“These modifications include faster turnover of histone acetylation marks and H3K36me3 [40–42] and the acquisition of ubiquitinated H2BK120 [43, 44].”
BackgroundAdamik, J., Jin, S., Sun, Q., Zhang, P., Weiss, K. R., Anderson, J. L., Silbermann, R., Roodman, G. D., & Galson, D. L. (2017) · Molecular Cancer Research · doi:10.1158/1541-7786.mcr-16-0242-t · Cited by 73
“Of note, LSD1 primarily acts on H3K4me1/2 substrates (42), but its presence regulating the H3K4 methylation state is primarily associated with gene repression and decreased levels of H3K4me3 at promoters (43).”
BackgroundSynthetic epigenetics—towards intelligent control of epigenetic states and cell identity
Jurkowski, T. P., Ravichandran, M., & Stepper, P. (2015) · Clinical Epigenetics · doi:10.1186/s13148-015-0044-x · Cited by 73
“This might be explained by the fact that in contrast to the not yet fully understood mechanism of maintenance of histone modifications during mitotic division [112], the mechanisms of setting up and inheritance of DNA methylation have been thoroughly studied (reviewed in [113]).”
BackgroundStructural analysis of nucleosomal barrier to transcription
Gaykalova, D. A., Kulaeva, O. I., Игоревна, В. О., Shaytan, A. К., Hsieh, F., Kirpichnikov, M. P., Sokolova, O. S., & Studitsky, V. M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1508371112 · Cited by 72
“(C) After formation of a small intranucleosomal DNA loop on the surface of the nucleosome (1), Pol II likely initiates uncoiling of nucleosomal DNA, starting from the promoter–distal end (2), and eventually involving all nucleosomal DNA in front of the enzyme (3).”
BackgroundAhR regulates the expression of human cytochrome P450 1A1 (CYP1A1) by recruiting Sp1
Ye, W., Chen, R., Chen, X., Huang, B., Lin, R., Xie, X., Chen, J., Jiang, J., Deng, Y., & Wen, J. (2019) · The FEBS Journal · doi:10.1111/febs.14956 · Cited by 71
Remodelling chromatin to shape development of plants
Gentry, M., & Hennig, L. (2013) · Experimental Cell Research · doi:10.1016/j.yexcr.2013.11.010 · Cited by 71
The chromatin remodelers RSC and ISW1 display functional and chromatin-based promoter antagonism
Parnell, T. J., Schlichter, A., Wilson, B. G., & Cairns, B. R. (2015) · eLife · doi:10.7554/elife.06073 · Cited by 70
The “ART” of Epigenetics in Melanoma: From histone “Alterations, to Resistance and Therapies”
Strub, T., Ballotti, R., & Bertolotto, C. (2020) · Theranostics · doi:10.7150/thno.36218 · Cited by 73
“The balance of these histone modifications orchestrates the above mentioned states by modifying the charges of the nucleosomal structure by respectively decreasing or increasing the histone-DNA interactions and therefore modulation of transcriptional activation and repression [15].”
BackgroundReading the Combinatorial Histone Language
Su, Z., & Denu, J. M. (2015) · ACS Chemical Biology · doi:10.1021/acschembio.5b00864 · Cited by 82
Shaping epigenetic memory via genomic bookmarking
Michieletto, D., Chiang, M., Colì, D., Papantonis, A., Orlandini, E., Cook, P. R., & Marenduzzo, D. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx1200 · Cited by 72
Accelerating the Field of Epigenetic Histone Modification Through Mass Spectrometry–Based Approaches
Lu, C., Coradin, M., Porter, E. G. P., & Garcia, B. A. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r120.002257 · Cited by 71
“, acetylation and phosphorylation, effectively reduce the positive charge of histones, influencing the overall structure of chromatin, facilitating or impairing DNA access (7, 85).”
BackgroundProteomics of post-translational modifications of mammalian spermatozoa
Baker, M. A. (2015) · Cell and Tissue Research · doi:10.1007/s00441-015-2249-x · Cited by 69
“As lysine acetylation neutralises the positive charge of the residue, this will weaken the ionic interaction between the positively charged lysine and the negatively charged phosphate DNA backbone, aiding the removal of the histone protein (Zentner and Henikoff 2013).”
Opposing roles of H3- and H4-acetylation in the regulation of nucleosome structure—a FRET study
Gansen, A., Tóth, K., Schwarz, N., & Langowski, J. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1354 · Cited by 69
“These mechanisms include posttranslational modifications (PTMs) on histones and DNA, such as histone acetylation or DNA methylation (1).”
BackgroundZhou, W., Zhu, Y., Dong, A., & Shen, W. (2015) · The Plant Journal · doi:10.1111/tpj.12830 · Cited by 70
“ribosylation, phosphorylation, and ubiquitination at various histone amino acid residues (Tessarz and Kouzarides, 2014; Zentner and Henikoff, 2013).”
BackgroundInfluentialThe impact of the vitamin D-modulated epigenome on VDR target gene regulation
Nurminen, V., Neme, A., Seuter, S., & Carlberg, C. (2018) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2018.05.006 · Cited by 69
Mohd-Sarip, A., Teeuwssen, M., Bot, A. G. M., Herdt, M. J. D., Willems, S. M., de Jong, R. J. B., Looijenga, L. H. J., Zatreanu, D. A., Bezstarosti, K., van Riet, J., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.020 · Cited by 68
“A second mechanism to control chromatin state involves a plethora of post-translational histone modifications, which can direct the recruitment of regulatory proteins (including remodel-ers) and modulate the folding of the chromatin fiber (Patel and Wang, 2013; Zentner and Henikoff, 2013).”
Epigenetic perspectives on systemic autoimmune disease
Karagianni, P., & Tzioufas, A. G. (2019) · Journal of Autoimmunity · doi:10.1016/j.jaut.2019.102315 · Cited by 68
Cognition-Enhancing Vagus Nerve Stimulation Alters the Epigenetic Landscape
Sanders, T. H., Weiss, J. B., Hogewood, L., Chen, L., Paton, C., McMahan, R. L., & Sweatt, J. D. (2019) · Journal of Neuroscience · doi:10.1523/jneurosci.2407-18.2019 · Cited by 71
“During systems consolidation, memories are uploaded from the hippocampus to the cortex for persistent storage (Levenson et al., 2004; Miller et al., 2010; Itzhak et al., 2013; Zentner and Henikoff, 2013).”
BackgroundInfluentialMelanocytes in the Skin – Comparative Whole Transcriptome Analysis of Main Skin Cell Types
Reemann, P., Reimann, E., Ilmjärv, S., Porosaar, O., Silm, H., Jaks, V., Vasar, E., Kingo, K., & Kõks, S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0115717 · Cited by 64
“For instance, the high prevalence of histone genes in MC reveal to intensified DNA synthesis as histones are responsible for nucleosome structure and proper DNA wrapping [31].”
BackgroundCharacterization of functional disordered regions within chromatin-associated proteins
Musselman, C. A., & Kutateladze, T. G. (2021) · iScience · doi:10.1016/j.isci.2021.102070 · Cited by 68
Park, J., Estrada, J., Johnson, G., Vincent, B. J., Ricci-Tam, C., Bragdon, M. D. J., Shulgina, Y., Cha, A., Wunderlich, Z., Gunawardena, J., et al. (2019) · eLife · doi:10.7554/elife.41266 · Cited by 69
“The eukaryotic transcriptional machinery involves not only TFs, but also chromatin remodeling machinery, and cofactors that relay information about TF binding to the basal transcriptional machinery (Allen and Taatjes, 2015; Hargreaves and Crabtree, 2011; Levine, 2010; Wang et al., 2013; Zentner and Henikoff, 2013).”
BackgroundEpe1 recruits BET family bromodomain protein Bdf2 to establish heterochromatin boundariesPreprint
Wang, J., Tadeo, X., Hou, H., Tu, P. G., Thompson, J. X., Yates, J. R., & Jia, S. (2013) · Genes & Development · doi:10.1101/gad.221010.113 · Cited by 76
“Chromatin regulates diverse DNA-based processes such as gene transcription, recombination, and DNA damage repair (Bannister and Kouzarides 2011; Zentner and Henikoff 2013).”
BackgroundJing, Y., Ding, D., Tian, G., Kwan, K. C. J., Liu, Z., Ishibashi, T., & Li, X. D. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa663 · Cited by 62
Roquis, D., Lepesant, J. M. J., Picard, M., Freitag, M., Parrinello, H., Groth, M., Emans, R., Cosseau, C., & Grunau, C. (2015) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0003853 · Cited by 70
Cancer cell migration in 3D tissue: Negotiating space by proteolysis and nuclear deformability
Krause, M., & Wolf, K. (2015) · Cell Adhesion & Migration · doi:10.1080/19336918.2015.1061173 · Cited by 66
“This induces increased transcription activity by enhanced accessibility for RNA polymerase and transcription factors.(59,60) Chromatin decondensation therefore leads to nuclear size increase as well as nuclear softening.”
BackgroundDNA repair goes hip-hop: SMARCA and CHD chromatin remodellers join the break dance
Rother, M. B., & van Attikum, H. (2017) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2016.0285 · Cited by 67
Ji, F., Liao, H., Pan, S. D., Ouyang, L., Jia, F., Fu, Z., Zhang, F., Geng, X., Wang, X., Li, T., et al. (2020) · Cell Research · doi:10.1038/s41422-020-0357-y · Cited by 65
Molecular features and gene expression signature of metastatic colorectal cancer (Review)
Poturnajova, M., Furielova, T., Balintova, S., Schmidtova, S., Kučerová, L., & Matúšková, M. (2021) · Oncology Reports · doi:10.3892/or.2021.7961 · Cited by 70
Role of Histone Acetylation in Cell Cycle Regulation
Koprinarova, M., Schnekenburger, M., & Diederich, M. F. (2015) · Current Topics in Medicinal Chemistry · doi:10.2174/1568026615666150825140822 · Cited by 67
The Chromatin Landscape of Kaposi’s Sarcoma-Associated Herpesvirus
Tóth, Z., Brulois, K., & Jung, J. U. (2013) · Viruses · doi:10.3390/v5051346 · Cited by 65
“Depending on whether a gene is destined for activation or silencing, different histone modifying enzyme complexes are recruited to the gene promoter to generate specific posttranslational modifications on histones called histone marks, which function as key modulators of gene expression (Figure 1B) [16].”
BackgroundRoquis, D., Taudt, A., Geyer, K. K., Padalino, G., Hoffmann, K. F., Holroyd, N. E., Berriman, M., Aliaga, B., Chaparro, C., Grunau, C., et al. (2018) · PLoS Pathogens · doi:10.1371/journal.ppat.1007066 · Cited by 64
Cell Heterogeneity and Phenotypic Plasticity in Metastasis Formation: The Case of Colon Cancer
Teeuwssen, M., & Fodde, R. (2019) · Cancers · doi:10.3390/cancers11091368 · Cited by 67
“In addition, post-translational histone modifications which modulate chromatin folding and influence recruitment of regulatory proteins and control gene expression [17].”
Tang, H., Fang, H., Yin, E., Brasier, A. R., Sowers, L. C., & Zhang, K. (2014) · Analytical Chemistry · doi:10.1021/ac500972x · Cited by 63
Chetty, R., & Serra, S. (2020) · Journal of Clinical Pathology · doi:10.1136/jclinpath-2020-206451 · Cited by 64
Winogradoff, D. N., Echeverria, I., Potoyan, D. A., & Papoian, G. A. (2015) · Journal of the American Chemical Society · doi:10.1021/jacs.5b00235 · Cited by 64
González, B., Jayanthi, S., Gomez, N. V., Torres, O. V., Sosa, M. H., Bernardi, A., Urbano, F. J., García‐Rill, E., Cadet, J. L., & Bisagno, V. (2017) · Progress in Neuro-Psychopharmacology and Biological Psychiatry · doi:10.1016/j.pnpbp.2017.12.009 · Cited by 62
“…can be recognized directly by specific enzymes that act as "readers" of lysine acetylation, translating this signal into various normal or abnormal phenotypes, that not necessarily correlates with gene transcription (Strahl and Allis, 2000; Robison and Nestler, 2011; Zentner and Henikoff, 2013).”
BackgroundJing, Y., Liu, Z., Tian, G., Bao, X., Ishibashi, T., & Li, X. (2017) · Cell chemical biology · doi:10.1016/j.chembiol.2017.11.005 · Cited by 65
Mind the gap: Epigenetic regulation of chromatin accessibility in plants
Candela-Ferre, J., Diego‐Martin, B., Pérez-Alemany, J., & Gallego‐Bartolomé, J. (2024) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiae024 · Cited by 69
“On the other hand, indirect effects are often mediated by specific reader proteins that modulate chromatin through diverse mechanisms (Zentner and Henikoff 2013).”
Singh, A., Compe, E., May, N. L., & Egly, J. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.12.012 · Cited by 63
Hill, B. G., Shiva, S., Ballinger, S. W., Zhang, J., & Darley-Usmar, V. M. (2019) · Biological Chemistry · doi:10.1515/hsz-2019-0268 · Cited by 66
“For example, the degree of histone acetylation influences nuclear gene expression through the regulation of chromatin structure (Zentner and Henikoff, 2013; Allis and Jenuwein, 2016).”
BackgroundLin, S., Wein, S. P., Gonzales-Cope, M., Otte, G. L., Yuan, Z., Afjehi‐Sadat, L., Maile, T. M., Berger, S. L., Rush, A. J., Lill, J. R., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o113.036459 · Cited by 68
“Multiple acetylation has been observed in many different organisms in vivo and is strongly correlated with active transcription (33, 34).”
BackgroundRivière, G. (2014) · Frontiers in Physiology · doi:10.3389/fphys.2014.00129 · Cited by 65
“…to CpG-binding proteins recruitment (Antequera, 2003; Deaton et al., 2011; Vinson and Chatterjee, 2012) and/or the regulation of DNA/histone interactions within nucleosomes (Cedar and Bergman, 2009; Zentner and Henikoff, 2013) thereby diminishing transcription (Hsieh, 1994; Rivière et al., 2011).”
BackgroundEpigenetics: The neglected key to minimize learning and memory deficits in Down syndrome
Dekker, A. D., Deyn, P. P. D., & Rots, M. G. (2014) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2014.05.004 · Cited by 64
“Epigenetic mechanisms 252 affect the nucleosomal packaging and thereby alter the accessibility of the DNA for molecular interactions that are required for transcription and replication (Cosgrove et al., 2004; Zentner and Henikoff, 2013).”
Klymenko, Y., & Nephew, K. P. (2018) · Cancers · doi:10.3390/cancers10090295 · Cited by 63
“Similarly, histone (de)phosphorylation utilizes protein kinases and phosphatases to attach or remove negatively charged phosphate groups, respectively, influencing chemical attraction between DNA and histone tails (reviewed in [60,61]).”
BackgroundRevisiting Histone Deacetylases in Human Tumorigenesis: The Paradigm of Urothelial Bladder Cancer
Giannopoulou, A. F., Velentzas, A. D., Konstantakou, E. G., Avgeris, M., Katarachia, S. A., Papandreou, N. C., Kalavros, N., Mpakou, V., Iconomidou, V. A., Anastasiadou, E., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20061291 · Cited by 62
Epigenetic Mechanisms of Abiotic Stress Response and Memory in Plants
Mozgová, I., Mikulski, P., Pečinka, A., & Farrona, S. (2019) · Springer eBooks · doi:10.1007/978-3-030-14760-0_1 · Cited by 63
Xin, B., & Rohs, R. (2018) · Genome Research · doi:10.1101/gr.220079.116 · Cited by 63
“Given the multiple layers that contribute to in vivo binding (Levo and Segal 2014; Slattery et al. 2014; Zentner et al. 2015; Mathelier et al. 2016b), it is clear that DNA sequence and shape at core binding sites, which in vitro experiments have identified as determinants of DNA binding specificity…”
BackgroundLiu, K., Yu, Y., Dong, A., & Shen, W. (2017) · New Phytologist · doi:10.1111/nph.14596 · Cited by 60
Dilweg, I. W., & Dame, R. T. (2018) · Biochemical Society Transactions · doi:10.1042/bst20180488 · Cited by 60
Organocatalytic Control over a Fuel‐Driven Transient‐Esterification Network**
van der Helm, M. P., Wang, C., Fan, B., Macchione, M., Mendes, E., & Eelkema, R. (2020) · Angewandte Chemie International Edition · doi:10.1002/anie.202008921 · Cited by 60
Rossetto, D., Cramet, M., Wang, A. Y., Steunou, A., Lacoste, N., Schulze-Hentrich, J. M., Côté, V., Saksouk, J., Piquet, S., Nourani, A., et al. (2014) · The EMBO Journal · doi:10.15252/embj.201386433 · Cited by 57
“Multiple other histone modifications such as phosphorylation, methylation, and ubiquitination have also since emerged as important players in transcription regulation, defining the chromatin state (Bannister & Kouzarides, 2011; Zentner & Henikoff, 2013).”
BackgroundMultiple dimensions of epigenetic gene regulation in the malaria parasite Plasmodium falciparum
Ay, F., Bunnik, E. M., Varoquaux, N., Vert, J., Noble, W. S., & Roch, K. G. L. (2014) · BioEssays · doi:10.1002/bies.201400145 · Cited by 60
Bomsztyk, K., Mar, D., An, D., Sharifian, R., Mikuła, M., Gharib, S. A., Altemeier, W. A., Liles, W. C., & Denisenko, O. N. (2015) · Critical Care · doi:10.1186/s13054-015-0943-4 · Cited by 64
“Acetylation of histone lysine residues removes positive charges, reducing chromatin compaction and thereby permitting higher rates of Pol II transcription (Additional file 1: Figure S1) [37].”
BackgroundInfluentialShaping epigenetic memory via genomic bookmarking
Michieletto, D., Chiang, M., Colì, D., Papantonis, A., Orlandini, E., Cook, P. R., & Marenduzzo, D. (2018) · Kölner Universitäts PublikationsServer (Universität zu Köln) · Cited by 59
Exploiting epigenetic dependencies in ovarian cancer therapy
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“The compaction state of a DNA region— influenced by its histone PTM status—is the central control to transcriptional output, either allowing or restricting its access to downstream transcription factors.(32,33) Some of the most common histone modifications include methylation, acetylation, ubiquitination and phosphory…”
BackgroundUllius, A., Lüscher‐Firzlaff, J., Costa, I. G., Walsemann, G., Forst, A. H., Gusmao, E. G., Kapelle, K., Kleine, H. O., Kremmer, E., Vervoorts, J., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku312 · Cited by 58
“ASH2L was of interest to us because it has been described as a component of KMT2 group MTase complexes (14,58,59).”
BackgroundSaxon, E., & Peng, X. (2021) · ChemBioChem · doi:10.1002/cbic.202100366 · Cited by 60
Mechanisms of DNA methylation and histone modifications
Acharjee, S., Chauhan, S. K., Pal, R., & Tomar, R. S. (2023) · Progress in molecular biology and translational science · doi:10.1016/bs.pmbts.2023.01.001 · Cited by 61
The emerging role of epigenetics in pulmonary hypertension
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CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks
Rother, M. B., Pellegrino, S., Smith, R., Gatti, M., Meisenberg, C., Wiegant, W. W., Luijsterburg, M. S., Imhof, R., Downs, J. A., Vertegaal, A. C. O., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19502-5 · Cited by 62
Metadata
- Authors
- Zentner, G. E., & Henikoff, S.
- Affiliations
- Fred Hutch Cancer Center (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Henikoff, Steven
- Venue
- Nature Structural & Molecular Biology
- Published
- 2013-03
- Volume
- 20
- Issue
- 3
- Pages
- 259-266
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- OpenAlex
- W2034340491
- Cited by
- 923
- References
- 111
- Citations by year
- 2026: 22 · 2025: 33 · 2024: 57 · 2023: 39 · 2022: 45 · 2021: 60 · 2020: 63 · 2019: 82 · 2018: 75 · 2017: 84 · 2016: 76 · 2015: 106 · 2014: 125 · 2013: 52
- FWCI
- 11.25
- Type
- journal article
- Language
- en
- Open access
- closed
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (5u01hg004274-04)
- National Human Genome Research Institute (5U01 HG004274)
- National Cancer Institute (T32CA009657, U54CA143862)
- National Institute of Environmental Health Sciences (R01ES020116)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- nucleosome dynamics, histone modifications, chromatin, nucleosome mobility, nucleosome turnover, transcription, DNA replication, DNA repair
- MeSH terms
- Acetylation, Acylation, Adenosine Diphosphate, Chromatin, DNA, DNA Replication, Gene Expression Regulation, Glycosylation, Histones, Lysine, Methylation, Nucleosomes
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