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Role of Histone H3 Lysine 9 Methylation in Epigenetic Control of Heterochromatin Assembly

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RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

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Dynamics and Memory of Heterochromatin in Living Cells

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Functional mammalian homologues of the Drosophila PEV‐modifier Su(var)3‐9 encode centromere‐associated proteins which complex with the heterochromatin component M31

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Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin

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Cell cycle control of centromeric repeat transcription and heterochromatin assembly

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Polymerase pausing induced by sequence-specific RNA-binding protein drives heterochromatin assemblyPreprint

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Histone deacetylation primes self-propagation of heterochromatin domains to promote epigenetic inheritance

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Noncoding RNA-nucleated heterochromatin spreading is intrinsically labile and requires accessory elements for epigenetic stability

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Shelterin and subtelomeric DNA sequences control nucleosome maintenance and genome stability

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Histone H3K9 methylation regulates chronic stress and IL‐6–induced colon epithelial permeability and visceral pain

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The molecular basis of cell memory in mammals: The epigenetic cycle

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Nucleosome remodeler exclusion by histone deacetylation enforces heterochromatic silencing and epigenetic inheritance

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An H3K9 methylation-dependent protein interaction regulates the non-enzymatic functions of a putative histone demethylase

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Epigenomic insights into common human disease pathology

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Cis-acting determinants of paramutation

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Establishment of expression-state boundaries by Rif1 and Taz1 in fission yeast

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Insulator-based loops mediate the spreading of H3K27me3 over distant micro-domains repressing euchromatin genes

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A composite DNA element that functions as a maintainer required for epigenetic inheritance of heterochromatin

Wang, X., Paulo, J. A., Li, X., Zhou, H., Yu, J., Gygi, S. P., & Moazed, D. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.07.017 · Cited by 26

The Inherent Asymmetry of DNA Replication

Snedeker, J. C., Wooten, M., & Chen, X. (2017) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100616-060447 · Cited by 34

Heterodimerization of H3K9 histone methyltransferases G9a and GLP activates methyl reading and writing capabilities

Sanchez, N. A., Kallweit, L. M., Trnka, M. J., Clemmer, C. L., & Al‐Sady, B. (2021) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2021.101276 · Cited by 25

Transgenerational epigenetic inheritance: a critical perspective

Bird, A. P. (2024) · Frontiers in Epigenetics and Epigenomics · doi:10.3389/freae.2024.1434253 · Cited by 32

Establishment of heterochromatin in domain-size-dependent bursts

Nickels, J. F., Edwards, A., Charlton, S. J., Mortensen, A. M., Hougaard, S. C. L., Trusina, A., Sneppen, K., & Thon, G. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2022887118 · Cited by 27

Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory

Abdulla, A. Z., Vaillant, C., & Jost, D. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac702 · Cited by 26

Regulation of ectopic heterochromatin-mediated epigenetic diversification by the JmjC family protein Epe1

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Distinct H3K9me3 heterochromatin maintenance dynamics govern different gene programmes and repeats in pluripotent cells

Zhang, J., Donahue, G., Gilbert, M. B., Lapidot, T., Nicetto, D., & Zaret, K. S. (2024) · Nature Cell Biology · doi:10.1038/s41556-024-01547-z · Cited by 33

How Communication Between Nucleosomes Enables Spreading and Epigenetic Memory of Histone Modifications

Erdel, F. (2017) · BioEssays · doi:10.1002/bies.201700053 · Cited by 28

Symmetry from Asymmetry or Asymmetry from Symmetry?Preprint

Kahney, E. W., Ranjan, R., Gleason, R. J., & Chen, X. (2017) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2017.82.034272 · Cited by 23

Disruption of promoter memory by synthesis of a long noncoding RNA

Yu, Y., Yarrington, R. M., Chuong, E. B., Elde, N. C., & Stillman, D. J. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1601793113 · Cited by 26

The euchromatic histone mark H3K36me3 preserves heterochromatin through sequestration of an acetyltransferase complex in fission yeast

Georgescu, P. R., Capella, M., Fischer‐Burkart, S., & Braun, S. J. (2020) · Microbial Cell · doi:10.15698/mic2020.03.711 · Cited by 24

The INO80 Complex Regulates Epigenetic Inheritance of Heterochromatin

Shan, C., Bao, K., Diedrich, J. K., Chen, X., Lü, C., Yates, J. R., & Jia, S. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108561 · Cited by 24

Coordination of histone chaperones for parental histone segregation and epigenetic inheritancePreprint

Fang, Y., Hua, X., Shan, C.-M., Toda, T., Qiao, F., Zhang, Z., & Jia, S. (2024) · Genes & Development · doi:10.1101/gad.351278.123 · Cited by 21

A unifying model of epigenetic regulation

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Requirements for establishment and epigenetic stability of mammalian heterochromatin

Tatarakis, A., Saini, H., Yu, J., Feng, W., Pinzón-Arteaga, C. A., & Moazed, D. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.08.025 · Cited by 24

H3K9 demethylases IBM1 and JMJ27 are required for male meiosis in Arabidopsis thaliana

Cheng, J., Xu, L., Bergér, V., Bruckmann, A., Yang, C., Schubert, V., Grasser, K. D., Schnittger, A., Zheng, B., & Jiang, H. L. (2022) · New Phytologist · doi:10.1111/nph.18286 · Cited by 21

Specialized replication of heterochromatin domains ensures self-templated chromatin assembly and epigenetic inheritance

Nathanailidou, P., Dhakshnamoorthy, J., Xiao, H., Zofall, M., Holla, S., O’Neill, M. J., Andrésson, Þ., Wheeler, D. L., & Grewal, S. I. S. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2315596121 · Cited by 21

The evolutionary consequences of interactions between the epigenome, the genome and the environment

Baduel, P., Sammarco, I., Barrett, R. D. H., Coronado‐Zamora, M., Crespel, A., Rodríguez, B. D., Fox, J. A., Galanti, D., González, J., Jueterbock, A., et al. (2024) · Evolutionary Applications · doi:10.1111/eva.13730 · Cited by 23

H3K9me3 maintenance on a human artificial chromosome is required for segregation but not centromere epigenetic memory

Martins, N. M. C., Cisneros-Soberanis, F., Pesenti, E., Kochanova, N. Y., Shang, W.-H., Hori, T., Nagase, T., Kimurâ, H., Larionov, V., Masumoto, H., et al. (2020) · Journal of Cell Science · doi:10.1242/jcs.242610 · Cited by 21

Proteasome-dependent truncation of the negative heterochromatin regulator Epe1 mediates antifungal resistance

Yaseen, I., White, S. A., Torres-Garcia, S., Spanos, C., Lafos, M., Gaberdiel, E., Yeboah, R., El Karoui, M., Rappsilber, J., Pidoux, A. L., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00801-y · Cited by 20

Distinct silencer states generate epigenetic states of heterochromatin

Saxton, D. S., & Rine, J. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.08.002 · Cited by 21

Environmental epigenetics: new horizons in redefining biological and health outcomes

Faraji, J., & Metz, G. A. S. (2026) · Environment International · doi:10.1016/j.envint.2026.110072 · Cited by 22

Epigenetic Mechanisms of Tree Responses to Climatic Changes

Kurpisz, B., & Pawłowski, T. A. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms232113412 · Cited by 21

RNA quality control factors nucleate Clr4/SUV39H and trigger constitutive heterochromatin assembly

Khanduja, J. S., Joh, R. I., Perez, M. M., Paulo, J. A., Palmieri, C. M., Zhang, J., Gulka, A. O. D., Haas, W., Gygi, S. P., & Motamedi, M. (2024) · Cell · doi:10.1016/j.cell.2024.04.042 · Cited by 20

Recruitment and reinforcement: maintaining epigenetic silencing

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Exposomes to Exosomes: Exosomes as Tools to Study Epigenetic Adaptive Mechanisms in High-Altitude Humans

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RNAi epimutations conferring antifungal drug resistance are inheritable

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Retrieving Chromatin Patterns from Deep Sequencing Data Using Correlation Functions

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Uncoupling the distinct functions of HP1 proteins during heterochromatin establishment and maintenance

Seman, M., Levashkevich, A., Larkin, A., Huang, F., & Ragunathan, K. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113428 · Cited by 16

Inheritance of epigenetic transcriptional memory through read–write replication of a histone modification

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A Heterochromatin Domain Forms Gradually at a New Telomere and Is Dynamic at Stable Telomeres

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Nuclear Envelope Proteins Modulating the Heterochromatin Formation and Functions in Fission Yeast

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Molecular and cellular bases of trained immunity

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Depositing centromere repeats induces heritable intragenic heterochromatin establishment and spreading in Arabidopsis

Liu, Z., Liu, J., Liu, F., & Zhong, X. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad306 · Cited by 15

Chromatin‐associated noncoding RNAs in development and inheritance

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Paraquat Reduces the Female Fertility by Impairing the Oocyte Maturation in Mice

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Evolution of epigenetic chromatin states

Yung, P. Y. K., & Elsässer, S. J. (2017) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2017.10.001 · Cited by 15

Competition between local erasure and long-range spreading of a single biochemical mark leads to epigenetic bistability

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A histone H3K9 methyltransferase Dim5 mediates repression of sorbicillinoid biosynthesis in Trichoderma reesei

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Histone H3K9 demethylase JMJD1A is a co-activator of erythropoietin expression under hypoxia

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Recycling of parental histones preserves the epigenetic landscape during embryonic development

Mühlen, D., Li, X., Dovgusha, O., Jäckle, H., & Günesdogan, U. (2023) · Science Advances · doi:10.1126/sciadv.add6440 · Cited by 13

Beyond Tethering and the LEM domain: MSCellaneous functions of the inner nuclear membrane Lem2

Braun, S. J., & Barrales, R. R. (2016) · Nucleus · doi:10.1080/19491034.2016.1252892 · Cited by 13

Programmed suppression of oxidative phosphorylation and mitochondrial function by gestational alcohol exposure correlate with widespread increases in H3K9me2 that do not suppress transcription

Chang, R. C.-A., Thomas, K. N., Mehta, N. A., Veazey, K. J., Parnell, S. E., & Golding, M. C. (2021) · Epigenetics & Chromatin · doi:10.1186/s13072-021-00403-w · Cited by 13

Sensitive and Quantitative Three-Color Protein Imaging in Fission Yeast Using Spectrally Diverse, Recoded Fluorescent Proteins with Experimentally-Characterized In Vivo Maturation Kinetics

Al‐Sady, B., Greenstein, R., El‐Samad, H., Braun, S. J., & Madhani, H. D. (2016) · PLoS ONE · doi:10.1371/journal.pone.0159292 · Cited by 13

High-throughput assessment of context-dependent effects of chromatin proteins

Brueckner, L., van Arensbergen, J., Akhtar, W., Pagie, L., & van Steensel, B. (2016) · Epigenetics & Chromatin · doi:10.1186/s13072-016-0096-y · Cited by 13

Mkt1 is required for RNAi-mediated silencing and establishment of heterochromatin in fission yeast

Taglini, F., Chapman, E., van Nues, R. W., Théron, E., & Bayne, E. H. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1157 · Cited by 13

Epigenome Editing in the Brain

Bashtrykov, P., & Jeltsch, A. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-53889-1_21 · Cited by 12

Establishment of centromere identity is dependent on nuclear spatial organization

Wu, W., McHugh, T., Kelly, D. A., Pidoux, A. L., & Allshire, R. C. (2022) · Current Biology · doi:10.1016/j.cub.2022.06.048 · Cited by 11

The Catalytic-Dependent and -Independent Roles of Lsd1 and Lsd2 Lysine Demethylases in Heterochromatin Formation in Schizosaccharomyces pombe

Marayati, B. F., Tucker, J. F., de la Cerda, D. A., Hou, T.-C. J., Chen, R., Sugiyama, T., Pease, J. B., & Zhang, K. (2020) · Cells · doi:10.3390/cells9040955 · Cited by 11

A Key Silencing Histone Mark on Chromatin Is Lost When Colorectal Adenocarcinoma Cells Are Depleted of Methionine by Methionine γ-Lyase

Raboni, S., Montalbano, S., Stransky, S., Garcia, B. A., Buschini, A., Bettati, S., Sidoli, S., & Mozzarelli, A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.735303 · Cited by 19

Tandemly repeated genes promote RNAi-mediated heterochromatin formation via an antisilencing factor, Epe1, in fission yeastPreprint

Asanuma, T., Inagaki, S., Kakutani, T., Aburatani, H., & Murakami, Y. (2022) · Genes & Development · doi:10.1101/gad.350129.122 · Cited by 10

Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation

Larkin, A., Kunze, C., Seman, M., Levashkevich, A., Curran, J., Morris-Evans, D., Lemieux, S., Khalil, A. S., & Ragunathan, K. (2024) · Developmental Cell · doi:10.1016/j.devcel.2024.07.006 · Cited by 10

Disabling leading and lagging strand histone transmission results in parental histones loss and reduced cell plasticity and viability

Kollenstart, L., Biran, A., Alcaraz, N., Reverón-Gómez, N., Solis‐Mezarino, V., Völker-Albert, M. C., Jenkinson, F., Flury, V., & Groth, A. (2025) · Science Advances · doi:10.1126/sciadv.adr1453 · Cited by 10

Clr4 specificity and catalytic activity beyond H3K9 methylation

Kušević, D., Kudithipudi, S., Iglesias, N., Moazed, D., & Jeltsch, A. (2017) · Biochimie · doi:10.1016/j.biochi.2017.01.013 · Cited by 10

Adaptive Evolution and Epigenetics

Kronholm, I. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-805388-1.00028-6 · Cited by 11

The cAMP signaling pathway regulates Epe1 protein levels and heterochromatin assembly

Bao, K., Shan, C., Chen, X., Raiymbek, G., Monroe, J. G., Fang, Y., Toda, T., Koutmou, K. S., Ragunathan, K., Lü, C., et al. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010049 · Cited by 9

Tissue homogeneity requires inhibition of unequal gene silencing during development

Lê, H. M. N., Looney, M. M., Strauss, B., Bloodgood, M., & Jose, A. M. (2016) · The Journal of Cell Biology · doi:10.1083/jcb.201601050 · Cited by 9

Leaving histone unturned for epigenetic inheritance

Shan, C., Fang, Y., & Jia, S. (2021) · FEBS Journal · doi:10.1111/febs.16260 · Cited by 9

Histone variant H2A.Z plays multiple roles in the maintenance of heterochromatin integrity

Tsukii, K., Takahata, S., & Murakami, Y. (2021) · Genes to Cells · doi:10.1111/gtc.12911 · Cited by 9

Stress controls heterochromatin inheritance via histone H3 ubiquitylation

Bhatt, B., Wei, Y., Pradhan, A. K., Dhakshnamoorthy, J., Zofall, M., Xiao, H., Vijayakumari, D., Jain, S., Folco, H. D., Qi, H., et al. (2026) · Nature · doi:10.1038/s41586-025-09899-8 · Cited by 8

Transgenerational epigenetic control of constitutive heterochromatin, transposons, and centromeres

Fukagawa, T., & Kakutani, T. (2023) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2023.102021 · Cited by 8

The level and distribution pattern of HP1β in the embryonic brain correspond to those of H3K9me1/me2 but not of H3K9me3

Bártová, E., Večeřa, J., Krejčí, J., Legartová, S., Pachernı́k, J., & Kozubek, S. (2016) · Histochemistry and Cell Biology · doi:10.1007/s00418-015-1402-7 · Cited by 8

Passing epigenetic silence to the next generation

De, S., & Kassis, J. A. (2017) · Science · doi:10.1126/science.aan1493 · Cited by 8

Deposition Bias of Chromatin Proteins Inverts under DNA Replication Stress Conditions

Zwinderman, M. R. H., Lobo, T. J., van der Wouden, P. E., Spierings, D. C. J., van Vugt, M. A. T. M., Lansdorp, P. M., Guryev, V., & Dekker, F. J. (2021) · ACS Chemical Biology · doi:10.1021/acschembio.1c00321 · Cited by 7

Antimicrobial resistance in the wild: Insights from epigenetics

de la Peña, M. V., & Kronholm, I. (2024) · Evolutionary Applications · doi:10.1111/eva.13707 · Cited by 7

Analysis of Heterochromatin in Schizosaccharomyces pombePreprint

Cam, H. P., & Whitehall, S. K. (2016) · Cold Spring Harbor Protocols · doi:10.1101/pdb.top079889 · Cited by 7

Replication-coupled inheritance of chromatin states

Song, A., Wang, Y., Liu, C., Yu, J., Zhang, Z., Lan, L., Lin, H., Zhao, J., & Li, G. (2024) · Cell Insight · doi:10.1016/j.cellin.2024.100195 · Cited by 6

Minimal requirements for the epigenetic inheritance of engineered silent chromatin domains

Yuan, A. H., & Moazed, D. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2318455121 · Cited by 6

time-ChIP: A Method to Determine Long-Term Locus-Specific Nucleosome Inheritance

Siwek, W., Rodríguez, M. G., Sobral, D., Junior, I. R. C., & Jansen, L. E. T. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8663-7_7 · Cited by 6

Application of Recombination -Induced Tag Exchange (RITE) to study histone dynamics in human cells

Molenaar, T. M., Pagès-Gallego, M., Meyn, V., & van Leeuwen, F. (2020) · Epigenetics · doi:10.1080/15592294.2020.1741777 · Cited by 7

Unprogrammed epigenetic variation mediated by stochastic formation of ectopic heterochromatin

Sorida, M., & Murakami, Y. (2019) · Current Genetics · doi:10.1007/s00294-019-01031-4 · Cited by 5

Adaptive evolution and epigenetics

Kronholm, I. (2022) · Elsevier eBooks · doi:10.1016/b978-0-323-91909-8.00014-1 · Cited by 5

Histone Methyltransferase SsDim5 Regulates Fungal Virulence through H3K9 Trimethylation in Sclerotinia sclerotiorum

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