Heterochromatin: Guardian of the Genome

Hallmarks of Cancer: The Next Generation

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Initial sequencing and analysis of the human genome

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The DNA Damage Response: Making It Safe to Play with Knives

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Phase separation drives heterochromatin domain formation

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Loss of the Suv39h Histone Methyltransferases Impairs Mammalian Heterochromatin and Genome Stability

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Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

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The impact of retrotransposons on human genome evolution

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Liquid–liquid phase separation in human health and diseases

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Heterochromatin protein 1α interacts with parallel RNA and DNA G-quadruplexes

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Histone Modifications Regulate Chromatin Compartmentalization by Contributing to a Phase Separation Mechanism

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Liquid-liquid phase separation in biology: mechanisms, physiological functions and human diseases

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The relationship between genome structure and function

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Role of H3K9me3 heterochromatin in cell identity establishment and maintenance

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Crosstalk between epitranscriptomic and epigenetic mechanisms in gene regulation

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Epigenetic patterns in a complete human genome

Gershman, A., Sauria, M. E. G., Guitart, X., Vollger, M. R., Hook, P. W., Hoyt, S. J., Jain, M., Shumate, A., Razaghi, R., Koren, S., et al. (2022) · Science · doi:10.1126/science.abj5089 · Cited by 297

On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability

Khristich, A. N., & Mirkin, S. M. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.rev119.007678 · Cited by 289

Chromatin Organization in Early Land Plants Reveals an Ancestral Association between H3K27me3, Transposons, and Constitutive Heterochromatin

Montgomery, S. A., Tanizawa, Y., Gálik, B., Wang, N., Ito, T., Mochizuki, T., Akimcheva, S., Bowman, J. L., Cognat, V., Maréchal‐Drouard, L., et al. (2020) · Current Biology · doi:10.1016/j.cub.2019.12.015 · Cited by 252

Transcription-mediated replication hindrance: a major driver of genome instabilityPreprint

Gómez‐González, B., & Aguilera, A. (2019) · Genes & Development · doi:10.1101/gad.324517.119 · Cited by 235

The molecular basis of heterochromatin assembly and epigenetic inheritance

Grewal, S. I. S. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.04.020 · Cited by 224

Endogenous Retroelements and the Viral Mimicry Response in Cancer Therapy and Cellular Homeostasis

Chen, R. E., Ishak, C. A., & Carvalho, D. D. D. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0506 · Cited by 213

MeCP2 links heterochromatin condensates and neurodevelopmental disease

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Anticancer Therapy with HDAC Inhibitors: Mechanism-Based Combination Strategies and Future Perspectives

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The control of gene expression and cell identity by H3K9 trimethylation

Ninova, M., Tóth, K. F., & Aravin, A. A. (2019) · Development · doi:10.1242/dev.181180 · Cited by 170

Losing DNA methylation at repetitive elements and breaking bad

Pappalardo, X. G., & Barra, V. (2021) · Epigenetics & Chromatin · doi:10.1186/s13072-021-00400-z · Cited by 165

Taming transposable elements in vertebrates: from epigenetic silencing to domestication

Almeida, M. V., Vernaz, G., Putman, A. L. K., & Miska, E. A. (2022) · Trends in Genetics · doi:10.1016/j.tig.2022.02.009 · Cited by 150

Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

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Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers

Spracklin, G., Abdennur, N. A., Imakaev, M., Chowdhury, N., Pradhan, S., Mirny, L. A., & Dekker, J. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00892-7 · Cited by 144

Liquid–Liquid Phase Separation in ChromatinPreprint

Rippe, K. (2021) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a040683 · Cited by 147

Paradoxical association of TET loss of function with genome-wide DNA hypomethylation

López-Moyado, I. F., Tsagaratou, A., Yuita, H., Seo, H., Delatte, B., Heinz, S., Benner, C. W., & Rao, A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1903059116 · Cited by 130

Double-edged sword: The evolutionary consequences of the epigenetic silencing of transposable elements

Choi, J. Y., & Lee, Y. C. G. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008872 · Cited by 122

Multi-omic profiling of primary mouse neutrophils predicts a pattern of sex- and age-related functional regulation

Lu, R. J., Taylor, S., Contrepois, K., Kim, M., Bravo, J. I., Ellenberger, M., Sampathkumar, N. K., & Benayoun, B. A. (2021) · Nature Aging · doi:10.1038/s43587-021-00086-8 · Cited by 132

Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis

Xu, J., Ma, H., Ma, H., Jiang, W., Mela, C. A., Duan, M.-H., Zhao, S., Gao, C., Hahm, E., Lardo, S. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15718-7 · Cited by 120

Single-cell nuclear architecture across cell types in the mouse brain

Takei, Y., Zheng, S., Yun, J., Shah, S., Pierson, N. G., White, J. A., Schindler, S., Tischbirek, C. H., Yuan, G., & Cai, L. (2021) · Science · doi:10.1126/science.abj1966 · Cited by 115

Roles of chromatin and genome instability in cellular senescence and their relevance to ageing and related diseases

Wu, Z., Qu, J., & Liu, G.-H. (2024) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-024-00775-3 · Cited by 118

Transposable elements in mammalian chromatin organization

Lawson, H. A., Liang, Y., & Wang, T. (2023) · Nature Reviews Genetics · doi:10.1038/s41576-023-00609-6 · Cited by 124

TET Enzymes in the Immune System: From DNA Demethylation to Immunotherapy, Inflammation, and Cancer

López-Moyado, I. F., Ko, M., Hogan, P. G., & Rao, A. (2024) · Annual Review of Immunology · doi:10.1146/annurev-immunol-080223-044610 · Cited by 121

In Vivo Reprogramming Ameliorates Aging Features in Dentate Gyrus Cells and Improves Memory in Mice.

Rodríguez-Matellán, A., Alcazar, N., Hernández, F., Serrano, M., & Ávila, J. (2020) · Stem Cell Reports · doi:10.1016/j.stemcr.2020.09.010 · Cited by 116

Stabilization of heterochromatin by CLOCK promotes stem cell rejuvenation and cartilage regeneration

Liang, C., Liu, Z., Song, M., Li, W., Wu, Z., Wang, Z., Wang, Q., Wang, S., Yan, K., Sun, L., et al. (2020) · Cell Research · doi:10.1038/s41422-020-0385-7 · Cited by 119

Complete loss of H3K9 methylation dissolves mouse heterochromatin organization

Montavon, T., Shukeir, N., Erikson, G. A., Engist, B., Onishi‐Seebacher, M., Ryan, D. P., Musa, Y., Mittler, G., Meyer, A. G., Genoud, C., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24532-8 · Cited by 115

Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries

Bizhanova, A., & Kaufman, P. D. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194666 · Cited by 112

Confined migration induces heterochromatin formation and alters chromatin accessibility

Hsia, C.-R., McAllister, J., Hasan, O., Judd, J., Lee, S. Y., Agrawal, R., Chang, C., Soloway, P. D., & Lammerding, J. (2022) · iScience · doi:10.1016/j.isci.2022.104978 · Cited by 109

53BP1 regulates heterochromatin through liquid phase separation

Zhang, L., Geng, X., Wang, F., Tang, J., Ichida, Y., Sharma, A., Jin, S., Chen, M., Tang, M., Pozo, F. M., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28019-y · Cited by 107

Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains

Gopi, L. K., & Kidder, B. L. (2021) · Nature Communications · doi:10.1038/s41467-021-21707-1 · Cited by 101

Contributions of Histone Variants in Nucleosome Structure and Function

Kurumizaka, H., Kujirai, T., & Takizawa, Y. (2020) · Journal of Molecular Biology · doi:10.1016/j.jmb.2020.10.012 · Cited by 99

The American lobster genome reveals insights on longevity, neural, and immune adaptations

Polinski, J. M., Zimin, A. V., Clark, K. F., Kohn, A. B., Sadowski, N., Timp, W., Ptitsyn, A. A., Khanna, P., Romanova, D. Y., Williams, P., et al. (2021) · Science Advances · doi:10.1126/sciadv.abe8290 · Cited by 93

Phase separation drives decision making in cell division

Liu, X., Liu, X., Wang, H., Dou, Z., Ruan, K., Hill, D. L., Li, L., Shi, Y., & Yao, X. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.rev120.011746 · Cited by 88

Rapid embryonic cell cycles defer the establishment of heterochromatin by Eggless/SetDB1 in DrosophilaPreprint

Seller, C. A., Cho, C.-Y., & O’Farrell, P. H. (2019) · Genes & Development · doi:10.1101/gad.321646.118 · Cited by 90

Epigenetic modifications affect the rate of spontaneous mutations in a pathogenic fungus

Habig, M., Lorrain, C., Feurtey, A., Komluski, J., & Stukenbrock, E. H. (2021) · Nature Communications · doi:10.1038/s41467-021-26108-y · Cited by 85

Role of Polycomb in the control of transposable elements

Deleris, A., Berger, F., & Duharcourt, S. (2021) · Trends in Genetics · doi:10.1016/j.tig.2021.06.003 · Cited by 85

Phase separation of DNA: From past to present

King, J. T., & Shakya, A. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.01.033 · Cited by 80

Molecular interactions underlying the phase separation of HP1α: role of phosphorylation, ligand and nucleic acid binding

Her, C., Phan, T. M., Jovic, N., Kapoor, U., Ackermann, B. E., Rizuan, A., Kim, Y. C., Mittal, J., & Debelouchina, G. T. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1194 · Cited by 69

Transposable elements as new players in neurodegenerative diseases

Ravel‐Godreuil, C., Znaidi, R., Bonnifet, T., Joshi, R. L., & Fuchs, J. (2021) · FEBS Letters · doi:10.1002/1873-3468.14205 · Cited by 77

DNA methylation in disease: Immunodeficiency, Centromeric instability, Facial anomalies syndrome

Vukić, M., & Daxinger, L. (2019) · Essays in Biochemistry · doi:10.1042/ebc20190035 · Cited by 67

Haplotypes spanning centromeric regions reveal persistence of large blocks of archaic DNA

Langley, S. A., Miga, K. H., Karpen, G. H., & Langley, C. H. (2019) · eLife · doi:10.7554/elife.42989 · Cited by 64

Physical Chemistry of Cellular Liquid‐Phase Separation

Bentley, E. P., Frey, B. B., & Deniz, A. A. (2018) · Chemistry - A European Journal · doi:10.1002/chem.201805093 · Cited by 67

Decoding p53 tumor suppression: a crosstalk between genomic stability and epigenetic control?

Janic, A., Abad, E., & Amelio, I. (2024) · Cell Death and Differentiation · doi:10.1038/s41418-024-01259-9 · Cited by 72

Establishment and evolution of heterochromatin

Liu, J., Ali, M., & Zhou, Q. (2020) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.14303 · Cited by 74

The Polycomb repressive complex 2 deposits H3K27me3 and represses transposable elements in a broad range of eukaryotes

Hisanaga, T., Romani, F., Wu, S., Kowar, T., Wu, Y., Lintermann, R., Fridrich, A., Cho, C. H., Chaumier, T., Jamge, B., et al. (2023) · Current Biology · doi:10.1016/j.cub.2023.08.073 · Cited by 60

Imaging the response to DNA damage in heterochromatin domains reveals core principles of heterochromatin maintenance

Fortuny, A., Chansard, A., Caron, P., Chevallier, O., Leroy, O., Renaud, O., & Polo, S. E. (2021) · Nature Communications · doi:10.1038/s41467-021-22575-5 · Cited by 66

Nuclear cGAS: guard or prisoner?

Mann, C. C. D. O., & Hopfner, K. (2021) · The EMBO Journal · doi:10.15252/embj.2021108293 · Cited by 65

Is euchromatin really open in the cell?

Maeshima, K., Iida, S., Shimazoe, M. A., Tamura, S., & Ide, S. (2023) · Trends in Cell Biology · doi:10.1016/j.tcb.2023.05.007 · Cited by 66

Satellite repeat transcripts modulate heterochromatin condensates and safeguard chromosome stability in mouse embryonic stem cells

Novo, C. L., Wong, E. V., Hockings, C., Poudel, C., Sheekey, E., Wiese, M., Okkenhaug, H., Boulton, S. J., Basu, S., Walker, S. A., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31198-3 · Cited by 64

Metabolic regulation by p53 prevents R-loop-associated genomic instability

Panatta, E., Butera, A., Mammarella, E., Pitolli, C., Mauriello, A., Leist, M., Knight, R. A., Melino, G., & Amelio, I. (2022) · Cell Reports · doi:10.1016/j.celrep.2022.111568 · Cited by 60

The SUMO Ligase Su(var)2-10 Controls Hetero- and Euchromatic Gene Expression via Establishing H3K9 Trimethylation and Negative Feedback Regulation

Ninova, M., Godneeva, B. K., Chen, Y.-C. A., Luo, Y., Prakash, S. J., Jankovics, F., Erdélyi, M., Aravin, A. A., & Tóth, K. F. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.09.033 · Cited by 59

Non-complementary strand commutation as a fundamental alternative for information processing by DNA and gene regulation

Nikitin, M. P. (2023) · Nature Chemistry · doi:10.1038/s41557-022-01111-y · Cited by 63

Transposable Elements as a Source of Novel Repetitive DNA in the Eukaryote Genome

Zattera, M. L., & Bruschi, D. P. (2022) · Cells · doi:10.3390/cells11213373 · Cited by 52

A unique chromatin profile defines adaptive genomic regions in a fungal plant pathogen

Cook, D. E., Kramer, H. M., Torres, D. E., Seidl, M. F., & Thomma, B. P. H. J. (2020) · eLife · doi:10.7554/elife.62208 · Cited by 53

Alzheimer’s disease and related tauopathies: disorders of disrupted neuronal identity

Frost, B. E. (2023) · Trends in Neurosciences · doi:10.1016/j.tins.2023.07.006 · Cited by 57

The Telomere Paradox: Stable Genome Preservation with Rapidly Evolving Proteins

Saint‐Leandre, B., & Levine, M. T. (2020) · Trends in Genetics · doi:10.1016/j.tig.2020.01.007 · Cited by 51

Nematode chromosomes

Carlton, P. M., Davis, R. E., & Ahmed, S. C. (2022) · Genetics · doi:10.1093/genetics/iyac014 · Cited by 49

Multifunctional histone variants in genome function

Wong, L. H., & Tremethick, D. J. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00759-1 · Cited by 54

DNA sequence-dependent formation of heterochromatin nanodomains

Thorn, G. J., Clarkson, C. T., Rademacher, A., Mamayusupova, H., Schotta, G., Rippe, K., & Teif, V. B. (2022) · Nature Communications · doi:10.1038/s41467-022-29360-y · Cited by 49

Aberrant liquid-liquid phase separation and amyloid aggregation of proteins related to neurodegenerative diseases

Ahmad, A., Uversky, V. N., & Khan, R. H. (2022) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2022.08.132 · Cited by 53

Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin

Lee, Y. C. G., Ogiyama, Y., Martins, N. M. C., Beliveau, B. J., Acevedo, D., Wu, C.-T., Cavalli, G., & Karpen, G. H. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008673 · Cited by 49

Emerging Implications of Phase Separation in Cancer

Ren, J., Zhang, Z., Zong, Z., Zhang, L., & Zhou, F. (2022) · Advanced Science · doi:10.1002/advs.202202855 · Cited by 48

Diverse heterochromatin states restricting cell identity and reprogramming

McCarthy, R. L., Zhang, J., & Zaret, K. S. (2023) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2023.02.007 · Cited by 47

Timely double-strand break repair and pathway choice in pericentromeric heterochromatin depend on the histone demethylase dKDM4APreprint

Janssen, A., Colmenares, S. U., Lee, T., & Karpen, G. H. (2018) · Genes & Development · doi:10.1101/gad.317537.118 · Cited by 48

Mechanical regulation of histone modifications and cell plasticity

Song, Y., Soto, J., & Li, S. (2020) · Current Opinion in Solid State and Materials Science · doi:10.1016/j.cossms.2020.100872 · Cited by 48

Heterochromatin-dependent transcription of satellite DNAs in the Drosophila melanogaster female germline

Wei, X., Eickbush, D. G., Speece, I., & Larracuente, A. M. (2021) · eLife · doi:10.7554/elife.62375 · Cited by 44

Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery

Andreev, V. I., Yu, C., Wang, J., Schnabl, J., Tirián, L., Gehre, M., Handler, D., Duchek, P., Novatchkova, M., Baumgartner, L., et al. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00721-x · Cited by 48

Emerging roles of telomeric chromatin alterations in cancer

Cacchione, S., Biroccio, A., & Rizzo, A. (2019) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-019-1030-5 · Cited by 47

Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing

Osumi, K., Sato, K., Murano, K., Siomi, H., & Siomi, M. C. (2019) · EMBO Reports · doi:10.15252/embr.201948296 · Cited by 47

Role of Connexins 30, 36, and 43 in Brain Tumors, Neurodegenerative Diseases, and Neuroprotection

Sánchez, O. F., Rodríguez, A. V., Velasco-España, J. M., Murillo, L. C., Sutachan, J. J., & Albarracin, S.-L. (2020) · Cells · doi:10.3390/cells9040846 · Cited by 46

OUP accepted manuscript

Liang, C., Ke, Q., Liu, Z., Ren, J., Zhang, W., Hu, J., Wang, Z., Chen, H., Xia, K., Lai, X., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac146 · Cited by 50

The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders

Frost, B., & Dubnau, J. (2024) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-082823-020615 · Cited by 45

Euchromatin Activity Enhances Segregation and Compaction of Heterochromatin in the Cell Nucleus

Mahajan, A., Yan, W., Zidovska, A., Saintillan, D., & Shelley, M. (2022) · Physical Review X · doi:10.1103/physrevx.12.041033 · Cited by 44

Heterochromatin organization and phase separation

Zhang, H., Qin, W., Romero, H., Leonhardt, H., & Cardoso, M. C. (2023) · Nucleus · doi:10.1080/19491034.2022.2159142 · Cited by 46

The Molecular Mechanism of Polyphenols in the Regulation of Ageing Hallmarks

Pereira, Q. C., dos Santos, T. W., Fortunato, I. M., & Ribeiro, M. L. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24065508 · Cited by 51

Toward a Unified Theory of Aging and Regeneration

West, M. D., Sternberg, H., Labat, I., Janus, J., Chapman, K. B., Malik, N. N., de Grey, A. D., & Larocca, D. (2019) · Regenerative Medicine · doi:10.2217/rme-2019-0062 · Cited by 48

The Chromatin Landscape Channels DNA Double-Strand Breaks to Distinct Repair Pathways

Chen, Z., & Tyler, J. K. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.909696 · Cited by 44

Neutrophil dynamics and inflammaging in acute ischemic stroke: A transcriptomic review

Bui, T. A., Jickling, G. C., & Winship, I. R. (2022) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2022.1041333 · Cited by 46

Targeting pericentric non-consecutive motifs for heterochromatin initiation

Ma, R., Zhang, Y., Zhang, J., Zhang, P., Liu, Z., Fan, Y., Wang, H., Zhang, Z., & Zhu, B. (2024) · Nature · doi:10.1038/s41586-024-07640-5 · Cited by 43

SUV39 SET domains mediate crosstalk of heterochromatic histone marks

Stirpe, A., Guidotti, N., Northall, S. J., Kilic, S., Hainard, A., Vadas, O., Fierz, B., & Schalch, T. (2021) · eLife · doi:10.7554/elife.62682 · Cited by 44

Karyotype variation, spontaneous genome rearrangements affecting chemical insensitivity, and expression level polymorphisms in the plant pathogen Phytophthora infestans revealed using its first chromosome-scale assembly

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DONSON and FANCM associate with different replisomes distinguished by replication timing and chromatin domain

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