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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...cancers. Our work reveals that misregulation of the Polycomb-mediated H3K27me3 histone modification in differentiated cells during aging not only underlies tissue decline but also mirrors transcriptional changes in cancer, suggesting a common mechanism linking aging and cancer progression...
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Research: Polycomb-dependent differential chromatin compartmentalization determines gene coregulation in Arabidopsis
- Ying Huang,
- Sanchari Sicar,
- Juan S. Ramirez-Prado,
- Deborah Manza-Mianza,
- Javier Antunez-Sanchez,
- Rim Brik-Chaouche,
- Natalia Y. Rodriguez-Granados,
- Jing An,
- Catherine Bergounioux,
- Magdy M. Mahfouz,
- Heribert Hirt,
- Martin Crespi,
- Lorenzo Concia,
- Fredy Barneche,
- Simon Amiard,
- Aline V. Probst,
- Jose Gutierrez-Marcos,
- Federico Ariel,
- Cécile Raynaud,
- David Latrasse,
- and Moussa Benhamed
Genome Res. July 2021 31: 1230-1244; Published in Advance June 3, 2021, doi:10.1101/gr.273771.120
...et al. 2011).Growing evidence indicates that H3K27me3 plays an important role in the spatial organization of chromatin in eukaryotes, a phenomenon that has been associated with its repressive role in transcription. For instance, it has been shown in animals that Polycomb targets marked with H3K27me3...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...heterochromatic H3K9me3 deposition. We reveal a paradoxical repression of protein-coding genes in Suv39DKO cells, with these differentially expressed genes principally in euchromatic (Tn5-accessible, H3K4me3- and H3K27ac-marked) rather than heterochromatic (H3K9me3-marked) or polycomb (H3K27me3-marked) regions...
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Research: Characterization of the distribution and dynamics of chromatin states in the C. elegans germline reveals substantial H3K4me3 remodeling during oogenesis
- Mariateresa Mazzetto,
- Lauren E. Gonzalez,
- Nancy Sanchez,
- and Valerie Reinke
Genome Res. January 2024 34: 57-69; Published in Advance December 26, 2023, doi:10.1101/gr.278247.123
...,” because it had high levels of H3K9me3. The second state, “heterochromatin 2” is characterized by high levels of both H3K9me3 and H3K27me3. The third state had high levels of H3K27me3 alone and is called “Polycomb (PC) repressed,” whereas state 4 had low levels of any mark and is termed “quiescent.” States...
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Research: Polycomb repressive complex 1 shapes the nucleosome landscape but not accessibility at target genes
- Hamish W. King,
- Nadezda A. Fursova,
- Neil P. Blackledge,
- and Robert J. Klose
Genome Res. October 2018 28: 1494-1507; Published in Advance August 28, 2018, doi:10.1101/gr.237180.118
...authors: h.king@qmul.ac.uk, drhamishking@gmail.com, rob.klose@bioch.ox.ac.ukAbstractPolycomb group (PcG) proteins are transcriptional repressors that play important roles in regulating gene expression during animal development. In vitro experiments have shown that PcG protein complexes can compact...
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Research: Dynamics of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes
- Mohamed Belhocine,
- Mathieu Simonin,
- José David Abad Flores,
- Agata Cieslak,
- Iris Manosalva,
- Lydie Pradel,
- Charlotte Smith,
- Eve-Lyne Mathieu,
- Guillaume Charbonnier,
- Joost H.A. Martens,
- Hendrik G. Stunnenberg,
- Muhammad Ahmad Maqbool,
- Aneta Mikulasova,
- Lisa J. Russell,
- Daniel Rico,
- Denis Puthier,
- Pierre Ferrier,
- Vahid Asnafi,
- and Salvatore Spicuglia
Genome Res. July 2022 32: 1328-1342; Published in Advance June 23, 2021, doi:10.1101/gr.266924.120
..., the absence of broad H3K4me3 domain at these loci is often associated with repressive chromatin enriched with Polycomb-associated states. As described before for cell lines and primary tissues, here we showed that broad H3K4me3 domains dynamically associate with cell identity genes throughout T cell...
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Research: Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors
- Martin Cusack,
- Hamish W. King,
- Paolo Spingardi,
- Benedikt M. Kessler,
- Robert J. Klose,
- and Skirmantas Kriaucionis
Genome Res. October 2020 30: 1393-1406; Published in Advance September 22, 2020, doi:10.1101/gr.257576.119
...poorly understood. HDAC inhibition, or disruption of the interaction between MBD proteins and the HDAC-containing complexes, has been shown to alleviate transcriptional silencing mediated by DNA methylation in reporter gene assays (Jones et al. 1998; Nan et al. 1998; Ng et al. 1999; Lyst et al. 2013...
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Research: The loss of heterochromatin is associated with multiscale three-dimensional genome reorganization and aberrant transcription during cellular senescence
- Xianglin Zhang,
- Xuehui Liu,
- Zhenhai Du,
- Lei Wei,
- Huan Fang,
- Qiongye Dong,
- Jing Niu,
- Yanda Li,
- Juntao Gao,
- Michael Q. Zhang,
- Wei Xie,
- and Xiaowo Wang
Genome Res. July 2021 31: 1121-1135; Published in Advance June 17, 2021, doi:10.1101/gr.275235.121
...the loss of heterochromatin is not clear. One hypothesis is that relatively increased occupation of H3K27me3 in heterochromatin (Polycomb repressor complex has been shown as mediator of chromatin organization) is responsible for the maintenance of A/B compartment structure (Penagos-Puig and Furlan...
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Research: Reprogramming of the human intestinal epigenome by surgical tissue transposition
- Fides D. Lay,
- Timothy J. Triche, Jr.,
- Yvonne C. Tsai,
- Sheng-Fang Su,
- Sue Ellen Martin,
- Siamak Daneshmand,
- Eila C. Skinner,
- Gangning Liang,
- Yoshitomo Chihara,
- and Peter A. Jones
Genome Res. April 2014 24: 545-553; Published in Advance February 10, 2014, doi:10.1101/gr.166439.113
...enhancer regions, with the remaining probes in the cluster distributed across the heterochromatic/quiescent state, transcribed regions, the polycomb repressed state, and to a lesser extent, the promoter regions. (Fig. 4B, left panel; Supplemental Fig. 7E). The enrichment of the enhancer regions is specific...
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Research: The role of DNA methylation in directing the functional organization of the cancer epigenome
- Fides D. Lay,
- Yaping Liu,
- Theresa K. Kelly,
- Heather Witt,
- Peggy J. Farnham,
- Peter A. Jones,
- and Benjamin P. Berman
Genome Res. April 2015 25: 467-477; Published in Advance March 6, 2015, doi:10.1101/gr.183368.114
...likely to be expressed in a tissue-specific pattern, be associated with TATA boxes, and initiate transcription from a particular base pair rather than many possible initiation sites within a “broad” region (Rach et al. 2011); they are also almost never repressed by Polycomb-associatedH3K27me3 (Mohn et al...
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