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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...fate determinants plays a critical role in specifying these identities. Epigenetic mechanisms, such as histones and their post-translational modifications, regulate chromatin compaction, transcription, and DNA replication timing to influence cell fate decisions. In stem cells, epigenetic regulation...
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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
..., and transcription factor occupancy in wild-type or DNA methylation-deficient mouse embryonic stem cells following HDAC inhibition. We observe widespread increases in chromatin accessibility at retrotransposons when HDACs are inhibited, and this is magnified when cells also lack DNA methylation. A subset...
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Resource: A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
- Salam Idriss,
- Mohammad Hallal,
- Abdullah El-Kurdi,
- Hasan Zalzali,
- Inaam El-Rassi,
- Erik A. Ehli,
- Christel M. Davis,
- Philip E.D. Chung,
- Deena M.A. Gendoo,
- Eldad Zacksenhaus,
- Raya Saab,
- and Pierre Khoueiry
Genome Res. February 2023 33: 269-282; Published in Advance January 17, 2023, doi:10.1101/gr.277037.122
...chromatin, independent of ChromHMM. For that, we compiled available ENCODE peaks for the following histone marks generated on mouse cell lines: H3K27ac (marks active promoters and enhancers), H3K4me1 (marks enhancer regions), H3K27me3 (repressive mark, usually on gene body), H3K9me3 (marks constitutive...
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Research: TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity
- Morgan A. Sammons,
- Jiajun Zhu,
- Adam M. Drake,
- and Shelley L. Berger
Genome Res. February 2015 25: 179-188; Published in Advance November 12, 2014, doi:10.1101/gr.181883.114
...dynamic. H4K16ac enrichment at TP53-bound enhancers supports a recent report of H4K16acmarking active enhancers inmouse embryonic stem cells (mES) and suggests that classes of enhancers may be differentially marked with histone acetylation (Taylor et al. 2013). Dynamic deposition of H3K27ac after...
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Research: DNA replication and transcription programs respond to the same chromatin cues
- Yoav Lubelsky,
- Joseph A. Prinz,
- Leyna DeNapoli,
- Yulong Li,
- Jason A. Belsky,
- and David M. MacAlpine
Genome Res. July 2014 24: 1102-1114; Published in Advance July 1, 2014, doi:10.1101/gr.160010.113
...acetylation levels. We examined the median enrichment of different chromatin marks in the early and late replicating domains in Kc167 and S2 cells. We found that there was an X chromosome-specific hyperacetylation of H4K16 in both the early and late replicating domains in the male S2 cells (Fig. 5C...
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Research: Histone deacetylases maintain expression of the pluripotent gene network via recruitment of RNA polymerase II to coding and noncoding loci
- Richard D.W. Kelly,
- Kristy R. Stengel,
- Aditya Chandru,
- Lyndsey C. Johnson,
- Scott W. Hiebert,
- and Shaun M. Cowley
Genome Res. January 2024 34: 34-46; Published in Advance January 30, 2024, doi:10.1101/gr.278050.123
...(HDACs). Deacetylation of histone tails results in chromatin tightening, and therefore, HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of Hdac1 and Hdac2 in embryonic stem cells (ESCs) reduces expression of the pluripotency-associated transcription...
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Research: Genes for embryo development are packaged in blocks of multivalent chromatin in zebrafish sperm
- Shan-Fu Wu,
- Haiying Zhang,
- and Bradley R. Cairns
Genome Res. April 2011 21: 578-589; Published in Advance March 7, 2011, doi:10.1101/gr.113167.110
...associated with regulating compaction is the acetylation of lysine 16 on histone H4 (H4K16ac), which alone deters the transition of 10-nm nucleosome arrays to more compact 30-nm fibers (Shogren-Knaak et al. 2006; Zhou et al. 2007; Robinson et al. 2008; Kan et al. 2009). Furthermore, H4K16ac uniquely...
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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
...whether PcG proteins define chromatin accessibility or other chromatin features. To address this important question, we examine the chromatin accessibility and nucleosome landscape at PcG protein-bound promoters in mouse embryonic stem cells using the assay for transposase accessible chromatin (ATAC...
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Method: One minute analysis of 200 histone posttranslational modifications by direct injection mass spectrometry
- Simone Sidoli,
- Yekaterina Kori,
- Mariana Lopes,
- Zuo-Fei Yuan,
- Hee Jong Kim,
- Katarzyna Kulej,
- Kevin A. Janssen,
- Laura M. Agosto,
- Julia Pinheiro Chagas da Cunha,
- Andrew J. Andrews,
- and Benjamin A. Garcia
Genome Res. June 2019 29: 978-987; Published in Advance May 23, 2019, doi:10.1101/gr.247353.118
...acetylations, i.e., H4K16ac, H3K23ac, and H3K18ac, and the heterochromatic marker H3K9me3 (Fig. 6E). On the other hand, other acetylations like H4K5ac and H4K12ac were found to be more abundant in liver cells. This also proved that our method can accurately discriminate the relative abundance of isomeric PTMs...
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Research: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
- Ray Marin,
- Diego Cortez,
- Francesco Lamanna,
- Madapura M. Pradeepa,
- Evgeny Leushkin,
- Philippe Julien,
- Angélica Liechti,
- Jean Halbert,
- Thoomke Brüning,
- Katharina Mössinger,
- Timo Trefzer,
- Christian Conrad,
- Halie N. Kerver,
- Juli Wade,
- Patrick Tschopp,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1974-1987; Published in Advance November 13, 2017, doi:10.1101/gr.223727.117
..., including residue K16 of histone 4 (Fig. 4A; Stante et al. 2009; Taylor et al. 2013). H4K16 acetylation is crucial for chromatin structure and function in eukaryotes; by hampering nucleosome interactions, it reduces levels of chromatin compaction, facilitating transcription (Dion et al. 2005; Shogren...
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