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Research: Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development
- Hiroto S. Fukushima,
- Hiroyuki Takeda,
- and Ryohei Nakamura
Genome Res. April 2023 33: 572-586; Published in Advance April 28, 2023, doi:10.1101/gr.277577.122
...and H3K9me3 marks were only detected in mitotic phase chromatin at the 16-cell, 64-cell, and late morula stages, but detected in both mitotic phase and interphase chromatin at the late blastula stage (Fig. 1B,C). This suggests that H3K27me3 and H3K9me3 mostly accumulate during or after ZGA, consistent...
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Research: Broad domains of histone marks in the highly compact Paramecium macronuclear genome
- Franziska Drews,
- Abdulrahman Salhab,
- Sivarajan Karunanithi,
- Miriam Cheaib,
- Martin Jung,
- Marcel H. Schulz,
- and Martin Simon
Genome Res. April 2022 32: 710-725; Published in Advance March 9, 2022, doi:10.1101/gr.276126.121
...Broad domains of histone marks in the highly compact Paramecium macronuclear Franziska Drews1,2, Abdulrahman Salhab3,7, Sivarajan Karunanithi4,5,7,8, Miriam Cheaib2, Martin Jung6, Marcel H. Schulz4,5 and Martin Simon1,2 1Molecular Cell Biology and Microbiology, Faculty for Mathematics and Natural...
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Research: Epigenetic activation of meiotic recombination near Arabidopsis thaliana centromeres via loss of H3K9me2 and non-CG DNA methylation
- Charles J. Underwood,
- Kyuha Choi,
- Christophe Lambing,
- Xiaohui Zhao,
- Heïdi Serra,
- Filipe Borges,
- Joe Simorowski,
- Evan Ernst,
- Yannick Jacob,
- Ian R. Henderson,
- and Robert A. Martienssen
Genome Res. April 2018 28: 519-531; Published in Advance March 12, 2018, doi:10.1101/gr.227116.117
...dimethylation (H3K9me2), and DNA methylation in CG and non-CG sequence contexts. However, the role of these chromatin modifications in control of meiotic recombination in the pericentromeres is not fully understood. Here, we show that disruption of Arabidopsis thaliana H3K9me2 and non-CG DNA methylation...
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Research: Sense–antisense miRNA pairs constitute an elaborate reciprocal regulatory circuit
- Yulong Song,
- Lishi Li,
- Wenbing Yang,
- Qiang Fu,
- Wanying Chen,
- Zeng Fang,
- Wen Li,
- Nannan Gu,
- and Rui Zhang
Genome Res. May 2020 30: 661-672; Published in Advance May 18, 2020, doi:10.1101/gr.257121.119
...as a previously unknown reciprocal regulatory circuit of sense–antisense miRNA pairs.One of the greatest surprises of recent transcriptome analysis is the discovery that the mammalian is pervasively transcribed (Kapranov et al. 2002; Carninci et al. 2005) and many of the protein-coding genes have antisense...
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Research: Ancient antagonism between CELF and RBFOX families tunes mRNA splicing outcomes
- Matthew R. Gazzara,
- Michael J. Mallory,
- Renat Roytenberg,
- John P. Lindberg,
- Anupama Jha,
- Kristen W. Lynch,
- and Yoseph Barash
Genome Res. August 2017 27: 1360-1370; Published in Advance May 16, 2017, doi:10.1101/gr.220517.117
...family antagonism in mouse heart and muscle, we wished to examine if this Figure 3. Reciprocal regulation of CELF2-repressed exons by RBFOX2 in T cells. (A–E)Quantification of splicingby RT-PCR (see Supplemental Fig. S1 for gels) of MAJIQ-identified CELF2-repressed exons that contain proximal intronic...
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Method: Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes
- Yinxiu Zhan,
- Luca Mariani,
- Iros Barozzi,
- Edda G. Schulz,
- Nils Blüthgen,
- Michael Stadler,
- Guido Tiana,
- and Luca Giorgetti
Genome Res. March 2017 27: 479-490; Published in Advance January 5, 2017, doi:10.1101/gr.212803.116
...if their reciprocal insulation is smaller than a given threshold. (C) (Left three panels) Examples of sets of domains defined in mouse ESCs Hi-C data (20-kb binning) imposing different threshold on RI. (Right) Number of domains detected in ESC as a function of RI. (D) Sub-TAD contact domains (left), directionality...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
.... Each group is defined by a different heterochromatin modification (H3K9me3, H3K9me2, or H3K27me3), suggesting that all three of these marks play important roles in regulation of LAD chromatin and potentially of lamina association. We also discover unique features of LAD borders, including a LAD border...
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Research: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
- Agustín F. Fernández,
- Gustavo F. Bayón,
- Rocío G. Urdinguio,
- Estela G. Toraño,
- María G. García,
- Antonella Carella,
- Sandra Petrus-Reurer,
- Cecilia Ferrero,
- Pablo Martinez-Camblor,
- Isabel Cubillo,
- Javier García-Castro,
- Jesús Delgado-Calle,
- Flor M. Pérez-Campo,
- José A. Riancho,
- Clara Bueno,
- Pablo Menéndez,
- Anouk Mentink,
- Katia Mareschi,
- Fabian Claire,
- Corrado Fagnani,
- Emanuela Medda,
- Virgilia Toccaceli,
- Sonia Brescianini,
- Sebastián Moran,
- Manel Esteller,
- Alexandra Stolzing,
- Jan de Boer,
- Lorenza Nisticò,
- Maria A. Stazi,
- and Mario F. Fraga
Genome Res. January 2015 25: 27-40; Published in Advance September 30, 2014, doi:10.1101/gr.169011.113
..., aging is associated with hypermethylation of DNA regions enriched in repressive histone post-translational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal...
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Research: Novel H3K4me3 marks are enriched at human- and chimpanzee-specific cytogenetic structures
- Giuliana Giannuzzi,
- Eugenia Migliavacca,
- and Alexandre Reymond
Genome Res. September 2014 24: 1455-1468; Published in Advance June 10, 2014, doi:10.1101/gr.167742.113
...was observed in two recent comparisons: the 5-hydroxymethylcytosine epigenetic mark between induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs) in human (Wang et al. 2013) and higher order chromatin structure between human andmouse (Chambers et al. 2013). Moreover, an example...
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LETTER: Chicken Microchromosomes Are Hyperacetylated, Early Replicating, and Gene Rich
- Heather A. McQueen,
- Giorgia Siriaco,
- and Adrian P. Bird
Genome Res. June 1, 1998 8: 621-630; doi:10.1101/gr.8.6.621
...Chicken Microchromosomes Are Hyperacetylated, Early Replicating, and Gene Rich Heather A. McQueen 1 , 2 , Giorgia Siriaco 1 , and Adrian P. Bird Institute of Cell and Molecular Biology, University of Edinburgh, Darwin Building, King’s Buildings...

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