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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
...experimentally showed the functional roles of such retained modifications at early stages: (i) H3K27ac premarks promoters during the cleavage stage, and inhibition of histone acetyltransferases disrupts proper patterning of H3K4 and H3K27 methylation at CpG-dense promoters, but does not affect chromatin...
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Research: Genome-wide variability in recombination activity is associated with meiotic chromatin organization
- Xiaofan Jin,
- Geoff Fudenberg,
- and Katherine S. Pollard
Genome Res. September 2021 31: 1561-1572; Published in Advance July 23, 2021, doi:10.1101/gr.275358.121
...-C, CTCF, RNAPII, and cohesin RAD21 subunit) from embryonic stem (ES) cells, serving as an example of interphase chromatin organization (Nitzsche et al. 2011; Shen et al. 2012; Bonev et al. 2017), allowing the identification of meiosis-specific patterns.PRDM9 sites associated with DSB formation show...
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Research: Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control
- Valentina Casa,
- Macarena Moronta Gines,
- Eduardo Gade Gusmao,
- Johan A. Slotman,
- Anne Zirkel,
- Natasa Josipovic,
- Edwin Oole,
- Wilfred F.J. van IJcken,
- Adriaan B. Houtsmuller,
- Argyris Papantonis,
- and Kerstin S. Wendt
Genome Res. April 2020 30: 515-527; Published in Advance April 6, 2020, doi:10.1101/gr.253211.119
...of the cohesin complex is still unclear. STAG1- and STAG2-cohesin were initially proposed to organize cohesion at telomeres and centromeres, respectively. Here, we uncover redundant and specific roles of STAG1 and STAG2 in gene regulation and chromatin looping using HCT116 cells with an auxin-inducible degron...
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Research: The gene repressor complex NuRD interacts with the histone variant H3.3 at promoters of active genes
- Daniel C. Kraushaar,
- Zuozhou Chen,
- Qingsong Tang,
- Kairong Cui,
- Junfang Zhang,
- and Keji Zhao
Genome Res. November 2018 28: 1646-1655; Published in Advance September 25, 2018, doi:10.1101/gr.236224.118
...access of active and repressive complexes to chromatin in embryonic stem cell self-renewal and differentiation. Cell Stem Cell 12: 180–192. ↵Jin C, Felsenfeld G. 2007. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev 21: 1519–1529. ↵Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K...
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Research: PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX
- Erwan Delbarre,
- Kristina Ivanauskiene,
- Jane Spirkoski,
- Akshay Shah,
- Kristin Vekterud,
- Jan Øivind Moskaug,
- Stig Ove Bøe,
- Lee H. Wong,
- Thomas Küntziger,
- and Philippe Collas
Genome Res. June 2017 27: 913-921; Published in Advance March 24, 2017, doi:10.1101/gr.215830.116
..., AndersonMA,Mann J, et al. 2009. Histone H3.3 incorporation provides a unique and functionally essential telomeric chromatin in embryonic stem cells. Genome Res 19: 404–414. WongLH,McGhie JD, SimM, AndersonMA, Ahn S, Hannan RD,George AJ, Morgan KA, Mann JR, Choo KH. 2010. ATRX interacts with H3...
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Method: A synergistic DNA logic predicts genome-wide chromatin accessibility
- Tatsunori Hashimoto,
- Richard I. Sherwood,
- Daniel D. Kang,
- Nisha Rajagopal,
- Amira A. Barkal,
- Haoyang Zeng,
- Bart J.M. Emons,
- Sharanya Srinivasan,
- Tommi Jaakkola,
- and David K. Gifford
Genome Res. October 2016 26: 1430-1440; Published in Advance July 25, 2016, doi:10.1101/gr.199778.115
...assay could additionally be paired with assays for DNA methylation, histone modification, or gene expression to gain insight into how DNA sequence encodes these functions in controlled genomic contexts as well as elucidating cell-state–specific chromatin accessibility and gene regulation when applying...
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Research: SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells
- A. Rasim Barutcu,
- Bryan R. Lajoie,
- Andrew J. Fritz,
- Rachel P. McCord,
- Jeffrey A. Nickerson,
- Andre J. van Wijnen,
- Jane B. Lian,
- Janet L. Stein,
- Job Dekker,
- Gary S. Stein,
- and Anthony N. Imbalzano
Genome Res. September 2016 26: 1188-1201; Published in Advance July 19, 2016, doi:10.1101/gr.201624.115
...stem cells (Hu et al. 2011; RadaIglesias et al. 2011) and B-cells (Bossen et al. 2015) and colocalizes with pluripotency factors (Ho et al. 2009), suggesting important roles in enhancer function. Furthermore, previouswork classifying -wide interactions according to their histone modifications...
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Method: Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression
- Maxwell W. Libbrecht,
- Ferhat Ay,
- Michael M. Hoffman,
- David M. Gilbert,
- Jeffrey A. Bilmes,
- and William Stafford Noble
Genome Res. April 2015 25: 544-557; Published in Advance February 12, 2015, doi:10.1101/gr.184341.114
...compared the 1D genomics data at pairs of statistically significantly interacting loci (Supplemental Fig. 1). As expected, we found that chromatin signalswere highly consistent at pairs of positions nearby in 3D. First, histone modification and replication signal values at pairs of significantly...
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Letter: ATRX interacts with H3.3 in maintaining telomere structural integrity in pluripotent embryonic stem cells
- Lee H. Wong,
- James D. McGhie,
- Marcus Sim,
- Melissa A. Anderson,
- Soyeon Ahn,
- Ross D. Hannan,
- Amee J. George,
- Kylie A. Morgan,
- Jeffrey R. Mann,
- and K.H. Andy Choo
Genome Res. March 2010 20: 351-360; Published in Advance January 28, 2010, doi:10.1101/gr.101477.109
...to be a transcriptional regulator, its precise roles remain undefined. We demonstrate ATRX localization at the telomeres in interphase mouse embryonic stem (ES) cells in synchrony with the incorporation of H3.3 during telomere replication at S phase. Moreover, we found that chromobox homolog 5 (CBX5) (also known...
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Research: The PML-associated protein DEK regulates the balance of H3.3 loading on chromatin and is important for telomere integrity
- Kristina Ivanauskiene,
- Erwan Delbarre,
- James D. McGhie,
- Thomas Küntziger,
- Lee H. Wong,
- and Philippe Collas
Genome Res. October 2014 24: 1584-1594; Published in Advance July 21, 2014, doi:10.1101/gr.173831.114
...thalassemia/mental retardation syndrome X-linked (ATRX), a chromatin remodeler (Gibbons et al. 1997; Argentaro et al. 2007), loads H3.3 on pericentric chromatin and, in embryonic stem cells (ESCs), on telomeres (Drane et al. 2010; Goldberg et al. 2010; Lewis et al. 2010; Wong et al. 2010; Eustermann et al...

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