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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...are linked to active chromatin remodeling and reduced DNA methylation. Nucleosomes lost or gained in CLL marks differential binding of 3D chromatin organizers such as CTCF as well as immune response–related transcription factors and delineated mechanisms of epigenetic deregulation. The principal component...
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Research: DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries
- Laura Wiehle,
- Graeme J. Thorn,
- Günter Raddatz,
- Christopher T. Clarkson,
- Karsten Rippe,
- Frank Lyko,
- Achim Breiling,
- and Vladimir B. Teif
Genome Res. May 2019 29: 750-761; Published in Advance April 4, 2019, doi:10.1101/gr.239707.118
...binding, DNA methylation, and gene expression in DKO ESCs and developed biophysical models to predict differential CTCF binding. Methylation-sensitive nucleosome repositioning accounted for a significant portion of CTCF binding loss in DKO ESCs, whereas unmethylated and nucleosome-depleted CpG islands...
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Research: CTCF sites display cell cycle–dependent dynamics in factor binding and nucleosome positioning
- Marlies E. Oomen,
- Anders S. Hansen,
- Yu Liu,
- Xavier Darzacq,
- and Job Dekker
Genome Res. February 2019 29: 236-249; Published in Advance January 17, 2019, doi:10.1101/gr.241547.118
..., dissociates from chromatin during mitosis. Along these lines, CTCF becomes highly phosphorylated in mitosis (Dovat et al. 2002; Dephoure et al. 2008; Rizkallah and Hurt 2009), and in vitro assays show that DNA binding capability of phosphorylated CTCF is dramatically reduced (Jantz and Berg 2004; Sekiya et al...
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Research: Transcription factor activity and nucleosome organization in mitosis
- Nicola Festuccia,
- Nick Owens,
- Thaleia Papadopoulou,
- Inma Gonzalez,
- Alexandra Tachtsidi,
- Sandrine Vandoermel-Pournin,
- Elena Gallego,
- Nancy Gutierrez,
- Agnès Dubois,
- Michel Cohen-Tannoudji,
- and Pablo Navarro
Genome Res. February 2019 29: 250-260; Published in Advance January 17, 2019, doi:10.1101/gr.243048.118
...show that localization of a TF to the chromatin does not necessarily imply DNA sequence-specific binding in mitosis (Fig. 7A). This is exemplified by SOX2 and, as shown by others, by CTCF (Oomen et al. 2019): While these TFs are both chromosomally retained, they are largely evicted from the sites...
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Research: Study of mitotic chromatin supports a model of bookmarking by histone modifications and reveals nucleosome deposition patterns
- Elisheva Javasky,
- Inbal Shamir,
- Shashi Gandhi,
- Shawn Egri,
- Oded Sandler,
- Scott B. Rothbart,
- Noam Kaplan,
- Jacob D. Jaffe,
- Alon Goren,
- and Itamar Simon
Genome Res. October 2018 28: 1455-1466; Published in Advance August 30, 2018, doi:10.1101/gr.230300.117
...of nucleosomes during mitosis.The cell cycle is a dynamic orchestrated process that involves major changes to the chromatin structure (Raynaud et al. 2014) and the expression of hundreds of genes (Spellman et al. 1998; Cho et al. 2001; Whitfield et al. 2002; Bar-Joseph et al. 2008). During the cell cycle, DNA...
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Research: DNA methylation profiling in human B cells reveals immune regulatory elements and epigenetic plasticity at Alu elements during B-cell activation
- Anne Y. Lai,
- Deepak Mav,
- Ruchir Shah,
- Sara A. Grimm,
- Dhiral Phadke,
- Katerina Hatzi,
- Ari Melnick,
- Cissy Geigerman,
- Steve E. Sobol,
- David L. Jaye,
- and Paul A. Wade
Genome Res. December 2013 23: 2030-2041; Published in Advance September 6, 2013, doi:10.1101/gr.155473.113
...differentiation in an immune response. [Supplemental material is available for this article.] Epigenetic modifications play important roles in regulating cellular differentiation events. One such epigenetic modification, DNA methylation, occurs on cytosine residues primarily at CpG dinucleotides in mammals...
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Research: Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
- Gangqing Hu,
- Dustin E. Schones,
- Kairong Cui,
- River Ybarra,
- Daniel Northrup,
- Qingsong Tang,
- Luca Gattinoni,
- Nicholas P. Restifo,
- Suming Huang,
- and Keji Zhao
Genome Res. October 2011 21: 1650-1658; Published in Advance July 27, 2011, doi:10.1101/gr.121145.111
...HSCs and CD36+ cells using MNase-seq as describedpreviously (Schones et al. 2008). As shown in Figure 1A, nucleosomes were well positioned surrounding the binding sites of the constitutively expressed insulator protein, CTCF, and little difference was detected after differentiation. In striking contrast...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
..., independent features. This may be due to the popularity of “single-profile” methods which provide rich data for only one aspect of chromatin at a time (Box 1). However, features such as chromatin accessibility (Fig. 1A), DNA methylation (Fig. 1B), compartments (Fig. 1C), CTCF loops, E–P, and other...
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Method: A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs
- Christian Pflueger,
- Dennis Tan,
- Tessa Swain,
- Trung Nguyen,
- Jahnvi Pflueger,
- Christian Nefzger,
- Jose M. Polo,
- Ethan Ford,
- and Ryan Lister
Genome Res. August 2018 28: 1193-1206; Published in Advance June 15, 2018, doi:10.1101/gr.233049.117
.... Furthermore, we used dC9Sun-D3A to demonstrate the binding sensitivity to DNA methylation for CTCF and NRF1 in situ. Overall, this modular dC9Sun-D3A system enables precise DNA methylation deposition with the lowest off-target DNA methylation levels reported to date, allowing accurate functional determination...
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Research: Cytosine modifications modulate the chromatin architecture of transcriptional enhancers
- Elise A. Mahé,
- Thierry Madigou,
- Aurélien A. Sérandour,
- Maud Bizot,
- Stéphane Avner,
- Frédéric Chalmel,
- Gaëlle Palierne,
- Raphaël Métivier,
- and Gilles Salbert
Genome Res. June 2017 27: 947-958; Published in Advance April 10, 2017, doi:10.1101/gr.211466.116
...influence nucleosome stability in a direct or indirect manner. This is consistent with reports showing (1) that nucleosomes found at hydroxymethylated CTCF binding sites are more sensitive to MNase digestion (Teif et al. 2014), and (2) that nucleosomes formed in vitro on a hydroxymethylated DNA template...

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