DNA-binding factors shape the mouse methylome at distal regulatory regions

By Michael B. Stadler, Rabih Murr, Lukas Burger, R. Ivanek, F. Lienert, A. Schöler, C. Wirbelauer, E. Oakeley, Dimos Gaidatzis, V. Tiwari and 1 more. 2011

1,338 citations recorded by the source corpus.

Subfields: Molecular Biology

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In Molecular Biology

1. Hao Wu
2. Yi Zhang
3. Chuan He
4. Bing Ren
5. V. Corces
6. Daniel R. Zerbino
7. Yang Shi
8. Christoph Bock

Citations in the corpus

• Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, methodology): “(8) and heatmaps were generated using deepTools (version 2.”
• CG methylated microarrays identify a novel methylated sequence bound by the CEBPB|ATF4 heterodimer that is active in vivo (2013, background): “…in vivo binding of CEBPB to the unmethylated CEBP se- quences, even though they are bound more poorly on the array, is because the unmethylated occurrences are in more accessible Genome Research 993 www.genome.org regions of the genome (Biddie et al. 2011; John et al. 2011; Stadler et al. 2011).”
• YY1 Is a Structural Regulator of Enhancer-Promoter Loops (2017, neutral): “…et al., 1993); Lin et al. (2010); Lobanenkov et al. (1990); Mendenhall et al. (2010); Moore et al. (2012); Natesan and Gilman (1993); Nora et al. (2016); Pope et al. (2014); Seto et al. (1991); Stadler et al. (2011); Wang et al. (2012); Wu et al. (2007); Xu et al. (2007); Yusufzai et al. (2004).”
• Architectural protein subclasses shape 3D organization of genomes during lineage commitment. (2013, positive): “Genome-wide binding sites for CTCF, mediator subunit Med12, and cohesin subunit Smc1 have been previously identified in ES cells by ChIP-seq (Kagey et al., 2010; Stadler et al., 2011).”
• Widespread plasticity in CTCF occupancy linked to DNA methylation (2012, neutral): “Indeed, there is evidence that the binding of some transcription factors, including CTCF, is sufficient to effect a local demethyl-ated state (Matsuo et al. 1998; Lin et al. 2000; Stadler et al. 2011).”
• Modification of enhancer chromatin: what, how and why? (2013, background): “…been detected in genomes of several cell types, including ESCs, where it positively correlates with gene activity and is found at promoters, gene bodies, and enhancers (Ficz et al., 2011; Pastor et al., 2011; Stroud et al., 2011; Szulwach et al., 2011; Valinluck et al., 2004; Wu and Zhang, 2010).”
• DNA methylation: a historical perspective. (2022, positive): “Elevated levels of 5hmC have been found at LMRs, suggesting a role for active demethylation at LMRs [222].”