Competition between DNA methylation and transcription factors determines binding of NRF1

By Silvia Domcke, A. Bardet, Paul Adrian Ginno, Dominik Hartl, Lukas Burger, Dirk Schübeler. 2015

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In Molecular Biology

Citations in the corpus

Impact of cytosine methylation on DNA binding specificities of human transcription factors (2017, methodology): “Peaks containing motif 2 matches whose methylation does not change or changes less than the cut-off (from ≤ 20% in Dnmt-TKO to ≥80% in Tet-TKO) are in gray.”
Mapping genome-wide transcription-factor binding sites using DAP-seq (2017, methodology): “…Enrichment (HT-SELEX) have achieved the highest throughput for deducing TF binding specificities in vitro 9–11 , but these methods use short synthetic oligonucleotides lacking secondary DNA modifications and genomic context, both important determinants of selective TF binding in vivo 12–16 .”
DNA methylation: a historical perspective. (2022, unknown): “To quantify this effect, high-throughput in vitro screens were developed [225,226], finding that the affinity of 90% of the studied TFs containing a CpG in their motif was influenced by DNAmethylation [226], but only few studies have gone on to demonstrate this in vivo [227,228].”
Epigenomic diversity in a global collection of Arabidopsis thaliana accessions (2016, unknown): “As TF binding provides a mechanism for how methylation may affect gene expression, we compared the genetic and methylation variants to the 2.7 million TFBS of 329 TFs identified on Col-0 leaf DNA with methylcytosines (Col-0 cistrome) and the additional 180,000 TFBS identified on methylation-free DNA”
Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape (2016, unknown): “We examined several primary sequence properties of genomic DNA known to impact in vivo binding, including motif clusters (Pott and Lieb, 2015) and TF sensitivity to DNA methylation in motifs (Domcke et al., 2015), by restricting predictions to peaks containing a single motif with no strong motifs wi”