Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers

Abstract

Methylation of cytosines on DNA is a prominent modification associated with gene expression regulation. Aberrant DNA methylation patterns have recurrently been linked to dysregulation of the regulatory program in cancer cells. To shed light on the underlying molecular mechanism driving this process, we hypothesised that aberrant methylation patterns could be controlled by the binding of specific transcription factors (TFs) across cancer types. By combining DNA methylation arrays and gene expression data with TF binding sites (TFBSs), we explored the interplay between TF binding and DNA methylation in 19 cancer types. We performed emQTL (expression–methylation quantitative trait loci) analyses independently in each cancer type and identified 13 TFs whose expression levels are correlated with local DNA methylation patterns around their binding sites in at least 2 cancer types. The 13 TFs are mainly associated with local demethylation and are enriched for pioneer function, suggesting a specific role for these TFs in modulating chromatin structure and transcription in cancer patients. Furthermore, we confirmed that de novo methylation is precluded across cancers at CpGs lying in genomic regions enriched for TF binding signatures associated with SP1, CTCF, NRF1, GABPA, KLF9, and/or YY1. The modulation of DNA methylation associated with TF binding was observed at cis-regulatory regions controlling immune- and cancer-associated pathways, corroborating that the emQTL signals were derived from both cancer and tumor-infiltrating cells. As a case example, we experimentally confirmed that FOXA1 knock-down is associated with higher methylation in regions bound by FOXA1 in breast cancer MCF-7 cells. Finally, we reported physical interactions between FOXA1 with TET1 and TET2 both in an in vitro setup and in vivo at physiological levels in MCF-7 cells, adding further support for FOXA1 attracting TET1 and TET2 to induce local demethylation in cancer cells.

Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data

“…3 e), these motifs are potential TF complex motifs, with both parts to be known as single motifs. An exemplary case is shown for a DENIS motif that matches KLF9 and CTCF, both assigned to have a protective role against DNA methylation 46 . Other examples were found with one of the parts to be a known database motif, while the second part is novel.…”

Role of TET1-mediated epigenetic modulation in Alzheimer's disease

“…These TFs are involved in nervous system development, cell senescence, cell proliferation, cell death, tumorigenesis, and metabolic homeostasis. Furthermore, six of these TFs, including FOXO1, FOXA2, FLI1, MYB, and P53, function as pioneer transcription factors ( Lemma et al, 2022 ). Additionally, in the TF binding motifs lost in 5xFAD/Tet1 (+/−) , we observe several ETS family TFs including ETS1, ELF1, and ERG which have been previously shown to have methylation and hydroxymethylation sensitive binding ( Song et al, 2021 ).…”

DMRT1 regulates human germline commitment

“…We observed a localized enhancement of 5hmC and a decrease in 5mC with DMRT1 binding. Similarly, localized DNA demethylation occurs by recruitment of TET1 and TET2 by FOXA1, a pioneer TF, to its binding sites 78 . The direct targets of DMRT1, TET1 and QSER1 , protect DNA hypomethylated regions from de novo methylation 79 .…”