Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation

Abstract

Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats in mammalian genomes. To what extent this entails direct inhibition of transcription factor (TF) binding versus indirect inhibition via recruitment of methyl-CpG-binding domain (MBD) proteins is unclear. Here we show that combinatorial genetic deletions of all four proteins with functional MBDs in mouse embryonic stem cells, derived neurons or a human cell line do not reactivate genes or repeats with methylated promoters. These do, however, become activated by methylation-restricted TFs if DNA methylation is removed. We identify several causal TFs in neurons, including ONECUT1, which is methylation sensitive only at a motif variant. Rampantly upregulated retrotransposons in methylation-free neurons feature a CRE motif, which activates them in the absence of DNA methylation via methylation-sensitive binding of CREB1. Our study reveals methylation-sensitive TFs in vivo and argues that direct inhibition, rather than indirect repression by the tested MBD proteins, is the prevailing mechanism of methylation-mediated repression at regulatory regions and repeats.

Epigenetic Modification of Cytosines in Hematopoietic Differentiation and Malignant Transformation

“…Mechanistically, this disturbed hematopoietic lineage commitment was attributed to opposing biases in transcriptional priming, with TET2 and DNMT3A LOF favoring the myelomonocytic and erythroid lineages, respectively, in uncommitted HSCs. Consistent with the notion that direct inhibition of TF binding is considered the primary mode of gene silencing by DNA methylation [ 114 , 115 ], the chromatin accessibility of key lineage-determining TFs was particularly susceptible to methylation changes, and strikingly, its sensitivity was determined by the CpG density of the binding motifs [ 113 ]. As the TF binding motif had a higher CpG enrichment, it was more readily inactivated by hypermethylation.…”

Systematic identification of factors involved in the silencing of germline genes in mouse embryonic stem cells

“…Many factors that we found enriched at germline genes in Figure 1 were recovered in this list (PRC1.6 components, RIF1, KDM5C, EHMT2/G9a). Yet, genes coding for MBD proteins were not enriched in the screen, suggesting lack of repressive function ( 39 ). Unexpectedly, Setdb1 was also not recovered in the screen.…”

Loss of BLK expression as a potential predictor of poor prognosis and immune checkpoint blockade response in NSCLC and contribute to tumor progression

“…Therefore, biomarkers based on DNA methylation have been used to predict prognosis and immunotherapy response in cancer [ 52 , 53 ]. Direct inhibition of transcription factor (TF) binding is the main form of DNA methylation inhibiting gene expression and duplication [54] . BLK expression is regulated by the transcription factor PAX5 [55] , and DNA methylation participates in the silencing of PAX5, resulting in the inhibition of BLK expression [56] .…”