A screening system to identify transcription factors that induce binding site-directed DNA demethylation

Abstract

BackgroundDNA methylation is a fundamental epigenetic modification that is involved in many biological systems such as differentiation and disease. We and others recently showed that some transcription factors (TFs) are involved in the site-specific determination of DNA demethylation in a binding site-directed manner, although the reports of such TFs are limited.ResultsHere, we develop a screening system to identify TFs that induce binding site-directed DNA methylation changes. The system involves the ectopic expression of target TFs in model cells followed by DNA methylome analysis and overrepresentation analysis of the corresponding TF binding motif at differentially methylated regions. It successfully identified binding site-directed demethylation of SPI1, which is known to promote DNA demethylation in a binding site-directed manner. We extended our screening system to 15 master TFs involved in cellular differentiation and identified eight novel binding site-directed DNA demethylation-inducing TFs (RUNX3, GATA2, CEBPB, MAFB, NR4A2, MYOD1, CEBPA, and TBX5). Gene ontology and tissue enrichment analysis revealed that these TFs demethylate genomic regions associated with corresponding biological roles. We also describe the characteristics of binding site-directed DNA demethylation induced by these TFs, including the targeting of highly methylated CpGs, local DNA demethylation, and the overlap of demethylated regions between TFs of the same family.ConclusionsOur results show the usefulness of the developed screening system for the identification of TFs that induce DNA demethylation in a site-directed manner.Electronic supplementary materialThe online version of this article (10.1186/s13072-017-0169-6) contains supplementary material, which is available to authorized users.

Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes

“…A recent survey of the mutations occurring within the T-box domain in those TBX genes known to cause the different genetic syndromes did show that they abrogate either the interaction with the known methyl or dimethyl transferases ( 47 ). However, the direct supporting evidence to our data came from a study that showed using a newly described screening system that TBX5 is one of few transcription factors that induce binding site-directed DNA demethylation ( 49 ). These findings coupled to the global methylation process that underscores all lung cancer subtypes and mainly the nicotine-induced types will thus potentially position the effect of the for TBX genes in the pathway that includes demethylating agent in clinical trials like 5-AZA ( 50 , 51 ).…”

LTRs activated by Epstein-Barr virus-induced transformation of B cells alter the transcriptome

“…To our knowledge, this is the first report of RUNX3 involved in LTR activation. There has also been recent report that RUNX3 can induced site-specific DNA hypomethylation (Suzuki et al 2017). Along with our finding that RUNX3 binds to >50% of all EBV-activated LTRs, EBVinduced RUNX3 activity may be an important factor in the hypomethylation of EBV-activated LTRs.…”

5-Hydroxymethylcytosine (5hmC), or How to Identify Your Favorite Cell

“…Although this is better supported at the level of pioneer factors, it is feasible that other TFs involved in lineage commitment are also able to recruit TETs to specific genomic loci. While several TFs are involved in DNA demethylation by interacting with TET proteins (e.g., Nanog during establishment of pluripotency [101], the hematopoiesis-related RUNX1 [102] and EBF1 [103], PU.1 in osteoclast differentiation [104], and PPARγ in adipogenesis [105]), screening systems suggest that many others may share this property [106]. Alternatively, enhancer elements that distinguish cell types may be specifically targeted by TETs based on their chromatin conformation and histone mark profile.…”