Everyone knows one of those couples who keeps getting together and breaking up, as if they’re trying to decide how much they like each other. Well the chromatin architectural protein CTCF and DNA methylation have one of those relationships, and it just got more complicated!
For years, we’ve been trying to decipher whether DNA methylation always prevents CTCF binding, or not, and a new study from the labs of Vladimir Teif (University of Essex, UK) and Achim Breiling (German Cancer Research Center, Germany) suggests that it’s not a simple “will they?” or “won’t they?”
The talented team decided to take DNA demethylation out of the equation and developed mouse embryonic stem cells that had both DNA demethylase enzymes, Tet1 and Tet2, genetically knocked out. Using whole genome bisulfite sequencing, RNAseq, and ChIP-seq against CTCF, and the histone protein H3 to measure nucleosome occupancy, they compared their double knock out cells (DKO) to wildtype cells (WT) and found that:
- DKO cells gain nucleosomes in regions that didn’t have them in WT cells much more often than they lose nucleosomes
- The few regions where DKO cells lose nucleosomes are enriched for 5hmC in WT cells, according to a separate dataset
- DKO cells lose thousands of CTCF peaks, which are mostly within regions of low CpG density and are associated with changes in 5mC or nucleosome occupancy outside of the CTCF binding site itself
- Sites missing CTCF peaks in DKO cells occur most often at regions that are hydroxymethylated in WT cells, but methylated in DKO cells
- In regions that lose CTCF binding, distance from CpGs is a better predictor of WT CTCF binding than methylation
- Lack of CTCF binding allows the boundaries of DNA methylation to spread, and when those boundaries were pushed close to promoters, gene expression was reduced
Ultimately, it looks like CTCF may be avoiding 5mC in order to spend time with its oxidized cousins 5hmC and 5fmC, at least in specific genomic contexts. It sounds like things could get awkward at the next chromatin family reunion!
Catch up on all the juicy gossip in Genome Research, April 2019