Enhancers Under TET Control

RESEARCH HIGHLIGHTS

EPIGENETICS Morgan/NPG Patrick Enhancers under TET control DNA methylation at the cytosine C-5 bisulphite sequencing revealed that altered epigenetic status seen in the position (5mC) is an epigenetic mark in TKO ES cells, hypermethylation absence of TET affects gene expres- of promoter gene silencing that regu- (resulting from a deficiency in TET- sion during differentiation. They lates important biological processes. mediated demethylation) occurred observed that during their differentia- The establishment and maintenance in clusters at specific genomic loci tion to neural progenitor cells (NPCs), of 5mC depends on several DNA with regulatory functions, such as Tet2-deleted mouse ES cells exhibited methyltransferases, whereas the ten- promoters, enhancers and gene delayed induction of neuronal-specific eleven-tanslocation (TET) family of bodies, but that the most affected by genes during early differentiation. protein dioxygenases initiates active TET-dependent demethylation were Moreover, the hypermethylated DNA demethylation. TET proteins enhancer regions. Hon et al. found enhancers and the delayed genes were oxidise 5mC to 5-hydroxymethyl that TET2 is the major hydroxy located in the same genomic topo- cytosine (5hmC), which is further methylase in mouse ES cells, as cells logical domains, suggesting that TET oxidized to 5-formylcytosine (5fC) in which Tet2 was deleted lost over proteins mediate enhancer and gene and 5-carboxylcytosine (5caC) 90% of their 5hmC, and report that activity during differentiation. — 5hmC, 5fC and 5caC are inter- Tet2 deletion results in global deple- In addition, Lu et al. found mediates of DNA demethylation. tion of 5hmC at promoters, gene that TET TKO led to an increased Although the function of DNA bodies, enhancers and sequences number of cells in the two-cell methylation in promoter silencing is bound by the insulator binding pro- embryo-like state, which is a well-established, its role in the regula- tein CCCTC-binding factor (CTCF), transient state required for ES cell tion of enhancer activity is less clear. as well as in an increase in 5mC at long-term maintenance. They further Moreover, the exact distribution of enhancers and other distal-regulatory showed that TKO cells have longer TET-mediated demethylation across elements. Thus, both studies report telomeres owing to increased sister the genome and its physiological that TET proteins are directly chromosome telomere exchange. function remain to be clarified. involved in the demethylation of Together, these studies underscore By mapping DNA methylation at regulatory elements, and in particular the importance of TET in regulating base-pair resolution, two studies now of enhancers. enhancer methylation and activ- report that TET-mediated demethyl Next, the authors of both studies ity. Further studies are required ation occurs primarily at enhancer went on to analyse whether the to elucidate the mechanisms that regions, and that it functions to observed enhancer hypermethylation determine which specific enhancers modulate enhancer activity and the is connected to enhancer activity. are targeted and whether similar gene expression programmes that In both Tet2-deleted cells and TET mechanisms regulate gene expression are important for establishing cell TKO cells, active or poised enhancers in somatic cells. identity and for differentiation. were extensively hypermethylated. Kim Baumann Lu et al. generated mouse Importantly, the expression levels of ORIGINAL RESEARCH PAPERS Lu, F. et al. Role embryonic stem (ES) cells deficient their associated genes were substan- of Tet proteins in enhancer activity and telomere TET-mediated for all three TET family members tially reduced following loss of TET elongation. Genes Dev. 28, 2103–2119 (2014) | — TET1, TET2 and TET3 — using activity, indicating that, at least for a Hon, G. C. et al. 5mC oxidation by Tet2 modulates demethylation enhancer activity and timing of transcriptome occurs the CRISPR-Cas9 technology. subset of enhancers, hypermethylation reprogramming during differentiation. Mol. Cell No self-renewal defects were seen in reduces their activity. http://dx.doi.org/10.1016/j.molcel.2014.08.026 primarily at (2014) these triple knockout (TKO) ES cells, As enhancers are involved in FURTHER READING Pastor, W. A., Aravind, L. & enhancer which were used for base-resolution the early steps of cell fate commit- Rao, A. TETonic shift: biological roles of TET DNA methylome and transcrip- ment during ES cell differentiation, proteins in DNA demethylation and transcription. regions Nature Reviews Mol. Cell Biol. 14, 341–356 (2013) tome analyses. Whole-genome Hon et al. analysed whether the

NATURE REVIEWS | MOLECULAR CELL BIOLOGY VOLUME 15 | NOVEMBER 2014