kits are based on DNA methylation. Nevertheless, several questions remain to be
addressed, and chemical tools can be of help. The most potent inhibitors of DNA
methylation are the nucleoside analogues 5azaC and 5azadC that have their limitations as described above. Non-nucleoside inhibitors have been designed or screened
to overcome this. Several have shown to demethylate promoters and reactivate
tumour suppressor genes, but none have the potency of the nucleoside inhibitors
in cells and in vivo. There are ongoing efforts to further improve the design of these
compounds, and novel strategies, such as the design of dual inhibitors or bisubstrate
analogues, are providing promise. Isoform-selective inhibitors of DNMTs (Dnmt1,
Dnmt2 or Dnmt3) will be of great use for the understanding of the roles of each, as
well as compounds that specifically demethylate DNA, which are devoid of
off-target effects.
In parallel, it is crucial to understand the downstream chemical fate of DNA
methylation. While sequential oxidations of 5mC to 5hmC, 5fC and 5caC are key
steps in the passive and active demethylation pathways, each oxidised 5mC mark
themselves has important regulatory functions, including active recruitment of
chromatin reader modules and protein complexes. TETs are thus involved in multiple levels of epigenetic regulation, making them an interesting protein family to
study. TETs play key roles in development and in disease. In cancer, TETs have
been shown to have both oncogenic and tumour suppressor functions. However, the
catalytic and non-catalytically dependent TET functions remain unclear in many
biological processes.
Recent progresses in structural and biochemical studies have provided great
insight into the functions of TET proteins. The substrate specificity, the allosteric
regulation with respect to other domains (e.g. CXXC domain, LCI domain) and the
biological impact, however, are not fully understood. Selective domain targeting
chemical probes for TETs will be valuable to investigate the regulation of cytosine
modifications on chromatin and transcription. Efforts have been made towards
developing inhibitors targeting the catalytic domain of TETs; however, many of
the small molecule inhibitors reported to date are weak inhibitors and are not
selective. Potent cyclic peptide inhibitors show promise, but cell permeability
remains a challenge. It is anticipated that the recent advancements in (highthroughput) assays and structural information will aid in the development of chemical probes for the TET proteins.
Acknowledgement RB is supported by the Engineering and Physical Science Research Council
and University of Oxford. AK gratefully acknowledges the Royal Society for the Dorothy Hodgkin
Fellowship and the European Research Council Starting Grant (EPITOOLS-679479) and the
Cancer Research UK Oxford Centre Development Fund (C5255/A18085). We apologise for the
incomplete citations of research due to space constraints.
The authors acknowledge the EU COST Action CM1406. PBA is supported by
PlanCancer2014-2019 (EPIG-2014-01).
Chemical Compounds Targeting DNA Methylation and Hydroxymethylation
277
addressed, and chemical tools can be of help. The most potent inhibitors of DNA
methylation are the nucleoside analogues 5azaC and 5azadC that have their limitations as described above. Non-nucleoside inhibitors have been designed or screened
to overcome this. Several have shown to demethylate promoters and reactivate
tumour suppressor genes, but none have the potency of the nucleoside inhibitors
in cells and in vivo. There are ongoing efforts to further improve the design of these
compounds, and novel strategies, such as the design of dual inhibitors or bisubstrate
analogues, are providing promise. Isoform-selective inhibitors of DNMTs (Dnmt1,
Dnmt2 or Dnmt3) will be of great use for the understanding of the roles of each, as
well as compounds that specifically demethylate DNA, which are devoid of
off-target effects.
In parallel, it is crucial to understand the downstream chemical fate of DNA
methylation. While sequential oxidations of 5mC to 5hmC, 5fC and 5caC are key
steps in the passive and active demethylation pathways, each oxidised 5mC mark
themselves has important regulatory functions, including active recruitment of
chromatin reader modules and protein complexes. TETs are thus involved in multiple levels of epigenetic regulation, making them an interesting protein family to
study. TETs play key roles in development and in disease. In cancer, TETs have
been shown to have both oncogenic and tumour suppressor functions. However, the
catalytic and non-catalytically dependent TET functions remain unclear in many
biological processes.
Recent progresses in structural and biochemical studies have provided great
insight into the functions of TET proteins. The substrate specificity, the allosteric
regulation with respect to other domains (e.g. CXXC domain, LCI domain) and the
biological impact, however, are not fully understood. Selective domain targeting
chemical probes for TETs will be valuable to investigate the regulation of cytosine
modifications on chromatin and transcription. Efforts have been made towards
developing inhibitors targeting the catalytic domain of TETs; however, many of
the small molecule inhibitors reported to date are weak inhibitors and are not
selective. Potent cyclic peptide inhibitors show promise, but cell permeability
remains a challenge. It is anticipated that the recent advancements in (highthroughput) assays and structural information will aid in the development of chemical probes for the TET proteins.
Acknowledgement RB is supported by the Engineering and Physical Science Research Council
and University of Oxford. AK gratefully acknowledges the Royal Society for the Dorothy Hodgkin
Fellowship and the European Research Council Starting Grant (EPITOOLS-679479) and the
Cancer Research UK Oxford Centre Development Fund (C5255/A18085). We apologise for the
incomplete citations of research due to space constraints.
The authors acknowledge the EU COST Action CM1406. PBA is supported by
PlanCancer2014-2019 (EPIG-2014-01).
Chemical Compounds Targeting DNA Methylation and Hydroxymethylation
277