Cell identity and 5-hydroxymethylcytosine

Abstract

Epigenetic factors underlie cellular identity through the regulation of transcriptional networks that establish a cell's phenotype and function. Cell conversions are directed by transcription factor binding at target DNA which induce changes to identity-specific gene regulatory programs. The degree of cell plasticity is determined by the interplay of epigenetic mechanisms to create a landscape susceptible to such binding events. 5-hydroxymethylcytosine, a key intermediate during the process of DNA demethylation, is an epigenetic modification involved in controlling these epigenetic dynamics related to cell identity. Here, the role of 5-hydroxcymethylcytosine during cell identity conversions, including its relationship with other main epigenetic mechanisms, is reviewed.

Keywords: 5-hydroxymethylcytosine; Cell conversions; Cell identity; Epigenetic barriers; Epigenetic mechanisms.

Fig. 1

5hmC as an intermediate during passive and active DNA demethylation of cytosine modifications. Cytosine is methylated to 5-methylcytosine by DNA methyltransferases. Ten-eleven translocation enzymes convert 5-methylcytosine into 5-hydroxymethylcytosine (highlighted in green), and subsequently into 5-formylcytosine and 5-carboxylcytosine via oxidation reactions in a stepwise manner. Passive demethylation of all cytosine modifications happens during DNA replication through DNA methyltransferases dysfunction or suppression. Active demethylation occurs via base excision repair following excision of 5-formylcytosine or 5-carboxylcytosine by thymine glycosylases. Created in BioRender: https://BioRender.com/w40a603

Fig. 2

Cell conversion routes displayed on Waddington’s epigenetic landscape. (A) The several trajectories through the valleys of Waddington’s landscape encompass the stepwise progression of (pluripotent) stem cells to distinct specialised, mature cells. (B) The scaling up the hill represents the reversion of a cell to a less differentiated identity known as somatic cell reprogramming. (C) Transdifferentiation (or direct reprogramming) is illustrated by trajectories across ridges between specialised cell identities. Adapted from Waddington’s original model [31]. Created in BioRender: https://BioRender.com/n40n501

Fig. 3

5hmC dynamics during cell conversions. 5hmC remodelling takes place at identity genes and associated regulatory regions during cell conversions, thereby activating identity-specific gene expression. Created in BioRender: https://BioRender.com/r59v578

Fig. 4

The interplay between 5hmC and epigenetic mechanisms modulate chromatin states to regulate identity-specific gene expression. Closed chromatin is associated with repressive epigenetic marks, including 5mC, H3K27me3 and H3K9me3, and is transcriptionally inactive. 5hmC comes together with other epigenetic marks, including H3K27ac and H3K4me1-3, at gene regulatory regions to establish chromatin permissive for transcription factor binding and active gene transcription. This transition between closed and accessible chromatin is mediated by TET enzymes and histone transferases. Created in BioRender: https://BioRender.com/w40a603

Fig. 5

5hmC levels during neoplastic transformation. Colon villi represent a good example of committed adult progenitor cells (present in the crypts*) and epithelial differentiation along transit-amplifying cells. (1) Upon normal differentiation 5hmC levels that are low in the stem cells (light grey nuclei) accumulate in transit-amplifying and differentiated cells (black nuclei) (2–3) Neoplastic transformation in the colon is associated with reduced 5hmC in tumour cells profile of the progenitor stem cell identity. Reasons for reduced levels of 5hmC in tumours may include: (2) Aberrant differentiation: where the tumours initiate from the crypt but fail to accumulate 5hmC linked to a lack of 5hmC production, (3) Transdifferentiation: where differentiated cells acquire mutations leading to fast replicating neoplastic cells that fail to maintain 5hmC levels, and dedifferentiation: where differentiated cells revert back to a stem-like state during neoplastic transformation and lose 5hmC. *Paneth cells in the crypt are not depicted in this figure for simplicity. Created in BioRender: https://BioRender.com/f16f504