Selective capture of 5-hydroxymethylcytosine from genomic DNA

Coordinated removal of repressive epigenetic modifications during induced reversal of cell identity

Epigenetic modifications operate in concert to maintain cell identity, yet how these interconnected networks suppress alternative cell fates remains unknown. Here, we uncover a link between the removal of repressive histone H3K9 methylation and DNA methylation during the reprogramming of somatic cells to pluripotency. The H3K9me2 demethylase, Kdm3b, transcriptionally controls DNA hydroxymethylase Tet1 expression. Unexpectedly, in the absence of Kdm3b, loci that must be DNA demethylated are trapped in an intermediate hydroxymethylated (5hmC) state and do not resolve to unmethylated cytosine. Ectopic 5hmC trapping precludes the chromatin association of master pluripotency factor, POU5F1, and pluripotent gene activation. Increased Tet1 expression is important for the later intermediates of the reprogramming process. Taken together, coordinated removal of distinct chromatin modifications appears to be an important mechanism for altering cell identity.

A method for the efficient and selective identification of 5-hydroxymethyluracil in genomic DNA

Recently, 5-hydroxymethyluracil (5hmU) was identified in mammalian genomic DNA as an oxidative product of thymine by the ten-eleven translocation (TET) proteins. While the biological role of this modification remains unclear, identifying its genomic location will assist in elucidating function. Here we present a rapid and robust method to selectively tag and enrich genomic regions containing 5hmU. This method involves the selective glucosylation of 5hmU residues by the base J glucosyltransferase from trypanosomes creating glucosylhydroxymethyluracil (base J). The base J can then be efficiently and selectively pulled down by antibodies against base J or by J-binding protein 1. DNA that is enriched is suitable for analysis by quantitative PCR or sequencing. We utilized this tagging reaction to provide proof of concept for the enrichment of 5hmU containing DNA from a pool that contains modified and unmodified DNA. Furthermore, we demonstrate that the base J pull-down assay identifies 5hmU at specific regions of the trypanosome genome involved in transcriptional repression. The method described here will allow for a greater understanding of the functional role and dynamics of 5hmU in biology.

DNA methylation: old dog, new tricks?

DNA methylation is an epigenetic modification that is generally associated with repression of transcription initiation at CpG-island promoters. Here we argue that, on the basis of recent high-throughput genomic and proteomic screenings, DNA methylation can also have different outcomes, including activation of transcription. This is evidenced by the fact that transcription factors can interact with methylated DNA sequences. Furthermore, in certain cellular contexts, genes containing methylated promoters are highly transcribed. Interestingly, this uncoupling between methylated DNA and repression of transcription seems to be particularly evident in germ cells and pluripotent cells. Thus, contrary to previous assumptions, DNA methylation is not exclusively associated with repression of transcription initiation.