Regulation of DNA demethylation by the XPC DNA repair complex in somatic and pluripotent stem cells

Abstract

Faithful resetting of the epigenetic memory of a somatic cell to a pluripotent state during cellular reprogramming requires DNA methylation to silence somatic gene expression and dynamic DNA demethylation to activate pluripotency gene transcription. The removal of methylated cytosines requires the base excision repair enzyme TDG, but the mechanism by which TDG-dependent DNA demethylation occurs in a rapid and site-specific manner remains unclear. Here we show that the XPC DNA repair complex is a potent accelerator of global and locus-specific DNA demethylation in somatic and pluripotent stem cells. XPC cooperates with TDG genome-wide to stimulate the turnover of essential intermediates by overcoming slow TDG-abasic product dissociation during active DNA demethylation. We further establish that DNA demethylation induced by XPC expression in somatic cells overcomes an early epigenetic barrier in cellular reprogramming and facilitates the generation of more robust induced pluripotent stem cells, characterized by enhanced pluripotency-associated gene expression and self-renewal capacity. Taken together with our previous studies establishing the XPC complex as a transcriptional coactivator, our findings underscore two distinct but complementary mechanisms by which XPC influences gene regulation by coordinating efficient TDG-mediated DNA demethylation along with active transcription during somatic cell reprogramming.

Nucleotide Excision Repair and Transcription‐Associated Genome Instability

“…B) The XPC/RAD23B/CETN2 is known to be part of a SCC complex required for coactivating Oct4/Sox2‐dependent transcription of Nanog for stem cell pluripotency . C) XPC also facilitates TDG‐mediated DNA demethylation during somatic cell reprogramming independently of its function in DNA repair . D) XPG and ERCC1–XPF may also promote active DNA demethylation of nuclear receptor (NR) genes (as in C) or facilitate gene looping for optimal gene transcription .…”

“…In further support, Zhang et al also proposed the regions of contact between the XPC complex and OCT4, SOX2, XPA, and TFIIH. XPC may also impinge on gene expression by facilitating TDG‐mediated DNA demethylation during somatic cell reprogramming (Figure C) . Arguably, the functional role of XPC in stem cell pluripotency contrasts with the lack of any apparent developmental defects seen in Xpc −/− mice .…”

“…XPC may also impinge on gene expression by facilitating TDG-mediated DNA demethylation during somatic cell reprogramming ( Figure 2C). [81] Arguably, the functional Figure 2. The functional role of NER factors outside the canonical DNA repair mechanism.…”

“…[79,80] C) XPC also facilitates TDG-mediated DNA demethylation during somatic cell reprogramming independently of its function in DNA repair. [81] D) XPG and ERCC1-XPF may also promote active DNA demethylation of nuclear receptor (NR) genes (as in C) or facilitate gene looping for optimal gene transcription. [82] E) ERCC1-XPF also interacts with CTCF to facilitate the postnatal silencing of imprinted genes.…”

Impact of DNA sequences in the DNA duplex opening by the Rad4/XPC nucleotide excision repair complex

“…In principle, such mechanisms have a potential to allow the protein to act as more than a lesion-sensing protein. Interestingly, more and more studies report that XPC functions as a transcriptional coactivator that localizes to and functions around DNA in the absence of an apparent NER lesion (20)(21)(22)(23)(24). The detailed mechanistic insights into the protein's action can thus be illuminating for these studies as well.…”