ERCC1–XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes

Abstract

Inborn defects in DNA repair are associated with complex developmental disorders whose causal mechanisms are poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the nucleotide excision repair (NER) structure-specific endonuclease ERCC1-XPF complex interacts with the insulator binding protein CTCF, the cohesin subunits SMC1A and SMC3 and with MBD2; the factors co-localize with ATRX at the promoters and control regions (ICRs) of imprinted genes during postnatal hepatic development. Loss of Ercc1 or exposure to MMC triggers the localization of CTCF to heterochromatin, the dissociation of the CTCF-cohesin complex and ATRX from promoters and ICRs, altered histone marks and the aberrant developmental expression of imprinted genes without altering DNA methylation. We propose that ERCC1-XPF cooperates with CTCF and cohesin to facilitate the developmental silencing of imprinted genes and that persistent DNA damage triggers chromatin changes that affect gene expression programs associated with NER disorders.

Nucleotide Excision Repair and Transcription‐Associated Genome Instability

“…Abrogation of XPG or XPF due to gene silencing or a mutation in their catalytic sites substantially hampers the recruitment of CTCF in chromatin, the formation of appropriate chromatin loops, and the fine tuning of RARb2 mRNA synthesis. In further support, a recent in vivo biotinylation tagging approach revealed that the heterodimer ERCC1–XPF complex interacts with CTCF, the cohesin subunits SMC1A and SMC3, and with MBD2 to facilitate the postnatal silencing of imprinted genes during murine development (Figure E) . Abrogation of ERCC1 in Ercc1 −/− mice or exposure of primary embryonic fibroblasts to the DNA interstrand cross‐linker mitomycin triggers the localization of CTCF to heterochromatin and the dissociation of the CTCF–cohesin complex and ATRX from promoters and imprinted control regions.…”

“…Promoter recruitment occurred in the absence of any exposure to exogenous genotoxic insults and was sensitive to transcription inhibitors . Subsequently, ERCC1–XPF was shown to interact with multiple TFIID subunits, i.e., TATA‐associated factors and the TBP in vitro and in vivo and to assemble together with RNAPII and the basal transcription machinery at promoters of growth genes. In further support, the DNA repair‐deficient Ercc1 −/− animals share genome‐wide gene expression similarities with those of the transcription‐defective (but otherwise DNA repair‐proficient) Taf10 −/− mice .…”

“…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 . E) ERCC1–XPF also interacts with CTCF to facilitate the postnatal silencing of imprinted genes . Black lollipops, methylated cytosine; white lollipops, nonmethylated cytosine.…”

“…In spite of the recent progress, the precise biochemical functions of NER proteins in transcription‐associated DNA damage and repair, in fine‐tuning gene expression or in shaping the chromatin architecture remain obscure. With the advent of more sophisticated, functional animal models, e.g., biotin‐tagged or cell‐specific knockout mice coupled to high‐throughput mass spectrometry, and next‐generation sequencing approaches, however, we may soon be able to gain more insights into the role of NER‐associated protein complexes and gene targets in distinct cell types at any stage during mammalian development. Moreover, the recent advances in genome‐wide chromosome conformation capture approaches for characterizing the 3D architectures of genomes will allow us to gain insights into the functional relevance of distinct NER factors in genome‐wide looping formation.…”

Topological demarcation by HMGB2 is disrupted early upon senescence entry across cell types and induces CTCF clustering

“…Notably, both senescent and HMGB2-knockdown cells are characterized by the dramatic clustering of CTCF foci into SICCs -this, in conjunction with the heterochromatic remodeling seen in senescence cells (but not upon HMGB2 knock-down), give rise to the strong reorganization seen in Hi-C data. Notably, such a stress-induced clustering was very recently observed in vivo in mice with deficient DNA repair mechanism (Chatzinikolaou et al, 2017). Inevitably, the differential regulation of additional chromatin-binding factors, like topoisomerase II (Uuskula-Reimand et al, 2016) or HMGB1, will also contribute to chromosome refolding in senescence.…”