Pericentromeric hypomethylation elicits an interferon response in an animal model of ICF syndrome

Abstract

Pericentromeric satellite repeats are enriched in 5-methylcytosine (5mC). Loss of 5mC at these sequences is common in cancer and is a hallmark of Immunodeficiency, Centromere and Facial abnormalities (ICF) syndrome. While the general importance of 5mC is well-established, the specific functions of 5mC at pericentromeres are less clear. To address this deficiency, we generated a viable animal model of pericentromeric hypomethylation through mutation of the ICF-gene ZBTB24. Deletion of zebrafish zbtb24 caused a progressive loss of 5mC at pericentromeres and ICF-like phenotypes. Hypomethylation of these repeats triggered derepression of pericentromeric transcripts and activation of an interferon-based innate immune response. Injection of pericentromeric RNA is sufficient to elicit this response in wild-type embryos, and mutation of the MDA5-MAVS dsRNA-sensing machinery blocks the response in mutants. These findings identify activation of the innate immune system as an early consequence of pericentromeric hypomethylation, implicating derepression of pericentromeric transcripts as a trigger of autoimmunity.Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

A functional assay to classify ZBTB24 missense variants of unknown significance

“…Specifically, we showed that ZBTB24 is a transcription factor that positively regulates CDCA7 expression by binding to and activating the CDCA7 promoter (Wu et al, ). This observation has subsequently been validated in different studies using additional cell lines (Rajshekar et al, ; Thompson et al, ), demonstrating that this regulation is highly conserved. To dissect how missense variants of ZBTB24 affect its biological function, we established two independent experimental assays that used Cdca7 promoter activity and ZBTB24 binding to the CDCA7 promoter as a readout.…”

Keeping the Centromere under Control: A Promising Role for DNA Methylation

“…Although HELLS was already known to contribute to DNA methylation at murine centromeric repeats through direct interaction with DNMT3B [133,134], a role for ZBTB24 and CDCA7 in DNA methylation maintenance at murine centromeric repeats was only recently elucidated [130]. HELLS and CDCA7 act as a complex, namely CHIRRC (CDCA7-HELLS ICF-Related nucleosome Remodeling Complex), to regulate nucleosome structure, likely modulating its accessibility to DNA methyltransferase activities [135].…”

“…In addition, a role for ZBTB24 in the positive transcriptional regulation of CDCA7 has been demonstrated both in mouse and human [131,138,139]. Methylation reduction of the pericentromeric satellite 1 scored in a Zebrafish model of ICF 2 (ZBTB24 mutation) elicited an increased generation of satellite transcripts, which in turn activated innate immunity [134]. It will be interesting to address whether this phenomenon contributes to the clinical signs of ICF patients, or to the etiology of some autoimmune pathologies.…”

“…Another factor likely contributing to the genomic instability in ICF cells is the presence of RNA:DNA hybrids, otherwise known as R loops, which have a deleterious effect on the maintenance of genome integrity. Indeed, an increased occurrence of R loops was observed at telomeres of ICF1 cells, and this has been correlated with chromosome end DNA damage [134]. Given that R loops accumulate at the centromere [142,143], it is likely that ICF mutations induce R loops accumulation and satellite repeats instability.…”

DNA methylation in disease: Immunodeficiency, Centromeric instability, Facial anomalies syndrome

“…Recent genome-wide ChIP-seq studies reported that ZBTB24 is mainly enriched at CpG-rich promoters [77,78] and that its C2H2 zinc fingers direct sequence-specific binding [78]. Down-regulation of cdca7 has also been observed in a zbtb24 knockout zebrafish model [80], demonstrating that CDCA7 is probably a highly conserved ZBTB24 target.…”