Telomeres in ICF syndrome cells are vulnerable to DNA damage due to elevated DNA:RNA hybrids

Abstract

DNA:RNA hybrids, nucleic acid structures with diverse physiological functions, can disrupt genome integrity when dysregulated. Human telomeres were shown to form hybrids with the lncRNA TERRA, yet the formation and distribution of these hybrids among telomeres, their regulation and their cellular effects remain elusive. Here we predict and confirm in several human cell types that DNA:RNA hybrids form at many subtelomeric and telomeric regions. We demonstrate that ICF syndrome cells, which exhibit short telomeres and elevated TERRA levels, are enriched for hybrids at telomeric regions throughout the cell cycle. Telomeric hybrids are associated with high levels of DNA damage at chromosome ends in ICF cells, which are significantly reduced with overexpression of RNase H1. Our findings suggest that abnormally high TERRA levels in ICF syndrome lead to accumulation of telomeric hybrids that, in turn, can result in telomeric dysfunction.

DNA:RNA hybrids at telomeres – when it is better to be out of the (R) loop

“…In line with this prediction, in vitro studies demonstrated that plasmids containing human telomeric repeats form RLs with telomere‐containing RNA transcribed off the C‐rich strand . Utilizing the S9.6‐DNA:RNA hybrid‐specific antibody, human TRLs were observed in cancer cells, in particular those that maintain their telomeres by the ALT pathway , as well as in cells of patients with immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome . In both ALT and ICF cells, abnormally high levels of TERRA are transcribed , explaining the high levels of TRLs detected in these cells.…”

“…The binding of TERRA to telomeres in cis is supported by several lines of evidence in yeast as well as in human cells . Therefore, identifying the telomeres that transcribe TERRA should inform us which telomeres are potentially capable of generating TRLs.…”

“…Most TERRA promoters are embedded in regions positioned within 2 kb of the telomere tract , although TERRA promoters positioned 5–10 kb from the telomere tract have been described for several human telomeres . Despite sharing high sequence similarity , a bioinformatic analysis of the distal 2 kb of the majority of human chromosome ends revealed that subtelomeres differ in characteristics such as CpG richness, GC content, and GC‐skewing . In addition, this analysis indicated that a significant number of subtelomeres, but not all, possess positive GC skew immediately downstream to the putative transcription start site (TSS).…”

“…A clear positive correlation was established between TERRA and TRL levels in yeast . Normal human cells, in which TERRA levels are very low , are unsuitable for studying whether a similar correlation exists in humans. However, ICF syndrome type I provides a powerful platform to study this correlation.…”

“…Assuming that the majority of TRLs form cotranscriptionally, can we expect the subtelomeric component of TERRA to influence TRL formation? Most TERRA promoters are embedded in regions positioned within 2 kb of the telomere tract , although TERRA promoters positioned 5–10 kb from the telomere tract have been described for several human telomeres . Despite sharing high sequence similarity , a bioinformatic analysis of the distal 2 kb of the majority of human chromosome ends revealed that subtelomeres differ in characteristics such as CpG richness, GC content, and GC‐skewing .…”