Expression and differential regulation of human TERRA at several chromosome ends

Abstract

The telomeric long noncoding RNA TERRA has been implicated in regulating telomere maintenance by telomerase and homologous recombination, and in influencing telomeric protein composition during the cell cycle and the telomeric DNA damage response. TERRA transcription starts at subtelomeric regions resembling the CpG islands of eukaryotic genes extending toward chromosome ends. TERRA contains chromosome-specific subtelomeric sequences at its 5 ′ ′ ′ ′ ′ end and long tracts of UUAGGG-repeats toward the 3 ′ ′ ′ ′ ′ end. Conflicting studies have been published as to whether TERRA is expressed from one or several chromosome ends. Here, we quantify TERRA species by RT-qPCR in normal and several cancerous human cell lines. By using chromosome-specific subtelomeric DNA primers, we demonstrate that TERRA is expressed from a large number of telomeres. Deficiency in DNA methyltransferases leads to TERRA up-regulation only at the subset of chromosome ends that contain CpG-island sequences, revealing differential regulation of TERRA promoters by DNA methylation. However, independently of the differences in TERRA expression, short telomeres were uniformly present in a DNA methyltransferase deficient cell line, indicating that telomere length was not dictated by TERRA expression in cis. Bioinformatic analyses indicated the presence of a large number of putative transcription factors binding sites at TERRA promoters, and we identified a subset of them that repress TERRA expression. Altogether, our study confirms that TERRA corresponds to a large gene family transcribed from multiple chromosome ends where we identified two types of TERRA promoters, only one of which is regulated by DNA methylation.

Increased amounts and stability of telomeric repeat-containing RNA (TERRA) following DNA damage induced by etoposide

“…reported that transcripts arising from the subtelomeres of chromosomes 1p, 9p, 12p, 15q, 16p, 19p, and XqYq are unlikely to be true TERRAs and that telomere transcripts are generated mainly from the 20q and XpYp loci [13]. These findings are unexpected because it has been widely accepted that transcription occurs at many chromosome terminals [19–21]. In our study, the primers for 9p, 15q, 16p, and XqYq targeted the subtelomeres of undesignated chromosome loci (S1 Table).…”

“…A recent work from Feretzaki et al . showed that the absolute levels of TERRA from different telomeres vary significantly: TERRA 17p is very abundant, while TERRA 2p is barely detected in HeLa cells [21], suggesting that each telomere may be transcribed at different levels by RNAPII. This raises the possibility that global RNAPII distribution at telomeres may not reflect RNAPII interaction at each single telomere.…”

“…Recently, Feretzaki et al . demonstrated that TERRA is expressed from numerous chromosome ends and that the relative expression values vary among the different cell types [21]. In contrast, Montero et al .…”

The Long Non-coding RNA Cyrano Is Dispensable for Pluripotency of Murine and Human Pluripotent Stem Cells

“…The copy number of Cyrano was quantified by qPCR and a plasmid standard curve as described previously ( Feretzaki et al., 2019 ).…”

Subtelomeric Transcription and its Regulation

“…In the same line, only two mouse chromosome ends have been shown to be responsible for TERRA production (chromosome 18 and 9 [ 92 ]). TERRA proximal promoters in mice and humans contain CpG-island sequences, but only in mouse cells are these sequences sensitive to DNA methylation by DNMT1 and 3b to repress TERRA transcription [ 93 ]. The chromatin at TERRA TSSs is enriched for active promoter histone-dedicated marks (such as H3K4me3) even though the predominant histone marks at the subtelomeres remain those associated with transcriptional repression and condensed chromatin, H3K9me3, and H4K20me3, respectively.…”