TERRA: telomeric repeat-containing RNA

Abstract

Telomeres, the physical ends of eukaryotic chromosomes, consist of tandem arrays of short DNA repeats and a large set of specialized proteins. A recent analysis has identified telomeric repeat-containing RNA (TERRA), a large non-coding RNA in animals and fungi, which forms an integral component of telomeric heterochromatin. TERRA transcription occurs at most or all chromosome ends and it is regulated by RNA surveillance factors and in response to changes in telomere length. TERRA functions that are emerging suggest important roles in the regulation of telomerase and in orchestrating chromatin remodelling throughout development and cellular differentiation. The accumulation of TERRA at telomeres can also interfere with telomere replication, leading to a sudden loss of telomere tracts. Such a phenotype can be observed upon impairment of the RNA surveillance machinery or in cells from ICF (Immunodeficiency, Centromeric region instability, Facial anomalies) patients, in which TERRA is upregulated because of DNA methylation defects in the subtelomeric region. Thus, TERRA may mediate several crucial functions at the telomeres, a region of the genome that had been considered to be transcriptionally silent.

Figure 1

TERRA Biogenesis, telomere association and displacement from telomeres. TERRA Biogenesis (upper panel)—TERRA is an RNAPII-dependent transcript whose transcription initiates within the subtelomeric sequences and proceeds into the telomeric tract. Human TRF1 may promote transcription through the telomere tract through its association with RNAPII. A fraction of TERRA is polyadenylated through the canonical poly(A) polymerase, Pap1. The 5′-end structure that exists on TERRA molecules has not yet been reported. Telomere association (middle panel)—TERRA colocalizes with telomeres as visualized by RNA-FISH experiments on human interphase and metaphase chromosomes. Indirect evidence suggests that at least a portion of TERRA is bound to telomeres through base pairing with telomeric DNA. Undefined RNA–protein interactions or intermolecular G-quadruplex structures (Gquad) may also tether TERRA to telomeric DNA. Telomere removal and degradation (lower panel)—the 5′ to 3′ exonuclease, Rat1, directly degrades TERRA molecules and can itself be found associated with telomeres. Rat1 can degrade its other target RNAs in a co-transcriptional manner (as depicted here), whether TERRA is degraded by Rat1 in a similar manner has yet to be determined. The poly(A) polymerase, Trf4, also contributes to TERRA degradation, although likely as a minor contributor compared with Rat1. The NMD factors, UPF1, SMG1 and EST1A/SMG6, all contribute to TERRA removal from telomeres. Inhibition of any of these factors results in both more and brighter TERRA foci, although overall TERRA levels as assessed by northern blot analysis remain largely unchanged. RNaseH overexpression also reduces cellular TERRA levels when Rat1 function is impaired.

Figure 2

Telomere dysfunction associated with TERRA. TERRA removal upon DNA replication (upper panel): As the replication fork passes into the subtelomeric and telomeric regions, TERRA may potentially create an obstacle through the formation of an RNA/DNA hybrid. DNA methylation within the subtelomeric tract is one potential means of ensuring that the levels of the telomeric transcript remain low. hUPF1, which associates with the replicative polymerase, may encounter such hybrids and be involved in their active displacement through its helicase activity. EST1A/SMG6 may also be involved in actively removing TERRA molecules, perhaps through its endonuclease activity. Moreover, EST1A could potentially be involved in the recruitment of telomerase to irreversible fork pausing/collapse events in which rapid de novo telomere addition is required. TERRA accumulation and telomere dysfuntion (lower panel): In ICF patient cells, levels of DNA methylation in the subtelomeric regions are greatly reduced because of mutations in the DNA methyltransferase, DNMT3b. These cells consequently express higher levels of TERRA and may, as a result, experience an increased frequency of replication fork collapse resulting in the observed increase in telomere loss events. These effects would potentially be augmented in these cells because of the inherent ability of TERRA to inhibit telomerase activity and therefore to prevent telomere healing at the collapsed fork. These phenotypes are re-capitulated in cells in which SMG protein function has been experimentally reduced, in that TERRA accumulates at telomeres and cells lose large tracts of telomeric DNA. In this instance, the combination of TERRA accumulation and lack of SMG proteins may together inhibit telomerase activity and prevent its recruitment, respectively, to collapsed forks within the telomeric tracts.