Non-Coding RNA: a Protective Role for TERRA at Telomeres

RESEARCH HIGHLIGHTS

Nature Reviews Genetics | Published online 17 Jul 2017; doi:10.1038/nrg.2017.58

Finally, depletion of TERRA NON-CODING RNA led to increased telomerase RNA levels and activity in mouse ES cells, concomitant with an increase in A protective role for telomere dysfunction and defects, indicating a role for TERRA in maintaining telomere integrity. The TERRA at telomeres authors propose that TERRA expression may promote ALT in cancer cells by specifically suppressing From yeast to humans, telomeric Using an in vivo proteomic ATRX and telomerase in this context. DNA is transcribed by RNA poly- approach, the authors used identi- In a second study, Graf et al. merase II into the long non-coding fication of direct RNA interacting focused on yeast cells, in which one (lnc) telomeric repeat-containing proteins (iDRiP) to determine critically short telomere is sufficient RNA (TERRA), but the exact the protein interactome of TERRA. to trigger senescence. It was known functions of this RNA and its mode The analysis identified 134 enriched that in the absence of telomerase, of action have remained poorly proteins belonging to several func- homology-directed repair (HDR) understood. Two studies in Cell now tional groups, including chromatin between sister chromatids can par- reveal a protective role for TERRA at and transcription factors, cell cycle tially compensate telomere shorten- chromosome ends. regulators and DNA replication pro- ing to prevent early-onset senescence. Telomeric DNA is composed teins, as well as proteins involved in Using quantitative PCR (qPCR) of long repetitive sequences with a alternative lengthening of telomeres and DNA–RNA hybrid immunopre- single-stranded 3ʹ overhang several (ALT), a mechanism that relies cipitation (DRIP), the authors could hundred nucleotides in length. The on homologous recombination- show that TERRA accumulates at length of telomeres, which shorten mediated DNA copying to critically short telomeres, forming with every cell division, is maintained counteract telomere shortening. RNA–DNA hybrids (R-loops). by the ribonucleoprotein complex TERRA levels and TERRA R-loops telomerase, the lack of which leads were found to be tightly regulated to progressive telomere shortening through the cell cycle, forming in and activation of the DNA damage marked changes in gene the S phase before telomere replica- response, resulting in irreversible cell expression resulting from tion, before being degraded. Upon cycle arrest (senescence) or cell death. TERRA depletion telomere shortening, however, the To map chromatin regions bound accumulation of TERRA R-loops by TERRA, Chu et al. combined two leads to the activation of the DNA established methods, chromatin iso- ALT has previously been associ- damage response, which promotes lation by RNA purification (ChIRP) ated with mutations in the chromatin HDR, thereby protecting against and capture hybridization analysis of remodeller α-thalassaemia/mental premature senescence. RNA targets (CHART), to develop a retardation syndrome X-linked Taken together, the two studies new approach they call CHIRT-seq, (ATRX) both in vitro and in several provide pivotal insights into the which identified thousands of bind- human cancers, where it is activated regulatory function of TERRA in ing sites in mouse embryonic stem to promote telomere lengthening in mice and yeast. Given the essential (ES) cells. RNA fluorescence in situ the absence of telomerase. Chu et al. role of telomeres for maintaining hybridization (FISH) also showed observed that ATRX colocalized genome integrity, and the detrimen- that TERRA was not restricted with TERRA in vivo. Moreover, the tal impact of telomere crisis (a state to telomeres. proteins were found to share a subset of extensive genome instability) Functional effects of TERRA were of target genes, displaying antag- in cancer, it will be interesting to

Macmillan Publishers Limited assessed through antisense oligo onistic effects on gene expression, determine how far these novel nucleotide-mediated degradation of with TERRA promoting and ATRX findings translate to humans. the lncRNA in vivo, and successful suppressing gene expression of both Linda Koch depletion was confirmed by RNA- telomeric and non-telomeric targets. ORIGINAL ARTICLES Chu, H.-P. et al. TERRA RNA FISH and northern blot analysis. In vitro and in vivo analyses showed antagonizes ATRX and protects telomeres. Cell Transcriptomic analysis showed further that TERRA modulates ATRX 170, 86–101 (2017) | Graf, M. et al. Telomere length marked changes in gene expression distribution and competes with determines TERRA and R-loop regulation through the cell cycle. Cell 170, 72–85 (2017) resulting from TERRA depletion. telomeric DNA for ATRX binding.