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REVIEW
The Rockefeller University, New York, New York 10021, USA
| Abstract |
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Six shelterin subunits: TRF1, TRF2, TIN2, Rap1, TPP1, and POT1
[Keywords: Shelterin; telomere; telomerase; cancer; DNA damage response]
All six shelterin subunits can be found in a single complex in fractionated nuclear extracts (Liu et al. 2004a
; Ye et al. 2004a
). The linchpin of shelterin is TIN2, which tethers TPP1/POT1 to TRF1 and TRF2. TIN2 also connects TRF1 to TRF2 and this link contributes to the stabilization of TRF2 on telomeres (Liu et al. 2004a
; Ye et al. 2004a
). Shelterin subcomplexes containing either TRF1 or TRF2 in association with the other subunits can also be isolated. Although these subcomplexes could be an isolation artifact of the salt sensitivity of the TIN2-TRF2 link (Ye et al. 2004a
), photobleaching experiments also suggest that some of TRF1 and TRF2 are in separate complexes (Mattern et al. 2004
). Further work is needed to establish the number of shelterin units bound per telomere, the stoichiometry of the shelterin subunits, and the significance of shelterin subcomplexes.
Not all proteins at chromosome ends are part of shelterin. Several criteria distinguish the shelterin components from the non-shelterin proteins observed at telomeres (Table 1). Shelterin is abundant at chromosome ends but does not accumulate elsewhere; it is present at telomeres throughout the cell cycle, and its known function is limited to telomeres. Non-shelterin proteins at chromosome ends fail to meet two or three of these criteria, yet can play important roles at telomeres.
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| Shelterin shapes telomeres |
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A crucial way in which shelterin is thought to affect the structure of telomeric DNA is by forming t-loops (Fig. 2; Griffith et al. 1999
; Stansel et al. 2001
). Telomeres have a long single-stranded array of TTAGGG repeats at the 3' end (Makarov et al. 1997
). This overhang has been proposed to invade the double-stranded telomeric DNA, base pairing with the C-strand and displacing the G-strand. The strand invasion takes place at a distance from the physical end of the telomeres and therefore results in a large duplex lariat structure, the t-loop (Fig. 2). The key feature of t-loops is that the end of the telomere is tucked in. The size of the circle part is probably not relevant since t-loops with very large (25-kb) and very small (1-kb) loops have been observed in human cells.
T-loops were first identified by electron microscopy of purified telomeric restriction fragments from human and mouse cells (Griffith et al. 1999
). In order to observe t-loops in protein-free DNA, it is necessary to introduce interstrand cross-links with psoralen and UV. Without cross-links or proteins that stabilize the strand invasion, branch migration can dissociate them. Lariats have now also been observed in telomeric chromatin that was isolated without the use of psoralen, and in this analysis nucleosomes were found to be present on the loop as well as on the adjacent tail DNA (Nikitina and Woodcock 2004
).
In vitro, shelterin components have DNA remodeling activities that are relevant to t-loop formation. TRF2 can remodel an artificial telomeric substrate into loops (Griffith et al. 1999
; Stansel et al. 2001
). These loops are stabilized by psoralen cross-linking, suggesting a strand-invasion event. The t-loop formation by purified TRF2 is puzzling since the reaction does not require ATP and TRF2 lacks a recognizable helicase domain. The reaction is not efficient, however, and it is likely that in vivo, TRF2 requires help of other factors to generate t-loops. As shelterin associates with several proteins involved in recombinational repair (Table 1), it is anticipated that these factors could contribute to t-loop formation and maintenance (de Lange and Petrini 2000
).
TRF1 also has DNA remodeling activity. In vitro, TRF1 can loop, bend, and pair telomeric repeat arrays, activities that might stimulate the folding of telomeres in vivo, (Bianchi et al. 1997
, 1999
; Griffith et al. 1998
) and TIN2 can enhance some of TRF1's architectural effects (Kim et al. 2003
). The DNA gymnastics of TRF1 are probably due to its unusually flexible binding mode. The two SANT/Myb domains of a TRF1 dimer reside at the end of flexible regions, explaining how they can engage their 5'-YTAGGGTTR-3' half-sites in different orientations and at variable distance. Now that the other components are largely known, it will be important to further define how shelterin remodels telomeric DNA in vitro and to test the contribution of the shelterin subunits to t-loop formation and maintenance in vivo.
T-loops are a conserved aspect of telomere structure and have been speculated to protect telomeres and regulate telomerase. Yet much about them remains to be determined. The exact structure at the base of the t-loop is not known and the role of TRF1 and TRF2 in t-loop formation has not (yet) been tested in vivo. It is also not clear whether t-loops are the only (or even the predominant) state of protected chromosome ends. Although the replication fork should dissociate the strand-invasion, it is not known whether DNA replication leads to a temporary "open" state. Addressing these questions is not simple because the detection of t-loops is currently constrained by the requirements of EM analysis.
Shelterin also affects the structure of the 3' end. When either TRF2 or POT1 are inhibited, the overall amount of single-stranded TTAGGG repeats is diminished by 30%-50% (van Steensel et al. 1998
; Hockemeyer et al. 2005
). In the case of TRF2 inhibition, the loss of single-stranded TTAGGG DNA involves ERCC1/XPF, a flap endonuclease that can cleave next to a 3' overhang just inside the neighboring duplex DNA (Zhu et al. 2003
). The involvement of ERCC1/XPF predicts that some of the telomeres lose all of their ssDNA when TRF2 is inhibited. To address this issue, it will be necessary to apply techniques that measure changes in the length of the overhangs rather than loss of the overall single-stranded TTAGGG repeat signal. The protection of the 3' overhang by shelterin could be an indirect effect of the formation of t-loops. For instance, the strand invasion of the 3' overhang may be sufficient to protect the ssDNA from cleavage by ERCC1/XPF and other 3' flap nucleases. In addition, the binding of POT1 to the ssDNA could block nucleolytic degradation (Hockemeyer et al. 2005
; Lei et al. 2005
; Yang et al. 2005
).
How is the 3' overhang generated? Nuclease activity may be required to modify the telomere end generated by leading strand DNA synthesis, as its replication product may be a blunt end. Although the nuclease involved has not yet been identified, recent data shows that the nucleolytic processing of the 5' strand is controlled by shelterin. In a tour de force, Sfeir et al. (2005
) were able to determine the sequence at the 3' and 5' ends of human chromosomes. They found that while the 3' end is more or less randomly positioned within the TTAGGG repeats, the 5' end is remarkably precise (Fig. 2A). Almost all human chromosomes have the sequence AATC CCAATC-5', indicating that the nucleolytic processing is regulated. The shelterin subunit POT1 is implicated in this control. When POT1 is inhibited, 5' ends lose their homogeneity and now end with AA, AT, TC, CC, CA, or AT (Hockemeyer et al. 2005
).
A simple model for how POT1 controls the 5' end sequence is suggested by its DNA-binding features (Fig. 2). In the natural structure of telomere, the first POT1 site in the 3' overhang is just 2 nucleotides (nt) from the end of the duplex telomeric DNA. This configuration is a preferred binding substrate for POT1 in vitro (F. Ishikawa, pers. comm.; D. Hockemeyer and T. de Lange, unpubl.) suggesting that POT1 has an interaction with the duplex end of the telomere. So, once this terminal structure has been generated by a 5' exonuclease, POT1 bound near the double-strand-single-strand transition may simply occlude the 5' end from further processing. Obviously, the tethering of POT1 to the adjacent duplex telomeric DNA through the other shelterin proteins could further enhance the formation of a POT1 cap over the 5' end.
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| Shelterin inhibition activates the canonical DNA damage response |
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B
M), that heterodimerizes with the endogenous TRF2, blocking its binding to DNA (van Steensel et al. 1998
Telomere dysfunction can lead to either apoptosis or senescence. The outcome appears to be dictated by the cell type; fibroblasts undergo senescence upon TRF2 inhibition (and treatment with DNA damaging agents), whereas apoptosis is a more prominent outcome in lymphocytes and epithelial cells (Karlseder et al. 1999
). The activation of the ATM pathway does not require the secondary DNA damage that can be generated when cells with dicentric chromosomes progress through mitosis. Rather, it is the damage at the telomere itself that activates the ATM kinase pathway (Fig. 3).
The view that deprotected telomeres activate the DNA damage response has been solidified by experiments in which DNA damage response factors were observed at telomeres (d'Adda di Fagagna et al. 2003
; Takai et al. 2003
). After inhibition of TRF2 or when telomeres become critically short, 53BP1,
-H2AX, the Mre11 complex, Rif1, and the phosphorylated form of ATM, ATM S1981-P, accumulate at chromosome ends. The cytological structures formed by the DNA damage factors are referred to as Telomere dysfunction Induced Foci (TIFs) (Takai et al. 2003
). TIFs are also formed when other components of shelterin are inhibited (e.g., TIN2 or POT1) (Kim et al. 2004
; Hockemeyer et al. 2005
). ATM-deficient (A-T) cells have a decreased ability to form TIFs and the response is further reduced upon treatment with caffeine, an inhibitor of ATM, ATR, and other PI3 like kinases (PIKKs) (Takai et al. 2003
). Based on these findings, it seems likely that both ATM and a second PIKK are responsible for the telomere damage response. ATR has been implicated as the second transducer by experiments on cells with shortened telomeres (Herbig et al. 2004
). Simultaneous repression of ATM and ATR can reverse some of the phenotypes of telomere-directed senescence (d'Adda di Fagagna et al. 2003
). Collectively, the data argue that dysfunctional telomeres are detected by the canonical DNA damage response. So far, there is no need to invoke a telomere "checkpoint" or specific signaling pathways to explain how cells respond to loss of telomere function.
Many aspects of the telomere damage response still need to be worked out. For instance, it is not known which sensors and mediators (e.g., the Mre11 complex, the 9-1-1 complex, the Rad17 complex, RPA, 53BP1, MDC1) function in the telomere damage pathway, the relative contribution of ATM and ATR (and perhaps other PIKKs) are not understood, and the nature of the telomere damage signal(s) has not been established.
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| How does shelterin prevent a telomere damage signal? |
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If overhang protection is not sufficient to prevent the telomere damage response, shelterin must have at least one other mechanism to prevent detection of telomeres by the DNA damage surveillance. An interesting possibility is that t-loops create a nucleosomal organization that conceals the chromosome ends from the DNA damage surveillance. Recent work on ATM, 53BP1, and fission yeast Crb2 has suggested that a key event in the DNA damage response is a change in the nucleosomal organization at the site of DNA damage (Bakkenist and Kastan 2003
; Huyen et al. 2004
; Sanders et al. 2004
). In the case of 53BP1, the critical interaction is with the dimethylated form of K79 of histone H3 (Huyen et al. 2004
). This residue is constitutively methylated but may not be accessible in intact chromatin. The proposal is that when a DNA break occurs, the nucleosomal organization changes, exposing the binding site for 53BP1. With this mechanism in mind, it is easy to see how t-loops could hide the crucial nucleosome surface from the DNA damage surveillance. When a telomere is in the open state, the last nucleosome might have an exposed 53BP1 interaction site. In the t-loop, this penultimate nucleosome could be positioned such that the H3-K79 and other signaling residues are buried against other nucleosomes. However, 53BP1 is not the only (or the major) factor that senses DNA damage. The signal for other sensors, such as the Mre11 complex and 9-1-1/RFC, have not been worked out. Once their sensing mechanisms are known, the counter-tactics of shelterin can be addressed. And vice versa, a better understanding of shelterin could provide a hint about how the DNA damage response detects damage at telomeres and elsewhere.
| An ATM inhibitor in shelterin? |
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| Avoiding inappropriate repair |
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| Preventing NHEJ and overhang processing |
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One way in which shelterin could protect chromosome ends from NHEJ is by promoting t-loop formation. Without an accessible end, the NHEJ machinery will not be able to form the synaptic complex that is thought to be required for processing and ligation of the ends. By blocking access, t-loops would also protect the telomeric overhang from being removed by nucleases that depend on the NHEJ machinery (Fig. 4).
| Repression of HR |
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A second HR reaction that threatens telomeres is referred to as t-loop HR (Wang et al. 2004
) (Fig. 5). T-loops are at risk for resolution by Holliday junction (HJ) resolvases because an HJ could be formed if the 5' end of the telomere base pairs with the displacement loop (D loop). Branch migration in the direction of the centromere could generate a double HJ and resolution of this structure with crossover would delete the whole loop segment, leaving a drastically shortened telomere at the chromosome end. T-loop HR was discovered through a separation of function mutant of TRF2, TRF2
B, which protects telomeres from NHEJ but induces sudden telomere truncations. These deletions are dependent on two proteins implicated in HR, the Mre11 recombination repair complex and XRCC3, a Rad51 paralog associated with HJ resolution activity. Cells expressing TRF2
B also contain extrachromosomal telomeric DNA that is circular. On two-dimensional gels, these circles show a broad size distribution consistent with their representing the loop part of the t-loops. How the N terminus of TRF2 represses t-loop HR has not been established. As unperturbed cells contain small amounts of circular telomeric DNA, suppression of the t-loop HR reaction at telomeres may be incomplete. The control of t-loop HR appears to be further relaxed in ALT cells, which contain abundant telomeric circles (Cesare and Griffith 2004
; Wang et al. 2004
). As T-SCE and t-loop HR are similar reactions (one taking place in cis, the other in trans), their prevalence in ALT cells may be due to loss of a repressor that controls both.
There may be a third type of HR with detrimental outcomesthe recombination between a telomere and interstitial telomeric DNA. Chromosome internal telomeric DNA is not frequent in human cells, but in many other vertebrates, such sequences are abundant throughout the chromosomes. Recombination between telomeres and these elements could generate terminal deletions, extrachromosomal fragments, inversions, and translocations. This type of recombination appears to take place in mouse cells lacking ERCC1, which generate large extrachromosomal elements that contain a single stretch of telomeric DNA, presumably at a chromosome internal site (Zhu et al. 2003
). These elements, referred to as Telomeric DNA-containing Double Minute chromosomes (TDMs) could be formed by recombination between a telomere and interstitial telomeric DNA on the same chromosome. Perhaps shelterin carries ERCC1/XPF is on its "tool-belt" to prevent inappropriate recombination events.
| Shelterin's affiliations with DNA repair factors |
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A particularly perplexing case of telomere-associated DNA repair factors are DNA-PKcs and the Ku70/80 heterodimer (Hsu et al. 1999
, 2000
; d'Adda di Fagagna et al. 2001
; O'Connor et al. 2004
). These proteins promote NHEJ and are thought to associate with telomeres through interactions with shelterin (Table 1). How DNA-PKcs and Ku contribute to telomere function is not known; regardless, their behavior will have to be closely controlled so that NHEJ of chromosome ends is avoided. A similar conundrum is presented by the association of shelterin with ERCC1/XPF (Zhu et al. 2003
), the nuclease implicated in the processing of the telomeric overhang after telomere damage. As suggested above, shelterin may be using this nuclease to block potentially harmful recombination between telomeres and interstitial telomeric DNA.
Another of shelterin's fair-weather friends is WRN, a RecQ helicase with 3' exonuclease activity. WRN interacts with TRF2 and can be detected at telomeres by ChIP and IF in S phase (Opresko et al. 2002
, 2004
; Crabbe et al. 2004
; Machwe et al. 2004
). The general function of WRN is to allow branch migration of HJs. In vitro, WRN can resolve the t-loop structure and degrade the 3' overhang, attributes that are potential threat to telomere integrity (Opresko et al. 2002
, 2004
). However, RecQ helicases also have the ability to remove G-quadruplex structures from TTAGGG repeats (Sun et al. 1998
; Huber et al. 2002
). This activity was recently proposed to be necessary for telomere replication based on the finding of S-phase-dependent telomere loss in the absence of WRN (Bai and Murnane 2003
; Crabbe et al. 2004
). WRN inhibition only affected lagging-strand DNA synthesis at telomeres, which copies the G-rich telomeric strand and is therefore expected to be inhibited by G-quadruplexes (Crabbe et al. 2004
). So perhaps shelterin can use WRN to prevent problems during lagging-strand synthesis while blocking WRN from inappropriately resolving t-loops after DNA replication is complete.
It is anticipated that the list of shelterin-affiliated factors will grow. The challenge will be to understand both the telomere-specific functions of these proteins and how shelterin manages to keep control over their un-wanted activities.
| Conclusions |
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| Acknowledgments |
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| Footnotes |
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1 Correspondence.
E-MAIL delange{at}mail.rockefeller.edu; FAX (212) 327-7147. ![]()
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