Super-Resolution Fluorescence Imaging of Telomeres Reveals TRF2- Dependent T-loop Formation Ylli Doksani, 1,5 John Y. Wu, 2,3,5 Titia de Lange, 1, * and Xiaowei Zhuang 3,4, * 1 Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA 2 Department of Molecular and Cellular Biology 3 Department of Chemistry and Chemical Biology 4 Department of Physics Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA 5 These authors contributed equally to this work *Correspondence: [email protected](T.d.L.), [email protected](X.Z.) http://dx.doi.org/10.1016/j.cell.2013.09.048 SUMMARY We have applied a super-resolution fluorescence imaging method, stochastic optical reconstruction microscopy (STORM), to visualize the structure of functional telomeres and telomeres rendered dysfunctional through removal of shelterin proteins. The STORM images showed that functional telo- meres frequently exhibit a t-loop configuration. Conditional deletion of individual components of shelterin showed that TRF2 was required for the for- mation and/or maintenance of t-loops, whereas dele- tion of TRF1, Rap1, or the POT1 proteins (POT1a and POT1b) had no effect on the frequency of t-loop occurrence. Within the shelterin complex, TRF2 uniquely serves to protect telomeres from two pathways that are initiated on free DNA ends: classical nonhomologous end-joining (NHEJ) and ATM-dependent DNA damage signaling. The TRF2- dependent remodeling of telomeres into t-loop struc- tures, which sequester the ends of chromosomes, can explain why NHEJ and the ATM signaling pathway are repressed when TRF2 is present. INTRODUCTION The telomere concept arose from cytological data indicating that natural chromosome ends are resistant to a fusion reaction that joins broken chromosomes (McClintock, 1938, 1941). DNA ends of linear plasmids, when introduced into cells, recombine with chromosomal DNA (Orr-Weaver et al., 1981), and double-strand breaks (DSBs), induced by genotoxic agents, activate a signaling pathways that can halt cell-cycle progression (reviewed in Call- egari and Kelly, 2007). As the natural ends of chromosomes are stable and do not activate the DNA damage response (DDR), a view has emerged that telomeres have an inherent abil- ity to repress inappropriate DSB repair and DNA damage signaling. How telomeres solve this end-protection problem is a question relevant to understanding telomeropathies and the role of telomere dysfunction in human cancer (reviewed in Ar- tandi and DePinho, 2010; Savage and Bertuch, 2010). Mammalian cells solve the end-protection problem through the agency of shelterin, a multisubunit protein complex bound to the telomeric TTAGGG repeats (reviewed in Palm and de Lange, 2008; O’Sullivan and Karlseder, 2010). Shelterin is anchored on the telomeric DNA by two duplex DNA-binding fac- tors, TRF1 and TRF2. These two proteins interact with TIN2, which in turn binds the TPP1-POT1 heterodimer. In the mouse, there are two functionally distinct forms of POT1, POT1a and POT1b. Once tethered to telomeres through this TPP1-TIN2 link, the POT1 proteins bind the single-stranded (ss) TTAGGG re- peats present at all mammalian chromosome ends in the form of a 50–400 nucleotide (nt) 3 0 overhang. An additional member of the shelterin complex, Rap1, associates with TRF2. Simultaneous deletion of TRF1 and TRF2 from mouse embryo fibroblasts (MEFs) has allowed the creation of telomeres devoid of all shelterin proteins (Sfeir and de Lange, 2012). These shel- terin-free telomeres are equivalent to the unprotected DNA ends, whose instability provided the first clues to telomere function. Together with prior data, this telomere deconstruction established that the telomeric DNA at the ends of mouse chro- mosomes is potentially a substrate for four distinct DSB processing reactions: classical Ku70/80- and DNA-ligase-4- dependent nonhomologous end-joining (c-NHEJ), microhomol- ogy-dependent alternative NHEJ (a-NHEJ) mediated by PARP1 and DNA ligase 3, homology-directed repair (HDR), and CtIP-dependent 5 0 end resection. In addition, the shel- terin-free telomeres activate DSB signaling by the ATM and ATR kinase pathways. Thus, telomeres require protection from six distinct pathways that together define the telomere end pro- tection problem in mammalian cells. Among these six pathways, c-NHEJ and ATM kinase signaling are the purview of TRF2 (Karlseder et al., 1999; van Steensel et al., 1998; Celli and de Lange, 2005; Denchi and de Lange, 2007; Smogorzewska et al., 2002). Deletion of TRF2 results in activation of the ATM kinase cascade at telomeres and very Cell 155, 345–356, October 10, 2013 ª2013 Elsevier Inc. 345
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Super-Resolution FluorescenceImaging of Telomeres Reveals TRF2-Dependent T-loop FormationYlli Doksani,1,5 John Y. Wu,2,3,5 Titia de Lange,1,* and Xiaowei Zhuang3,4,*1Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA2Department of Molecular and Cellular Biology3Department of Chemistry and Chemical Biology4Department of PhysicsHoward Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA5These authors contributed equally to this work
We have applied a super-resolution fluorescenceimaging method, stochastic optical reconstructionmicroscopy (STORM), to visualize the structure offunctional telomeres and telomeres rendereddysfunctional through removal of shelterin proteins.The STORM images showed that functional telo-meres frequently exhibit a t-loop configuration.Conditional deletion of individual components ofshelterin showed that TRF2 was required for the for-mation and/ormaintenance of t-loops, whereas dele-tion of TRF1, Rap1, or the POT1 proteins (POT1aand POT1b) had no effect on the frequency oft-loop occurrence. Within the shelterin complex,TRF2 uniquely serves to protect telomeres fromtwo pathways that are initiated on free DNA ends:classical nonhomologous end-joining (NHEJ) andATM-dependent DNA damage signaling. The TRF2-dependent remodeling of telomeres into t-loop struc-tures, which sequester the ends of chromosomes,can explain why NHEJ and the ATM signalingpathway are repressed when TRF2 is present.
INTRODUCTION
The telomere concept arose from cytological data indicating that
natural chromosome ends are resistant to a fusion reaction that
joins broken chromosomes (McClintock, 1938, 1941). DNA ends
of linear plasmids, when introduced into cells, recombine with
chromosomal DNA (Orr-Weaver et al., 1981), and double-strand
breaks (DSBs), induced by genotoxic agents, activate a signaling
pathways that can halt cell-cycle progression (reviewed in Call-
egari and Kelly, 2007). As the natural ends of chromosomes
are stable and do not activate the DNA damage response
(DDR), a view has emerged that telomeres have an inherent abil-
ity to repress inappropriate DSB repair and DNA damage
signaling. How telomeres solve this end-protection problem is
a question relevant to understanding telomeropathies and the
role of telomere dysfunction in human cancer (reviewed in Ar-
tandi and DePinho, 2010; Savage and Bertuch, 2010).
Mammalian cells solve the end-protection problem through
the agency of shelterin, a multisubunit protein complex bound
to the telomeric TTAGGG repeats (reviewed in Palm and de
Lange, 2008; O’Sullivan and Karlseder, 2010). Shelterin is
anchored on the telomeric DNA by two duplex DNA-binding fac-
tors, TRF1 and TRF2. These two proteins interact with TIN2,
which in turn binds the TPP1-POT1 heterodimer. In the mouse,
there are two functionally distinct forms of POT1, POT1a and
POT1b. Once tethered to telomeres through this TPP1-TIN2
link, the POT1 proteins bind the single-stranded (ss) TTAGGG re-
peats present at all mammalian chromosome ends in the form of
a 50–400 nucleotide (nt) 30 overhang. An additional member of
the shelterin complex, Rap1, associates with TRF2.
Simultaneous deletion of TRF1 and TRF2 from mouse embryo
fibroblasts (MEFs) has allowed the creation of telomeres devoid
of all shelterin proteins (Sfeir and de Lange, 2012). These shel-
terin-free telomeres are equivalent to the unprotected DNA
ends, whose instability provided the first clues to telomere
function. Together with prior data, this telomere deconstruction
established that the telomeric DNA at the ends of mouse chro-
mosomes is potentially a substrate for four distinct DSB
processing reactions: classical Ku70/80- and DNA-ligase-4-
Ku80+/� MEFs were described previously (Sfeir et al., 2009, 2010; Wu et al., 2010, 2012; Denchi and de Lange, 2007; Hockemeyer
et al., 2006; Sfeir and de Lange, 2012). Immortalized MEFs were grown in D-MEM supplemented with 10% fetal bovine serum
(GIBCO), 2 mM L-glutamine (GIBCO), 100 U/ml penicillin (Sigma), 0.1 mg/ml streptomycin (Sigma), and 0.1 mM non-essential amino
acids (Invitrogen).
For tamoxifen-inducible expression of Cre (Rosa26 Cre-ERT1 or Cre-ERT2) cells in 15 cmdishes were treated for 6-8 hr with 0.5mM
4-OH-tamoxifen (Sigma). Cells were washed with PBS andmedia was replaced. Experimental time points were counted as hours (h)
from the time ofmedia change. For introduction of Cre recombinase, MEFswere infected twice at 12 hr interval with pWZL-hygro-Cre
and selected with hygromycin or infected a Hit-and-run Cre retrovirus without selection. Experimental time points were counted as
hours (h) after the second infection.
ImmunoblottingImmunoblotting was performed as described previously (Celli and de Lange, 2005). Briefly, cells were suspended in 2xLaemmli buffer
(100 mM Tris-HCl pH 6.8, 200 mM DTT, 3% SDS, 20% glycerol, 0.05% bromophenol blue) at 104 cells/ml, denatured for 5 min at
100�C, and shearedwith an insulin needle before loading the equivalent of 23 105 cells per lane on SDS-PAGE. Proteins were blotted
onto nitrocellulose membranes. The membranes were blocked in 5% nonfat dry milk in PBS-T (0.05% Tween-20 in PBS) for 30 min
and incubated with primary antibodies in 0.1% or 5% milk in PBS-T at room temperature for at least for 1 hr. Antibodies used for
immunoblots were TRF2 (1254), TRF1 (1449), Rap1 (1253), POT1b (1223), POT1a (1221) (Sfeir et al., 2009, 2010; Hockemeyer
et al., 2006). Immunoblots for POT1a and POT1b were performed using the renaturation protocol described previously (Loayza
and De Lange, 2003).
Analysis of ss Telomeric 30 Overhang and Total Telomeric DNATelomeric DNAwas analyzed as described previously (Celli and de Lange, 2005). Briefly, cells were suspended in PBS andmixed 1:1
(v/v) with 2% agarose (SeaKem) in PBS to obtain between 5 3 105 to 1 3 106 cells per plug. Plugs were digested overnight with
1 mg/ml Proteinase K (in 10 mM Tris-HCl pH 8.0, 250 mM EDTA, 0.2% sodium deoxycholate, 1% sodium lauryl sarcosine), washed
four times for 1 hr each with TE, with 1 mMPMSF in the last wash. Plugs were washed once more with H2O and then digestion buffer.
Plugs were incubated overnight at 37�Cwith 60 UMboI. The following day, the plugs were washed once in TE, and once in 0.5xTBE,
and loaded onto a 1% agarose gel in 0.5xTBE gel. Samples were run for 22–24 hr on a CHEF-DRII PFGE apparatus (BioRad) in
0.5xTBE. The settings were as follows: initial pulse, 5 s; final pulse, 5 s; 6 V/cm; 14�C. The gel was stained with Ethidium Bromide
to visualize the molecular weight marker under UV. The DNA was then transferred on a Hybond-N membrane (Amersham) and
hybridized with telomeric repeat probe generated by [CCCTAA]3-primed Klenow labeling of a 800-bp TTAGGG repeat fragment
(from pSty11 [de Lange, 1992]) in the presence of [a32P]-dCTP.
For in-gel hybridization, the gels were dried and prehybridized in Church mix for 1 hr at 50�C. Hybridization was performed over-
night at 50�C in Churchmix with 50 ng of g-32P-ATP end-labeled [AACCCT]4 to obtained the ss overhang signal. The gel was washed
at 55�C three times for 30 min each in 4xSSC, once for 30 min in 4x SSC/0.1% SDS, and exposed to a PhosphoImager screen over-
night. After the imagewas captured, the gel was denatured in 0.5MNaOH, 1.5MNaCl for 30min, neutralized with two 15minwashes
in 0.5MTris-HCl pH 7.5, 3MNaCl, prehybridized in Churchmix for 1 hr at 55�C, and hybridized overnight with the same probe at 55�Cto obtained the total telomeric DNA signal. The gel was washed and exposed as above. The ss overhang signal in the native gel was
quantified with ImageQuant software and normalized to the total telomeric DNA quantified after the gel had been denatured and re-
hybridized with the telomeric probe.
Splenocyte Chromatin RelaxationSpleens from adult mice were harvested and kept in ice-cold PBS. To release splenocytes, spleens were cut into small pieces and
squeezed between two glass slides. The released material was washed with ice-cold PBS and passed through a cell-strainer with
70-mm pores. The resulting splenocytes were kept on ice in PBS before centrifugation onto glass coverslips using a Shandon Cyto-
spin 3 for 1 min and fixed in�20�Cmethanol for 10 min followed by 1 min in�20�C acetone. The coverslips were washed in PBS and
dehydrated through a 70%, 95%, 100% ethanol series before performing FISH. The centrifugation speed was varied from 600 to
2,000 rpm (1 min). In general the higher speeds produced more cells with relaxed telomere chromatin.
Preparation of MEF Nuclei, Psoralen Crosslinking, and Chromatin SpreadingMEF nuclei were isolated as described previously (Pipkin and Lichtenheld, 2006). Briefly, cells were collected by trypsinization,
washed in media containing serum, washed with ice-cold PBS, and resuspended in ice-cold fibroblast lysis buffer (12.5 mM Tris
pH 7.4, 5 mM KCl, 0.1 mM spermine, 0.25 mM spermidine, 175 mM sucrose, supplemented with protease inhibitor cocktail (Roche)
at a concentration of 8 3 106 cells/ml). After 10 min incubation on ice, 0.02 vol 10% NP-40 was added and cells were incubated for
Cell 155, 345–356, October 10, 2013 ª2013 Elsevier Inc. S1
5 min on ice. Nuclei were collected by centrifugation at 1,000 g for 5 min at 4�C and washed once with ice-cold Nuclei Wash Buffer
(NWB) (10 mM Tris-HCl pH 7.4, 15 mM NaCl, 60 mM KCl, 5 mM EDTA, 300 mM sucrose) and resuspended in NWB.
For crosslinking, 1-2 3 107 nuclei were resuspended in 3 ml of NWB and incubated for 5 min in the presence of 100 mg/ml Triox-
salen (Sigma, stock 2 mg/ml in DMSO, stored at �20�C). The incubation was carried out in a 6 cm dish, on ice, in the dark, while
stirring. Nuclei were then exposed to 365 nm UV light at 2-3 cm from the light source (model UVL-56, UVP) for 30 min, while stirring
on ice. After crosslinking, nuclei were collected, washed once with ice-cold NWB, and resuspended at 2-5 3 106 nuclei/ml. For
spreading, nuclei were diluted 1:10 in spreading buffer (10 mM Tris-HCl 7.4, 10 mM EDTA, 0.05% SDS, 1 M NaCl, pre-warmed at
37�C) and 100 ml of the suspension was immediately deposited on a coverslip using a Shandon Cytospin 3 at 600 rpm for 1min. Sam-
ples were fixed in methanol at �20�C for 10 min followed by 1 min in�20�C acetone. The coverslips were washed in PBS and dehy-
drated through a 70%, 95%, 100% ethanol series before performing FISH.
FISHTelomeres were detected by FISH on metaphase spreads using a previously described protocol (Lansdorp et al., 1996) with
minor modifications (Celli and de Lange, 2005). Briefly, MEFs at �80% confluence were incubated for 2 hr with 0.2 mg colcemid
(Sigma) per ml media, harvested by trypsinization, resuspended in 0.075 M KCl at 37�C for 30 min, and fixed overnight in meth-
anol/acetic acid (3:1) at 4�C. Cells were dropped onto glass slides in a Thermotron Cycler (20�C, 50% humidity) and dried overnight.
For imaging of telomeres in intact MEF nuclei, cells were grown on coverslips and fixed as previously described (Celli and de Lange,
2005). For STORM imaging of telomeres in psoralen-crosslinked spread chromatin, the slides were prepared as described above.
The slides were rehydrated with PBS for 15 min and then dehydrated with a 75%, 95%, and 100% ethanol series before processing
for telomeric FISH. A peptide nucleic acid (PNA) probe [CCCTAA]3 conjugated with Alexa Fluor 647 fluorophore (for conventional and
STORM imaging) or FITC (for conventional imaging only) was obtained from BioSynthesis and resuspended in 50% dimethylforma-
mide (DMF) at a stock concentration of 120 mM. FISH blocking reagent (Roche) was made as a 10% stock in maleic acid buffer
(100 mM maleic acid, 150 mM NaCl, pH 7.5) and stored at 4�C. For FISH labeling, fixed and ethanol-dried samples on coverslips
were spotted with 30 ml of hybridization solution (70% deionized formamide, 0.5% blocking reagent, 10 mM Tris-HCl pH 7.2)
containing 0.1 mM PNA probe. A glass slide was then put on top of the coverslip, sandwiching a thin layer of hybridization buffer
in between to form a hybridization chamber. The slide-coverslip chamber was then placed onto an 80�C heat block covered with
wet paper towel, with the slide-side facing the block, and incubated for 10 min to denature DNA. Subsequently, the hybridization
reaction was allowed to proceed overnight in the dark at room temperature in a humidified box. The coverslip was then removed
from the slide and washed twice for 15 min with 70% formamide; 10 mM Tris-HCl pH 7.2 and 3 times for 5 min with 0.1 M Tris-
HCl pH 7.2, 0.15 M NaCl, 0.08% Tween-20, at room temperature. Finally, the coverslip was dried with a 70%, 95%, 100% ethanol
series before storage in the dark until imaging.
STORM Imaging and AnalysisFor STORM imaging, a custommade microscope fitted with a 100X 1.4 NA oil immersion objective (Olympus, Center Valley, PA) was
used as described previously (Huang et al., 2008a, 2008b). The coverslip containing FISH-labeled sample was sealed in a well con-
taining �100 ml of imaging buffer (50 mM Tris-HCl pH 8.0, 10 mM NaCl, 100 mM MEA) supplemented with an oxygen scavenging
system consisting of 10%w/v glucose, 300 mg/ml glucose oxidase, and 40 mg/ml catalase. The presence of the thiol MEA facilitated
photoswitching of the Alexa Fluor 647 fluorophore (Bates et al., 2007; Heilemann et al., 2008; Dempsey et al., 2011) and the oxygen
scavenging system reduced photobleaching of the sample. Prior to STORM imaging, large areas of the coverslip were imaged at the
conventional resolution using a motorized stage scanner to identify areas of interest in which telomeres were abundant. Next, an im-
aging sequence was set up to allow sequential conventional and STORM imaging of dozens of 433 43 mm fields of view per sample.
STORM data acquisition was started with constant illumination of the sample with the imaging laser (656 nm, Crystalaser) at 60
frames per second, which both excite fluorescence from the Alexa Fluor 647 molecules and rapidly switch the molecules to a
non-fluorescent state, and continuous illumination of an activation laser (405 nm, Coherent Sapphire), which reactivates Alexa Fluor
647 from the dark state back to the fluorescent state (Folling et al., 2008; Dempsey et al., 2011; Heilemann et al., 2008). To maintain a
nearly constant number of photoswitching events per frame, the power of the 405 nm laser was ramped during imaging to counter
balance photobleaching of the dye molecules. The power of the activation laser was typically 1–5 mW entering the back port of the
microscope and that of the imaging laser was 50 mW. A dichroic mirror (T660LPXR, Chroma) and a band-pass filter (ET705/70 nm,
Chroma) separate the fluorescence signal collected by the objective from the scattered excitation light. The filtered images were then
recorded with an EMCCD camera (Ixon DU897, Andor). For 3D STORM imaging, a cylindrical lens (focal length = 1 m) was inserted
into the imaging path to introduce astigmatism, such that the single-molecule images appear elliptical (Huang et al., 2008b). In addi-
tion, a custom-built focus lock was used to maintain z-focus to within ± 20 nm.
Image analysis was performed as described previously (Bates et al., 2007; Huang et al., 2008b). Briefly, fluorescence peaks of in-
dividual molecules were identified and fitted to a 2D elliptical Gaussian to determine the centroid position (x, y) and ellipticity of each
peak. The z-coordinate of each localization was determined by comparing the fitted ellipticity against a predetermined calibration
curve of ellipticity versus z as described previously (Huang et al., 2008a, 2008b). Sample drift correction was performed using image
correlation as described previously (Bates et al., 2007; Huang et al., 2008b). All instrument control, data acquisition, and data analysis
was performed using custom written software.
S2 Cell 155, 345–356, October 10, 2013 ª2013 Elsevier Inc.
SUPPLEMENTAL REFERENCES
Dempsey, G.T., Vaughan, J.C., Chen, K.H., Bates, M., and Zhuang, X. (2011). Evaluation of fluorophores for optimal performance in localization-based super-
resolution imaging. Nat. Methods 8, 1027–1036.
Folling, J., Bossi, M., Bock, H., Medda, R., Wurm, C.A., Hein, B., Jakobs, S., Eggeling, C., and Hell, S.W. (2008). Fluorescence nanoscopy by ground-state deple-
tion and single-molecule return. Nat. Methods 5, 943–945.
Heilemann, M., van de Linde, S., Schuttpelz, M., Kasper, R., Seefeldt, B., Mukherjee, A., Tinnefeld, P., and Sauer, M. (2008). Subdiffraction-resolution fluores-
Lansdorp, P.M., Verwoerd, N.P., van de Rijke, F.M., Dragowska, V., Little, M.T., Dirks, R.W., Raap, A.K., and Tanke, H.J. (1996). Heterogeneity in telomere length
of human chromosomes. Hum. Mol. Genet. 5, 685–691.
Loayza, D., and De Lange, T. (2003). POT1 as a terminal transducer of TRF1 telomere length control. Nature 423, 1013–1018.
Wu, P., van Overbeek, M., Rooney, S., and de Lange, T. (2010). Apollo contributes to G overhang maintenance and protects leading-end telomeres. Mol. Cell 39,
606–617.
Cell 155, 345–356, October 10, 2013 ª2013 Elsevier Inc. S3
Figure S1. Examples of T-loops Imaged by STORM and Conventional Microscopy, Related to Figure 2
(A) Examples of t-loops imaged with STORM (top) and conventional fluorescence microscopy (bottom). Most t-loops (>75%) were not resolved by conventional
fluorescence microscopy. Scale bars: 1 mm.
(B) Additional examples of t-loops detected by STORM.
S4 Cell 155, 345–356, October 10, 2013 ª2013 Elsevier Inc.
Figure S2. Loss of T-loops at an Early Time Point after TRF2 Removal and T-loop Quantification with Inclusion of X Structures, Related to
Figure 3
(A) Representative STORM images of telomeres before and after TRF2 was deleted from the indicated MEFs. Cells were harvested at 72 hr after induction of Cre
with 4-OHT.
(B) T-loop fraction of the total unambiguously scored telomeres (ambiguous structures marked ‘‘x’’ excluded) detected by STORM imaging before and after
deletion of TRF2. Graphs show mean and ± SEM from one experiment.
(C) Table showing data obtained on MEFs with the indicated genotype before and after treatment with Cre for 156 hr using standard scoring (ambiguous ‘‘x’’
structures excluded) or with ‘‘x’’ structures included and counted as a separate category from linear and t-loop structures. The bottom line gives the average
frequency of t-loops (ambiguous ‘‘x’’ structures excluded) and the average frequency of ‘‘x’’ structures in the two conditions. Note that the fraction of ‘‘x’’
structures is lower in the +Cre samples, potentially because collapsed and/or broken t-loops are relegated to the ambiguous category in the -Cre samples. Upon
TRF2 deletion, the t-loop fraction diminished and hence fewer collapsed and/or broken t-loops would be included in the ‘‘x’’ category.
(D) Bar graph showing t-loop frequencies obtained with ‘‘x’’ structures included and counted as a separate category. Graphs show mean and SD values from 3
independent experiments with n > 600 molecules each. P value was derived from unpaired two-tailed Student’s t test.
Cell 155, 345–356, October 10, 2013 ª2013 Elsevier Inc. S5
Figure S3. ATM Does Not Affect T-loop Structure and Scoring of T-loop Frequencies in TRF2/ATM Null Cells with Inclusion of X Structures,
Related to Figure 4
(A) Comparison of t-loop contour lengths shows similar size distributions of telomeres for ATM-proficient and ATM-deficient MEFs (n = 58).
(B) Histogram showing that ATM-deficient cells contain t-loops with a loop size distribution similar to that of ATM-proficient cells (n = 58) (compare to Figure 2F).
(C) Table showing data obtained on MEFs with the indicated genotype before and after treatment with Cre using standard scoring (ambiguous ‘‘x’’ structures
excluded) or with ‘‘x’’ structures included and counted as a separate category from linear and t-loop structures.
(D) Bar graph showing t-loop frequencies obtained with ‘‘x’’ structures included and counted as a separate category. Graphs show mean and SD values from 3
independent experiments with n > 600 molecules each. P value was derived from unpaired two-tailed Student’s t test.
S6 Cell 155, 345–356, October 10, 2013 ª2013 Elsevier Inc.
Figure S4. Deletion of TRF1, Rap1, or Pot1 Proteins Is Not Associated with Loss of T-loops, whereas T-loops Are Lost from Shelterin-Free
Telomeres, Related to Figures 6 and 7
(A) The table shows the t-loop frequencies before and after Cre induction for the indicated shelterin-deletion mutants.
(B) Immunoblots and PCR assays to monitor the loss of the floxed alleles for (from left to right) POT1b, POT1a and POT1b, TRF1 and TRF2 after Cre induction of
the indicated MEFs. Loss of POT1b allele in the POT1b KO cells was monitored by PCR rather than by immunoblots because of poor performance of the POT1b
antibodies in these cells.
(C) Assay for analyzing the ss telomeric DNA overhang (left, indicated as ‘‘native’’) and total telomeric DNA (right, indicated as ‘‘denatured’’) for the indicated
genotypes before and after Cre treatment. Overhang signal intensity was normalized to the total telomeric DNA and the normalized intensity values are indicated
below the gel image. The -Cre value was set to 100 for each cell line. Increases in the overhang signals are due to nucleolytic degradation of the C-rich telomeric
strand.
Cell 155, 345–356, October 10, 2013 ª2013 Elsevier Inc. S7