POT1-TPP1 regulates telomeric overhang structural dynamics

Abstract

Human telomeres possess a single-stranded DNA (ssDNA) overhang of TTAGGG repeats, which can self-fold into a G-quadruplex structure. POT1 binds specifically to the telomeric overhang and partners with TPP1 to regulate telomere lengthening and capping, although the mechanism remains elusive. Here, we show that POT1 binds stably to folded telomeric G-quadruplex DNA in a sequential manner, one oligonucleotide/oligosaccharide binding fold at a time. POT1 binds from 3' to 5', thereby unfolding the G-quadruplex in a stepwise manner. In contrast, the POT1-TPP1 complex induces a continuous folding and unfolding of the G-quadruplex. We demonstrate that POT1-TPP1 slides back and forth on telomeric DNA and also on a mutant telomeric DNA to which POT1 cannot bind alone. The sliding motion is specific to POT1-TPP1, as POT1 and ssDNA binding protein gp32 cannot recapitulate this activity. Our results reveal fundamental molecular steps and dynamics involved in telomere structure regulation.

Figure 1. POT1 Binds a Telomeric Overhang One OB Fold at a Time

(A) Schematic of the G4 DNA construct. The strand with four TTAGGG repeats was attached to a single molecule surface by annealing a complementary biotinylated strand to form a duplex. G-quadruplex folding induces high FRET between Cy3 (green) and Cy5 (red) at both ends of the ssDNA. (B) Telomeric repeats for G4, G3, and G2 with POT1 binding sites marked in gray. (C) Single molecule traces of POT1 binding to G4, G3, and G2 show four, three, and two steps of FRET decrease (arrow), respectively. (D) Transition density plots are built from the FRET value before transition in the y axis and the FRET value after transition in the x axis. (E) Dwell times taken from the first (δt1) and second step (δt2) of FRET decrease obtained from the G4 construct with variable POT1 concentrations. See also Figure S1. Error bars indicate the SEM.

Figure 2. POT1 Binds Overhangs Directionally from 3′ to 5′

(A) Schematic of the G4 DNA with various dye positions. (B and C) Schematic diagram representing the dye positions with respect to the individual OB fold binding sites. CT indicates C-terminal domain of POT1. The positions 24, 18, and 6 nt represent the distances between Cy3 and Cy5. The faint ovals indicate the OB unit bindings that should not induce FRET decrease. The step number shown in the single molecule traces (C) expected from individual OB fold binding is written above each oval. Single molecule traces obtained from the three DNA constructs (C). The dt indicates the time interval between POT1 addition and the first step of FRET decrease. (D) The average dt from each DNA construct. The longest dt for the 6 nt DNA construct suggests POT1 binding initiates from the 3′ to 5′ direction. Error bars indicate the SEM. (E) Schematic of a plausible POT1 binding mode. See also Figure S2.

Figure 3. POT1-TPP1N Induces Folding-Unfolding Dynamics on Telomeric Overhangs

(A) Schematic of unlabeled TPP1N and POT1 on the G4 FRET construct with Cy3 dyes placed 24, 18, 12, and 6 nt from the duplex junction. (B) Single molecule traces collected from all DNA substrates shows initial FRET decreases representing POT1-TPP1N binding by POT1 recognition of the telomeric overhang sequence, followed by continuous FRET fluctuations of the 24 and 18 nt DNA and less pronounced FRET changes for the other DNA constructs. We interpret the FRET fluctuations as dynamic folding and unfolding of G-quadruplex DNA induced by POT1-TPP1N. (C) FRET histograms built from FRET values collected from 100 single molecule traces that exhibit dynamic folding-unfolding of unlabeled POT1-TPP1N on the G4 DNA FRET constructs. (D) Dwell time histograms from over several hundred events of 24 and 18 nt G4 DNA FRET constructs. See also Figure S3. Gaussian fit yields center of the histogram with the SEM.

Figure 4. POT1-TPP1N Slides on the Telomeric Overhang near the 3′ End

(A) Schematic of Alexa 647-labeled TPP1N and POT1 on the G4 DNA construct, with the Cy3 dye located 24, 18, 12, 6, and 0 nt from the duplex junction. (B) Single molecule traces show the initial FRET increase, followed by dynamic FRET fluctuations reflecting movement of POT1-TPP1N on the G4 DNA. (C) FRET histograms taken from over 100 single molecule traces that display FRET fluctuation. (D) Dwell times from several hundred events from the 24 and 18 nt G4 Cy3-DNA constructs. Gaussian fit yields center of the histogram with the SEM. (E) Schematic of Alexa 647-labeled TPP1N and POT1 on the G2-mut2 DNA construct. (F) Single molecule trace of POT1-TPP1N (Alexa 647) on G2-mut2 exhibits dynamic FRET fluctuations similar to the G4 DNA. (G) FRET histogram built from over 100 single molecule traces that exhibit dynamic FRET fluctuation on the G2mut2 DNA. (H) Dwell times from over several hundred events of sliding on the G2mut2 DNA construct. See also Figures S4 and S5. Gaussian fit yields center of the histogram with the SEM.

Figure 5. Proposed Mechanism of POT1-TPP1N Sliding

TPP1N-POT1 binds to the telomeric overhang from the 3′ end in a POT1-dependent manner and exhibits sliding clamp activity by diffusing along the telomeric overhang near the 3′ end. See also Figure S5.