Biology subjects

de Lange, T.

Publications and source records attributed to de Lange, T..

12 recordsLinked to original sources

bioRxiv2024

Tetrameric TRF2 forms t-loop to protect telomeres from ATM signaling and cNHEJ

Telomeres often occur in the t-loop structure, formed through the base-pairing of the 3 telomeric overhang is base-paired with more internal telomeric DNA. T-loops are proposed to avert ATM kinase signaling and classical non-homologous end joining (cNHEJ) by sequestering the telomere end. The shelterin subunit TRF2 is required for t-loop formation but how it generates t-loops is not known and the t-loop model for telomere protection remains untested. We show that TRF2 binds telomeric DNA as a tetramer using two dimerization domains and that tetramerization is critical for telomere protection. Furthermore, TRF1, the TRF2 paralog that binds DNA as a dimer and does not form t-loops, gained the ability to form t-loops in vivo upon its tetramerization through the addition of a second dimerization domain. We propose that TRF2 tetramers loop telomeric DNA, resulting in torsional stress and opening of the helix, which is a requirement for t-loop formation. Importantly, t-loops formed by tetrameric TRF1 were sufficient to avert ATM signaling and blocked most cNHEJ at telomeres, demonstrating that t-loops per se protect telomeres from these threats.

cell biology↗

bioRxiv2024

Replicative senescence is ATM driven, reversible, and accelerated by hyperactivation of ATM at normoxia

Replicative senescence, a powerful tumor suppressor pathway, occurs when a few critically-short telomeres activate the DNA damage response (DDR). We show that ATM is the sole DDR kinase responsible for the induction and maintenance of replicative senescence and that ATM inhibition can induce normal cell divisions in senescent cells. Compared to non-physiological atmospheric ([~]20%) oxygen, cells grown at physiological (3%) oxygen were more tolerant to critically-short telomeres, explaining their extended replicative lifespan. We show that this tolerance is due to attenuation of the ATM response to double-strand breaks (DSBs) and unprotected telomeres. Our data indicate that the reduced ATM response to DSBs at 3% oxygen is due to increased ROS, which induces disulfide-bridges in ATM, generating crosslinked ATM dimers that do not respond to DSBs. This regulation of cellular lifespan through attenuation of ATM at physiological oxygen has implications for tumor suppression through telomere shortening.

cell biology↗

bioRxiv2023

CST--Polymeraseα-primase solves a second telomere end-replication problem

Telomerase adds G-rich telomeric repeats to the 3' ends of telomeres1, counteracting telomere shortening caused by loss of telomeric 3' overhangs during leading-strand DNA synthesis ("the end-replication problem"2). We report a second end-replication problem that originates from the incomplete duplication of the C-rich telomeric repeat strand by lagging-strand synthesis. This problem is solved by CST-Polymerase(Pol)-primase fill-in synthesis. In vitro, priming for lagging-strand DNA replication does not occur on the 3 overhang and lagging-strand synthesis stops in an [~]150-nt zone more than 26 nt from the end of the template. Consistent with the in vitro data, lagging-end telomeres of cells lacking CST-Pol-primase lost [~]50-60 nt of CCCTAA repeats per population doubling (PD). The C-strands of leading-end telomeres shortened by [~]100 nt/PD, reflecting the generation of 3 overhangs through resection. The measured overall C-strand shortening in absence of CST-Pol-primase fill-in is consistent with the combined effects of incomplete lagging-strand synthesis and 5' resection at the leading-ends. We conclude that canonical DNA replication creates two telomere end-replication problems that require telomerase to maintain the G-strand and CST-Pol-primase to maintain the C-strand.

cell biology↗

bioRxiv2023

Structural basis of CST-Polα/Primase recruitment and regulation by POT1 at telomeres

Telomere maintenance requires extension of the G-rich telomeric repeat strand by telomerase and fill-in synthesis of the C-rich strand by Pol/Primase. Telomeric Pol/Primase is bound to Ctc1-Stn1-Ten1 (CST), a single-stranded DNA-binding complex. Like mutations in telomerase, mutations affecting CST-Pol/Primase result in pathological telomere shortening and cause a telomere biology disorder, Coats plus (CP). We determined cryogenic electron microscopy structures of human CST bound to the shelterin heterodimer POT1/TPP1 that reveal how CST is recruited to telomeres by POT1. Phosphorylation of POT1 is required for CST recruitment, and the complex is formed through conserved interactions involving several residues mutated in CP. Our structural and biochemical data suggest that phosphorylated POT1 holds CST-Pol/Primase in an inactive auto-inhibited state until telomerase has extended the telomere ends. We propose that dephosphorylation of POT1 releases CST-Pol/Primase into an active state that completes telomere replication through fill-in synthesis.

biophysics↗

bioRxiv2023

DNA-PK and the TRF2 iDDR inhibit MRN-initiated resection at leading-end telomeres

Telomeres replicated by leading-strand synthesis lack the 3 overhang required for telomere protection. Surprisingly, resection of these blunt telomere is initiated by the telomere-specific 5 exonuclease Apollo rather than the Mre11-Rad50-Nbs1 (MRN) complex, the nuclease that acts at DNA breaks. Without Apollo, leading-end telomeres undergo fusion, which, as demonstrated here, are mediated by alternative End Joining. Here, we show that DNA-PK and TRF2 coordinate the repression of MRN at blunt telomeres. DNA-PK represses an MRN-dependent long range resection at blunt telomeres, while the endonuclease activity of MRN/CtIP, which could cleave DNA-PK off of blunt telomere ends, is inhibited in vitro and in vivo by the iDDR of TRF2. AlphaFold-Multimer predicts a conserved association of the iDDR with Rad50 potentially interfering with CtIP binding and MRN endonuclease activation. We propose that repression of MRN-mediated resection is a conserved aspect of telomere maintenance and represents an ancient feature of DNA-PK and the iDDR.

molecular biology↗

bioRxiv2022

Neotelomere formation by human telomerase

The maintenance of genome integrity requires that telomerase action be limited to telomeres and not convert DSBs into neotelomeres. Using the breakpoint sequence from an apparent germline neotelomere formation event, we developed an assay to detect and quantify telomeric repeat addition at Cas9-programmed DSBs in human cells. The data show that telomerase can add telomeric repeats to DSBs and that this process can generate functional neotelomeres. Neotelomere formation is increased when telomerase is overexpressed, suggesting that in most human cells, low (or absent) telomerase activity limits the deleterious effects of de novo telomere addition. We show that neotelomere formation at DSBs is inhibited by long-range resection and the accompanying activation of ATR signaling. Our findings reveal that telomerase can cause genome instability by generating neotelomeres at DSBs. We propose that neotelomere formation can promote tumorigenesis by ending detrimental breakage-fusion-bridge cycles in cancer cells whose genome alterations engender dicentric chromosomes.

cancer biology↗

bioRxiv2022

Shelterin is a Dimeric Complex with Extensive Structural Heterogeneity

Human shelterin is a six-subunit complex - comprised of TRF1, TRF2, Rap1, TIN2, TPP1, and POT1 - that binds telomeres, protects them from the DNA-damage response, and regulates the maintenance of telomeric DNA. Although high-resolution structures have been generated of the individual structured domains within shelterin, the architecture and stoichiometry of the full complex are currently unknown. Here we report the purification of shelterin subcomplexes and reconstitution of the entire complex using full-length, recombinantly produced components. By combining negative-stain electron microscopy (EM), crosslinking mass spectrometry (XLMS), mass photometry, and native mass spectrometry (MS), we obtain stoichiometries as well as domain-scale architectures of shelterin subcomplexes and determine that they are extensively conformationally heterogenous. For POT1/TPP1 and POT1/TPP1/TIN2, we observe high variability in the positioning of the POT1 DNA-binding domain, the TPP1 OB fold, and the TIN2 TRFH domain with respect to the C-terminal domains of POT1. Truncation of unstructured linker regions in TIN2, TPP1, and POT1 did not reduce the conformational variability of the heterotrimer. Both shelterin and the TRF1/TIN2/TPP1/POT1 subcomplex primarily adopt fully dimeric complexes, even in the absence of DNA substrates. TRF1/TIN2/TPP1/POT1 and shelterin complex showed extensive conformational variability, regardless of the presence of DNA substrates. We conclude that shelterin adopts a multitude of conformations and argue that its unusual architectural variability is beneficial for its many functions at telomeres.

biochemistry↗

bioRxiv2021

Cryo-EM structure of the human CST·Polα/Primase complex in a recruitment state

The CST*Pol/Primase complex is essential for telomere overhang maintenance and additionally functions to counteract resection at double-strand breaks. We report a 4.6-[A] resolution cryo-EM structure of CST*Pol/Primase, captured prior to catalysis in a recruitment state, which provides insights into the architecture and stoichiometry of the fill-in machinery. Our model informs on human disease mutations that cause Coats plus syndrome.

biochemistry↗

bioRxiv2021

Loose ends in cancer genome structure

Recent pan-cancer studies have delineated patterns of structural genomic variation across thousands of tumor whole genome sequences. It is not known to what extent the shortcomings of short read ([≤] 150 bp) whole genome sequencing (WGS) used for structural variant analysis has limited our understanding of cancer genome structure. To formally address this, we introduce the concept of "loose ends" - copy number alterations that cannot be mapped to a rearrangement by WGS but can be indirectly detected through the analysis of junction-balanced genome graphs. Analyzing 2,319 pan-cancer WGS cases across 31 tumor types, we found loose ends were enriched in reference repeats and fusions of the mappable genome to repetitive or foreign sequences. Among these we found genomic footprints of neotelomeres, which were surprisingly enriched in cancers with low telomerase expression and alternate lengthening of telomeres phenotype. Our results also provide a rigorous upper bound on the role of non-allelic homologous recombination (NAHR) in large-scale cancer structural variation, while nominating INO80, FANCA, and ARID1A as positive modulators of somatic NAHR. Taken together, we estimate that short read WGS maps >97% of all large-scale (>10 kbp) cancer structural variation; the rest represent loose ends that require long molecule profiling to unambiguously resolve. Our results have broad relevance for future research and clinical applications of short read WGS and delineate precise directions where long molecule studies might provide transformative insight into cancer genome structure.

genomics↗

bioRxiv2020

Structural variant evolution after telomere crisis

Telomere crisis contributes to cancer genome evolution, yet only a subset of cancers display breakage-fusion-bridge (BFB) cycles and chromothripsis, hallmarks of previous experimental telomere crisis studies. We examine the spectrum of SVs instigated by natural telomere crisis. Spontaneous post-crisis clones from prior studies had both complex and simple SVs without BFB cycles or chromothripsis. In contrast, BFB cycles and chromothripsis occurred in clones that escaped from telomere crisis after CRISPR-controlled telomerase activation in MRC5 fibroblasts. This system revealed convergent evolutionary lineages altering one allele of 12p, where a short telomere likely predisposed to fusion. Remarkably, the 12p chromothripsis and BFB events were stabilized by independent fusions to 21. Telomere crisis can therefore generate a wide spectrum of SVs, and lack of BFB patterns and chromothripsis does not indicate absence of past crisis.

genomics↗

bioRxiv2019

APOBEC3B-dependent kataegis and TREX1-driven chromothripsis in telomere crisis

Chromothripsis and kataegis are frequently observed in cancer and can arise from telomere crisis, a period of genome instability during tumorigenesis when depletion of the telomere reserve generates unstable dicentric chromosomes1-5. Here we report on the mechanism underlying chromothripsis and kataegis using an in vitro telomere crisis model. We show that the cytoplasmic exonuclease TREX1, which promotes the resolution of dicentric chromosomes4, plays a prominent role in chromothriptic fragmentation. In absence of TREX1, the genome alterations induced by telomere crisis primarily involve Breakage-Fusion-Bridge cycles and simple genome rearrangements rather than chromothripsis. Furthermore, we show that the kataegis observed at chromothriptic breakpoints is the consequence of cytosine deamination by APOBEC3B. In addition, APOBEC3B increased the frequency of chromothriptic fragmentation, possibly due to strand breakage after cytosine deamination. These data reveal that chromothripsis and kataegis arise from a combination of nucleolytic processing by TREX1 and cytosine editing by APOBEC3B.

molecular biology↗

bioRxiv2018

ATR repression at telomeres by POT1a and POT1b: RPA exclusion and interference by CST

Telomeres carry a constitutive 3 overhang that can bind RPA and activate ATR signaling. POT1a, a single-stranded (ss) DNA binding protein in mouse shelterin, has been proposed to repress ATR signaling by preventing RPA binding. Repression of ATR at telomeres requires the TPP1/TIN2 mediated tethering of POT1a to the the rest of the shelterin complex situated on the ds telomeric DNA. The simplest version of the tethered exclusion model for ATR repression suggests that the only critical features of POT1a are its connection to shelterin and its binding to ss telomeric DNA binding. In agreement with the model, we show that a shelterin-tethered RPA70 mutant, lacking the ATR recruitment domain, is effective in repressing ATR signaling at telomeres. However, arguing against the simple tethered exclusion model, the nearly identical POT1b subunit of shelterin is much less proficient in ATR repression than POT1a. We now show that POT1b has the intrinsic ability to fully repress ATR but is prevented from doing so when bound to the CST/Pol/primase complex. The data establish that shelterin represses ATR with a tethered ssDNA-binding domain that excludes RPA from the 3 overhang and suggest that ATR repression does not require the interaction of POT1 with the 3 end or G4 DNA.

cell biology↗