PrimPol is required for replicative tolerance of G quadruplexes in vertebrate cells

G quadruplexes (G4s) can present potent blocks to DNA replication. Accurate and timely replication of G4s in vertebrates requires multiple specialized DNA helicases and polymerases to prevent genetic and epigenetic instability. Here we report that PrimPol, a recently described primase-polymerase (PrimPol), plays a crucial role in the bypass of leading strand G4 structures. While PrimPol is unable to directly replicate G4s, it can bind and reprime downstream of these structures. Disruption of either the catalytic activity or zinc-finger of PrimPol results in extreme G4-dependent epigenetic instability at the BU-1 locus in avian DT40 cells, indicative of extensive uncoupling of the replicative helicase and polymerase. Together, these observations implicate PrimPol in promoting restart of DNA synthesis downstream of, but closely coupled to, G4 replication impediments

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Les 25 et 26 novembre 2010 se sont tenues, à l’initiative de Thomas Lienhard (IFHA), trois demi-journées de rencontre consacrées à la présentation du paysage historique français à l’usage des historiens allemands, jeunes ou confirmés. Le but de cette manifestation était d’offrir une information groupée et (donc) efficace sur trois grands thèmes : les institutions de recherche et d’enseignement supérieur, l’accès à la documentation et un aperçu de la situation actuelle de l’historiographie fra..

The KRAB Zinc Finger Protein Roma/Zfp157 Is a Critical Regulator of Cell-Cycle Progression and Genomic Stability.

Regulation of DNA replication and cell division is essential for tissue growth and maintenance of genomic integrity and is particularly important in tissues that undergo continuous regeneration such as mammary glands. We have previously shown that disruption of the KRAB-domain zinc finger protein Roma/Zfp157 results in hyperproliferation of mammary epithelial cells (MECs) during pregnancy. Here, we delineate the mechanism by which Roma engenders this phenotype. Ablation of Roma in MECs leads to unscheduled proliferation, replication stress, DNA damage, and genomic instability. Furthermore, mouse embryonic fibroblasts (MEFs) depleted for Roma exhibit downregulation of p21Cip1 and geminin and have accelerated replication fork velocities, which is accompanied by a high rate of mitotic errors and polyploidy. In contrast, overexpression of Roma in MECs halts cell-cycle progression, whereas siRNA-mediated p21Cip1 knockdown ameliorates, in part, this phenotype. Thus, Roma is an essential regulator of the cell cycle and is required to maintain genomic stability.This work was supported by a PhD studentship from A*STAR Singapore to T.L.F.H. and funding from the Medical Research Council to C.J.W. G.G. and J.E.S. are supported by an MRC core grant to LMB (U105178808).This is the final version of the article. It first appeared from Cell Press via http://dx.doi.org/10.1016/j.celrep.2016.03.07

DNA polymerase stalling at structured DNA constrains the expansion of short tandem repeats.

BACKGROUND: Short tandem repeats (STRs) contribute significantly to de novo mutagenesis, driving phenotypic diversity and genetic disease. Although highly diverse, their repetitive sequences induce DNA polymerase slippage and stalling, leading to length and sequence variation. However, current studies of DNA synthesis through STRs are restricted to a handful of selected sequences, limiting our broader understanding of their evolutionary behaviour and hampering the characterisation of the determinants of their abundance and stability in eukaryotic genomes. RESULTS: We perform a comprehensive analysis of DNA synthesis at all STR permutations and interrogate the impact of STR sequence and secondary structure on their genomic representation and mutability. To do this, we developed a high-throughput primer extension assay that allows monitoring of the kinetics and fidelity of DNA synthesis through 20,000 sequences comprising all STR permutations in different lengths. By combining these measurements with population-scale genomic data, we show that the response of a model replicative DNA polymerase to variously structured DNA is sufficient to predict the complex genomic behaviour of STRs, including abundance and mutational constraints. We demonstrate that DNA polymerase stalling at DNA structures induces error-prone DNA synthesis, which constrains STR expansion. CONCLUSIONS: Our data support a model in which STR length in eukaryotic genomes results from a balance between expansion due to polymerase slippage at repeated DNA sequences and point mutations caused by error-prone DNA synthesis at DNA structures

R-loop formation during S phase is restricted by PrimPol-mediated repriming

During DNA replication conflicts with ongoing transcription are frequent and require careful management to avoid genetic instability. R-loops, three stranded nucleic acid structures comprising a DNA:RNA hybrid and displaced single stranded DNA, are important drivers of damage arising from such conflicts. How R-loops stall replication and the mechanisms that restrain their formation during S phase are incompletely understood. Here we show in vivo how R-loop formation drives a short purine-rich repeat, (GAA)10, to become a replication impediment that engages the repriming activity of the primase-polymerase PrimPol. Further, the absence of PrimPol leads to significantly increased R-loop formation around this repeat during S phase. We extend this observation by showing that PrimPol suppresses R-loop formation in genes harbouring secondary structure-forming sequences, exemplified by G quadruplex and H-DNA motifs, across the genome in both avian and human cells. Thus, R- loops promote the creation of replication blocks at susceptible structure-forming sequences, while PrimPol-dependent repriming limits the extent of unscheduled R-loop formation at these sequences, mitigating their impact on replication

Contribution of epigenetic landscapes and transcription factors to X-chromosome reactivation in the inner cell mass.

X-chromosome inactivation is established during early development. In mice, transcriptional repression of the paternal X-chromosome (Xp) and enrichment in epigenetic marks such as H3K27me3 is achieved by the early blastocyst stage. X-chromosome inactivation is then reversed in the inner cell mass. The mechanisms underlying Xp reactivation remain enigmatic. Using in vivo single-cell approaches (allele-specific RNAseq, nascent RNA-fluorescent in situ hybridization and immunofluorescence), we show here that different genes are reactivated at different stages, with more slowly reactivated genes tending to be enriched in H3meK27. We further show that in UTX H3K27 histone demethylase mutant embryos, these genes are even more slowly reactivated, suggesting that these genes carry an epigenetic memory that may be actively lost. On the other hand, expression of rapidly reactivated genes may be driven by transcription factors. Thus, some X-linked genes have minimal epigenetic memory in the inner cell mass, whereas others may require active erasure of chromatin marks

DNA replication initiation shapes the mutational landscape and expression of the human genome

The interplay between active biological processes and DNA repair is central to mutagenesis. Here, we show that the ubiquitous process of replication initiation is mutagenic, leaving a specific mutational footprint at thousands of early and efficient replication origins. The observed mutational pattern is consistent with two distinct mechanisms, reflecting the two-step process of origin activation, triggering the formation of DNA breaks at the center of origins and local error-prone DNA synthesis in their immediate vicinity. We demonstrate that these replication initiation–dependent mutational processes exert an influence on phenotypic diversity in humans that is disproportionate to the origins’ genomic size: By increasing mutational loads at gene promoters and splice junctions, the presence of an origin significantly influences both gene expression and mRNA isoform usage. Last, we show that mutagenesis at origins not only drives the evolution of origin sequences but also contributes to sculpting regulatory domains of the human genome

Extreme-ultraviolet vector-vortex beams from high harmonic generation

[EN]Structured light in the short-wavelength regime opens exciting avenues for the study of ultrafast spin and electronic dynamics. Here, we demonstrate theoretically and experimentally the generation of vector-vortex beams (VVB) in the extreme ultraviolet through high-order harmonic generation (HHG). The up-conversion of VVB, which are spatially tailored in their spin and orbital angular momentum, is ruled by the conservation of the topological Pancharatnam charge in HHG. Despite the complex propagation of the driving beam, high-harmonic VVB are robustly generated with smooth propagation properties. Remarkably, we find out that the conversion efficiency of high-harmonic VVB increases with the driving topological charge. Our work opens the possibility to synthesize attosecond helical structures with spatially varying polarization, a unique tool to probe spatiotemporal dynamics in inhomogeneous media or polarization-dependent systems.European Research Council (851201); Ministerio de Ciencia de Innovación y Universidades, Agencia Estatal de Investigación and European Social Fund (PID2019-106910GB-I00, RYC-2017-22745); Junta de Castilla y León and FEDER Funds (SA287P18); Université Paris-Saclay (2012-0333T-OASIS, 50110000724-OPTX, PhOM REC-2019-074-MAOHAm); Conseil Régional, Île-de-France (501100003990); Barcelona Supercomputing Center (FI-2020-3-0013)

Extreme-ultraviolet structured beams via high harmonic generation

Funding European Research Council (851201); Ministerio de Ciencia de Innovación y Universidades, Agencia Estatal de Investigaci ́on and European Social Fund (PID2019106910GB-I00, RYC-2017-22745); Junta de Castilla y León and FEDER Funds (SA287P18); Université ParisSaclay (2012-0333TOASIS, 50110000724-OPTX, PhOM REC-2019-074-MAOHAm); Conseil Régional, I ˆle-de-France (501100003990); Barcelona Supercomputing Center (FI2020-3-0013).Vigorous efforts to harness the topological properties of light have enabled a multitude of novel applications. Translating the applications of structured light to higher spatial and temporal resolutions mandates their controlled generation, manipulation, and thorough characterization in the short-wavelength regime. Here, we resort to high-order harmonic generation (HHG) in a noble gas to upconvert near-infrared (IR) vector, vortex, and vector-vortex driving beams that are tailored, respectively, in their spin angular momentum (SAM), orbital angular momentum (OAM), and simultaneously in their SAM and OAM. We show that HHG enables the controlled generation of extreme-ultraviolet (EUV) vector beams exhibiting various spatially dependent polarization distributions, or EUV vortex beams with a highly twisted phase. Moreover, we demonstrate the generation of EUV vector-vortex beams (VVB) bearing combined characteristics of vector and vortex beams. We rely on EUV wavefront sensing to unambiguously affirm the topological charge scaling of the HHG beams with the harmonic order. Interestingly, our work shows that HHG allows for a synchronous controlled manipulation of SAM and OAM. These EUV structured beams bring in the promising scenario of their applications at nanometric spatial and sub-femtosecond temporal resolutions using a table-top harmonic source

Extreme-ultraviolet structured beams via high harmonic generation

Funding European Research Council (851201); Ministerio de Ciencia de Innovación y Universidades, Agencia Estatal de Investigaci ́on and European Social Fund (PID2019106910GB-I00, RYC-2017-22745); Junta de Castilla y León and FEDER Funds (SA287P18); Université ParisSaclay (2012-0333TOASIS, 50110000724-OPTX, PhOM REC-2019-074-MAOHAm); Conseil Régional, I ˆle-de-France (501100003990); Barcelona Supercomputing Center (FI2020-3-0013).Vigorous efforts to harness the topological properties of light have enabled a multitude of novel applications. Translating the applications of structured light to higher spatial and temporal resolutions mandates their controlled generation, manipulation, and thorough characterization in the short-wavelength regime. Here, we resort to high-order harmonic generation (HHG) in a noble gas to upconvert near-infrared (IR) vector, vortex, and vector-vortex driving beams that are tailored, respectively, in their spin angular momentum (SAM), orbital angular momentum (OAM), and simultaneously in their SAM and OAM. We show that HHG enables the controlled generation of extreme-ultraviolet (EUV) vector beams exhibiting various spatially dependent polarization distributions, or EUV vortex beams with a highly twisted phase. Moreover, we demonstrate the generation of EUV vector-vortex beams (VVB) bearing combined characteristics of vector and vortex beams. We rely on EUV wavefront sensing to unambiguously affirm the topological charge scaling of the HHG beams with the harmonic order. Interestingly, our work shows that HHG allows for a synchronous controlled manipulation of SAM and OAM. These EUV structured beams bring in the promising scenario of their applications at nanometric spatial and sub-femtosecond temporal resolutions using a table-top harmonic source