The recruitment of ACF1 and SMARCA5 to DNA lesions relies on ADP-ribosylation dependent chromatin unfolding

ADP-ribosylation signaling orchestrates the recruitment of various repair actors and chromatin remodeling processes promoting access to lesions during the early stages of the DNA damage response. The chromatin remodeler complex ACF, composed of the ATPase subunit SMARCA5/SNF2H and the cofactor ACF1/BAZ1A, is among the factors that accumulate at DNA lesions in an ADP-ribosylation dependent manner. In this work, we show that each subunit of the ACF complex accumulates to DNA breaks independently from its partner. Furthermore, we demonstrate that the recruitment of SMARCA5 and ACF1 to sites of damage is not due to direct binding to the ADP-ribose moieties but due to facilitated DNA binding at relaxed ADP-ribosylated chromatin. Therefore, our work provides new insights regarding the mechanisms underlying the timely accumulation of ACF1 and SMARCA5 to DNA lesions, where they contribute to efficient DNA damage resolution.

Multi-Scale Imaging of the Dynamic Organization of Chromatin

Chromatin is now regarded as a heterogeneous and dynamic structure occupying a non-random position within the cell nucleus, where it plays a key role in regulating various functions of the genome. This current view of chromatin has emerged thanks to high spatiotemporal resolution imaging, among other new technologies developed in the last decade. In addition to challenging early assumptions of chromatin being regular and static, high spatiotemporal resolution imaging made it possible to visualize and characterize different chromatin structures such as clutches, domains and compartments. More specifically, super-resolution microscopy facilitates the study of different cellular processes at a nucleosome scale, providing a multi-scale view of chromatin behavior within the nucleus in different environments. In this review, we describe recent imaging techniques to study the dynamic organization of chromatin at high spatiotemporal resolution. We also discuss recent findings, elucidated by these techniques, on the chromatin landscape during different cellular processes, with an emphasis on the DNA damage response.

Identification of key residues of the DNA glycosylase OGG1 controlling efficient DNA sampling and recruitment to oxidized bases in living cells

The DNA-glycosylase OGG1 oversees the detection and clearance of the 7,8-dihydro-8-oxoguanine (8-oxoG), which is the most frequent form of oxidized base in the genome. This lesion is deeply buried within the double-helix and its detection requires careful inspection of the bases by OGG1 via a mechanism that remains only partially understood. By analyzing OGG1 dynamics in the nucleus of living human cells, we demonstrate that the glycosylase constantly samples the DNA by rapidly alternating between diffusion within the nucleoplasm and short transits on the DNA. This sampling process, that we find to be tightly regulated by the conserved residue G245, is crucial for the rapid recruitment of OGG1 at oxidative lesions induced by laser micro-irradiation. Furthermore, we show that residues Y203, N149 and N150, while being all involved in early stages of 8-oxoG probing by OGG1 based on previous structural data, differentially regulate the sampling of the DNA and recruitment to oxidative lesions.

Modular antibodies reveal DNA damage-induced mono-ADP-ribosylation as a second wave of PARP1 signaling

PARP1, an established anti-cancer target that regulates many cellular pathways, including DNA repair signaling, has been intensely studied for decades as a poly(ADP-ribosyl)transferase. Although recent studies have revealed the prevalence of mono-ADP-ribosylation upon DNA damage, it was unknown whether this signal plays an active role in the cell or is just a byproduct of poly-ADP-ribosylation. By engineering SpyTag-based modular antibodies for sensitive and flexible detection of mono-ADP-ribosylation, including fluorescence-based sensors for live-cell imaging, we demonstrate that serine mono-ADP-ribosylation constitutes a second wave of PARP1 signaling shaped by the cellular HPF1/PARP1 ratio. Multilevel chromatin proteomics reveals histone mono-ADP-ribosylation readers, including RNF114, a ubiquitin ligase recruited to DNA lesions through a zinc-finger domain, modulating the DNA damage response and telomere maintenance. Our work provides a technological framework for illuminating ADP-ribosylation in a wide range of applications and biological contexts and establishes mono-ADP-ribosylation by HPF1/PARP1 as an important information carrier for cell signaling.

HPF1-dependent histone ADP-ribosylation triggers chromatin relaxation to promote the recruitment of repair factors at sites of DNA damage

Poly(ADP-ribose) polymerase 1 (PARP1) activity is regulated by its co-factor histone poly(ADP-ribosylation) factor 1 (HPF1). The complex formed by HPF1 and PARP1 catalyzes ADP-ribosylation of serine residues of proteins near DNA breaks, mainly PARP1 and histones. However, the effect of HPF1 on DNA repair regulated by PARP1 remains unclear. Here, we show that HPF1 controls prolonged histone ADP-ribosylation in the vicinity of the DNA breaks by regulating both the number and length of ADP-ribose chains. Furthermore, we demonstrate that HPF1-dependent histone ADP-ribosylation triggers the rapid unfolding of chromatin, facilitating access to DNA at sites of damage. This process promotes the assembly of both the homologous recombination and non-homologous end joining repair machineries. Altogether, our data highlight the key roles played by the PARP1/HPF1 complex in regulating ADP-ribosylation signaling as well as the conformation of damaged chromatin at early stages of the DNA damage response.

The N-terminal domain of TET1 promotes the formation of dense chromatin regions refractory to transcription

TET (ten-eleven translocation) enzymes initiate active cytosine demethylation via the oxidation of 5-methylcytosine. TET1 is composed of a C-terminal domain, which bears the catalytic activity of the enzyme, and a N-terminal region that is less well characterized except for the CXXC domain responsible for the targeting to CpG islands. While cytosine demethylation induced by TET1 promotes transcription, this protein also interacts with chromatin-regulating factors that rather silence this process, the coordination between these two opposite functions of TET1 being unclear. In the present work, we uncover a new function of the N-terminal part of the TET1 protein in the regulation of the chromatin architecture. This domain of the protein promotes the establishment of a compact chromatin architecture displaying reduced exchange rate of core histones and partial dissociation of the histone linker. This chromatin reorganization process, which does not rely on the CXXC domain, is associated with a global shutdown of transcription and an increase in heterochromatin-associated histone epigenetic marks. Based on these findings, we propose that the dense chromatin organization generated by the N-terminal domain of TET1 could contribute to restraining the transcription enhancement induced by the DNA demethylation activity of this enzyme.

Zinc finger protein ZNF384 is an adaptor of Ku to DNA during classical non-homologous end-joining

DNA double-strand breaks (DSBs) are among the most deleterious types of DNA damage as they can lead to mutations and chromosomal rearrangements, which underlie cancer development. Classical non-homologous end-joining (cNHEJ) is the dominant pathway for DSB repair in human cells, involving the DNA-binding proteins XRCC6 (Ku70) and XRCC5 (Ku80). Other DNA-binding proteins such as Zinc Finger (ZnF) domain-containing proteins have also been implicated in DNA repair, but their role in cNHEJ remained elusive. Here we show that ZNF384, a member of the C2H2 family of ZnF proteins, binds DNA ends in vitro and is recruited to DSBs in vivo. ZNF384 recruitment requires the poly(ADP-ribosyl) polymerase 1 (PARP1)-dependent expansion of damaged chromatin, followed by binding of its C2H2 motifs to the exposed DNA. Moreover, ZNF384 interacts with Ku70/Ku80 via its N-terminus, thereby promoting Ku70/Ku80 assembly and the accrual of downstream cNHEJ factors, including APLF and XRCC4/LIG4, for efficient repair at DSBs. Altogether, our data suggest that ZNF384 acts as a 'Ku-adaptor' that binds damaged DNA and Ku70/Ku80 to facilitate the build-up of a cNHEJ repairosome, highlighting a role for ZNF384 in DSB repair and genome maintenance.

New Methodologies to Study DNA Repair Processes in Space and Time Within Living Cells

DNA repair requires a coordinated effort from an array of factors that play different roles in the DNA damage response from recognizing and signaling the presence of a break, creating a repair competent environment, and physically repairing the lesion. Due to the rapid nature of many of these events, live-cell microscopy has become an invaluable method to study this process. In this review we outline commonly used tools to induce DNA damage under the microscope and discuss spatio-temporal analysis tools that can bring added information regarding protein dynamics at sites of damage. In particular, we show how to go beyond the classical analysis of protein recruitment curves to be able to assess the dynamic association of the repair factors with the DNA lesions as well as the target-search strategies used to efficiently find these lesions. Finally, we discuss how the use of mathematical models, combined with experimental evidence, can be used to better interpret the complex dynamics of repair proteins at DNA lesions.

RhoA- and Cdc42-induced antagonistic forces underlie symmetry breaking and spindle rotation in mouse oocytes

Mammalian oocyte meiotic divisions are highly asymmetric and produce a large haploid gamete and 2 small polar bodies. This relies on the ability of the cell to break symmetry and position its spindle close to the cortex before anaphase occurs. In metaphase II–arrested mouse oocytes, the spindle is actively maintained close and parallel to the cortex, until fertilization triggers sister chromatid segregation and the rotation of the spindle. The latter must indeed reorient perpendicular to the cortex to enable cytokinesis ring closure at the base of the polar body. However, the mechanisms underlying symmetry breaking and spindle rotation have remained elusive. In this study, we show that spindle rotation results from 2 antagonistic forces. First, an inward contraction of the cytokinesis furrow dependent on RhoA signaling, and second, an outward attraction exerted on both sets of chromatids by a Ran/Cdc42-dependent polarization of the actomyosin cortex. By combining live segmentation and tracking with numerical modeling, we demonstrate that this configuration becomes unstable as the ingression progresses. This leads to spontaneous symmetry breaking, which implies that neither the rotation direction nor the set of chromatids that eventually gets discarded are biologically predetermined.

Mammalian oocyte meiotic divisions are highly asymmetric and produce a large haploid gamete and two small polar bodies, but the mechanisms underlying the required symmetry breaking and spindle rotation have remained elusive. This study shows that spindle rotation in activated mouse oocytes relies on spontaneous symmetry breaking resulting from an unstable configuration generated by cleavage furrow ingression and cortical chromosome attraction.

Label-free microscopy of mitotic chromosomes using the polarization orthogonality breaking technique

We report how a recently developed polarization imaging technique, implementing micro-wave photonics and referred to as orthogonality-breaking (OB) imaging, can be adapted on a classical confocal fluorescence microscope, and is able to provide informative polarization images from a single scan of the cell sample. For instance, the comparison of the images of various cell lines at different cell-cycle stages obtained by OB polarization microscopy and fluorescence confocal images shows that an endogenous polarimetric contrast arizes with this instrument on compacted chromosomes during cell division.

Serine-linked PARP1 auto-modification controls PARP inhibitor response

Poly(ADP-ribose) polymerase 1 (PARP1) and PARP2 are recruited and activated by DNA damage, resulting in ADP-ribosylation at numerous sites, both within PARP1 itself and in other proteins. Several PARP1 and PARP2 inhibitors are currently employed in the clinic or undergoing trials for treatment of various cancers. These drugs act primarily by trapping PARP1 on damaged chromatin, which can lead to cell death, especially in cells with DNA repair defects. Although PARP1 trapping is thought to be caused primarily by the catalytic inhibition of PARP-dependent modification, implying that ADP-ribosylation (ADPr) can counteract trapping, it is not known which exact sites are important for this process. Following recent findings that PARP1- or PARP2-mediated modification is predominantly serine-linked, we demonstrate here that serine ADPr plays a vital role in cellular responses to PARP1/PARP2 inhibitors. Specifically, we identify three serine residues within PARP1 (499, 507, and 519) as key sites whose efficient HPF1-dependent modification counters PARP1 trapping and contributes to inhibitor tolerance. Our data implicate genes that encode serine-specific ADPr regulators, HPF1 and ARH3, as potential PARP1/PARP2 inhibitor therapy biomarkers.

Multisite evaluation of phenotypic plasticity for specialized metabolites, some involved in carrot quality and disease resistance

Renewed consumer demand motivates the nutritional and sensory quality improvement of fruits and vegetables. Specialized metabolites being largely involved in nutritional and sensory quality of carrot, a better knowledge of their phenotypic variability is required. A metabolomic approach was used to evaluate phenotypic plasticity level of carrot commercial varieties, over three years and a wide range of cropping environments spread over several geographical areas in France. Seven groups of metabolites have been quantified by HPLC or GC methods: sugars, carotenoids, terpenes, phenolic compounds, phenylpropanoids and polyacetylenes. A large variation in root metabolic profiles was observed, in relation with environment, variety and variety by environment interaction effects in decreasing order of importance. Our results show a clear diversity structuration based on metabolite content. Polyacetylenes, β-pinene and α-carotene were identified mostly as relatively stable varietal markers, exhibiting static stability. Nevertheless, environment effect was substantial for a large part of carrot metabolic profile and various levels of phenotypic plasticity were observed depending on metabolites and varieties. A strong difference of environmental sensitivity between varieties was observed for several compounds, particularly myristicin, 6MM and D-germacrene, known to be involved in responses to biotic and abiotic stress. This work provides useful information about plasticity in the perspective of carrot breeding and production. A balance between constitutive content and environmental sensitivity for key metabolites should be reached for quality improvement in carrot and other vegetables.

[Impact of the type of incubator (non-humidified versus humidified) on embryo culture media osmolality]

INTRODUCTION

Benchtop incubators with small individual chambers have been developed in order to improve the stability of embryo culture conditions reducing the environmental stress during the embryo development. These new dry incubators were designed without any air humidification system in order to prevent bacterial proliferation and to enable the use of time-lapse system. However, an elevated evaporation of the culture media could occur in these conditions. The main objective of the study is to analyse the impact of the used incubator type on the embryo culture media osmolality.

MATERIALS AND METHODS

Microdrops of 50μL of culture media were placed in 60mm diameter culture dishes, and quickly covered with either 7 or 8mL of mineral oil in an IVF workstation with laminar airflow. Two series of culture dishes have been randomly placed either in a humidified incubator or in a dry benchtop incubator. The microdrops of each culture dishes were sampled at D0, D1, D2, D3, and D5 respectively to measure the osmolality in triplicate using a cryoscopic osmometer. The mean values of osmolality in each incubator have been compared respectively on D0, D1, D2, D3 and D5 with appropriate statistical tests, and considered statistically significant when P<0.05.

RESULTS

The osmolality of the microdrops placed in the dry benchtop incubator differed significantly after the third day of culture, regardless of the level of mineral oil in the culture dishes. Indeed, using Petri dishes covered respectively with 7 or 8mL of mineral oil, osmolality values of samples from the dry incubator were significantly higher than those from the humidified one, at D3 and D5 (D3/7mL: 273±2.1 vs. 268±1.0mOsm/kg; P=0.02; D3/8mL: 282±8.0 vs. 270±0.7mOsm/kg; P=0.04) and D5 (D5/7mL: 283±1.5 vs. 270±3.6mOsm/kg; P=0.004; D5/8mL: 287±5.6 vs. 268±2.3mOsm/kg; P=0.005). Furthermore, the analysis on paired samples showed that the osmolality in the dry benchtop incubator at D5 using 7mL of oil (283±1.5mOsm/kg; P=0.003) and at D3 (273±2.1mOsm/kg; P=0.016) and D5 (287±5.6mOsm/kg; P=0.009) using 8mL of oil was significantly higher than that measured at D0 (265±1.9mOsm/kg).

CONCLUSION

A significant increase of the embryo culture media osmolality was observed in the dry benchtop incubator with ambient hygrometry in our standard conditions. Adding 1mL of oil was not sufficient to reduce the evaporation of the media. Although maintained at a physiological level, the impact of the osmolality changes on the in vitro embryo development has to be further determined.

The chromatin remodeler ALC1 underlies resistance to PARP inhibitor treatment

Poly(ADP-ribose) polymerase (PARP) inhibitors are used in the treatment of BRCA-deficient cancers, with treatments currently extending toward other homologous recombination defective tumors. In a genome-wide CRISPR knockout screen with olaparib, we identify ALC1 (Amplified in Liver Cancer 1)-a cancer-relevant poly(ADP-ribose)-regulated chromatin remodeling enzyme-as a key modulator of sensitivity to PARP inhibitor. We found that ALC1 can remove inactive PARP1 indirectly through binding to PARylated chromatin. Consequently, ALC1 deficiency enhances trapping of inhibited PARP1, which then impairs the binding of both nonhomologous end-joining and homologous recombination repair factors to DNA lesions. We also establish that ALC1 overexpression, a common feature in multiple tumor types, reduces the sensitivity of BRCA-deficient cells to PARP inhibitors. Together, we conclude that ALC1-dependent PARP1 mobilization is a key step underlying PARP inhibitor resistance.

CHD7 and 53BP1 regulate distinct pathways for the re-ligation of DNA double-strand breaks

Chromatin structure is dynamically reorganized at multiple levels in response to DNA double-strand breaks (DSBs). Yet, how the different steps of chromatin reorganization are coordinated in space and time to differentially regulate DNA repair pathways is insufficiently understood. Here, we identify the Chromodomain Helicase DNA Binding Protein 7 (CHD7), which is frequently mutated in CHARGE syndrome, as an integral component of the non-homologous end-joining (NHEJ) DSB repair pathway. Upon recruitment via PARP1-triggered chromatin remodeling, CHD7 stimulates further chromatin relaxation around DNA break sites and brings in HDAC1/2 for localized chromatin de-acetylation. This counteracts the CHD7-induced chromatin expansion, thereby ensuring temporally and spatially controlled 'chromatin breathing' upon DNA damage, which we demonstrate fosters efficient and accurate DSB repair by controlling Ku and LIG4/XRCC4 activities. Loss of CHD7-HDAC1/2-dependent cNHEJ reinforces 53BP1 assembly at the damaged chromatin and shifts DSB repair to mutagenic NHEJ, revealing a backup function of 53BP1 when cNHEJ fails.

Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage

The addition of poly(ADP-ribose) (PAR) chains along the chromatin fiber due to PARP1 activity regulates the recruitment of multiple factors to sites of DNA damage. In this manuscript, we investigated how, besides direct binding to PAR, early chromatin unfolding events controlled by PAR signaling contribute to recruitment to DNA lesions. We observed that different DNA-binding, but not histone-binding, domains accumulate at damaged chromatin in a PAR-dependent manner, and that this recruitment correlates with their affinity for DNA. Our findings indicate that this recruitment is promoted by early PAR-dependent chromatin remodeling rather than direct interaction with PAR. Moreover, recruitment is not the consequence of reduced molecular crowding at unfolded damaged chromatin but instead originates from facilitated binding to more exposed DNA. These findings are further substantiated by the observation that PAR-dependent chromatin remodeling at DNA lesions underlies increased DNAse hypersensitivity. Finally, the relevance of this new mode of PAR-dependent recruitment to DNA lesions is demonstrated by the observation that reducing the affinity for DNA of both CHD4 and HP1α, two proteins shown to be involved in the DNA-damage response, strongly impairs their recruitment to DNA lesions.

Carrot Genotypes Contrasted by Root Color and Grown under Different Conditions Displayed Differential Pharmacological Profiles in Vascular and Metabolic Cells

Carrots' genotype and growing conditions influence their potential properties to fight against cardiovascular and metabolic diseases. The present study evaluated the influence of carrot genotypes contrasted by root color (Bolero, Presto, Karotan, Deep Purple, Kintoki and Blanche des Vosges) growing under standard, water-restricted, biotic stress (Alternaria dauci inoculation), and combined stress conditions (water restriction and A.dauci inoculation). The effect of carrots' polyphenol and carotenoid content was assessed on endothelial and smooth muscle cells, hepatocytes, adipocytes and macrophages functions (oxidative stress, apoptosis, proliferation, lipid accumulation and inflammation). Independently of varieties or growing conditions, all carrot extracts affected vascular cells' oxidative stress and apoptosis, and metabolic cells' oxidative stress and lipid accumulation. Three clusters were revealed and displayed beneficial properties mostly for adipocytes function, smooth muscle cells and hepatocytes, and endothelial cells and hepatocytes, respectively. Karotan and Presto varieties exhibited endothelial tropism while Blanche des Vosges targeted adipocytes. Carrots under biotic stress are more efficient in inducing beneficial effects, with the Bolero variety being the most effective. However, extracts from carrots which grew under combined stress conditions had limited beneficial effects. This report underscores the use of certain carrot extracts as potential effective nutraceutical supplements for metabolic diseases.

The RNA export factor Mex67 functions as a mobile nucleoporin

Derrer et al. show that the mRNA export factor Mex67 can perform its essential function when stably tethered to the nuclear pore complex.

The RNA export factor Mex67 is essential for the transport of mRNA through the nuclear pore complex (NPC) in yeast, but the molecular mechanism of this export process remains poorly understood. Here, we use quantitative fluorescence microscopy techniques in live budding yeast cells to investigate how Mex67 facilitates mRNA export. We show that Mex67 exhibits little interaction with mRNA in the nucleus and localizes to the NPC independently of mRNA, occupying a set of binding sites offered by FG repeats in the NPC. The ATPase Dbp5, which is thought to remove Mex67 from transcripts, does not affect the interaction of Mex67 with the NPC. Strikingly, we find that the essential function of Mex67 is spatially restricted to the NPC since a fusion of Mex67 to the nucleoporin Nup116 rescues a deletion of MEX67. Thus, Mex67 functions as a mobile NPC component, which receives mRNA export substrates in the central channel of the NPC to facilitate their translocation to the cytoplasm.

CHD3 and CHD4 recruitment and chromatin remodeling activity at DNA breaks is promoted by early poly(ADP-ribose)-dependent chromatin relaxation

One of the first events to occur upon DNA damage is the local opening of the compact chromatin architecture, facilitating access of repair proteins to DNA lesions. This early relaxation is triggered by poly(ADP-ribosyl)ation by PARP1 in addition to ATP-dependent chromatin remodeling. CHD4 recruits to DNA breaks in a PAR-dependent manner, although it lacks any recognizable PAR-binding domain, and has the ability to relax chromatin structure. However, its role in chromatin relaxation at the site of DNA damage has not been explored. Using a live cell fluorescence three-hybrid assay, we demonstrate that the recruitment of CHD4 to DNA damage, while being poly(ADP-ribosyl)ation-dependent, is not through binding poly(ADP-ribose). Additionally, we show that CHD3 is recruited to DNA breaks in the same manner as CHD4 and that both CHD3 and CHD4 play active roles in chromatin remodeling at DNA breaks. Together, our findings reveal a two-step mechanism for DNA damage induced chromatin relaxation in which PARP1 and the PAR-binding remodeler activities of Alc1/CHD1L induce an initial chromatin relaxation phase that promotes the subsequent recruitment of CHD3 and CHD4 via binding to DNA for further chromatin remodeling at DNA breaks.

Link between carrot leaf secondary metabolites and resistance to Alternaria dauci

Alternaria Leaf Blight (ALB), caused by the fungus Alternaria dauci, is the most damaging foliar disease affecting carrots (Daucus carota). In order to identify compounds potentially linked to the resistance to A. dauci, we have used a combination of targeted and non-targeted metabolomics to compare the leaf metabolome of four carrot genotypes with different resistance levels. Targeted analyses were focused on terpene volatiles, while total leaf methanolic extracts were subjected to non-targeted analyses using liquid chromatography couple to high-resolution mass spectrometry. Differences in the accumulation of major metabolites were highlighted among genotypes and some of these metabolites were identified as potentially involved in resistance or susceptibility. A bulk segregant analysis on F3 progenies obtained from a cross between one of the resistant genotypes and a susceptible one, confirmed or refuted the hypothesis that the metabolites differentially accumulated by these two parents could be linked to resistance.

Correlative live and super-resolution imaging reveals the dynamic structure of replication domains

Combining fluorescence labeling with live-cell confocal and correlative super-resolution microscopy, Xiang et al. characterize biophysical parameters defining the internal organization, spacing, and mechanical coupling of replication domains.

Chromosome organization in higher eukaryotes controls gene expression, DNA replication, and DNA repair. Genome mapping has revealed the functional units of chromatin at the submegabase scale as self-interacting regions called topologically associating domains (TADs) and showed they correspond to replication domains (RDs). A quantitative structural and dynamic description of RD behavior in the nucleus is, however, missing because visualization of dynamic subdiffraction-sized RDs remains challenging. Using fluorescence labeling of RDs combined with correlative live and super-resolution microscopy in situ, we determined biophysical parameters to characterize the internal organization, spacing, and mechanical coupling of RDs. We found that RDs are typically 150 nm in size and contain four co-replicating regions spaced 60 nm apart. Spatially neighboring RDs are spaced 300 nm apart and connected by highly flexible linker regions that couple their motion only <550 nm. Our pipeline allows a robust quantitative characterization of chromosome structure in situ and provides important biophysical parameters to understand general principles of chromatin organization.

Carotenoid gene expression explains the difference of carotenoid accumulation in carrot root tissues

Main conclusion Variations in gene expression can partially explain the difference of carotenoid accumulation in secondary phloem and xylem of fleshy carrot roots. The carrot root is well divided into two different tissues separated by vascular cambium: the secondary phloem and xylem. The equilibrium between these two tissues represents an important issue for carrot quality, but the knowledge about the respective carotenoid accumulation is sparse. The aim of this work was (i) to investigate if variation in carotenoid biosynthesis gene expression could explain differences in carotenoid content in phloem and xylem tissues and (ii) to investigate if this regulation is differentially modulated in the respective tissues by water-restricted growing conditions. In this work, five carrot genotypes contrasting by their root color were studied in control and water-restricted conditions. Carotenoid content and the relative expression of 13 genes along the carotenoid biosynthesis pathway were measured in the respective tissues. Results showed that in orange genotypes and the purple one, carotenoid content was higher in phloem compared to xylem. For the red one, no differences were observed. Moreover, in control condition, variations in gene expression explained the different carotenoid accumulations in both tissues, while in water-restricted condition, no clear association between gene expression pattern and variations in carotenoid content could be detected except in orange-rooted genotypes. This work shows that the structural aspect of carrot root is more important for carotenoid accumulation in relation with gene expression levels than the consequences of expression changes upon water restriction.

Analysis of DNA Replication by Optical Mapping in Nanochannels

DNA replication is essential to maintain genome integrity in S phase of the cell division cycle. Accumulation of stalled replication forks is a major source of genetic instability, and likely constitutes a key driver of tumorigenesis. The mechanisms of regulation of replication fork progression have therefore been extensively investigated, in particular with DNA combing, an optical mapping technique that allows the stretching of single molecules and the mapping of active region for DNA synthesis by fluorescence microscopy. DNA linearization in nanochannels has been successfully used to probe genomic information patterns along single chromosomes, and has been proposed to be a competitive alternative to DNA combing. Yet this conjecture remains to be confirmed experimentally. Here, two complementary techniques are established to detect the genomic distribution of tracks of newly synthesized DNA in human cells by optical mapping in nanochannels. Their respective advantages and limitations are compared, and applied them to detect deregulations of the replication program induced by the antitumor drug hydroxyurea. The developments here thus broaden the field of applications accessible to nanofluidic technologies, and can be used in the future as part for molecular diagnostics in the context of high throughput cancer drug screening.

The poly(ADP-ribose)-dependent chromatin remodeler Alc1 induces local chromatin relaxation upon DNA damage

PARP1 and its effector, the ATP-dependent chromatin remodeler Alc1/Chd1L, are identified as key players during the rapid chromatin relaxation at DNA damage sites.

Chromatin relaxation is one of the earliest cellular responses to DNA damage. However, what determines these structural changes, including their ATP requirement, is not well understood. Using live-cell imaging and laser microirradiation to induce DNA lesions, we show that the local chromatin relaxation at DNA damage sites is regulated by PARP1 enzymatic activity. We also report that H1 is mobilized at DNA damage sites, but, since this mobilization is largely independent of poly(ADP-ribosyl)ation, it cannot solely explain the chromatin relaxation. Finally, we demonstrate the involvement of Alc1, a poly(ADP-ribose)- and ATP-dependent remodeler, in the chromatin-relaxation process. Deletion of Alc1 impairs chromatin relaxation after DNA damage, while its overexpression strongly enhances relaxation. Altogether our results identify Alc1 as an important player in the fast kinetics of the NAD⁺- and ATP-dependent chromatin relaxation upon DNA damage in vivo.

Differential Pigment Accumulation in Carrot Leaves and Roots during Two Growing Periods

Carotenoids are important secondary metabolites involved in plant growth and nutritional quality of vegetable crops. These pigments are highly accumulated in carrot root, but knowledge about the impact of environmental factors on their accumulation is limited. The purpose of this work was to investigate the impact of environmental variations on carotenoid accumulation in carrot leaves and roots. In this work, carrots were grown during two contrasting periods to maximize bioclimatic differences. In leaves, carotenoid and chlorophyll contents were lower in the less favorable growing conditions, whereas relative contents were well conserved for all genotypes, suggesting a common regulatory mechanism. The down-regulation of all genes under environmental constraints demonstrates that carotenoid accumulation is regulated at the transcriptional level. In roots, the decrease in α-carotene and lutein contents was accompanied by an increase of β-carotene relative content. At the transcriptional level, LCYB and ZEP expression increased, whereas LCYE expression decreased, in the less favorable conditions, suggesting that carotenoid biosynthesis is switched toward the β-branch.

QTL mapping of carrot resistance to leaf blight with connected populations: stability across years and consequences for breeding

Combining biparental and multiparental connected population analyses was useful for the identification of 11 QTLs in two new genetic backgrounds of carrot resistance to Alternaria dauci and for breeding recommendations. Leaf blight due to the fungus Alternaria dauci is the major carrot foliar disease worldwide. Some resistance QTLs have been previously identified in one population, but the evaluation of additional genetic backgrounds with higher level of resistance would give opportunities for breeders to combine them by pyramiding. For this purpose, two segregating populations were evaluated twice across 4 years in the same environment (1) to compare the efficiency of the single vs. the connected populations approach for characterizing the new sources of carrot resistance to Alternaria dauci; (2) to evaluate the stability of QTLs over the years; and (3) to give recommendations to breeders for marker-assisted selection. Single and connected analyses were complementary; their combination allowed the detection of 11 QTLs. Connected analyses allowed the identification of common and specific QTLs among the two populations and the most favorable allele at each QTL. Important contrasts between allelic effects were observed with four and five most favorable alleles coming from the two resistant parental lines, whereas two other favorable alleles came from the susceptible parental line. While four QTLs were consistent across years, seven were detected within a single year. The heritabilities for both populations PC2 and PC3 were high (75 and 78%, respectively), suggesting that the resistance of carrot to A. dauci was little affected by these environmental conditions, but the instability of QTL over years may be due to changing environmental conditions. The complementarity between these parental lines in terms of interesting allelic combinations is also discussed.

[Urinary, infectious and digestive adverse events related to benign hysterectomy and the associated surgery on the Fallopian tube: Guidelines]

OBJECTIVES

To provide clinical practice guidelines from the French College of Obstetrics and Gynecology (CNGOF) based on the best evidence available, concerning the urinary, infectious and digestive adverse events related to benign hysterectomy and the associated surgery including opportunistic salpingectomy and adnexectomy.

MATERIAL AND METHOD

Review of literature using following keywords: benign hysterectomy; urinary injury; bladder injury; ureteral injury; vesicovaginal fistula; infection; bowel injury; salpingectomy.

RESULTS

Urinary catheter should be removed before 24h following uncomplicated hysterectomy (grade B). In case of urinary catheter during hysterectomy, immediate postoperative removal is possible (grade C). No hemostasis technics can be recommended to avoid urinary injury (grade C). There is not any evidence to recommend to perform a window in the broad ligament or an ureterolysis, to put ureteral stent or a uterine manipulator in order to avoid ureteral injury. An antibiotic prophylaxis by a cephalosporin is always recommended (grade B). Mechanical bowel preparation before hysterectomy is not recommended (grade B). If there is no ovarian cyst/disease and no familial or personal history of ovarian/breast cancer, ovarian conservation is recommended in premenopausal women (grade B). In postmenopausal women, informed consent and surgical approach should be taken in account to perform a salpingo-oophorectomy. Since the association salpingectomy and hysterectomy is not assessed in the prevention of ovarian cancer, systematic bilateral salpingectomy is not recommended (expert consensus).

CONCLUSIONS

Practical application of these guidelines should decrease the prevalence of visceral complications associated with benign hysterectomy.

[Hysterectomy for benign pathology: Guidelines for clinical practice]

OBJECTIVE

The objective of the study was to provide guidelines for clinical practice from the French college of obstetrics and gynecology (CNGOF), based on the best evidence available, concerning hysterectomy for benign pathology.

METHODS

Each recommendation for practice was allocated a grade which depends on the level of evidence (guidelines for clinical practice method).

RESULTS

Hysterectomy should be performed by a high volume surgeon (>10 procedures of hysterectomy per year) (grade C). Rectal enema stimulant laxatives are not recommended prior to hysterectomy (grade C). It is recommended to carry out vaginal disinfection using povidone iodine solution prior to an hysterectomy (grade B). Antibioprophylaxis is recommended during a hysterectomy, regardless of the surgical route (grade B). The vaginal or the laparoscopic routes are recommended for hysterectomy for benign pathology (grade B), even if the uterus is large and/or the patient is obese (grade C). The choice between these two surgical approaches depends on others parameters, such as the surgeon's experience, the mode of anesthesia and organizational constraints (operative duration and medico economic factors). Hysterectomy by vaginal route is not contraindicated in nulliparous women (grade C) or in women with previous c-section (grade C). No specific technique to achieve hemostasis is recommended with a view to avoid urinary tract injuries (grade C). In the absence of ovarian pathology and personal or family history of breast/ovarian carcinoma, it is recommended to conserve ovaries in pre-menopausal women (grade B). Subtotal hysterectomy is not recommended in order to diminish the risk of per- or postoperative complications (grade B).

CONCLUSION

The application of these recommendations should minimize risks associated with hysterectomy.

Diffusion and partitioning of macromolecules in casein microgels: evidence for size-dependent attractive interactions in a dense protein system

Understanding the mechanisms that determine the diffusion and interaction of macromolecules (such as proteins and polysaccharides) that disperse through dense media is an important fundamental issue in the development of innovative technological and medical applications. In the current work, the partitioning and diffusion of macromolecules of different sizes (from 4 to 10 nm in diameter) and shapes (linear or spherical) within dispersions of casein micelles (a protein microgel) is studied. The coefficients for diffusion and partition are measured using FRAP (fluorescence recovery after photobleaching) and analyzed with respect to the structural characteristics of the microgel determined by the use of TEM (transmission electron microscopy) tomography. The results show that the casein microgel displays a nonspecific attractive interaction for all macromolecules studied. When the macromolecular probes are spherical, this affinity is clearly size-dependent, with stronger attraction for the larger probes. The current data show that electrostatic effects cannot account for such an attraction. Rather, nonspecific hydration molecular forces appear to explain these results. These findings show how weak nonspecific forces affect the diffusion and partitioning of proteins and polysaccharides in a dense protein environment. These results could be useful to better understand the mechanisms of diffusion and partitioning in other media such as cells and tissues. Furthermore, there arises the possibility of using the casein micelle as a size-selective molecular device.

Carotenoid content and root color of cultivated carrot: a candidate-gene association study using an original broad unstructured population

Accumulated in large amounts in carrot, carotenoids are an important product quality attribute and therefore a major breeding trait. However, the knowledge of carotenoid accumulation genetic control in this root vegetable is still limited. In order to identify the genetic variants linked to this character, we performed an association mapping study with a candidate gene approach. We developed an original unstructured population with a broad genetic basis to avoid the pitfall of false positive detection due to population stratification. We genotyped 109 SNPs located in 17 candidate genes – mostly carotenoid biosynthesis genes – on 380 individuals, and tested the association with carotenoid contents and color components. Total carotenoids and β-carotene contents were significantly associated with genes zeaxanthin epoxydase (ZEP), phytoene desaturase (PDS) and carotenoid isomerase (CRTISO) while α-carotene was associated with CRTISO and plastid terminal oxidase (PTOX) genes. Color components were associated most significantly with ZEP. Our results suggest the involvement of the couple PDS/PTOX and ZEP in carotenoid accumulation, as the result of the metabolic and catabolic activities respectively. This study brings new insights in the understanding of the carotenoid pathway in non-photosynthetic organs.

Dynamic estrogen receptor interactomes control estrogen-responsive trefoil Factor (TFF) locus cell-specific activities

Estradiol signaling is ideally suited for analyzing the molecular and functional linkages between the different layers of information directing transcriptional regulations: the DNA sequence, chromatin modifications, and the spatial organization of the genome. Hence, the estrogen receptor (ER) can bind at a distance from its target genes and engages timely and spatially coordinated processes to regulate their expression. In the context of the coordinated regulation of colinear genes, identifying which ER binding sites (ERBSs) regulate a given gene still remains a challenge. Here, we investigated the coordination of such regulatory events at a 2-Mb genomic locus containing the estrogen-sensitive trefoil factor (TFF) cluster of genes in breast cancer cells. We demonstrate that this locus exhibits a hormone- and cohesin-dependent reduction in the plasticity of its three-dimensional organization that allows multiple ERBSs to be dynamically brought to the vicinity of estrogen-sensitive genes. Additionally, by using triplex-forming oligonucleotides, we could precisely document the functional links between ER engagement at given ERBSs and the regulation of particular genes. Hence, our data provide evidence of a formerly suggested cooperation of enhancers toward gene regulation and also show that redundancy between ERBSs can occur.

Ensconsin/Map7 promotes microtubule growth and centrosome separation in Drosophila neural stem cells

Ensconsin cooperates with its binding partner, Kinesin-1, during interphase to trigger centrosome separation, but it promotes microtubule polymerization independently of Kinesin-1 to control spindle length during mitosis.

The mitotic spindle is crucial to achieve segregation of sister chromatids. To identify new mitotic spindle assembly regulators, we isolated 855 microtubule-associated proteins (MAPs) from Drosophila melanogaster mitotic or interphasic embryos. Using RNAi, we screened 96 poorly characterized genes in the Drosophila central nervous system to establish their possible role during spindle assembly. We found that Ensconsin/MAP7 mutant neuroblasts display shorter metaphase spindles, a defect caused by a reduced microtubule polymerization rate and enhanced by centrosome ablation. In agreement with a direct effect in regulating spindle length, Ensconsin overexpression triggered an increase in spindle length in S2 cells, whereas purified Ensconsin stimulated microtubule polymerization in vitro. Interestingly, ensc-null mutant flies also display defective centrosome separation and positioning during interphase, a phenotype also detected in kinesin-1 mutants. Collectively, our results suggest that Ensconsin cooperates with its binding partner Kinesin-1 during interphase to trigger centrosome separation. In addition, Ensconsin promotes microtubule polymerization during mitosis to control spindle length independent of Kinesin-1.

[Temporal evolution of the genetic diversity of Chaerophyllum bulbosum: consequences on the genetic resources management]

To increase the germplasm necessary for varietal improvement of tuberous-rooted chervil, a food apiaceae of increasing importance, two successive surveys of wild populations were carried out in Germany, in the Rhine and the Weser River basins. These mainly riparian populations are likely to be shaped by changes in hydrographic networks that characterize their habitat. Molecular studies have shown a strong structuration between wild populations (GST∼32%), but did not reveal any structuring effect of the hydrographic network on diversity or any global phenomenon of genetic erosion. A discussion about the strategy for maintaining the diversity of this species on a long-term period is proposed.

Wapl is an essential regulator of chromatin structure and chromosome segregation

Mammalian genomes contain several billion base pairs of DNA that are packaged in chromatin fibres. At selected gene loci, cohesin complexes have been proposed to arrange these fibres into higher-order structures, but how important this function is for determining overall chromosome architecture and how the process is regulated are not well understood. Using conditional mutagenesis in the mouse, here we show that depletion of the cohesin-associated protein Wapl stably locks cohesin on DNA, leads to clustering of cohesin in axial structures, and causes chromatin condensation in interphase chromosomes. These findings reveal that the stability of cohesin-DNA interactions is an important determinant of chromatin structure, and indicate that cohesin has an architectural role in interphase chromosome territories. Furthermore, we show that regulation of cohesin-DNA interactions by Wapl is important for embryonic development, expression of genes such as c-myc (also known as Myc), and cell cycle progression. In mitosis, Wapl-mediated release of cohesin from DNA is essential for proper chromosome segregation and protects cohesin from cleavage by the protease separase, thus enabling mitotic exit in the presence of functional cohesin complexes.

Functional gene polymorphism to reveal species history: the case of the CRTISO gene in cultivated carrots

Background

Carrot is a vegetable cultivated worldwide for the consumption of its root. Historical data indicate that root colour has been differentially selected over time and according to geographical areas. Root pigmentation depends on the relative proportion of different carotenoids for the white, yellow, orange and red types but only internally for the purple one. The genetic control for root carotenoid content might be partially associated with carotenoid biosynthetic genes. Carotenoid isomerase (CRTISO) has emerged as a regulatory step in the carotenoid biosynthesis pathway and could be a good candidate to show how a metabolic pathway gene reflects a species genetic history.

Methodology/Principal Findings

In this study, the nucleotide polymorphism and the linkage disequilibrium among the complete CRTISO sequence, and the deviation from neutral expectation were analysed by considering population subdivision revealed with 17 microsatellite markers. A sample of 39 accessions, which represented different geographical origins and root colours, was used. Cultivated carrot was divided into two genetic groups: one from Middle East and Asia (Eastern group), and another one mainly from Europe (Western group). The Western and Eastern genetic groups were suggested to be differentially affected by selection: a signature of balancing selection was detected within the first group whereas the second one showed no selection. A focus on orange-rooted carrots revealed that cultivars cultivated in Asia were mainly assigned to the Western group but showed CRTISO haplotypes common to Eastern carrots.

Conclusion

The carotenoid pathway CRTISO gene data proved to be complementary to neutral markers in order to bring critical insight in the cultivated carrot history. We confirmed the occurrence of two migration events since domestication. Our results showed a European background in material from Japan and Central Asia. While confirming the introduction of European carrots in Japanese resources, the history of Central Asia material remains unclear.

A fractal model for nuclear organization: current evidence and biological implications

Chromatin is a multiscale structure on which transcription, replication, recombination and repair of the genome occur. To fully understand any of these processes at the molecular level under physiological conditions, a clear picture of the polymorphic and dynamic organization of chromatin in the eukaryotic nucleus is required. Recent studies indicate that a fractal model of chromatin architecture is consistent with both the reaction-diffusion properties of chromatin interacting proteins and with structural data on chromatin interminglement. In this study, we provide a critical overview of the experimental evidence that support a fractal organization of chromatin. On this basis, we discuss the functional implications of a fractal chromatin model for biological processes and propose future experiments to probe chromatin organization further that should allow to strongly support or invalidate the fractal hypothesis.

Fluorescence perturbation techniques to study mobility and molecular dynamics of proteins in live cells: FRAP, photoactivation, photoconversion, and FLIP

The technique of fluorescence recovery after photobleaching (FRAP) was introduced in the mid-1970s to study the diffusion of biomolecules in living cells. For several years, it was used mainly by a small number of biophysicists who had developed their own photobleaching systems. Since the mid-1990s, FRAP has gained increasing popularity because of the conjunction of two factors: First, photobleaching techniques are easily implemented on confocal laser-scanning microscopes (CLSMs), and so FRAP has become available to anyone who has access to such equipment. Second, the advent of green fluorescent protein (GFP) has allowed easy fluorescent tagging of proteins and their observation in living cells. Thanks both to the versatility of modern CLSMs, which allow control of laser intensity at any point of the image, and to the development of new fluorescent probes, additional photoperturbation techniques have emerged during the last few years. After the photoperturbation event, one observes and then analyzes how the fluorescence distribution relaxes toward the steady state. Because the photochemical perturbation of suitable fluorophores is essentially irreversible, changes of fluorescence intensity in the perturbed and unperturbed regions are due to the exchange of tagged molecules between those regions. This article first discusses the materials required for performing FRAP experiments on a CLSM and the software for data analysis. It then describes general considerations on how to perform FRAP experiments as well as the necessary controls. Finally, different possible ways to analyze the data are presented.