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.