HiChIP and Hi-C Protocol Optimized for Primary Murine T Cells

The functional implications of the three-dimensional genome organization are becoming increasingly recognized. The Hi-C and HiChIP research approaches belong among the most popular choices for probing long-range chromatin interactions. A few methodical protocols have been published so far, yet their reproducibility and efficiency may vary. Most importantly, the high frequency of the dangling ends may dramatically affect the number of usable reads mapped to valid interaction pairs. Additionally, more obstacles arise from the chromatin compactness of certain investigated cell types, such as primary T cells, which due to their small and compact nuclei, impede limitations for their use in various genomic approaches. Here we systematically optimized all the major steps of the HiChIP protocol in T cells. As a result, we reduced the number of dangling ends to nearly zero and increased the proportion of long-range interaction pairs. Moreover, using three different mouse genotypes and multiple biological replicates, we demonstrated the high reproducibility of the optimized protocol. Although our primary goal was to optimize HiChIP, we also successfully applied the optimized steps to Hi-C, given their significant protocol overlap. Overall, we describe the rationale behind every optimization step, followed by a detailed protocol for both HiChIP and Hi-C experiments.

Bio-Functional Sperm Parameters: Does Age Matter?

The evaluation of biofunctional sperm parameters can explain some cases of idiopathic male infertility. Among these, sperm DNA fragmentation (fDNA) is the most studied biofunctional sperm parameter. Mitochondrial membrane potential (MMP) correlates positively with sperm motility, the evaluation of sperm apoptosis by flow cytometry allows us to identify a population of spermatozoa not recognizable at the optical microscopy and finally, lipid peroxidation (LP) and mitochondrial superoxide levels measurements are rational oxidative stress indices. Male age seems to affect sperm concentration and sperm fDNA. For these reasons, this study was undertaken to evaluate the correlation, if any, between male age and biofunctional sperm parameters evaluating their possible impact on fDNA. To accomplish this, MMP, degree of chromatin compactness, sperm apoptosis/vitality, fDNA, LP, and mitochondrial superoxide levels were evaluated by flow cytometry in a cohort of 874 men. A significant negative correlation was found between age and the percentage of alive spermatozoa (r = -0.75, p < 0.05). The percentage of spermatozoa with low MMP (L-MMP) correlated positively with the percentage of spermatozoa with abnormal chromatin compactness (r = 0.24, p < 0.05). Spermatozoa with abnormal chromatin compactness and L-MMP correlated negatively with the percentage of alive spermatozoa (r = 0.83, p < 0.05) and positively with spermatozoa with PS externalization (r = 0.13, p < 0.01). The percentage of alive spermatozoa correlated negatively with both the percentage of spermatozoa with PS externalization (r = 0.24, p < 0.01) and of the spermatozoa with fDNA (r = 0.10, p < 0.05). Spermatozoa with PS externalization correlated positively with the percentage of spermatozoa with fDNA (r = 0.09, p < 0.05). Spermatozoa with LP correlated positively with the percentage of spermatozoa with increased mitochondrial superoxide (r = 0.11, p < 0.01) In conclusion, these findings in a large number of men suggest that age, mitochondrial damage, and alteration of chromatin compactness could activate the apoptotic cascade which could result in an increased fDNA rate.

From Spermiogram to Bio-Functional Sperm Parameters: When and Why Request Them?

The aim of this experimental study was to evaluate whether infertile patients may benefit from the evaluation of bio-functional sperm parameters in addition to the conventional semen analysis. To accomplish this, we evaluated the correlation between conventional and bio-functional sperm parameters based on their percentile distribution in search of a potential threshold of these latter that associates with conventional sperm parameter abnormalities. The study was conducted on 577 unselected patients with infertility lasting at least 12 months. We identified cut-off values according to the median of the population for mitochondrial membrane potential (MMP), number of alive spermatozoa, and chromatin abnormality. High MMP (HMMP) (≥46.25%) was associated with sperm concentration, sperm count, progressive motility, and normal form. Low MMP (LMMP) (≥36.5%) was found to be associated with semen volume, sperm concentration, total sperm count, progressive motility, total motility, and normal form. The number of alive spermatozoa (≥71.7%) was associated with sperm concentration and progressive motility whereas abnormal chromatin compactness (≥21.10%) was associated with sperm concentration, total sperm count, and progressive motility. The data would suggest that, for every increase in the percentile category of sperm concentration, the risk of finding an HMMP≤46.25 is reduced by 0.4 and by 0.66 for a total sperm count. This risk is also reduced by 0.60 for every increase in the percentile category of sperm progressive motility and by 0.71 for total sperm motility. Each increment of percentile category of the following sperm parameter was followed by a decrease in the risk of finding an LMMP≤36.5: sperm concentration 1.66, total sperm count 1.28, sperm progressive motility 1.27, total sperm motility 1.76, and normal form 1.73. Lastly, the data showed that, for every increase in the percentile category of total sperm count, the risk of finding an abnormal chromatin compactness ≤21.10 is reduced by 1.25 (1.04–1.51, p < 0.05) and an increase of total sperm motility is associated with a reduced risk by 1.44 (1.12–1.85, p < 0.05). Results suggest a correlation between bio-functional and conventional sperm parameters that impact the sperm fertilizing potential. Therefore, the evaluation of bio-functional sperm parameters by flow cytometry may be useful to explain some cases of idiopathic male infertility.

Environment and Male Fertility: Effects of Benzo-α-Pyrene and Resveratrol on Human Sperm Function In Vitro

Lifestyle, cigarette smoking and environmental pollution have a negative impact on male fertility. Therefore, the aim of this study was to evaluate the in-vitro effects of benzo-α-pyrene (BaP) and aryl hydrocarbon receptor (AHR) agonists on motility and bio-functional sperm parameters. We further assessed whether resveratrol (RES), an AHR antagonist and antioxidant molecule, had any protective effect. To accomplish this, 30 normozoospermic, healthy, non-smoker men not exposed to BaP were enrolled. Spermatozoa of 15 men were incubated with increasing concentrations of BaP to evaluate its effect and to establish its dose response. Then, spermatozoa of the 15 other men were incubated with BaP (15 µM/mL), chosen according to the dose-response and/or RES to evaluate its antagonistic effects. The effects of both substances were evaluated after 3 h of incubation on total and progressive sperm motility and on the following bio-functional sperm parameters evaluated by flow cytometry: Degree of chromatin compactness, viability, phosphatidylserine externalization (PS), late apoptosis, mitochondrial membrane potential (MMP), DNA fragmentation, degree of lipoperoxidation (LP), and concentrations of mitochondrial superoxide anion. Benzo-α-pyrene decreased total and progressive sperm motility, impaired chromatin compactness, and increased sperm lipoperoxidation and mitochondrial superoxide anion levels. All these effects were statistically significant at the lowest concentration tested (15 µM/mL) and they were confirmed at the concentration of 45 µM/mL. In turn, RES was able to counteract the detrimental effects of BaP on sperm motility, abnormal chromatin compactness, lipid peroxidation, and mitochondrial superoxide. This study showed that BaP alters sperm motility and bio-functional sperm parameters and that RES exerts a protective effect on BaP-induced sperm damage.

Protamine composition of koala and wombat spermatozoa provides new insights into DNA stability following cryopreservation

To investigate differences in the post-thaw DNA stability of koala and wombat spermatozoa, protamine amino acid sequences were compared and it was found that there were three more arginine residues for the wombat. Koala and wombat spermatozoa, cryopreserved using identical protocols, were examined for changes in sperm DNA fragmentation (SDF) dynamics over 24h of post-thaw incubation. Following validation of a wombat sperm chromatin dispersion test, wombat DNA showed a rate of SDF that was 6-fold higher than for koala spermatozoa (P=0.038). Finally, we examined whether expected differences in chromatin compactness, associated with protamine sequence, had an effect on restriction site accessibility of sperm DNA. Thawed spermatozoa were exposed to Alu I and EcoR1 endonuclease restriction enzymes and the SDF dynamics were observed. Koala spermatozoa exposed to Alu I showed a greater rate of SDF (P=0.01), whereas wombat spermatozoa exposed to EcoR1 showed a greater rate of SDF (P=0.032). We conclude that restriction sites in these species are differentially present or exposed and potentially account for differences in SDF dynamics. Although differences in the arginine composition of protamine may explain relative differences in SDF following cryopreservation, they do not support the hypothesis that increased arginine composition increases DNA stability; rather, increased arginine composition in the wombat may reduce post-thaw chromatin swelling.

Előprogramozott gének

Cells feel good and carry on perfect functions when they contain the right types of proteins in the right concentration, at the right time and sites. There are mechanisms that ensure the right level of gene expression in the different cell types: the formation of protein molecules based on the DNA-encoded genetic information. Gene expression can also be regulated through the compactness of chromatin, i.e. the accessibility of the genes. The chromosomes are repositories of the genetic information – the sequence of base pairs – and also of the so-called epigenetic mechanisms that control gene expression through the regulation of chromatin compactness. The epigenetic mechanisms operate through DNA methylation and/or the regulation of chromatin compactness. The present overview takes a look into the phenomenon of epigenesis. It summarizes how genetic crosses reveal the involvement of epigenesis, explains its meaning and impact on life of the organisms. An understanding of epigenesis provides guidance to improve our life. Orv Hetil. 2017; 158(34): 1323–1330.

Relationship between Testicular Volume and Conventional or Nonconventional Sperm Parameters

Background. Reduced testicular volume (TV) (<12 cm3) is associated with lower testicular function. Several studies explored the conventional sperm parameters (concentration, motility, and morphology) and the endocrine function (gonadotropins and testosterone serum concentrations) in the patients with reduction of TV. No other parameters have been examined.Aim. This study aims at evaluating some biofunctional sperm parameters by flow cytometry in the semen of men with reduced TV compared with that of subjects with normal TV.Methods. 78 patients without primary scrotal disease were submitted to ultrasound evaluation of the testis. They were divided into two groups according to testicular volume: A Group, including 40 patients with normal testicular volume (TV > 15 cm3) and B Group, including 38 patients with reduced testicular volume (TV ≤ 12 cm3). All patients underwent serum hormone concentration, conventional and biofunctional (flow cytometry) sperm parameters evaluation.Results. With regard to biofunctional sperm parameters, all values (mitochondrial membrane potential, phosphatidylserine externalization, chromatin compactness, and DNA fragmentation) were strongly negatively correlated with testicular volume ().Conclusions. This study for the first time in the literature states that the biofunctional sperm parameters worsen and with near linear correlation, with decreasing testicular volume.

Heterochromatin heterogeneity in the holocentric X chromatin of Megoura viciae (Homoptera, Aphididae)

Holocentric chromosomes, prepared by spreading embryo cells obtained from Megoura viciae parthenogenetic females, have been C-banded, enzymatically digested in situ using the specific endonucleases DdeI (C↓TNAG), DraI (TTT↓AAA), Tru9I (TT↓AA), and CfoI (GCG↓C), and subsequently stained with Giemsa, DAPI, CMA3, and AgNO3. We observed that the X chromosome had the best defined banding patterns. In the M. viciae X chromosome there is a certain amount of heterogeneity in heterochromatic DNA composition. In fact, the GC-rich NOR-associated heterochromatin differs from other heterochromatic bands that are characterized by AT-rich DNAs. Our data also indicate that, in M. viciae holocentric chromosomes, all heterochromatic blocks are accessible to in situ enzyme attack, the only limit to the digestion being the presence or absence of recognition targets. This is an interesting point, since, in monocentric chromosomes, it is well known that in situ endonuclease digestion is heavily affected not only by DNA base composition but also by chromatin compactness that may limit enzyme accessibility to their specific targets. Key words : heterochromatin, holocentric chromosomes, aphids.