Trisomies Reorganize Human 3D Genome.

Trisomy is the presence of one extra copy of an entire chromosome or its part in a cell nucleus. In humans, autosomal trisomies are associated with severe developmental abnormalities leading to embryonic lethality, miscarriage or pronounced deviations of various organs and systems at birth. Trisomies are characterized by alterations in gene expression level, not exclusively on the trisomic chromosome, but throughout the genome. Here, we applied the high-throughput chromosome conformation capture technique (Hi-C) to study chromatin 3D structure in human chorion cells carrying either additional chromosome 13 (Patau syndrome) or chromosome 16 and in cultured fibroblasts with extra chromosome 18 (Edwards syndrome). The presence of extra chromosomes results in systematic changes of contact frequencies between small and large chromosomes. Analyzing the behavior of individual chromosomes, we found that a limited number of chromosomes change their contact patterns stochastically in trisomic cells and that it could be associated with lamina-associated domains (LAD) and gene content. For trisomy 13 and 18, but not for trisomy 16, the proportion of compacted loci on a chromosome is correlated with LAD content. We also found that regions of the genome that become more compact in trisomic cells are enriched in housekeeping genes, indicating a possible decrease in chromatin accessibility and transcription level of these genes. These results provide a framework for understanding the mechanisms of pan-genome transcription dysregulation in trisomies in the context of chromatin spatial organization.

Domain Model of Eukaryotic Genome Organization: From DNA Loops Fixed on the Nuclear Matrix to TADs.

The article reviews the development of ideas on the domain organization of eukaryotic genome, with special attention on the studies of DNA loops anchored to the nuclear matrix and their role in the emergence of the modern model of eukaryotic genome spatial organization. Critical analysis of results demonstrating that topologically associated chromatin domains are structural-functional blocks of the genome supports the notion that these blocks are fundamentally different from domains whose existence was proposed by the domain hypothesis of eukaryotic genome organization formulated in the 1980s. Based on the discussed evidence, it is concluded that the model postulating that eukaryotic genome is built from uniformly organized structural-functional blocks has proven to be untenable.

Conservative and Atypical Ferritins of Sponges.

Ferritins comprise a conservative family of proteins found in all species and play an essential role in resistance to redox stress, immune response, and cell differentiation. Sponges (Porifera) are the oldest Metazoa that show unique plasticity and regenerative potential. Here, we characterize the ferritins of two cold-water sponges using proteomics, spectral microscopy, and bioinformatic analysis. The recently duplicated conservative HdF1a/b and atypical HdF2 genes were found in the Halisarca dujardini genome. Multiple related transcripts of HpF1 were identified in the Halichondria panicea transcriptome. Expression of HdF1a/b was much higher than that of HdF2 in all annual seasons and regulated differently during the sponge dissociation/reaggregation. The presence of the MRE and HRE motifs in the HdF1 and HdF2 promotor regions and the IRE motif in mRNAs of HdF1 and HpF indicates that sponge ferritins expression depends on the cellular iron and oxygen levels. The gel electrophoresis combined with specific staining and mass spectrometry confirmed the presence of ferric ions and ferritins in multi-subunit complexes. The 3D modeling predicts the iron-binding capacity of HdF1 and HpF1 at the ferroxidase center and the absence of iron-binding in atypical HdF2. Interestingly, atypical ferritins lacking iron-binding capacity were found in genomes of many invertebrate species. Their function deserves further research.

Hair Mineral and Trace Element Content in Children with Down's Syndrome.

The objective of the present study was to assess the level of minerals and trace elements in 40 children with Down's syndrome and 40 controls aged 1-2 years old. Hair mineral and trace element analysis was performed using inductively coupled plasma mass spectrometry. The obtained data demonstrate that hair levels of Mg, P, I, Cr, Si, Zn, and Pb in Down's syndrome patients exceeded the respective control values by 36, 36, 93, 57, 45, 28, and 54%, whereas hair mercury was more than twofold lower in children with Down's syndrome. The observed difference in the levels of trace elements was age-dependent. In particular, in 1-year-olds, major differences were observed for essential elements (Cr, Si, Zn), whereas in 2-year-olds-for toxic elements (Hg, Pb). At the same time, hair P levels in Down's syndrome patients were 14 and 35% higher at the age of 1 and 2 years in comparison to the respective controls. Multiple regression analysis demonstrated that a model incorporating all elements, being characterized by a significant group difference, accounted for 42.5% of status variability. At the same time, only hair phosphorus was significantly interrelated with Down's syndrome status (ß = 0.478; p < 0.001). Principal component analysis (PCA) used As, Ca, Cr, Fe, Hg, I, Mg, P, Pb, Se, Si, Sn, and Zn as predictors, with the resulting R2 = 0.559. The OPLS-DA models also separated between Down's and health control groups. Therefore, 1-2-year-old patients with Down's syndrome are characterized by significant alterations of mineral and trace element status.

Trace element levels are associated with neuroinflammatory markers in children with autistic spectrum disorder.

The objective of the present study was to estimate the association between brain inflammatory markers and serum trace element levels as assessed by inductively coupled plasma mass spectrometry at NexION 300D. Leukocyte elastase (LE), α1-proteinase inhibitor (α1-PI) activity, anti-nerve growth factor-antibodies (anti-NGF-Ab), and anti-myelin basic protein-antibodies (anti-MBP-Ab) levels were assessed as inflammatory markers. The obtained data demonstrate that the increase in LE and α1-PI activity is associated with higher serum Cr and Cu levels, respectively. The increase in Anti-NGF-Ab levels was associated with a nearly significant 16% increase in serum Mn levels. Autistic children with high MBP-Ab levels were characterized by 28% higher serum Mn and lower Mg concentration. The results of correlation analysis were generally in agreement with the outcome of group comparisons. Regression analysis demonstrated that serum Mg was significantly negatively associated with LE activity, whereas both serum Fe and V concentrations were characterized by a positive influence on the parameter. In turn, serum Cu was a significant predictor of α1-PI, as well as Cr levels. At the same time, the serum concentrations of Cd and Fe were found to be inversely associated with α1-PI levels. Serum Cd and Mn levels were significant positive predictors of anti-MBP-Ab levels, whereas Mg levels had a negative impact on anti-MBP-Ab values. Generally, the obtained data demonstrate the interrelationship between trace element homeostasis and neuroinflammation in autism. Hypothetically, modulation of trace element status may be used for reduction of neuroinflammatory response, although further studies are required to reveal the underlying mechanisms of the observed associations.

The Level of Toxic Elements in Edible Crops from Seleniferous Area (Punjab, India).

The primary objective of the present study was to assess the level of selenium and toxic trace elements in wheat, rice, maize, and mustard from seleniferous areas of Punjab, India. The content of selenium (Se) and toxic trace elements, including aluminum (Al), arsenic (As), cadmium (Cd), mercury (Hg), nickel (Ni), lead (Pb), and tin (Sn), in crop samples was assessed using inductively coupled plasma mass-spectrometry after microwave digestion of the samples. The obtained data demonstrate that cultivation of crops on seleniferous soils significantly increased Se level in wheat, mustard, rice, and maize by a factor of more than 590, 111, 85, and 64, respectively. The study also showed that Se exposure affected toxic metal content in crops. In particular, Se-rich wheat was characterized by a significant decrease in Al, As, Ni, Pb, and Sn levels. The level of As, Cd, Ni, Pb, and Sn was significantly decreased in Se-rich rice, whereas As content was increased. In turn, the decrease in Al, As, Cd, Ni, Pb, and Sn levels in Se-rich maize was associated with a significant elevation of Hg content. Finally, Se-rich mustard was characterized by a significant increase in Al, As, and Hg levels, while the content of Ni, Pb, and Sn was significantly lower than the control levels. These findings should be taken into account while developing the nutritional strategies for correction of Se status. At the same time, the exact mechanisms underlying the observed differences are to be estimated.

Comparative Hair Trace Element Profile in the Population of Sakhalin and Taiwan Pacific Islands.

The objective of the current study is to perform a comparative analysis of hair trace element content in 393 apparently healthy adults living in Taipei, Taiwan, Republic of China (94 women and 46 men) and Yuzhno-Sakhalinsk, Sakhalin, Russia (186 women and 67 men). The obtained data indicate that Yuzhno-Sakhalinsk inhabitants were characterized by significantly higher hair Co, Cr, Mn, and V levels, exceeding the respective Taipei values by a factor of 3, 2, 7, and 5, respectively (all p < 0.001). Hair Cu, Fe, and Si levels were also higher in examinees from Yuzhno-Sakhalinsk than those from Taipei by 10% (p = 0.001), 61% (p < 0.001), and 68% (p < 0.001), respectively. It is notable that the only essential element, being significantly higher (+ 30%; p < 0.001) in Taipei inhabitants, is selenium. Yuzhno-Sakhalinsk inhabitants were characterized by 60% higher levels of hair Sn, and nearly two- and threefold higher scalp hair content of Be and Cd in comparison to Taipei values, respectively (all p < 0.001). Oppositely, the examinees from Taipei had 14% (p = 0.040) and 47% (p = 0.001) higher levels of hair As and Hg as compared to Yuzhno-Sakhalinsk inhabitants. Further analysis demonstrated that men from both Yuzhno-Sakhalinsk and Taipei were characterized by significantly higher hair Mn, As, and Pb levels in comparison to women. The intensive development of heavy industry in Yuzhno-Sakhalinsk may result in increased metal emissions, whereas fish consumption may result in elevation of hair Hg, As, and Se levels in Taiwan inhabitants.