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Background: The three-dimensional configuration of the eukaryotic genome is an emerging area of research. Chromosome conformation capture outlined genome segregation into large scale A and B compartments corresponding mainly to transcriptionally active and repressive chromatin. It remains unknown how the compartmentalization of the genome changes in growing oocytes of animals with hypertranscriptional type of oogenesis. Such oocytes are characterized by highly elongated chromosomes, called lampbrush chromosomes, which acquire a typical chromomere-loop appearance, representing one of the classical model systems for exploring the structural and functional organization of chromatin domains. Results: Here, we compared the distribution of A/B compartments in chicken somatic cells with chromatin domains in lampbrush chromosomes. We found that in lampbrush chromosomes, the extended chromatin domains, restricted by compartment boundaries in somatic cells, disintegrate into individual chromomeres. Next, we performed FISH-mapping of the genomic loci, which belong to A or B chromatin compartments as well as to A/B compartment transition regions in embryonic fibroblasts on isolated lampbrush chromosomes. We found, that in chicken lampbrush chromosomes, clusters of dense compact chromomeres bearing short lateral loops and enriched with repressive epigenetic modifications generally correspond to constitutive B compartments in somatic cells. A compartments align with lampbrush chromosome segments with smaller, less compact chromomeres, longer lateral loops, and a higher transcriptional status. Clusters of small loose chromomeres with relatively long lateral loops show no obvious correspondence with either A or B compartment identity. Some genes belonging to facultative B (sub-) compartments can be tissue-specifically transcribed during oogenesis, forming distinct lateral loops. Conclusions: Here, we established a correspondence between the A/B compartments in somatic interphase nucleus and chromatin segments in giant lampbrush chromosomes from diplotene stage oocytes. The chromomere-loop structure of the genomic regions corresponding to interphase A and B compartments reveals the difference in how they are organized at the level of chromatin domains. The results obtained also suggest that gene-poor regions tend to be packed into chromomeres. [ABSTRACT FROM AUTHOR]

In the cell nuclei, various types of nuclear domains assemble as a result of transcriptional activity at specific chromosomal loci. Giant transcriptionally active lampbrush chromosomes, which form in oocyte nuclei of amphibians and birds enable the mapping of genomic sequences with high resolution and the visualization of individual transcription units. This makes avian and amphibian oocyte nuclei an advantageous model for studying locus-specific nuclear domains. We developed two strategies for identification and comprehensive analysis of the genomic loci involved in nuclear domain formation on lampbrush chromosomes. The first approach was based on the sequential FISH-mapping of BAC clones containing genomic DNA fragments with a known chromosomal position close to the locus of a nuclear domain. The second approach involved mechanical microdissection of the chromosomal region adjacent to the nuclear domain followed by the generation of FISH-probes and DNA sequencing. Furthermore, deciphering the DNA sequences from the dissected material by high throughput sequencing technologies and their mapping to the reference genome helps to identify the genomic region responsible for the formation of the nuclear domain. For those nuclear domains structured by nascent transcripts, identification of genomic loci of their formation is a crucial step in the identification of scaffold RNAs. [ABSTRACT FROM AUTHOR]

One of the most important sources of soil contamination with metals and metalloids is mining and processing of mined ores. Old tailing ponds and dumps affect the surrounding environment mainly by releasing potentially toxic trace elements, and thus contribute to contamination of the natural environment, including soils. The area of abandoned antimony deposit Čučma (eastern Slovakia) with unliquidated and unsecured mining wastes belongs to environmental burden, which should be monitored and eventually remediated. The main objective of this article was to (i) determine the basic physicochemical properties of mining soils at the former Čučma antimony deposit and total concentrations of selected trace elements with the emphasis on antimony (Sb) and arsenic (As), (ii) characterize mineralogy of these soils and (iii) evaluate the mobility of the two metalloids by means of extraction experiments with distilled water. The soils of the former antimony deposit Čučma showed a wide range of pH values (2.84 - 7.45 for a soil depth of 0 - 15 cm and 2.82 - 7.74 for a soil depth of 15 - 30 cm) and the organic carbon content varied from 0.13 wt. % to 19.1 wt. % with a median value of 3.67 wt. % in the soil surface layer, with a decrease to a median value of 1.21 wt. %. Total concentrations of the main contaminants Sb and As in the soils from 0 - 15 cm were in the range from 6.2 mg . kg-1 to 142 322 mg . kg-1 with a median of 433 mg . kg-1 and 16 - 2 253 mg . kg-1 with a median of 116 mg . kg-1, respectively, and significantly correlated with each other (R2 = 0.87 at p < 0.000 1). The indication (ID = 65 mg . kg-1 for As and 25 mg . kg-1 for Sb) and intervention (IT = 140 mg . kg-1 for As and 80 mg . kg-1 for Sb) criteria for industrial areas were exceeded in most soil samples and the median concentrations of Sb and As were far higher than their median concentrations within the soils of Slovakia (0.70 mg . kg-1 and 7.20 mg . kg-1 for Sb and As in A-horizon, respectively). Despite the high total concentrations of these metalloids in some soils irrespective of depth, the extractable proportions of Sb and As were low (median of 0.46 % and 0.50 % for Sb and 0.60 % and 0.70 % for As at soil depths of 0 - 15 cm and 15 - 30 cm, respectively). The low mobility of Sb and As has been interpreted as a result of their incorporation into stable secondary mineral phases under oxidizing conditions, in particular Fe-oxy-hydroxides and, in the case of Sb, also due to the formation of separate secondary mineral phases such as romeite (Ca2Sb2O7), cervantite (Sb2O4) and stibiconite [Sb3O6(OH)]. The presence of all these secondary solid phases in the investigated soils was confirmed by optical microscopy, X-ray diffraction and electron micro-probe analyses. Slightly higher mobility of As and Sb in soils from 15 - 30 cm depth than their mobility in soils from the top layer does not exclude the influence of organic matter on the release of these elements into natural waters. [ABSTRACT FROM AUTHOR]