Variations in heterochromatin content reveal important polymorphisms for studies of genetic improvement in garlic (Allium sativum L.)

Allium sativum L. is an herb of the Alliaceae family with a specific taste and aroma and medicinal and nutraceutical properties that are widely marketed in several countries. Brazil is one of the largest importers of garlic in the world, despite of its production is restricted and limited to internal consumption. Thus, explore the genetic diversity of commercial garlic conserved at germplasm banks is essential to generate additional genetic information about its economically important crop. A suitable tool for this purpose is the cytogenetic characterisation of these accessions. This study aimed to characterise the cytogenetic diversity among seven accessions of garlic from a Germplasm Bank in Brazil. The karyotypes were obtained by conventional staining and with chromomycin A3 (CMA) and 4,6-diamidino-2-phenylindole (DAPI) fluorochromes. All accessions analysed showed chromosome number 2n = 16, karyotype formula 6M+2SM, symmetrical karyotypes, reticulate interphase nuclei, and chromosomes with uniform chromatin condensation from prophase to metaphase. The fluorochromes staining showed differences in the amount and distribution of heterochromatin along the chromosomes and between accessions studied. Based on the distribution pattern of these small polymorphisms, it was possible to separate the seven accessions into three groups. It was also possible to differentiate some of the accessions individually. One of the results obtained showed a heteromorphic distension of the nucleolar organiser region observed on the chromosome pairs 6 or 7 with peculiar characteristics. It was suggested for example, that the heteromorphic block of heterochromatin (CMA+++/DAPI-) on chromosome 6 of the “Branco Mineiro Piauí” accession can be used as a marker to identify this genotype or may be associated with some character of economic interest.

Chromosomal Rearrangements and Altered Nuclear Organization: Recent Mechanistic Models in Cancer

The last decade has seen significant progress in understanding how the genome is organized spatially within interphase nuclei. Recent analyses have confirmed earlier molecular cytogenetic studies on chromosome positioning within interphase nuclei and provided new information about the topologically associated domains (TADs). Examining the nuances of how genomes are organized within interphase nuclei will provide information fundamental to understanding gene regulation and expression in health and disease. Indeed, the radial spatial positioning of individual gene loci within nuclei has been associated with up- and down-regulation of specific genes, and disruption of normal genome organization within nuclei will result in compromised cellular health. In cancer cells, where reorganization of the nuclear architecture may occur in the presence of chromosomal rearrangements such as translocations, inversions, or deletions, gene repositioning can change their expression. To date, very few studies have focused on radial gene positioning and the correlation to gene expression in cancers. Further investigations would improve our understanding of the biological mechanisms at the basis of cancer and, in particular, in leukemia initiation and progression, especially in those cases where the molecular consequences of chromosomal rearrangements are still unclear. In this review, we summarize the main milestones in the field of genome organization in the nucleus and the alterations to this organization that can lead to cancer diseases.

Orcein and DAPI-stained karyotype analysis of Alocasia macrorrhizos (L.) G. Don

Karyotype analyses are required for the identification, characterization, and genetic improvement of any organism. Alocasia macrorrhizos (L.) G. Don. was investigated cytogenetically to determine the karyotypic features. Complex chromocenter type, of interphase nuclei, and gradient type of prophase chromosomes were found in this study. Alocasia macrorrhizos was found to possesses 2n=28 chromosomes. The total length of the 2n chromosome complement was recorded as 98.83±1.39 μm. The range of chromosomal length was 2.50±0.10-4.70±0.10 μm. A gradual decrease in chromosomal length was observed. The total form (TF%) value was found to be 43.58%, Karyotype symmetry index (Syi %) was 77.00 % and karyotype asymmetry index (AsK %) was 56.66%. The centromeric formula was 18m+4sm+2ac, representing asymmetric karyotype. In DAPI banding, the 1.48% positive banded region indicates the lower amount of AT rich repeats in this material. Therefore, Alocasia macrorrhizos could be authentically characterized through karyotype analysis. J. Bangladesh Acad. Sci. 45(1); 27-35: June 2021

Somatic chromosome number and ploidy level in three Curcuma spp. from Bangladesh

Three Curcuma L. species were investigated cytogenetically which represent diversed staining pattern of heterochromatins in interphase nuclei and prophase chromosomes with orcein staining. Curcuma longa and C. caesia were found to possess 2n = 3x = 63 somatic chromosomes whereas 2n = 2x = 42 chromosome number in C. zedoaria is reported for the first time from Bangladesh. Total chromosome length recorded in C. longa, C. caesia and C. zedoaria were 145.08 ± 2.85 μm, 164.93 ± 4.29 μm and 97.78 ± 2.41 μm, respectively. This was the first attempt to measure the length of the chromosomes for these species. The experiment confirmed the basic chromosome number x = 21 with triploid (C. longa, C. caesia) and diploid (C. zedoaria) Curcuma plants. Polyploidy could be employed in the evolution and diversification of the genus Curcuma, which is an essential factor to characterize the species of this genus. Dhaka Univ. J. Biol. Sci. 30(2): 133-140, 2021 (July)

Generation of dynamic three-dimensional genome structure through phase separation of chromatin

Three-dimensional genome organization plays a critical role in DNA function. Flexible chromatin structure suggested that the genome is phase-separated to form A/B compartments in interphase nuclei. Here, we examined this hypothesis by developing a polymer model of the whole genome of human cells and assessing the impact of phase separation on genome structure. Upon entry to the G1 phase, the simulated genome expanded according to heterogeneous repulsion among chromatin chains, which moved chromatin heterogeneously, inducing phase separation. This repulsion-driven phase separation quantitatively reproduces the experimentally observed chromatin domains, A/B compartments, lamina-associated domains, and nucleolus-associated domains, consistently explaining nuclei of different human cells and predicting their dynamic fluctuations. We propose that phase separation induced by heterogeneous repulsive interactions among chromatin chains largely determines dynamic genome organization.

Karyology of Some Coastal and Water Plants from Far East (Russia)

Cytogenetic studies on four species of vascular coastal and water plants from Russian Far East are presented. During the present investigation the next chromosome numbers have been revealed: Gypsophila pacifica (2 n = 34), Allium sacculiferum (2 n = 32), Mertensia maritima (2 n = 24), and Nelumbo komarovii (2 n = 16). Unusual chromosome numbers for these species have not been noted but it was the first case of karyological studies of Nelumbo komarovii from the Jewish Autonomous Region and most northern habitat. The number of nucleoli in interphase nuclei of these species was counted. Interphase nuclei of studied species contain 1–4 nucleoli except in A. sacculiferum so far which have 1–2 nucleoli per cell. Different points of view on polyploidy of studied species are discussed.

Dynamic nuclear lamina-chromatin interactions during G1 progression

A large fraction of heterochromatin in the metazoan genome is associated with the nuclear lamina (NL) in interphase nuclei. This heterochromatin is often referred to as Lamina-Associated Domains (LADs) and are often mapped from cell populations asynchronously progressing through the cell cycle. We and others have recently reported that LADs are largely stable during G1, S, or G2 phases of the cell cycle, and appear similar to LADs mapped from bulk cell populations. LADs in senescent cells, however, are reported to be quite different from proliferating cells, and it remains unclear how senescent cell LADs are established. As cells finish mitosis and re-enter G1, reassembly of the nuclear envelope and NL appears to precede mitotic chromosome decondensation. Therefore, the initial NL interactions with the decondensing chromatin may be quite different from those reported in asynchronous or FACS isolated G1, S, or G2 populations. By developing a modified version of the Tyramide-Signal Amplification sequencing (TSA-seq), which we call chromatin pull down-based Tyramide Signal Amplification-sequencing (cTSA-seq), we uncover a dynamic NL-chromatin interaction as cells progress through G1. The appearance of stable LADs coincides with sufficient chromatin decondensation and active gene expression in G1. Interestingly, early G1 NL-chromatin interactions, which are found toward the telomeric ends of human chromosomes, are similar to those found in oncogene-induced senescent cells. We find that the assembly of LADs during the formation of the G1 nucleus is gradual and that the arrest of NL-chromatin interactions in early G1 may contribute to genome disorganization of senescence cells.

Karyotypic diversity among eight Zea mays L. varieties

Staining property of interphase nuclei and prophase chromosomes, diploid chromosome number, total chromosome length (TCL), symmetric and asymmetric indices of karyotype were studied in eight maize varieties released by BARI. 2n = 20 chromosomes were found in Barnali, Mohor, Khoi Vhutta, BS-1, B-5 and BM-7 whereas 2n = 22 chromosomes in China and 2n = 24 chromosomes in B-73 were observed. TCL was highest in Mohor (190.49 ± 5.61 μm) and lowest in B-73 (69.30 ± 2.51 μm). These varieties showed significant variation in cytogenetical parameters. Results obtained are expected to supplement genetic identification of maize varieties in variety conservation efforts.

Monochorionic diamniotic twin with a Down syndrome in one of the fetuses

A clinical observation of monochorionic diamniotic twins with discordance of cytogenetic and clinical manifestations of Down syndrome is presented. Pregnancy was complicated by feto-fetal transfusion syndrome at 17 weeks of gestation. An ultrasound scan revealed a ventriculomegaly in a donor. Laser coagulation of anastomoses was performed. Karyotype 46, XY was established in the recipient amniocytes. The pregnancy ended in childbirth at 33 weeks with newborn boys weighing 1789 and 2080g. One of the newborns (donor) had phenotypic signs of Down syndrome. When karyotyping peripheral blood lymphocytes of a child with clinical manifestations of Down syndrome, karyotype mos 47,XY,+21[12]/46,XY [88] was established, and a child with a normal phenotype was mos 47,XY,+21[14]/46,XY [86]. No malformations of internal organs were found. When analyzing the buccal epithelium by the FISH method, it was found that in all the analyzed interphase nuclei obtained from a child without clinical manifestations (recipient fetus), trisomy 21 was not detected. In 78% of the interphase nuclei of cells of a child with Down syndrome (fetus-donor), trisomy 21 was established. Thus, the presence of a clone of cells with trisomy 21 in the recipient is associated with twin chimerism.

Implementation of Novel Mode for Evaluation of MYCN Amplification that can Predict Outcome in Patients with Neuroblastoma

Background: Neuroblastoma tumorigenesis is a cascading process where several cytogenetic findings can be detected MYCN oncogene is a potent transcription factor that controls main cell functions. Several genetic methods can be applied in order to detect quantity of amplified MYCN oncogene. The purpose of this study is to improve the technique of determining the amplification of the MYCN oncogene in each evaluated tumor cell. Results: Standard G banded karyotype and fluorescence in-situ hybridization (FISH) on interphase nuclei using N-MYC amplification probe was performed in five patients with different clinical presentation of neuroblastoma. Both bone marrow and tumor tissue were analysed in four and in one patient only tumor tissue. Follow up study was performed in order to obtain additional prognostic information. Additional grading system was implemented to obtain MYCN amplification status. Significant amount of amplified units was detected in two patients with adverse outcome, which was not the case in other three patients who had minor or none amplification of MYCN. Furthermore, there were no cells with significant MYCN amplification in more than 30% of the cell surface in patient three and four that represented a good prognostic factor for their survival. Conclusion: Our study confirmed that patients with both chromosomal changes and significant MYCN amplification are characterized with aggressive clinical course. Accuracy in quantifying the amount of MYCN amplification is crucial in planning the therapeutic approach. FISH is proved to be rapid, sensitive, and reliable method for detection of MYCN oncogene amplification in routinely processed samples.