Distribution Of Heterochromatin Research Articles

New Cytogenetic Data for the Neottieae Tribe (Orchidaceae) in the Mediterranean Region.

This work presents a summary of cytogenetic data, including new information, on several species within the tribe Neottieae, with an update of the karyotype for 23 species belonging to the genera Cephalanthera, Limodorum, Epipactis, and Neottia (including Listera). Each of these four genera also presents distinctive chromosomal features, such as bimodal karyotypes. Our research includes insights into the distribution of constitutive heterochromatin, measured using C-banding and, in some cases, specific fluorochromes for the detection of A-T- and G-C-rich DNA. In the Epipactis group, it is noteworthy that when using the Giemsa banding technique, certain species (e.g., E. placentina, E. meridionalis) with a chromosome number of 2n = 38 were observed to exhibit a conspicuous wide band of constitutive heterochromatin on the long arm of the third pair in a subcentromeric position, resembling what has been observed in E. helleborine. These differences also have the potential to contribute to the diversification of these species. Based on the karyological results obtained, a hypothesis regarding the origin of certain species within the E. helleborine group is proposed. Additionally, karyological analyses conducted on a specimen of E. microphylla revealed chromosome counts ranging from 36 to 40. Somatic metaphases exhibited evident structural alterations in certain chromosomes, showing rearrangements probably caused by translocation phenomena. Based on the data obtained from the species within the studied genera, it is conceivable that variations in chromosomes, both structurally and in the distribution of constitutive heterochromatin, exert a significant influence on the evolution of the karyotype. Moreover, in many entities belonging to the Neottieae tribe, these processes may also contribute to the diversification of the phenotype in some instances.

Comparative Cytogenetics in Tyrannidae (Aves, Passeriformes): High Genetic Diversity despite Conserved Karyotype Organization

Introduction: Passeriformes has the greatest species diversity among Neoaves, and the Tyrannidae is the richest in this order with about 600 valid species. The diploid number of this family remains constant, ranging from 2n = 76 to 84, but the chromosomal morphology varies, indicating the occurrence of different chromosomal rearrangements. Cytogenetic studies of the Tyrannidae remain limited, with approximately 20 species having been karyotyped thus far. This study aimed to describe the karyotypes of two species from this family, Myiopagis viridicata and Sirystes sibilator. Methods: Skin biopsies were taken from each individual to establish fibroblast cell cultures and to obtain chromosomal preparations using the standard methodology. The chromosomal distribution of constitutive heterochromatin was investigated by C-banding, while the location of simple repetitive sequences (SSRs), 18S rDNA, and telomeric sequences was found through fluorescence in situ hybridization. Results: The karyotypes of both species are composed of 2n = 80. The 18S rDNA probes hybridized into two pairs of microchromosomes in M. viridicata, but only a single pair in S. sibilator. Only the telomeric portions of each chromosome in both species were hybridized by the telomere sequence probes. Most of the SSRs were found accumulated in the centromeric and telomeric regions of several macro- and microchromosomes in both species, which likely correspond to the heterochromatin-rich regions. Conclusion: Although both species analyzed showed a conserved karyotype organization (2n = 80), our study revealed significant differences in their chromosomal architecture, rDNA distribution, and SSR accumulation. These findings were discussed in the context of the evolution of Tyrannidae karyotypes.

Advances in the Study of Orchidinae Subtribe (Orchidaceae) Species with 40,42-Chromosomes in the Mediterranean Region

This study presents an updated analysis of cytogenetic data for several species within the 40,42-chromosome genera of the subtribe Orchidinae. The research includes insights into the distribution of heterochromatin obtained using C-banding and fluorochrome techniques. Our investigation confirmed variation in the distribution of heterochromatin and repetitive DNA sequences among species pertaining to Neotinea s.l. and Orchis s.str. These variations also potentially contribute to the diversification of these species. Cytogenetic analyses of the Neotinea group demonstrated that both H33258 and DAPI staining result in blocks of fluorescent regions on numerous chromosomes. Particular attention was paid to the cytological composition of the polyploid Neotinea commutata, focusing on its potential origin. Based on the karyological results acquired, a hypothesis concerning the origin of N. commutata is proposed. The most noteworthy revelations regard the O. mascula complex. In these species, the telomeric areas of all chromosome sets display extensive heterochromatin. Fluorochrome staining revealed telomeric blocks on many chromosomes that were not seen with Giemsa staining. This highlighted a distinct feature of O. mascula, where particularly large C-bands surrounding the centromeric regions of multiple chromosomes were found. However, in O. mascula, O. provincialis, O. pauciflora, and O. patens, C+ chromatin may not show a significant response to fluorochrome Hoechst or DAPI+ staining. The unique cytomorphological arrangement observed in the O. mascula species, unlike other members of the O. mascula complex, suggest epigenetic phenomena. Additional data are presented for the genera Dactylorhiza and Gymnadenia. A deeper understanding of the diversity of chromosomal structures among these orchids promises to shed light on the mechanisms underlying speciation, adaptation, and the remarkable diversity characteristic of the Orchidaceae family.

Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes

Abstract Karyotype divergence may strongly affect the degree of hybridization between species. Western Palearctic slow worms (Anguis) are legless lizards forming different types of secondary contact zones. To identify the level of chromosomal variation in slow worms, we examined karyotype in multiple populations of all species except one and Pseudopus apodus as an outgroup. We applied conventional and molecular cytogenetic methods and whole-chromosome painting using macrochromosome probes from Varanus komodoensis to interpret results within the evolutionary framework of the common clade Anguiformes. All Anguis species and P. apodus have conserved karyotype structures composed of 44 chromosomes. Despite the conserved chromosome morphology, the phylogenetically oldest Anguis cephallonica living in partial sympatry with Anguis graeca, and parapatric Anguis colchica vs. Anguis fragilis exhibit distinct patterns of constitutive heterochromatin distribution and telomeric repeat accumulation. In contrast, the sister species A. colchica and A. graeca living in allopatry display highly similar karyotype features. Our findings thus indicate karyotype stasis in Anguis and Pseudopus for > 20 Myr, with fixed species-specific differences present in sympatric and parapatric species. These differences in repetitive DNA patterns may play a role as intrinsic factors co-maintaining species divergence. They may also be used as cytotaxonomic markers to identify slow worm species in practice.

Survival, growth and digestive functions after exposure to nanodiamonds - Transgenerational effects beyond contact time in house cricket strains

The long-term exposure effects of nanodiamonds (NDs), spanning an organism's entire lifespan and continuing for subsequent generation, remain understudied. Most research has focused on evaluating their biological impacts on cell lines and selected organisms, typically over short exposure durations lasting hours or days. The study aimed to assess growth, mortality, and digestive functions in wild (H) and long-lived (D) strains of Acheta domesticus (Insecta: Orthoptera) after two-generational exposure to NDs in concentrations of 0.2 or 2 mg kg−1 of food, followed by their elimination in the third generation. NDs induced subtle stimulating effect that depended on the strain and generation. In the first generation, more such responses occurred in the H than in the D strain. In the first generation of H strain insects, contact with NDs increased survival, stimulated the growth of young larvae, and the activity of most digestive enzymes in mature adults. The same doses and exposure time did not cause similar effects in the D strain. In the first generation of D strain insects, survival and growth were unaffected by NDs, whereas, in the second generation, significant stimulation of those parameters was visible. Selection towards longevity appears to support higher resistance of the insects to exposure to additional stressor, at least in the first generation. The cessation of ND exposure in the third generation caused potentially harmful changes, which included, e.g., decreased survival probability in H strain insects, slowed growth of both strains, as well as changes in heterochromatin density and distribution in nuclei of the gut cells in both strains. Such a reaction may suggest the involvement of epigenetic inheritance mechanisms, which may become inadequate after the stress factor is removed.

C-banding characterization of centric fusion and heterochromatin polymorphisms in the water-hyacinth grasshopper, Cornops aquaticum (Orthoptera: Acrididae)

Abstract The water-hyacinth grasshopper, Cornops aquaticum (Orthoptera: Acrididae), shows a clinal variation for 3 Robertsonian translocation (centric fusion) polymorphisms in the southern extreme of its wide geographical distribution. It is a Neotropical semiaquatic grasshopper that lives, feeds, and lays eggs exclusively on floating plants of the family Pontederiaceae, or water-hyacinths, between 23° N (Southern Mexico) and 35° S (Central Argentina and Uruguay). Given the invasive-species status of Pontederia (formerly Eichhornia) crassipes and the voraciousness of these grasshoppers, they were considered as a potential biological control agent in addition to other natural enemies. We already described the association of the rearrangements with geographical and climatic variables, phenotypic variation, trivalent orientation, effects on recombination, and relationship with microsatellite variability. Here we analyze the distribution of constitutive heterochromatin in 2 populations of C. aquaticum in order to (i) provide consistent markers for a better distinction between all chromosomes, those which are involved in the centric fusions, and those which are not, and (ii) describe possible polymorphisms for C-positive supernumerary segments, given that, on conventional staining analysis, it was frequent to find heteromorphic autosomal bivalents. The cytogenetic analysis allowed us to get a detailed characterization of the constitutive heterochromatin distribution, providing unmistakable chromosome markers of the large, fusion-bearing chromosomes as well as the C-positive, polymorphic supernumerary segments.

TET2 modulates spatial relocalization of heterochromatin in aged hematopoietic stem and progenitor cells.

DNA methylation deregulation at partially methylated domains (PMDs) represents an epigenetic signature of aging and cancer, yet the underlying molecular basis and resulting biological consequences remain unresolved. We report herein a mechanistic link between disrupted DNA methylation at PMDs and the spatial relocalization of H3K9me3-marked heterochromatin in aged hematopoietic stem and progenitor cells (HSPCs) or those with impaired DNA methylation. We uncover that TET2 modulates the spatial redistribution of H3K9me3-marked heterochromatin to mediate the upregulation of endogenous retroviruses (ERVs) and interferon-stimulated genes (ISGs), hence contributing to functional decline of aged HSPCs. TET2-deficient HSPCs retain perinuclear distribution of heterochromatin and exhibit age-related clonal expansion. Reverse transcriptase inhibitors suppress ERVs and ISGs expression, thereby restoring age-related defects in aged HSPCs. Collectively, our findings deepen the understanding of the functional interplay between DNA methylation and histone modifications, which is vital for maintaining heterochromatin function and safeguarding genome stability in stem cells.

Cell nucleus elastography with the adjoint-based inverse solver

Background and objectivesThe mechanics of the nucleus depends on cellular structures and architecture, and impact a number of diseases. Nuclear mechanics is yet rather complex due to heterogeneous distribution of dense heterochromatin and loose euchromatin domains, giving rise to spatially variable stiffness properties. MethodsIn this study, we propose to use the adjoint-based inverse solver to identify for the first time the nonhomogeneous elastic property distribution of the nucleus. Inputs of the inverse solver are deformation fields measured with microscopic imaging in contracting cardiomyocytes. ResultsThe feasibility of the proposed method is first demonstrated using simulated data. Results indicate accurate identification of the assumed heterochromatin region, with a maximum relative error of less than 5%. We also investigate the influence of unknown Poisson's ratio on the reconstruction and find that variations of the Poisson's ratio in the range [0.3–0.5] result in uncertainties of less than 15% in the identified stiffness. Finally, we apply the inverse solver on actual deformation fields acquired within the nuclei of two cardiomyocytes. The obtained results are in good agreement with the density maps obtained from microscopy images. ConclusionsOverall, the proposed approach shows great potential for nuclear elastography, with promising value for emerging fields of mechanobiology and mechanogenetics.

Chromosome Diversity and Evolution of the Endemic Malagasy Velvet Geckos of the Genus Blaesodactylus (Reptilia, Gekkonidae).

We performed a molecular and phylogenetic analysis and a comparative cytogenetic study with standard karyotyping, silver staining (Ag-NOR) and sequential C-banding + Giemsa, + fluorochromes on several Blaesodactylus samples. The phylogenetic inference retrieved two main clades, the first comprises B. victori, B. microtuberculatus and B. boivini, while the second includes B. sakalava, B. antongilensis and B. ambonihazo. The available samples of B. sakalava form two different clades (here named B. sakalava clade A and clade B), which probably deserve a taxonomic re-evaluation. We found a karyological variability in Blaesodactylus in terms of chromosome number (2n = 40-42), morphology, location of NORs, and heterochromatin distribution pattern. Blaesodactylus antongilensis and B. sakalava clade A and B showed a karyotype of 2n = 40 mostly telocentric chromosomes. Pairs 1 and 6 were metacentric in B. sakalava clade A and B, while pair 1 was composed of subtelocentric/submetacentric elements in B. antongilensis. In contrast, B. boivini displayed a karyotype with 2n = 42 only telocentric chromosomes. NORs were on the first chromosome pair in B. boivini, and on the second pair in B. antongilensis. Adding our data to those available from the literature on evolutionarily related species, we highlight that the chromosome diversification in the genus probably proceeded towards a progressive reduction in the chromosome number and the formation of metacentric elements.

Cytogenetic characterization and karyotype evolution in six Macroptilium species (Leguminosae).

Macroptilium (Benth.) Urb. is a neotropical legume genus from the subtribe Phaseolinae. The investigated species present a stable chromosome number (2n=22), but differ in their karyotype formulae, suggesting the presence of chromosome rearrangements. In this work, we comparatively analysed the karyotypes of six species (Macroptilium atropurpureum, Macroptilium bracteatum, Macroptilium erythroloma, Macroptilium gracile, Macroptilium lathyroides, and Macroptilium martii) from the two main clades that form the genus. Heterochromatin distribution was investigated with chromomycin A3 (CMA)/4',6-diamidino-2-phenylindole (DAPI) staining and fluorescent in situ hybridization was used to localize the 5S and 35S ribosomal DNA (rDNA) sites. Single copy bacterial artificial chromosomes (BACs) previously mapped in the related genera Phaseolus L. and Vigna Savi were used to establish chromosome orthologies and to investigate possible rearrangements among species. CMA+/DAPI- bands were observed, mostly associated with rDNA sites. Additional weak, pericentromeric bands were observed on several chromosomes. Although karyotypes were similar, species could be differentiated mainly by the number and position of the 5S and 35S rDNA sites. BAC markers demonstrated conserved synteny of the main rDNA sites on orthologous chromosomes 6 and 10, as previously observed for Phaseolus and Vigna. The karyotypes of the six species could be differentiated, shedding light on its karyotype evolution.

Plasmodium falciparum gametocytes display global chromatin remodelling during sexual differentiation

BackgroundThe protozoan malaria parasite Plasmodium falciparum has a complex life cycle during which it needs to differentiate into multiple morphologically distinct life forms. A key process for transmission of the disease is the development of male and female gametocytes in the human blood, yet the mechanisms determining sexual dimorphism in these haploid, genetically identical sexual precursor cells remain largely unknown. To understand the epigenetic program underlying the differentiation of male and female gametocytes, we separated the two sexual forms by flow cytometry and performed RNAseq as well as comprehensive ChIPseq profiling of several histone variants and modifications.ResultsWe show that in female gametocytes the chromatin landscape is globally remodelled with respect to genome-wide patterns and combinatorial usage of histone variants and histone modifications. We identified sex specific differences in heterochromatin distribution, implicating exported proteins and ncRNAs in sex determination. Specifically in female gametocytes, the histone variants H2A.Z/H2B.Z were highly enriched in H3K9me3-associated heterochromatin. H3K27ac occupancy correlated with stage-specific gene expression, but in contrast to asexual parasites this was unlinked to H3K4me3 co-occupancy at promoters in female gametocytes.ConclusionsCollectively, we defined novel combinatorial chromatin states differentially organising the genome in gametocytes and asexual parasites and unravelled fundamental, sex-specific differences in the epigenetic code. Our chromatin maps represent an important resource for future understanding of the mechanisms driving sexual differentiation in P. falciparum.

Analysis in Proceratophrys boiei genome illuminates the satellite DNA content in a frog from the Brazilian Atlantic forest.

Satellite DNAs (satDNAs) are one of the most abundant elements in genomes. Characterized as tandemly organized sequences that can be amplified into multiple copies, mainly in heterochromatic regions. The frog P. boiei (2n = 22, ZZ♂/ZW♀) is found in the Brazilian Atlantic forest and has an atypical pattern of heterochromatin distribution when compared to other anuran amphibians, with large pericentromeric blocks on all chromosomes. In addition, females of Proceratophrys boiei have a metacentric sex chromosome W showing heterochromatin in all chromosomal extension. In this work, we performed high-throughput genomic, bioinformatic, and cytogenetic analyses to characterize the satellite DNA content (satellitome) in P. boiei, mainly due to high amount of C-positive heterochromatin and the highly heterochromatic W sex chromosome. After all the analyses, it is remarkable that the satellitome of P. boiei is composed of a high number of satDNA families (226), making P. boiei the frog species with the highest number of satellites described so far. Consistent with the observation of large centromeric C-positive heterochromatin blocks, the genome of P. boiei is enriched with high copy number of repetitive DNAs, with total satDNA abundance comprising 16.87% of the genome. We successfully mapped via Fluorescence in situ hybridization the two most abundant repeats in the genome, PboSat01-176 and PboSat02-192, highlighting the presence of certain satDNAs sequences in strategic chromosomal regions (e.g., centromere and pericentromeric region), which leads to their participation in crucial processes for genomic organization and maintenance. Our study reveals a great diversity of satellite repeats that are driving genomic organization in this frog species. The characterization and approaches regarding satDNAs in this species of frog allowed the confirmation of some insights from satellite biology and a possible relationship with the evolution of sex chromosomes, especially in anuran amphibians, including P. boiei, for which data were not available.

Cytotaxonomy and Molecular Analyses of Mycteria americana (Ciconiidae: Ciconiiformes): Insights on Stork Phylogeny.

Although molecular information for the wood stork (Mycteria americana) has been well described, data concerning their karyotypical organization and phylogenetic relationships with other storks are still scarce. Thus, we aimed to analyze the chromosomal organization and diversification of M. americana, and provide evolutionary insights based on phylogenetic data of Ciconiidae. For this, we applied both classical and molecular cytogenetic techniques to define the pattern of distribution of heterochromatic blocks and their chromosomal homology with Gallus gallus (GGA). Maximum likelihood analyses and Bayesian inferences (680 bp COI and 1007 bp Cytb genes) were used to determine their phylogenetic relationship with other storks. The results confirmed 2n = 72, and the heterochromatin distribution pattern was restricted to centromeric regions of the chromosomes. FISH experiments identified fusion and fission events involving chromosomes homologous to GGA macrochromosome pairs, some of which were previously found in other species of Ciconiidae, possibly corresponding to synapomorphies for the group. Phylogenetic analyses resulted in a tree that recovered only Ciconinii as a monophyletic group, while Mycteriini and Leptoptlini tribes were configured as paraphyletic clades. In addition, the association between phylogenetic and cytogenetic data corroborates the hypothesis of a reduction in the diploid number throughout the evolution of Ciconiidae.

New insights in Progerin-induced modifications of chromatin landscapes.

Genome structure, expression, and regulation are crucial in maintaining the physiological state of any cell. However, even a single variation in one of these processes can induce genomic instability, leading to different pathologies, including aging and cancer. Our work focuses on a particular model for of laminopathies disease, Hutchinson Gilford Progeria Syndrome, HGPS. HGPS is a genetic disorder in which patients show aging-related symptoms in the first years of their lives. HPGS is caused by a mutation in the Lamin A gene, LMNA, that causes the permanent anchoring of the mutated protein, named Progerin, to the nuclear membrane. This permanent bond causes abnormal tractions leading to a crumpled nuclear morphology that affects chromatin organization, inducing alteration in replication, transcription, and DNA repair. Indeed, one single point mutation in the LMNA gene results in massive damage to many cellular processes. Here, we exploit Structured Illumination microscopy, SIM, to investigate altered heterochromatin distribution in HGPS-model and compare the results with the control cell line. In particular, we explore how Progerin affects facultative heterochromatin organization in the proximity of the Nuclear Pore Complex, NUP, at the nuclear lamina level. To this aim, we perform multicolor SIM of DNA, Progerin or lamin (respectively HGPS or control), facultative heterochromatin (tagging histone H3K9me2) and NUP. Then, we combine SIM with Image Cross-Correlation Spectroscopy analysis, ICCS, to evaluate the differences in distances between NUP and H3K9me2. Our approach enables the visualization of Progerin-induced alterations of chromatin nanoscale organization at the single-cell level and will hopefully lead to a deeper understanding of the molecular mechanisms associated with HGPS development.

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.

First constitutive heterochromatin characterization and Karyotype of white stork Ciconia ciconia (Aves: Ciconiidae).

The karyotype and constitutive heterochromatin pattern of the white stork Ciconia ciconia samples obtained from Manzala lake, Dimiaat, Egypt was described. Somatic cells of Ciconia ciconia samples have diploid number 2n= 68 chromosomes. Out of 68 chromosomes, 11 pairs including sex chromosomes were macrochromosomes and the remaining pairs were microchromosomes. Of the 11 macrochromosome pairs, no.1, 2, 4 and 5 were submetacentric and pairs no. 6, 7 and 8 were described as metacentric. In addition, the autosome pair no.3 was subtelocentric, while autosome pair no.9 was acrocentric. Also, the sex chromosome Z represents the fourth one in size and it was classified as submetacentric while, W chromosome appeared as medium size and was acrocentric. Furthermore, C-banding pattern (constitutive heterochromatin) revealed variation in their sizes and occurrence between macrochromosomes. Pairs no. 7 and 8 of autosomes exhibited unusual distribution of heterochromatin, where they appeared as entirely heterochromatic. This may be related to the origin of sex chromosomes Z and W. However, there is no sufficient evidence illustrate the appearance of entirely heterochromatic autosomes. Therefore, there is no available cytogenetic literature that describes the C-banding and karyotype of Ciconia Ciconia, so the results herein are important and may assist in cytogenetic study and evolutionary pattern of Ciconiiformes.

Cytogenetic Characteristics of Gerbillus dasyurus and Meriones tristrami (Rodentia: Gerbillinae) from Kilis, Turkey: Conventional and C Banded Karyotypes

In this study, diploid chromosome number and constitutive heterochromatin distributions of chromosomes were determined in Gerbillus dasyurus and Meriones tristrami species. The diploid chromosome numbers (2n) and autosomal chromosome arms (NFa) of G. dasyurus and M. tristrami were determined as 2n=60, NFa= 68, and 2n=72, NFa= 73, respectively. It was found that there were differences in autosomal chromosomal arms (NFa) of two different gerbil species, the karyotypes of which were obtained in this study, compared to previously conducted studies in Türkiye. Heteromorphic chromosome pair (submetacentric/acrocentric) was found in the autosomal set of M. tristrami. There was an enlarged heterochromatin block on the short arm of submetacentric chromosome in heteromorphic chromosome pair.

Patterns of Heterochromatin Transitions Linked to Changes in the Expression of Plasmodium falciparum Clonally Variant Genes.

The survival of malaria parasites in the changing human blood environment largely depends on their ability to alter gene expression by epigenetic mechanisms. The active state of Plasmodium falciparum clonally variant genes (CVGs) is associated with euchromatin characterized by the histone mark H3K9ac, whereas the silenced state is characterized by H3K9me3-based heterochromatin. Expression switches are linked to euchromatin-heterochromatin transitions, but these transitions have not been characterized for the majority of CVGs. To define the heterochromatin distribution patterns associated with the alternative transcriptional states of CVGs, we compared H3K9me3 occupancy at a genome-wide level among several parasite subclones of the same genetic background that differed in the transcriptional state of many CVGs. We found that de novo heterochromatin formation or the complete disruption of a heterochromatin domain is a relatively rare event, and for the majority of CVGs, expression switches can be explained by the expansion or retraction of heterochromatin domains. We identified different modalities of heterochromatin changes linked to transcriptional differences, but despite this complexity, heterochromatin distribution patterns generally enable the prediction of the transcriptional state of specific CVGs. We also found that in some subclones, several var genes were simultaneously in an active state. Furthermore, the heterochromatin levels in the putative regulatory region of the gdv1 antisense noncoding RNA, a regulator of sexual commitment, varied between parasite lines with different sexual conversion rates. IMPORTANCE The malaria parasite P. falciparum is responsible for more than half a million deaths every year. P. falciparum clonally variant genes (CVGs) mediate fundamental host-parasite interactions and play a key role in parasite adaptation to fluctuations in the conditions of the human host. The expression of CVGs is regulated at the epigenetic level by changes in the distribution of a type of chromatin called heterochromatin. Here, we describe at a genome-wide level the changes in the heterochromatin distribution associated with the different transcriptional states of CVGs. Our results also reveal a likely role for heterochromatin at a particular locus in determining the parasite investment in transmission to mosquitoes. Additionally, this data set will enable the prediction of the transcriptional state of CVGs from epigenomic data, which is important for the study of parasite adaptation to the conditions of the host in natural malaria infections.

Dynamic Heterochromatin States in Anisotropic Nuclei of Cells on Aligned Nanofibers.

The cancer cell nucleus deforms as it invades the interstitial spaces in tissues and the tumor microenvironment. While alteration of the chromatin structure in a deformed nucleus is expected and documented, the chromatin structure in the nuclei of cells on aligned matrices has not been elucidated. In this work we elucidate the spatiotemporal organization of heterochromatin in the elongated nuclei of cells on aligned nanofibers with stimulated emission depletion nanoscopy and fluorescence correlation spectroscopy. We show that the anisotropy of nuclei is sufficient to drive H3K9me3-heterochromatin alterations, with enhanced H3K9me3 nanocluster compaction and aggregation states that otherwise are indistinguishable from diffraction-limited microscopy. We interrogated the higher-order heterochromatin structures within major chromatin compartments in anisotropic nuclei and discovered a wider spatial dispersion of nanodomain clusters in the nucleoplasm and condensed larger nanoclusters near the periphery and pericentromeric heterochromatin. Upon examining the spatiotemporal dynamics of heterochromatin in anisotropic nuclei, we observed reduced mobility of the constitutive heterochromatin mark H3K9me3 and the associated heterochromatin protein 1 (HP1α) at the nucleoplasm and periphery regions, correlating with increased viscosity and changes in gene expression. Since heterochromatin remodeling is crucial to genome integrity, our results reveal an unconventional H3K9me3 heterochromatin distribution, providing cues to an altered chromatin state due to perturbations of the nuclei in aligned fiber configurations.

Topotype-Based Chromosomal Diversity among Five Species of Freshwater Armored Catfishes in the Hypostomus auroguttatus Supergroup (Actinopterygii: Siluriformes).

Freshwater catfishes from the genus Hypostomus have been models for several cytogenetic studies, due to their intense variability in diploid number, chromosome morphology, and the distribution of repetitive DNAs. Taking into consideration the taxonomic complexity inherent to this group, the present study aims to describe the karyotypes of five species of Hypostomus collected in their type localities: Hypostomus albopunctatus (Regan, 1908), Hypostomus hermanni (Ihering, 1905), Hypostomus iheringii (Regan, 1908), and Hypostomus paulinus (Ihering, 1905) from the Piracicaba River (the Upper Paraná River Basin); and Hypostomus mutucae Knaack, 1999 from the Claro River (the Upper Paraguay River Basin). Our results evidenced a great inter-specific diploid-number variation: 2n = 72 (H. hermanni); 2n = 74 (H. albopunctatus); 2n = 76 (H. paulinus); 2n = 80 (H. iheringii); and 2n = 82 (H. mutucae), which reflects the important role of Robertsonian rearrangements in the karyotypic differentiation among these species. The distribution of heterochromatin also varied considerably among species, making it possible to distinguish each analyzed species, as well as to detect microstructural variations among populations of the same species. These data can support taxonomic revisions when further associated with molecular markers and morphological analyses to delimit, more consistently, the taxonomic status of these Hypostomus species, which have a complex taxonomic diagnosis history.