The occurrence, role and evolution of chromatin diminution in nematodes

Chromatin diminution as a tool to study some biological problems

This work reveals the opportunities to obtain additional information about some biological problems through studying species that possess chromatin diminution. A brief review of the hypothesized biological significance of chromatin diminution is discussed. This article analyzes the biological role of chromatin diminution as it relates to the C-value enigma. It is proposed to consider chromatin diminution as a universal mechanism of genome reduction, reducing the frequency of recombination events in the genome, which leads to specialization and adaptation of the species to more narrow environmental conditions. A hypothesis suggesting the role of non-coding DNA in homologous recombination in eukaryotes is proposed. Cyclopskolensis Lilljeborg, 1901 (Copepoda, Crustacea) is proposed as a model species for studying the mechanisms of transformation of the chromosomes and interphase nuclei structure of somatic line cells due to chromatin diminution. Chromatin diminution in copepods is considered as a stage of irreversible differentiation of embryonic cells during ontogenesis. The process of speciation in cyclopoids with chromatin diminution is considered.

Nematode chromosomes

The nematode Caenorhabditis elegans has shed light on many aspects of eukaryotic biology, including genetics, development, cell biology, and genomics. A major factor in the success of C. elegans as a model organism has been the availability, since the late 1990s, of an essentially gap-free and well-annotated nuclear genome sequence, divided among 6 chromosomes. In this review, we discuss the structure, function, and biology of C. elegans chromosomes and then provide a general perspective on chromosome biology in other diverse nematode species. We highlight malleable chromosome features including centromeres, telomeres, and repetitive elements, as well as the remarkable process of programmed DNA elimination (historically described as chromatin diminution) that induces loss of portions of the genome in somatic cells of a handful of nematode species. An exciting future prospect is that nematode species may enable experimental approaches to study chromosome features and to test models of chromosome evolution. In the long term, fundamental insights regarding how speciation is integrated with chromosome biology may be revealed.

Delete and survive: strategies of programmed genetic material elimination in eukaryotes

Genome stability is a crucial feature of eukaryotic organisms because its alteration drastically affects the normal development and survival of cells and the organism as a whole. Nevertheless, some organisms can selectively eliminate part of their genomes from certain cell types during specific stages of ontogenesis. This review aims to describe the phenomenon of programmed DNA elimination, which includes chromatin diminution (together with programmed genome rearrangement or DNA rearrangements), B and sex chromosome elimination, paternal genome elimination, parasitically induced genome elimination, and genome elimination in animal and plant hybrids. During programmed DNA elimination, individual chromosomal fragments, whole chromosomes, and even entire parental genomes can be selectively removed. Programmed DNA elimination occurs independently in different organisms, ranging from ciliate protozoa to mammals. Depending on the sequences destined for exclusion, programmed DNA elimination may serve as a radical mechanism of dosage compensation and inactivation of unnecessary or dangerous genetic entities. In hybrids, genome elimination results from competition between parental genomes. Despite the different consequences of DNA elimination, all genetic material destined for elimination must be first recognised, epigenetically marked, separated, and then removed and degraded.

NANOS3 downregulation in Down syndrome hiPSCs during primordial germ cell-like cell differentiation

Human infertility is a complex disorder at the genetic, molecular, cellular, organ, and hormonal levels. New developing technology based on the generation of human primordial germ cell-like cells (hPGCLCs) from induced pluripotent stem cells (hiPSCs) might improve understanding of early germ cell development (specification, migration, gametogenesis, and epigenetic reconstitutions), as well as offering a solution for infertility and hereditary disorders. In this study, we differentiated hiPSCs with trisomy 21 into hPGCLCs. In vitro-derived germ cells from hiPSCs with Down syndrome (DS) express hPGCLC core circuitry, EOMES, SOX17, and PRDM14 at relatively low levels. TFAP2C and PRDM1 were expressed and remained elevated, whereas NANOS3 and NANOG were downregulated in BMP4-induced hiPSCs with DS. The low level of NANOG and NANOS3 expression might negatively influence hPGCLC generation in DS hiPSCs. We suggest that DS hPGCLCs could be a suitable model for studying human early germ cell development, the epigenetic and molecular mechanisms of PGC specification and formation, as well as related infertility disorders, such as azoospermia and teratozoospermia.

Molecular diagnosis of scabies using a novel probe-based polymerase chain reaction assay targeting high-copy number repetitive sequences in the Sarcoptes scabiei genome

Background

The suboptimal sensitivity and specificity of available diagnostic methods for scabies hampers clinical management, trials of new therapies and epidemiologic studies. Additionally, parasitologic diagnosis by microscopic examination of skin scrapings requires sample collection with a sharp scalpel blade, causing discomfort to patients and difficulty in children. Polymerase chain reaction (PCR)-based diagnostic assays, combined with non-invasive sampling methods, represent an attractive approach. In this study, we aimed to develop a real-time probe-based PCR test for scabies, test a non-invasive sampling method and evaluate its diagnostic performance in two clinical settings.

Methodology/Principal findings

High copy-number repetitive DNA elements were identified in draft Sarcoptes scabiei genome sequences and used as assay targets for diagnostic PCR. Two suitable repetitive DNA sequences, a 375 base pair microsatellite (SSR5) and a 606 base pair long tandem repeat (SSR6), were identified. Diagnostic sensitivity and specificity were tested using relevant positive and negative control materials and compared to a published assay targeting the mitochondrial cox1 gene. Both assays were positive at a 1:100 dilution of DNA from a single mite; no amplification was observed in DNA from samples from 19 patients with other skin conditions nor from house dust, sheep or dog mites, head and body lice or from six common skin bacterial and fungal species. Moderate sensitivity of the assays was achieved in a pilot study, detecting 5/7 (71.4% [95% CI: 29.0% - 96.3%]) of clinically diagnosed untreated scabies patients). Greater sensitivity was observed in samples collected by FLOQ swabs compared to skin scrapings.

Conclusions/Significance

This newly developed qPCR assay, combined with the use of an alternative non-invasive swab sampling technique offers the possibility of enhanced diagnosis of scabies. Further studies will be required to better define the diagnostic performance of these tests.

As scabies control efforts continue to grow, scarcity of diagnostic options hinders success of elimination efforts in endemic areas. Efficiency in large-scale monitoring is further obstructed by invasive sample collection techniques, which are often uncomfortable for patients, and lack sensitivity. We have developed two PCR-based diagnostic assays targeting repetitive DNA elements. These were identified using new data on the S. scabiei genome. Targeting these elements by PCR improved the detection of scabies DNA. Enhanced sensitivity was demonstrated when tested against routine microscopy and a published PCR-based diagnostic assay. When combined with a non-invasive, effective FLOQ swab sampling method, the developed qPCR-based assays may provide a useful complementary tool for diagnosis of scabies, and its application will likely improve scabies control in target populations.

Epigenetics as an Evolutionary Tool for Centromere Flexibility

Centromeres are the complex structures responsible for the proper segregation of chromosomes during cell division. Structural or functional alterations of the centromere cause aneuploidies and other chromosomal aberrations that can induce cell death with consequences on health and survival of the organism as a whole. Because of their essential function in the cell, centromeres have evolved high flexibility and mechanisms of tolerance to preserve their function following stress, whether it is originating from within or outside the cell. Here, we review the main epigenetic mechanisms of centromeres’ adaptability to preserve their functional stability, with particular reference to neocentromeres and holocentromeres. The centromere position can shift in response to altered chromosome structures, but how and why neocentromeres appear in a given chromosome region are still open questions. Models of neocentromere formation developed during the last few years will be hereby discussed. Moreover, we will discuss the evolutionary significance of diffuse centromeres (holocentromeres) in organisms such as nematodes. Despite the differences in DNA sequences, protein composition and centromere size, all of these diverse centromere structures promote efficient chromosome segregation, balancing genome stability and adaptability, and ensuring faithful genome inheritance at each cellular generation.

Chromatin Diminution in Cyclops kolensis Lill. (Copepoda, Crustacea) as a Radical Way to Inactivate Redundant Genome in Somatic Cells

Chromatin diminution (CD) is a phenomenon of programmed DNA elimination which takes place in early embryogenesis in some eukaryotes. The mechanism and biological role of CD remain largely unknown. During CD in the freshwater copepod Cyclops kolensis, the genome of cells of the somatic lineage is reorganized and reduced in size by more than 90% without affecting the genome of germline cells. Although the diploid chromosome number is unchanged, chromosome size is dramatically reduced by CD. The eliminated DNA consists primarily of repetitive sequences and localizes within granules during the elimination process. In this review, we provide an overview of CD in C. kolensis including both cytological and molecular studies.

Holocentromere identity: from the typical mitotic linear structure to the great plasticity of meiotic holocentromeres

The centromere is the chromosomal site of kinetochore assembly and is responsible for the correct chromosome segregation during mitosis and meiosis in eukaryotes. Contrary to monocentrics, holocentric chromosomes lack a primary constriction, what is attributed to a kinetochore activity along almost the entire chromosome length during mitosis. This extended centromere structure imposes a problem during meiosis, since sister holocentromeres are not co-oriented during first meiotic division. Thus, regardless of the relatively conserved somatic chromosome structure of holocentrics, during meiosis holocentric chromosomes show different adaptations to deal with this condition. Recent findings in holocentrics have brought back the discussion of the great centromere plasticity of eukaryotes, from the typical CENH3-based holocentromeres to CENH3-less holocentric organisms. Here, we summarize recent and former findings about centromere/kinetochore adaptations shown by holocentric organisms during mitosis and meiosis and discuss how these adaptations are related to the type of meiosis found.

Gene silencing and sex determination by programmed DNA elimination in parasitic nematodes

Maintenance of genome integrity is essential. However, programmed DNA elimination removes specific DNA sequences from the genome during development. DNA elimination occurs in unicellular ciliates and diverse metazoa ranging from nematodes to vertebrates. Two distinct groups of nematodes use DNA elimination to silence germline-expressed genes in the soma (ascarids) or for sex determination (Strongyloides spp.). Data suggest that DNA elimination likely evolved independently in these nematodes. Recent studies indicate that differential CENP-A deposition within chromosomes defines which sequences are retained and lost during Ascaris DNA elimination. Additional studies are needed to determine the distribution, functions, and mechanisms of DNA elimination in nematodes.

Improved PCR-Based Detection of Soil Transmitted Helminth Infections Using a Next-Generation Sequencing Approach to Assay Design

BACKGROUND

The soil transmitted helminths are a group of parasitic worms responsible for extensive morbidity in many of the world's most economically depressed locations. With growing emphasis on disease mapping and eradication, the availability of accurate and cost-effective diagnostic measures is of paramount importance to global control and elimination efforts. While real-time PCR-based molecular detection assays have shown great promise, to date, these assays have utilized sub-optimal targets. By performing next-generation sequencing-based repeat analyses, we have identified high copy-number, non-coding DNA sequences from a series of soil transmitted pathogens. We have used these repetitive DNA elements as targets in the development of novel, multi-parallel, PCR-based diagnostic assays.

METHODOLOGY/PRINCIPAL FINDINGS

Utilizing next-generation sequencing and the Galaxy-based RepeatExplorer web server, we performed repeat DNA analysis on five species of soil transmitted helminths (Necator americanus, Ancylostoma duodenale, Trichuris trichiura, Ascaris lumbricoides, and Strongyloides stercoralis). Employing high copy-number, non-coding repeat DNA sequences as targets, novel real-time PCR assays were designed, and assays were tested against established molecular detection methods. Each assay provided consistent detection of genomic DNA at quantities of 2 fg or less, demonstrated species-specificity, and showed an improved limit of detection over the existing, proven PCR-based assay.

CONCLUSIONS/SIGNIFICANCE

The utilization of next-generation sequencing-based repeat DNA analysis methodologies for the identification of molecular diagnostic targets has the ability to improve assay species-specificity and limits of detection. By exploiting such high copy-number repeat sequences, the assays described here will facilitate soil transmitted helminth diagnostic efforts. We recommend similar analyses when designing PCR-based diagnostic tests for the detection of other eukaryotic pathogens.

Histone modifications related to chromosome silencing and elimination during male meiosis in Bengalese finch

We report here that a germline-restricted chromosome (GRC) is regularly present in males and females of the Bengalese finch (Lonchura domestica). While the GRC is euchromatic in oocytes, in spermatocytes this chromosome is cytologically seen as entirely heterochromatic and presumably inactive. The GRC is observed in the cytoplasm of secondary spermatocytes, indicating that its elimination from the nucleus occurs during the first meiotic division. By immunofluorescence on microspreads, we investigated the presence of histone H3 modifications throughout male meiosis, as well as in postmeiotic stages. We found that the GRC is highly enriched in di- and trimethylated histone H3 at lysine 9 during prophase I, in agreement with the presumed inactive state of this chromosome. At metaphase I, dimethylated histone H3 is no longer detectable on the GRC and its chromatin is more faintly stained with DAPI. The condensed GRC is underphosphorylated at serine 10 compared to the regular chromosomes during metaphase I, being phosphorylated later at this site after the first meiotic division. From these results, we proposed that trimethylation of histone H3 at lysine 9 on the GRC chromatin increases during metaphase I. This hypermethylated state at lysine 9 may preclude the phosphorylation of the adjacent serine 10 residue, providing an example of cross-talk of histone H3 modifications as described in experimental systems. The differential underphosphorylation of the GRC chromatin before elimination is interpreted as a cytologically detectable byproduct of deficient activity of Aurora B kinase, which is responsible for the phosphorylation of H3 at serine 10 during mitosis and meiosis.

Silencing of germline-expressed genes by DNA elimination in somatic cells

Chromatin diminution is the programmed elimination of specific DNA sequences during development. It occurs in diverse species, but the function(s) of diminution and the specificity of sequence loss remain largely unknown. Diminution in the nematode Ascaris suum occurs during early embryonic cleavages and leads to the loss of germline genome sequences and the formation of a distinct genome in somatic cells. We found that ∼43 Mb (∼13%) of genome sequence is eliminated in A. suum somatic cells, including ∼12.7 Mb of unique sequence. The eliminated sequences and location of the DNA breaks are the same in all somatic lineages from a single individual and between different individuals. At least 685 genes are eliminated. These genes are preferentially expressed in the germline and during early embryogenesis. We propose that diminution is a mechanism of germline gene regulation that specifically removes a large number of genes involved in gametogenesis and early embryogenesis.

Current knowledge on B chromosomes in natural populations of helminth parasites: a review

Helminths, traditionally classified into three phyla Platyhelminthes, Nemathelminthes and Acanthocephala, are a phylogenetically broadly diversified group of invertebrates, characterised by a parasitic life style. Current estimates of the helminth species diversity are at least 23-40,000 platyhelminthes, 10-26,000 nematodes and 1,200 acanthocephalans. Recent information on helminth karyotypes is fragmentary, and basic karyological data are known from approximately 1.1% of known species. Supernumerary chromosomes have been reported in selected populations of only 11 digenean flukes (Platyhelminthes), 1 thorny-headed worm (Acanthocephala) and 4 roundworms (Nematoda), which represent 3.6, 7.7 and 1.3% of the total number of species cytogenetically analysed to date within respective helminth groups. B chromosome presence was not generally associated with heteromorphic sex chromosomes as they occurred both in hermaphroditic flukes and dioecious helminths, and in species having male or female heterogametic sex chromosomes (ZW of schistosomes, XO of acanthocephalans and XY of nematodes). Numbers of B chromosomes varied from 1 to 10. Most often, Bs represented one or two of the smallest elements of the complement but they could be much bigger in some digenean flukes. B chromosomes showed a diverse morphology, including telocentric to metacentric structure. There is no detailed banding or ultrastructural study of Bs in the majority of helminth carriers. Assumptions on the possible relation between the occurrence of Bs in endoparasitic helminths and extreme environments are discussed.

Highly repetitive DNA families restricted to germ cells in a Japanese hagfish (Eptatretus burgeri): a hierarchical and mosaic structure in eliminated chromosomes

It is known that in eight hagfishes chromosome elimination occurs during early embryogenesis. The eliminated chromosomes are mostly C-band positive, so that none of the somatic cells have any C-band-positive chromatin. Recently, some highly repetitive DNA sequences have been reported as eliminated elements in these hagfishes based on molecular biological methods. However, no germline-restricted repetitive DNA have been directly isolated from the Japanese hagfish Eptatretus burgeri, from which approximately 21% of the total DNA is eliminated from presumptive somatic cells. Through electrophoretic investigation after digestion with restriction endonucleases, two DNA families that are restricted to germline DNA were isolated. Molecular cloning and sequence analysis revealed that these families are composed of closely related sequences of 64 and 57bp in length, respectively. Southern blot hybridization revealed that the two DNA families are restricted to germline DNA and were thus named EEEb1 and EEEb2, respectively. Moreover, these eliminated elements were highly and tandemly repeated, and it is predicted that they might amplify by saltatory replication and have evolved in a concerted manner. By densitometric scanning, EEEb1 and EEEb2 were found to amount to make up approximately 18.5 and 0.024% of the total germline genomic DNA, accounting for 88.6% of the total eliminated DNA. A fluorescence in situ hybridization experiment demonstrated that EEEb1 is located on all C-band-positive chromosomes that are limited to germ cells, suggesting that EEEb1 is the primary component of eliminated DNA of E. burgeri.

Chromosome elimination in sciarid flies

The programmed elimination of part of the genome through chromosome loss or chromatin diminution constitutes an exceptional biological process found to be present in several diverse groups of organisms. The occurrence of this phenomenon during early embryogenesis is generally correlated to somatic versus germ-line differentiation. A most outstanding example of chromosome elimination and genomic imprinting is found in sciarid flies, where whole chromosomes of exclusive parental origin are selectively eliminated at different developmental stages. Three types of tissue-specific chromosome elimination events occur in sciarids. During early cleavages, one or two X paternal chromosomes is/are discarded from somatic cells of embryos which then develop as females or males respectively. Thus, the sex of the embryo is determined by the number of eliminated paternal X chromosomes. In germ cells, instead, a single paternal X chromosome is eliminated in embryos of both sexes. In addition, while female meiosis is orthodox, male meiosis is highly unusual as the whole paternal chromosome set is discarded from spermatocytes. As a consequence, only maternally derived chromosomes are included in the functional sperm. This paper reviews current cytological and molecular knowledge on the tissue-specific cell mechanisms evolved to achieve chromosome elimination in sciarids.

Chromatin diminution in the parasitic nematodes ascaris suum and parascaris univalens

Chromatin diminution in Parascaris univalens and Ascaris suum undoubtedly represents an interesting case of developmentally programmed DNA rearrangement in higher eukaryotes. It is a complex mechanism involving chromosomal breakage, new telomere addition and DNA degradation, and occurs in all presomatic cells. The process is rather specific with respect to its developmental timing and the chromosomal regions that are eliminated. The functional significance of chromatin diminution still remains an enigma. The fact, however, that single-copy, protein-coding genes are contained in the eliminated DNA demonstrates that in P. univalens and A. suum, there is a qualitative difference between germ-line and somatic genomes, and suggests that chromatin diminution may be used as a "throw-away" approach to gene regulation. We present a hypothesis as to how, during evolution, a partial genome duplication might have been linked to the process of chromatin diminution, in order to provide a selective advantage to parasitic DNA-eliminating nematodes.

Host-like sequences in the schistosome genome

A series of recent papers has indicated that widespread genomic rearrangements take place in the genome of schistosomes during the life cycle of the parasite. These results have been controversial since genomic rearrangements are not common in eukaryotes, probably because excessive genome plasticity would carry a heavy evolutionary price. Here, Karen Clough, Alec Drew and Paul Brindley present data that ostensibly support the concept of widespread genomic rearrangements, but for which they suggest a different interpretation. They conclude that artefactual contamination of schistosome genome preparations with host DNA can probably explain the Southern hybridization results which led to the original hypothesis of developmental, genomic rearrangements.

Chromatin diminution in nematodes

The process of chromatin diminution in Parascaris and Ascaris is a developmentally controlled genome rearrangement, which results in quantitative and qualitative differences in DNA content between germ line and somatic cells. Chromatin diminution involves chromosomal breakage, new telomere formation and DNA degradation. The programmed elimination of chromatin in presomatic cells might serve as an alternative way of gene regulation. We put forward a new hypothesis of how an ancient partial genome duplication and chromatin diminution may have served to maintain the genetic balance in somatic cells and simultaneously endowed the germ line cells with a selective advantage.

Ribosomal heterogeneity from chromatin diminution in Ascaris lumbricoides

The genome of Ascaris lumbricoides encodes both germline- and soma-specific proteins homologous to the eukaryotic small ribosomal protein (Rp) S19. The two Ascaris homologs differ by 24 amino acid substitutions and are both components of the small ribosomal subunits. In oocytes, the germline RpS19 homolog (RpS19G) predominates. During chromatin diminution, however, the gene is eliminated from all presomatic cells, and RpS19G is replaced by the product of the somatic gene (RpS19S). Chromatin diminution in A. lumbricoides causes a change in the protein composition of ribosomes during development and represents an alternative means of gene regulation.