Research Article |
Corresponding author: Andrey Grishanin ( andreygrishanin@mail.ru ) Academic editor: Natalia Golub
© 2024 Andrey Grishanin.
This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Citation:
Grishanin A (2024) Chromatin diminution as a tool to study some biological problems. Comparative Cytogenetics 18: 27-49. https://doi.org/10.3897/compcytogen.17.112152
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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. Cyclops kolensis 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.
C-value enigma, differentiation, evolution, genome reorganization, recombination, speciation
All organisms exhibit genome variability produced by mutations, recombinations, deletions, insertions, mobile elements, etc. A small number of animals additionally exhibit a special, hard-coded form of genome modification called chromatin diminution, DNA elimination, programmed DNA elimination (PDE). As a result of this complex, genetically determined process chromosomes, and fragments of chromosomes undergo elimination. The phenomenon of chromatin diminution has a long history and was discovered by Theodor
Chromatin diminution in metazoans is the removal of chromosomal material (mostly heterochromatin) from the cells of the somatic line in early embryogenesis; chromatin diminution (programmed DNA elimination) in Protozoa is the removal of entire chromosomes or of sequences interspersed among genic loci in the somatic nucleus. The process of chromatin diminution is species-specific. The diploid number of chromosomes after diminution processes can remain the same or change. The biological role of chromatin diminution remains unknown. Despite being studied for over 100 years, chromatin diminution, in the author’s opinion, is an example of one of the most underestimated biological phenomena. The purpose of this work is to show that chromatin diminution is not only interesting as a biological phenomenon, but also provides researchers with a unique opportunity to work with species in which genome size changes during ontogeny, in some cases by more than 90%, which provides additional advantages when studying various biological structures and processes.
The biological role of chromatin diminution remains open. Theodor Boveri was the first to suggest a biological role for the eliminated chromatin. He suggested that the eliminated chromatin has important functions for germline cells, since centrifugation of Parascaris equorum Goeze, 1782 (Ascaridida, Nematoda) embryos in the early stages of development initiates diminution in all cells of the embryo, including germline cells (
As a result of chromatin diminution in Ascaris chromosomes, both preserved and eliminated chromosomes acquire new telomeres (
In some species, representatives of the order Diptera (Cecidomyiidae, Sciaridae, Chironomidae), elimination of individual chromosomes or entire chromosome sets is observed in the process of sexual differentiation; elimination of chromosomes is preceded by their heterochromatinization (
The most complete list of existing hypotheses about the biological significance of programmed DNA elimination (chromatin diminution) suggests the following functions: gene silencing and regulation, nucleotypic effects, mutation rate reduction, and energetic benefits (
The study of chromatin diminution in Cyclops strenuus strenuus Fisher, 1851 showed that throughout the prediminution interphase, the nucleus of somatic cells has a weak uniform color. Only 20 minutes before the start of division, numerous lumps of condensed chromatin appear in the nucleus, distributed along the periphery of the nucleus (
Thus, before chromatin diminution, C. kolensis embryonic cells have a typical structure of interphase nuclei of embryonic cells, while after chromatin diminution, the structure of interphase nuclei irreversibly changes and more closely resembles the structure of interphase nuclei observed in multicellular eukaryotic cells after differentiation.
As is known maternal genes of the eggs determine the pattern of embryonic formation before fertilization and during initial cleavage divisions, after which the genes localized in the nuclei of embryonic cells play a role in the developmental process (
It has been established that during the course of chromatin diminution, a decrease in the size of the nuclei in the somatic line cells occurs (
Hypothetical Matrix Attachment Region cutting scheme. Scheme of the Cyclops kolensis chromosome, in which, as a result of chromatin diminution, its part associated with the nuclear matrix (matrix attachment region, MAR) is cut out a chromosome before chromatin diminution b chromosome after chromatin diminution.
Thus, chromatin diminution in copepods can be considered as a stage of irreversible differentiation of embryonic cells during ontogenesis. The reduction of 94% of the nuclear genome in C. kolensis makes it impossible to return the cells of the somatic line to the potencies of the germ line cells. ChroTeMo, a tool (
The problem of non-coding DNA (C-value paradox, C-value enigma) was formulated in the middle of the 20th century and relates to the fact that the most DNA of eukaryotic genomes is non-coding (
Several authors have shown a correlation between genome size and various ecological or physiological parameters including the body’s resistance to cold and dryness in some plant species (
The C-value paradox poses another question for biologists to answer: why organisms occupying a lower position on the phylogenetic tree, being ancestral forms or contemporaries of ancestral forms, have a significantly larger genome than more evolutionarily advanced or more specialized species.
The study of the chromatin diminution process allows us to shed light on the fate of eliminated DNA (primarily constitutive heterochromatin), which was classified as non-coding or “junk”, and on the fate of some unique sequences that are also removed from the nuclear genome of somatic cells as a result of chromatin diminution. The idea of linking non-coding DNA to chromatin diminution belongs to Alexei Akifyev (
A unique objective for solving the C-value enigma can be a representative of freshwater copepods, C. kolensis, in which, during the 4th cleavage division, 94% of the DNA is excised from the chromosomes of somatic line cells, while germ-line cells retain their nuclear DNA unchanged throughout ontogeny. The diploid number of chromosomes remains unchanged (
According to the selectively neutral hypotheses (
The assumption that the role of non-coding DNA is in gene repression, which occurs during heterochromatinization of non-coding DNA, involving neighboring areas of euchromatin in this process (
Consider a model assuming the role of non-coding DNA in homologous recombination in C. kolensis. Suppose that the function of non-coding DNA is to increase the speed and frequency of recombination processes, the purpose of which is to increase the qualitative diversity of offspring that fall under the action of selection. At the same time, the more recombinant variants of the genome will be obtained, and the faster recombination events will take place, the more diverse offspring will be obtained. Given the interference rule, according to which two exchanges rarely occur in close proximity to each other, it can be assumed that the lower the density of genes in the genome, the higher the rate of recombination processes. It can be assumed that the role of non-coding DNA is to increase the distances between genes and their parts (exons and introns), as well as regulatory and structural elements (enhancers, silencers, insulators, MARs, etc.), in order to ensure the greatest freedom during recombination processes. The greater the distance between the coding regions of the genome, as well as coding and regulatory sequences, the greater the number of introns in the genes, and their magnitude, the less likely there will be violations of the structure of genes during recombination processes.
The more often recombination events that take place, the more different gene variants will appear during the rearrangement of coding and regulatory sections of the genome, and the more variants of structural and regulatory proteins will appear in this individual. In addition, non-coding DNA, creating a spatial three-dimensional structure in the interphase nucleus, largely determines the genome’s likelihood to undergo ectopic recombination. Thus, a genome “diluted” with non-coding DNA makes it possible to quickly search for a wide variety of gene variants. The evaluation of these variants is carried out through the phenotype of an individual during the implementation of various genome variants in the interaction of the organism with the external environment. A successful variant of the genome should be stabilized; therefore, a decrease in the rate of recombination processes due to genome reduction can be considered as a mechanism for reducing genome variability. In other words, with the specialization and adaptation of the species to narrow ecological conditions, the need to find the optimal variant of the genome decreases. A large genome makes it difficult to fix the optimal variant of linear and spatial relationships of various parts of the genome, which allows the species to interact within this ecological niche in the most successful way. A non-coding genome during the fluctuation of the environment provokes further changes during recombination processes, and the loss of the optimal structure is found by it under the conditions of the ecological niche to which it has adapted. There is a need to dump non-coding DNA. This is achieved by genome reduction in somatic and germline cells. All the mechanisms necessary for such a process in cells exist: restriction by endonucleases and crosslinking of free ends by ligases. Genetic regulation of the main events of meiosis is well studied. If meiosis is disrupted, then sterility occurs in one or both sexes (
Hypothetical scheme of the origin of Chromatin Diminution (CD) a genome reduction during evolution occurs in germ line cells and somatic line cells; genes responsible for meiosis are located in the part of chromosomes that is not subject to genome reduction b genome reduction during evolution occurs in germ line cells and somatic line cells; during genome reduction the genes responsible for meiosis are located in the part of chromosomes that is subject to reduction; as a result, the offspring become sterile due to the absence of genes controlling meiosis c genome reduction occurs only in somatic line cells while preserving the original genome in germ line cells; during chromatin diminution the genes responsible for meiosis are located in parts of the chromosome that are subject to reduction during chromatin diminution; but they are retained in the chromosomes of germline cells. The offspring are viable. Chromatin diminution does not affect development processes.
The appearance of chromatin diminution in the ontogenesis of a species of the genus Cyclops may also become a factor contributing to genetic isolation and further contribute to speciation. Due to the relatively short life cycle of freshwater copepods, genetic isolation can occur quite quickly (
A large-scale rearrangement of the genome has occurred apparently in the species Cyclops insignis Claus,1857 as evidenced by the German population which has chromatin diminution (
Consider a hypothetical scheme of speciation. The parental species (presumably Cyclops sp.) has a genome containing a large amount of non-coding DNA (Fig.
Hypothetical scheme in which reproductive isolation is determined by the appearance of chromatin diminution in one of the populations. Genome reduction of parental species (P) can take place in its descendants in two ways: population A, in which genome reduction occurred only in somatic line cells, and population B, in which genome reduction took place in somatic and germline cells. In population B due to inversion the linear order of the arrangement of functionally significant DNA sections has changed (population B1). In hybrids of individuals of populations A and B, partial conjugation will take place in meiosis. In hybrids of individuals of populations A and B1 conjugation in meiosis will be impossible and such hybrid individuals will be infertile.
The phenomenon of gonomery in fresh-water Copepoda species can be considered as an example of an intermediate stage of genome evolution in species with the phenomenon of chromatin diminution. Sigrid
Reduction of 94% of DNA in the somatic cell line as a result of chromatin diminution in C. kolensis, allowed us to consider the eliminated DNA as non-coding for cells of the somatic line, since the absence of this part of the genome in them does not interfere with the normal course of ontogenesis. At the same time, it suggests that the eliminated DNA does not carry any significant coding and regulatory functions in the somatic line.
Studies of chromatin diminution in C. kolensis have shown that as a result of chromatin diminution, a change in the structure of interphase nuclei occurs, which is characteristic of the interphase nucleus of a differentiated eukaryotic cell. The results obtained led to the conclusion that the process of chromatin diminution is an alternative form of regulation of cell differentiation into the somatic and germ lines.
Studies of different species of Cyclops have shown that the reason for the appearance of chromatin diminution in ontogenesis is not related to the need to remove non-coding DNA from the genome of somatic cells, as can be seen when comparing C. insignis from Moscow, Russia, which does not have chromatin diminution, and C. insignis from Germany, which has chromatin diminution (
The genome reduction is a tool aimed at reducing the speed of the evolutionary process of a species by reducing the frequency of recombination events, which leads to a decrease in the diversity of genotype variants in offspring when the necessary level of adaptability to environmental requirements is achieved. The chromatin diminution can be considered as one of the options for this process, when genome reduction in germ line cells is impossible due to localization of sequences there that are presumably important for the processes of meiosis and early stages of embryogenesis, but not necessary for subsequent development.
The author thanks Christopher Rose (Department of Biology, James Madison University, Harrisonburg, VA), Grace Wyngaard (Department of Biology, James Madison University, Harrisonburg, VA) and Natalia Golub (Editor of Comparative Cytogenetics Journal) for editing the article and valuable comments on its content, Maxim Zagoskin (Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN) for help in making figures.
Andrey Grishanin https://orcid.org/0000-0002-6368-5807