Somatic genome processing

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The genome of most cells of eukaryotes remains mainly constant during life. However, there are cases of genome being altered in specific cells or in different life cycle stages during development. For example, not every human cell has the same genetic content as red blood cells which are devoid of nucleus. One of the best known groups in respect of changes in somatic genome are ciliates. The process resulting in a variation of somatic genome that differs from germline genome is called somatic genome processing.

Contents

Genome loss

The result of this process is the removal of a whole genome from a cell. The most known example is the enucleation process of erythrocytes. A processed stem cell goes through changes causing it to lose a nucleus. In the beginning phase, pro-erythroblast goes through another mitotic divisions, in which an erythroblast with a smaller nucleus is created and moved to the side of the cell. The nucleus becomes isolated from cytoplasm and then erythroblast is divided into reticulocyte with cytoplasm and pyrenocyte with condensed nucleus. Pyrenocyte with all genetic material from cell is degraded then by a macrophage. Loss of genome is in this case advantageous, since pyrenocyte can accumulate more hemoglobin. Mature red blood cell without a nucleus, can properly deliver oxygen. [1]

Chromatin diminution

Chromatin diminution is a process of partial elimination of chromatin genetic material from genome of prospective somatic cells. This process was found to occur during the early developmental stage in three groups: nematodes, copepods, and hagfish [2] One of the first studies regarding somatic genome processing was observed by Boveri large-scale chromatin elimination in parasitic nematode Parascaris univalens . [3] During chromatin diminution, somatic chromosomes becomes fragmented with new telomeres added in many different places and devoid of heterochromatin so it differs from germline cell in respect of structure and genetic content. Germline cells of P. univalens contain only two chromosomes, but in early embryogenesis central euchromatic regions of the chromosomes fragment into diploid somatic set of 2×29 autosomes and 2×6 X chromosomes in females or 2×29 autosomes and 6 X chromosomes in males, which segregate to the two daughter nuclei. After all heterochromatin becomes degraded in cytoplasm. As a result of chromatin diminution P. univalens loses about 80–90% of the total nuclear germ line DNA. [4] [5] [6]

Chromatin diminution occurs also in unicellular eukaryotes, such as ciliates. Ciliates have two nuclei: micronucleus (germ-line cell nucleus) that does not express genes and macronucleus, where most genes are expressed, and is subject to chromatin elimination. During this process chromosomes are fragmented, chromatin eliminated and new DNA molecules with added telomeres are created. The final macronucleus has greater genetic content than micronucleus. In ciliates there are two types of diminution: the first is fragmentation of genome and loss of repetitive sequences and the second is deletion of internally eliminated sequences in chromosomes and the rejoining of remaining DNA fragments. [6]

Gene unscrambling

Gene unscrambling is type of genome-wide processing found particularly in ciliates. The germline genes in the micronucleus of ciliates are composed of protein-coding DNA fragments (MDSs) interrupted by many non-coding DNA sequences, also called internal eliminated (IESs).

In the Spirotrichea class, to which Oxytricha belongs, protein-coding DNA fragments in a micronucleus are located in permuted order. During sexual development the genetic content of somatic macronucleus is derived from micronucleus. First some parts, including IESs, of micronuclear DNA are removed to give transcriptionally active genome in macronucleus. Also micronuclear-encoded MDSs which are nonsequential must undergo gene unscrambling to be ligated in correct order to give functional genes [7] [8]

Local rearrangements

Local rearrangements affect specific loci only. Such rearrangements, for instance, help create genes that produce a great variation of immunoglobulins in vertebrates. During life, organisms have contact with a large number of antigens. Which means that the immune system needs to synthesize a wide range of antibodies. Each immunoglobulin is a tetramer consisting of four polypeptides connected by disulfide bridges. They form two long heavy chains and two short light chains. But vertebrate genome does not code entire genes of heavy and light immunoglobulins, only gene segments. Segments of heavy chain are located on chromosome 14, they include 11 constant gene segments (CH), that are preceded by 123-129 variable segments (VH), 27 diversity gene segments (DH) and 9 joining segments (JH), coding different versions of components V, D, J. Loci of light chains on chromosome 2 (locus κ) and chromosome 22 (locus λ) have similar structure, but they do not contain D segments. At the early stage of lymphocyte B development, loci of immunoglobulins are rearranged. During rearrangement, segment VH on heavy chain locus is connected with one DH segment, then V-D group is combined with JH segment. Eventually, exon with open reading frame coding segments: VH, DH, JH of immunoglobulin. Through RNA splicing during transcription, this exon becomes connected to exon for CH segment. Complementary mRNA of heavy chain can be translated into immunoglobulin specific only for one lymphocyte. [9]

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<i>Tetrahymena</i> Genus of single-celled organisms

Tetrahymena, a unicellular eukaryote, is a genus of free-living ciliates. The genus Tetrahymena is the most widely studied member of its phylum. It can produce, store and react with different types of hormones. Tetrahymena cells can recognize both related and hostile cells.

<span class="mw-page-title-main">Karyotype</span> Photographic display of total chromosome complement in a cell

A karyotype is the general appearance of the complete set of chromosomes in the cells of a species or in an individual organism, mainly including their sizes, numbers, and shapes. Karyotyping is the process by which a karyotype is discerned by determining the chromosome complement of an individual, including the number of chromosomes and any abnormalities.

<i>Paramecium</i> Genus of unicellular ciliates, commonly studied as a representative of the ciliate group

Paramecium is a genus of eukaryotic, unicellular ciliates, commonly studied as a model organism of the ciliate group. Paramecium are widespread in freshwater, brackish, and marine environments and are often abundant in stagnant basins and ponds. Because some species are readily cultivated and easily induced to conjugate and divide, they have been widely used in classrooms and laboratories to study biological processes. The usefulness of Paramecium as a model organism has caused one ciliate researcher to characterize it as the "white rat" of the phylum Ciliophora.

In cellular biology, a somatic cell, or vegetal cell, is any biological cell forming the body of a multicellular organism other than a gamete, germ cell, gametocyte or undifferentiated stem cell. Somatic cells compose the body of an organism and divide through the process of binary fission and mitotic division.

Double minutes are small fragments of extrachromosomal DNA, which have been observed in a large number of human tumors including breast, lung, ovary, colon, and most notably, neuroblastoma. They are a manifestation of gene amplification as a result of chromothripsis, during the development of tumors, which give the cells selective advantages for growth and survival. This selective advantage is as a result of double minutes frequently harboring amplified oncogenes and genes involved in drug resistance. DMs, like actual chromosomes, are composed of chromatin and replicate in the nucleus of the cell during cell division. Unlike typical chromosomes, they are composed of circular fragments of DNA, up to only a few million base pairs in size, and contain no centromere or telomere. Further to this, they often lack key regulatory elements, allowing genes to be constitutively expressed. The term ecDNA may be used to refer to DMs in a more general manner.

A macronucleus is the larger type of nucleus in ciliates. Macronuclei are polyploid and undergo direct division without mitosis. It controls the non-reproductive cell functions, such as metabolism. During conjugation, the macronucleus disintegrates, and a new one is formed by karyogamy of the micronuclei.

<span class="mw-page-title-main">Micronucleus</span>

Micronucleus is the name given to the small nucleus that forms whenever a chromosome or a fragment of a chromosome is not incorporated into one of the daughter nuclei during cell division. It usually is a sign of genotoxic events and chromosomal instability. Micronuclei are commonly seen in cancerous cells and may indicate genomic damage events that can increase the risk of developmental or degenerative diseases. Micronuclei form during anaphase from lagging acentric chromosome or chromatid fragments caused by incorrectly repaired or unrepaired DNA breaks or by nondisjunction of chromosomes. This incorrect segregation of chromosomes may result from hypomethylation of repeat sequences present in pericentromeric DNA, irregularities in kinetochore proteins or their assembly, dysfunctional spindle apparatus, or flawed anaphase checkpoint genes. Micronuclei can contribute to genome instability by promoting a catastrophic mutational event called chromothripsis. Many micronucleus assays have been developed to test for the presence of these structures and determine their frequency in cells exposed to certain chemicals or subjected to stressful conditions.

<span class="mw-page-title-main">Nuclear dimorphism</span>

Nuclear dimorphism is a term referred to the special characteristic of having two different kinds of nuclei in a cell. There are many differences between the types of nuclei. This feature is observed in protozoan ciliates, like Tetrahymena, and some foraminifera. Ciliates contain two nucleus types: a macronucleus that is primarily used to control metabolism, and a micronucleus which performs reproductive functions and generates the macronucleus. The compositions of the nuclear pore complexes help determine the properties of the macronucleus and micronucleus. Nuclear dimorphism is subject to complex epigenetic controls. Nuclear dimorphism is continuously being studied to understand exactly how the mechanism works and how it is beneficial to cells. Learning about nuclear dimorphism is beneficial to understanding old eukaryotic mechanisms that have been preserved within these unicellular organisms but did not evolve into multicellular eukaryotes.

V(D)J recombination is the mechanism of somatic recombination that occurs only in developing lymphocytes during the early stages of T and B cell maturation. It results in the highly diverse repertoire of antibodies/immunoglobulins and T cell receptors (TCRs) found in B cells and T cells, respectively. The process is a defining feature of the adaptive immune system.

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<span class="mw-page-title-main">Ciliate</span> Taxon of protozoans with hair-like organelles called cilia

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<i>Chilodonella uncinata</i> Species of single-celled organism

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<span class="mw-page-title-main">Chromothripsis</span> Massive chromosomal rearrangement process linked to cancer

Chromothripsis is a mutational process by which up to thousands of clustered chromosomal rearrangements occur in a single event in localised and confined genomic regions in one or a few chromosomes, and is known to be involved in both cancer and congenital diseases. It occurs through one massive genomic rearrangement during a single catastrophic event in the cell's history. It is believed that for the cell to be able to withstand such a destructive event, the occurrence of such an event must be the upper limit of what a cell can tolerate and survive. The chromothripsis phenomenon opposes the conventional theory that cancer is the gradual acquisition of genomic rearrangements and somatic mutations over time.

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<i>Sterkiella histriomuscorum</i> Species of single-celled organism

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<i>Tetrahymena thermophila</i> Species of ciliate protozoa

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This glossary of genetics is a list of definitions of terms and concepts commonly used in the study of genetics and related disciplines in biology, including molecular biology, cell biology, and evolutionary biology. It is intended as introductory material for novices; for more specific and technical detail, see the article corresponding to each term. For related terms, see Glossary of evolutionary biology.

References

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  2. ↑ Zufall, Rebecca A.; Robinson, Tessa; Katz, Laura A. (2005-09-15). "Evolution of developmentally regulated genome rearrangements in eukaryotes". Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 304 (5): 448–455. doi:10.1002/jez.b.21056. ISSN   1552-5007. PMID   16032699.
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  4. ↑ Bachmann-Waldmann, Christa; Jentsch, Stephan; Tobler, Heinz; Müller, Fritz (2004-03-01). "Chromatin diminution leads to rapid evolutionary changes in the organization of the germ line genomes of the parasitic nematodes A. suum and P. univalens" (PDF). Molecular and Biochemical Parasitology. 134 (1): 53–64. doi:10.1016/j.molbiopara.2003.11.001. ISSN   0166-6851. PMID   14747143.
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