4. Epigenetics
4.3. Epigenetic phenomena
The most important epigenetic events are: genomic imprinting and X chromosome inactivation. Furthermore, carcinogenesis, aging, some psychiatric disorders, and even conduct disorders can be associated with epigenetic processes. Some observations indicate that these changes - not altering DNA sequences, but affecting its function - can be transmitted not only somatically so from mitosis to mitosis, but instead through meiosis during gametogenesis to gametes, and thus after the fertilization they will be typical of the progeny as well so there are signs of the so called transgenerational epigenesis.
4.3.1. X-chromosome inactivation
Mammalians are diploid organisms and consequently both alleles of an autosomal locus responsible for a particular trait are functioning, i.e. biallelic gene expression is characteristic for them. If one of the autosomes is eliminated due to chromosome mutations so only one allele remains at a single locus, this generally results in severe or lethal symptoms. In contrast, the sex chromosomes form homologous pairs (XX) only in females, whereas in males the Y chromosome is not a functional homolog of the X chromosome. While the Y chromosome contains only a few genes mainly responsible for sex determination (SRY) and gametogenesis (e.g. AZF), the X chromosome has genes determining a large number of somatic traits. If genes coded by the single X chromosome of males are sufficient for the normal development and normal
physiological processes of the individual, it is obvious that one X chromosome has to be enough for the female body. This means that evolutionarily became necessary to equalize the different X chromosomal gene doses of the two sexes, so to compensate the dose differences. This dose compensation is also called Lyonisation after Mary Lyon, the scientist who described this phenomenon. In mammals, including humans, the dose compensation in females is achieved through the inactivation of one of the X chromosomes. However, it should be emphasized that other mechanisms also exist for dose compensation in other organisms with heteromorphic sex chromosomes. X chromosome inactivation takes place at the beginning of mammalian embryonic development, in the blastocyst stage. As a first step of dose compensation chromosome counting is carried out by a mechanism not yet fully understood in details.
This means that the cell acquires the information about the quantity of X chromosomes.
Where two or more X chromosomes are in the cell, only one is active and the other (or others) is (are) inactivated. This inactivation is random, i.e. either the maternal or the paternal X is inactivated. However, once the selected X is inactivated, the given status of the cell is maintained lifelong in each of its descendant daughter cells.
Due to the random X inactivation in females there are cells in which the maternal, and there are in which the paternal X chromosome becomes inactive. Thus a so-called functional mosaicism is typical for women. The inactive X chromosome is intact, most of its genes are not expressed, except the genes of the pseudoautosomal regions found near to the telomere of both arms of the X chromosome (PAR1 and PAR2 regions) and the few genes that escape X inactivation. These remain active on the inactive X chromosome. To find out why these genes remained and how, is the subject of intensive research today. Although the inactivation in somatic cells is passed from daughter cells to their progeny cells, it does not mean that it is the case in germ cells, too. During oogenesis the inactivated X chromosome is reactivated, and it remains active in the mature gamete. In X inactivation the so-called XIC = X inactivation center plays a crucial role. Here, in the Xq13 region the XIST gene is found that is transcribed only from the inactive X chromosome. The product is a large non-coding RNA which is covering the would-be inactive X by a not yet fully known mechanism. The XIST expression is followed by several other epigenetic events such as DNA methylation, histone methylation, a change in the histone composition as shown by the macroH2A histone variant, increased chromosome condensation, and ultimately late DNA replication will be characteristic to the inactive X chromosome, i.e. the DNA of the inactive X chromosome starts replication after the replication of the other chromosomes’ DNA.
The increased chromosome condensation leads to heterochromatinization, and then the transcription is inhibited, thus the chromosome becomes inactive.
4.3.2. Genomic imprinting
Based on the classical genetic experiments, it appeared that it does not matter even in heterozygosity which allele comes from which parent. Since both alleles are expressed, the origin is not important. However, some animal studies or rare human diseases, suggested that it is at least not true for each gene. During mouse embryo manipulations it was found that when the nucleus of a mouse oocyte was injected into another oocyte of the same mouse, then diploid cell created, a gynogenote just started the embryonic development, but soon died because the fetal membranes were not formed. When the experiment was repeated in a way that an enucleated oocyte got two sperm nuclei, although the embryonic development was also not normal, it was different from the
58 Genetics and genomics
former phenomenon. There was no embryo in such androgenote only hyperproliferated fetal membranes. In other words, on the basis of mouse experiments it is concluded that maternal and paternal halves of the genome are not functionally equivalent. Rare human diseases such as complete hydatidiform mole also suggest this. In this case only paternal chromosomes are found in the otherwise diploid sample. That is because an empty egg is fertilized by either two sperms or by a diploid one, which is also supported by the fact that the sample proved to be homozygous for all loci by further tests. The reverse of this was found when teratocarcinomas were analyzed the abnormal tissue had only maternal chromosomes. On the basis of these initial observations it is considered that each chromosome carries a marker which refers to the parental origin.
This signal is fixed at some point during gametogenesis, which somehow imprinted in the genetic material. The parental origin specific marking of the genome is called genomic imprinting.
To identify the mechanism of imprinting further attempts were made. When the mouse experiments were repeated in a way that only one pair of chromosomes or a distal or a proximal part of the chromosome was purely of paternal or maternal origin, it is found that not the total genome, but only certain chromosome segments, certain genes carry markers of parental origin. Such a phenomenon is the uniparental disomy (UPD) (see Chapter 3, Cytogenetics), where after rare chromosome segregation anomalies, regarding the chromosome number, normal diploid organisms are created with both homologues of certain chromosomes / chromosome segments derived from the same parent, and who have severe symptoms, depending on the chromosomes involved. From the point of DNA base sequence it is irrelevant, which comes from which parent, therefore the labeling should be epigenetic. If a father transmits an imprinted gene to his child, which he inherited from his mother, then the gene carries maternal imprinting in the father, but the kid will inherit paternal imprinting of this gene.
This means that imprinting is reversible. That is similar to X inactivation, where an epigenetic mark or pattern resulting in imprinting is inherited without further changes in somatic cells, but in germ cells the original inherited pattern is erased, and in the individual - appropriate to the gender - a new female or male epigenetic pattern, imprint is built up. To our knowledge, there are about 100 imprinted genes in humans, which generally play a role in ontogeny - especially around the implantation period – in growth and behavior. These genes are not completely dispersed in the genome, but form groups, so-called differentially imprinted regions (clusters). In mice, chromosome 7, in humans 11 and 15 are particularly rich in imprinted chromosomal regions.
4.3.2.1. Imprinting related diseases
The research of the imprinting related diseases is still in its infancy, as many very finely tuned mechanisms may lead to the development of these. The best known disorders due to imprinting are Prader-Willi and Angelman syndromes, where the 15q11-q13 region is affected. While in Prader-Willi syndrome the maternal UPD or paternal deletion of the above mentioned region is the cause of the disease, Angelman syndrome may be caused by maternal deletion or paternal UPD of this region or by mutation of the UBE3A (ubiquitin ligase) also located in this region. Moreover, in both cases, mutations of the center responsible for imprinting (IC) occur. Prader-Willi syndrome is characterized by obesity, small hands and feet, underdeveloped genitalia, mild mental retardation. Symptoms observed in Angelman syndrome are quite different.
Developmental retardation, compulsive movements, laughter (that is why the disease was formerly called happy puppet syndrome), poor speech ability or complete inability of the speech are the characteristic features.
More known rare diseases related to imprinting:
a. Beckwith-Wiedemann syndrome: in which two differentially imprinted regions (clusters) can be found in the 11p15.5 region with the H19, IGF2 and the KCNQ10T genes. The former cluster is associated with childhood kidney tumor disorders (Wilms' tumor, Beckwith-Wiedemann syndrome). During tumor formation loss of heterozygosity occurs in renal tissue (LOH; see chapter 2 Mutations), but then almost always (over 90%) the maternal allele is lost.
b. Silver-Russell syndrome (7p11.2 or 11p15.5);
c. the pseudo-hypoparathyroidism (20q13.2) d. transient neonatal diabetes mellitus (6q24).
4.3.2.2. Evolutionary causes of imprinting
There are several theories to explain the evolutionary origin of imprinting. One of the most well-known is the so-called conflict of parental interests theory. Thus, fathers will be able to spread their genes best when there is a lot of offspring. If, the maternal body is exhausted due to the numerous births, or the mother dies, the father can produce more offspring with another partner, and further transmits his genes. In contrast, the mothers interests are to save resources, i.e. that not one child will use all maternal resources they also can survive additional reproductive cycles and eventually successfully transmit their genes. That is, the paternal genes stimulate - even at the expense of the mother - fetal growth, while the maternal ones restrict the fetal access to nutrient resources. This concept is well suited to the hydatidiform mole and the observations in the case of ovarian teratomas and by the fact that the IGF2 (like growth factor 2 = insulin-like growth factor 2) and its receptor (IGFR) genes are imprinted as well. The imprinting of these two genes is specific: paternal IGF2 gene is weakly, and the IGFR gene is highly methylated, while in the mother the opposite is observed. The significance of this is that the effects of the two parents equalized in this way more growth factor is in vain when the amount of the receptor is reduced. As the Prader-Willi and Angelman syndromes do not confirm the above theory, therefore, there should be other unknown reasons for imprinting. According to one of these new theories upright position and balance shift during pregnancy may have a role. The maternal imprinting restricts fetal growth and thus shifting the center of gravity during pregnancy, thus making the upright posture and walking more stable, which could be crucial and life-saving for early human ancestors.