Skewed X-chromosome inactivation (skewed X-inactivation) occurs when the
X-inactivation
X-inactivation (also called Lyonization, after English geneticist Mary Lyon) is a process by which one of the copies of the X chromosome is inactivated in therian female mammals. The inactive X chromosome is silenced by being packaged into a ...
of one
X chromosome
The X chromosome is one of the two sex-determining chromosomes (allosomes) in many organisms, including mammals (the other is the Y chromosome), and is found in both males and females. It is a part of the XY sex-determination system and XO sex ...
is favored over the other, leading to an uneven number of cells with each
chromosome
A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
inactivated. It is usually defined as one
allele
An allele (, ; ; modern formation from Greek ἄλλος ''állos'', "other") is a variation of the same sequence of nucleotides at the same place on a long DNA molecule, as described in leading textbooks on genetics and evolution.
::"The chro ...
being found on the active X chromosome in over 75% of cells, and extreme skewing is when over 90% of cells have inactivated the same X chromosome.
It can be caused by primary nonrandom inactivation, either by chance due to a small cell pool or directed by genes, or by secondary nonrandom inactivation, which occurs by
selection
Selection may refer to:
Science
* Selection (biology), also called natural selection, selection in evolution
** Sex selection, in genetics
** Mate selection, in mating
** Sexual selection in humans, in human sexuality
** Human mating strateg ...
.
X-chromosome inactivation occurs in females to provide
dosage compensation Dosage compensation is the process by which organisms equalize the expression of genes between members of different biological sexes. Across species, different sexes are often characterized by different types and numbers of sex chromosomes. In order ...
between the sexes. If females kept both X chromosomes active, they would have twice the number of active X
genes
In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a ba ...
than males, who only have one copy of the X chromosome. At approximately the time of embryonic
implantation, one of the two X chromosomes in each cell of the female embryo is randomly selected for inactivation. Cells then undergo
transcriptional and
epigenetic changes to ensure this inactivation is permanent (such as
methylation and being modified into
Barr bodies). All progeny from these initial cells will maintain the inactivation of the same chromosome, resulting in a phenotypic mosaic pattern of cells in females
although not a
genotypic mosaic.
Most females will have some levels of skewing. It is relatively common in adult females; around 35% of women have a skewed ratio over 70:30, and 7% of women have an extreme skewed ratio of over 90:10. This is of medical significance, due to the potential for the expression of disease genes present on the X chromosome that are normally not expressed due to random X-inactivation.
Causes
Primary nonrandom inactivation
Nonrandom X-inactivation leads to skewed X-inactivation. Nonrandom X-inactivation can be caused by chance or directed by genes. If the initial pool of cells in which X-inactivation occurs is small, chance can cause skewing to occur in some individuals by causing a bigger proportion of the initial cell pool to inactivate one X chromosome. A reduction in the size of this initial cell pool would increase the likelihood of skewing occurring.
This skewing can then be inherited by progeny cells, or increased by secondary selection.
The X-chromosome controlling element (Xce) gene in mice has been found to influence genetically mediated skewing. It is unknown whether a similar gene plays a role in human X-inactivation, although a 2008 study found that skewing in humans is mostly caused by secondary events rather than a genetic tendency.
There is a much higher concordance rate in genetically identical (monozygotic) twins compared to non-identical (dizygotic) twins, which suggests a strong genetic input. A 10% difference in the skewing of genetically identical twins did exist however, so there are other contributing factors outside of genetics alone. It is difficult to identify primary nonrandom inactivation in humans, as early cell selection occurs in the embryo. Mutation and imprinting of the
XIST gene, a part of the X-inactivation centre, can result in skewing. This is rare in humans.
Xce
Skewed X-inactivation in mice is controlled by the Xce gene on the X chromosome. Xce acts in
cis
Cis or cis- may refer to:
Places
* Cis, Trentino, in Italy
* In Poland:
** Cis, Świętokrzyskie Voivodeship, south-central
** Cis, Warmian-Masurian Voivodeship, north
Math, science and biology
* cis (mathematics) (cis(''θ'')), a trigonome ...
, which means that it acts upon the chromosome from which it was transcribed.
There are four alleles of Xce, labeled ''a'', ''b'', ''c'', and ''d''. Each allele has a different likelihood of inactivation, with ''a'' < ''b'' < ''c'' < ''d'', where ''d'' is the most likely to remain active and ''a'' is the least likely. The strength differences between the four alleles are likely due to variations in the number of binding sites for a crucial actor in inactivation. The specific transfactor is not known currently.
Homozygotic mouse cells will have roughly even levels of inactivation due to both alleles having equal chance of being inactivated. For example, a mouse with the genotype ''dd'' will have an inactivation ratio very close to 50:50. Heterozygotes, will experience greater levels of skewing due to the differing inactivation likelihood of the two alleles. A mouse cell with the Xce genotype ''ad'' will have a greater number of the ''a''-carrying than ''d''-carrying X chromosomes inactivated, because the ''d''-carrying X chromosome is less likely to be inactivated.
There are two theories on the mechanism Xce uses to affect inactivation. The first is that genomic differences in the Xce alleles alter the sequence of the long non-coding RNA that is an integral part of X chromosome inactivation. The second is that Xce acts as a binding site for dosage factors that will affect
XIST gene and
Tsix
Tsix is a non-coding RNA gene that is antisense to the Xist RNA. Tsix binds Xist during X chromosome inactivation. The name Tsix comes from the reverse of Xist, which stands for X-inactive specific transcript.
Background
Female mammals have ...
expression (long non-coding RNAs involved in X chromosome inactivation).
Parent-of-origin
Skewing can also be influenced by the parent-of-origin effect, in which skewing becomes biased towards either the maternal or paternal X chromosome.
Studies have suggested an X-linked gene or genes that control this effect, but the exact gene has not yet been identified.
A 2010 study found a small but significant under-expression of the paternal X chromosome in mice. Extra-embryonic tissues are found to preferentially inactivate the paternal X chromosome.
Marsupial
Marsupials are any members of the mammalian infraclass Marsupialia. All extant marsupials are endemic to Australasia, Wallacea and the Americas. A distinctive characteristic common to most of these species is that the young are carried in a po ...
s will always inactivate the paternal X chromosome, in a process named
imprinting. Researchers hypothesized a link between the slight preference for inactivation of the paternal X in mice tissue, and the preference in extra-embryonic tissue and Marsupials. There may be a conserved epigenetic mark that drives this preference.
Promoter mutations
Skewed inactivation patterns can also emerge due to mutations that change the quantity of guanine on the Xist promoter. The Xist gene is responsible for inactivating the X chromosome from which it is transcribed. X-chromosome inactivation in general is influenced by the number of guanine-containing nucleotides on the Xist promoter, although generally inactivation still follows a random pattern. A rare mutation can occur, however, in which a cytosine residue is converted to guanine on the Xist promoter. It has been hypothesized that the mutation causes a change in the Xist transcript or in the levels of transcript produced, which causes the cell to differentiate between the two X chromosomes and causes the chromosome with the mutation to become preferentially inactivated. The mechanism has not been fully elucidated at this time, although research does point towards decreased promoter activity as a result of the mutation being a major part of the process.
Secondary skewing
Secondary skewing occurs when an X-linked mutation affects cell proliferation or survival. If a mutation on one X chromosome negatively affects a cell’s ability to proliferate or survive, there will end up being a larger proportion of cells with the other X chromosome active. This selection of one X chromosome can vary between tissue types, as it depends on the specific gene and its activity in the tissue, with rapidly dividing cells giving selection processes more time to work.
Blood cell
A blood cell, also called a hematopoietic cell, hemocyte, or hematocyte, is a cell produced through hematopoiesis and found mainly in the blood. Major types of blood cells include red blood cells (erythrocytes), white blood cells (leukocytes) ...
s, for example, tend to have the highest rates of skewing due to the extremely high dividing and replacement rate within the human body.
The strength of selection can also vary depending on the gene under selection, and so skewing can occur at different rates and to different extents.
Secondary selection tends to cause an increase in skewing with age. This is primarily due to a longer span over which selective pressure has room in which to act.
Skewing is still seen in young children, but with a lower frequency and at less extreme levels in most cases.
Clinical significance
Skewed X-inactivation has medical significance due to its impacts on X-linked diseases. X-chromosome skewing has an ability to amplify diseases on the X chromosome. In wildtype women, recessive diseases on the X chromosome are often unexpressed due to the roughly even inactivation process, which prevents mutated alleles from becoming heavily expressed. However, skewed inactivation can lead to a more severe expression of the disease.
The diseased X-linked allele can also cause strong selection in a heterozygote for the cells with the diseased allele on the inactive chromosome. Therefore, strong skewing in female members of a family can suggest they are carriers of an X-linked disease.
Cancer predisposition
Skewed X-inactivation has also been found to correlate with a higher rate of
ovarian cancer
Ovarian cancer is a cancerous tumor of an ovary. It may originate from the ovary itself or more commonly from communicating nearby structures such as fallopian tubes or the inner lining of the abdomen. The ovary is made up of three different c ...
, although the mechanism behind this is unknown. A 2013 study also found skewed X-inactivation to be a factor that predisposes individuals to
esophageal carcinomas. It has been postulated that skewed X-inactivation might lead to a decrease in the expression of X-linked
tumor suppressor gene
A tumor suppressor gene (TSG), or anti-oncogene, is a gene that regulates a cell during cell division and replication. If the cell grows uncontrollably, it will result in cancer. When a tumor suppressor gene is mutated, it results in a loss or red ...
s in an individual who also has a
germline mutation
A germline mutation, or germinal mutation, is any detectable variation within germ cells (cells that, when fully developed, become sperm and ova). Mutations in these cells are the only mutations that can be passed on to offspring, when either a m ...
in the expressed chromosome. This would cause the gene on that chromosome to become under-expressed, making it more difficult for cells to regulate themselves properly. Other researchers have contended that such a mutation would lead to higher rates of cancer among wild type females, as approximately half the cells would not express the gene due to random inactivation. One would also see a higher rate of cancer in males with the mutation. Instead, the researchers proposed that the cause of cancer and skewed inactivation could potentially be separate events, or both be caused by an unknown source.
Rett syndrome
Rett syndrome
Rett syndrome (RTT) is a genetic disorder that typically becomes apparent after 6–18 months of age and almost exclusively in females. Symptoms include impairments in language and coordination, and repetitive movements. Those affected often h ...
is a genetic disorder caused by a mutation of the ''
MECP2'' gene on the X chromosome. The disease occurs mostly in females and involves repetitive hand movements, frequent seizures and a loss of vocal skills and sometimes motor skills. Females with one copy of the mutated allele show symptoms of severe mental retardation. Asymptomatic carriers and patients with very mild symptoms have been described, who can show skewed X-inactivation that favors the inactivation of the mutated allele. Asymptomatic carriers can pass on the mutated allele to their daughters, who can show full symptoms if skewing does not occur. Most Rett syndrome cases show no skewing.
Autoimmunity
Skewed X-inactivation has been correlated with several
autoimmune diseases, including
autoimmune thyroid disease (ATD) and
scleroderma
Scleroderma is a group of autoimmune diseases that may result in changes to the skin, blood vessels, muscles, and internal organs. The disease can be either localized to the skin or involve other organs, as well. Symptoms may include areas ...
. Autoimmune thyroid disease is a disease involving the
thyroid gland
The thyroid, or thyroid gland, is an endocrine gland in vertebrates. In humans it is in the neck and consists of two connected lobe (anatomy), lobes. The lower two thirds of the lobes are connected by a thin band of Connective tissue, tissue cal ...
. The immune system of those who have the condition recognize the thyroid as foreign and attack it, causing it to
atrophy. Women have a predisposition towards the condition, and research indicates that this might in part be due to skewed X-inactivation. It was discovered that when twins with the disease were examined, the prevalence of skewing was above 30% as compared to 11% in the control group of wild type women, indicating that X-chromosome skewing could possibly be involved in the cause of the condition. Similar results have also been witnessed in scleroderma, which involves hardening of the skin and inner organs. Skewing levels were found in 64% of informative patients, as compared to only 8% of the control group, also indicating a strong correlation and possible cause. The mechanism behind both conditions is unclear at this time.
Autism
Higher levels of skewed X chromosome inactivation have been correlated with cases of
autism
The autism spectrum, often referred to as just autism or in the context of a professional diagnosis autism spectrum disorder (ASD) or autism spectrum condition (ASC), is a neurodevelopmental condition (or conditions) characterized by difficulti ...
in women. 33% of autistic women in a study had extreme levels of skewing, with only 11% of the wildtype control having extreme levels of skewing. The study also revealed that the mothers of the autistic daughters with skewing also had significant levels of skewing, indicating a higher level of heritability as compared to the wild type population. The reason behind this is currently unknown, as no mutations in the
Xist promoter were detected.
Klinefelter syndrome
Klinefelter 47,XXY and
48,XXYY patients were found to have significantly skewed X-chromosome levels in 31% of the patients examined, with researchers predicting that this skewing might be responsible for the mental deficiencies and abnormalities present. Different forms of the disease also showed preferential activation towards either the maternal or paternal X chromosome. This might indicate that parent-of-origin effects such as
imprinting might be involved with the X-chromosome skewing.
Metabolism
X-linked
glycogen storage disease (GSD IXa) is a
metabolic disorder
A metabolic disorder is a disorder that negatively alters the body's processing and distribution of macronutrients, such as proteins, fats, and carbohydrates. Metabolic disorders can happen when abnormal chemical reactions in the body alter t ...
typically only seen in males because of the X-linked inheritance pattern. Since women are
mosaic
A mosaic is a pattern or image made of small regular or irregular pieces of colored stone, glass or ceramic, held in place by plaster/mortar, and covering a surface. Mosaics are often used as floor and wall decoration, and were particularly pop ...
models when it comes to gene expression, they tend to mask X-linked mutations by using the other X to compensate. Skewed X-inactivation resulting in the expression of the defective X chromosome can cause X-linked mutations to be expressed in women.
The problem occurring in IXa is a defect in
phosphorylase b kinase (PHK). PHK activates
glycogen phosphorylase
Glycogen phosphorylase is one of the phosphorylase enzymes (). Glycogen phosphorylase catalyzes the rate-limiting step in glycogenolysis in animals by releasing glucose-1-phosphate from the terminal alpha-1,4-glycosidic bond. Glycogen phosphor ...
, which is a key enzyme to mobilize glucose from stored glycogen, through
phosphorylation
In chemistry, phosphorylation is the attachment of a phosphate group to a molecule or an ion. This process and its inverse, dephosphorylation, are common in biology and could be driven by natural selection. Text was copied from this source, wh ...
.
Glycogen
Glycogen is a multibranched polysaccharide of glucose that serves as a form of energy storage in animals, fungi, and bacteria. The polysaccharide structure represents the main storage form of glucose in the body.
Glycogen functions as one o ...
is the polymer storage unit of glucose in the body. When the body requires energy it can use enzymes such as PHK to break down the glycogen into glucose for the body to use. Some symptoms of the disease are altered blood glucose levels,
ketoacidosis
Ketoacidosis is a metabolic state caused by uncontrolled production of ketone bodies that cause a metabolic acidosis. While ketosis refers to any elevation of blood ketones, ketoacidosis is a specific pathologic condition that results in changes ...
, growth retardation, or liver distention.
Recurrent miscarriages
Skewed X-chromosome inactivation has been implicated in
miscarriages
Miscarriage, also known in medical terms as a spontaneous abortion and pregnancy loss, is the death of an embryo or fetus before it is able to survive independently. Miscarriage before 6 weeks of gestation is defined by ESHRE as biochemical ...
in the past. Recurrent pregnancy loss can be defined as either two or three consecutive lost pregnancies within five months. In most cases, the loss of pregnancy can be attributed to genetic, hormonal, anatomical and immunological problems. However, there are still about 50% of cases without a known cause. A study hypothesized that skewed X-inactivation may play a role in these miscarriages. However, a 2003 study found that there was no significant correlation between miscarriages and skewed X-inactivation, with only 6.6% of the patients showing significant skewing as compared to the 3.9% rate in the control group. It also stated that there had been a lack of controlling for age-related skewing in similar studies and concluded that it is unlikely for skewed X-inactivation to influence recurrent miscarriages.
Studying skewed X-inactivation
To study skewed X chromosome inactivation, there must be a detectable difference between the two parental chromosomes. This difference, or
polymorphism, will allow detection of which chromosome is active in the cell, so an inactivation ratio can be determined. Often, the
methylation levels of the inactive DNA are detected in order to identify the inactive chromosome.
Loci that are known to be polymorphic within the human population are selected. Assays that detect the methylation level of the highly polymorphic CAG trinucleotide at the 5’ end of the androgen receptor gene are often used in skewed X-inactivation studies. Other loci used include phosphoglycerate kinase,
hypoxanthine phosphoribosyl transferase and the DXS255 locus.
If these loci contain heavy methylation, it indicates the chromosome is inactive.
At the turn of the 21st century, ratio detection moved to more direct methods by using
mRNA
In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein.
mRNA is ...
or protein levels, and
whole exome sequencing
Exome sequencing, also known as whole exome sequencing (WES), is a genomic technique for sequencing all of the protein-coding regions of genes in a genome (known as the exome). It consists of two steps: the first step is to select only the sub ...
. With the exception of escaped genes, only the active X chromosome will transcribe mRNA and produce protein.
The exome sequencing provides a dataset that shows target sequences, giving an indication of disease-related protein coding regions. mRNA sequencing is then used on these regions to focus on the X chromosome and find
single nucleotide polymorphisms (SNP) that are associated with the disease. These SNPs are genotyped and traced to parental contributor to calculate the ratio of inactivation, based on how much genetic information each parent donated and how much of each parental allele is expressed. These levels of expression may give greater insight to the fundamental cause of the diseases seen from skewed X-inactivation.
Potential problems
There are several factors which must be taken into account when studying skewed X-inactivation. Escaped genes are ones found on the inactive X chromosome but are still expressed; this particular gene will be expressed from both chromosomes. It is estimated that 25% of the genes escape inactivation.
Genes used to study skewing must be carefully selected to ensure they do not escape inactivation, as they will not show any skewed pattern.
A skewed pattern might be more common in affected females than unaffected.
This must be considered when studying X-linked diseases. Due to the random nature of inactivation, women can have skewed inactivation due to simple statistical probability. This makes it difficult to determine when the ratio is abnormally skewed. Additionally, skewed activation can also be localized to specific cell lineages. For example, one woman might have skewed activation in her T cells but not the B cells, which in turn necessitates deep analysis work and adequate control of cell lines to ensure proper diagnosis.
References
{{reflist, 32em
Epigenetics