Genetic imprinting

Biology

Also known as: Genomic imprinting, parental imprinting

Anatomy or system affected: All

Definition: The silencing of specific genes by means of deoxyribonucleic acid (DNA) methylation that is initially established during sperm and oocyte production. Typically, gene expression is influenced by the genetic contribution from both parents. For an imprinted gene, expression in the offspring is determined by just one of the parents, the parent in whom the gene has not been silenced through methylation.

Key terms:

allele: alternative form of a gene

autosome: a nonsex chromosome of which there are 22 pairs in a normal human. Humans also have a 23rd pair of chromosomes, the sex chromosomes.

deacetylation: removal of an acetyl group

differentiation: process in which a cell becomes more specialized

gametogenesis: production of sperm in males and oocytes in females

gene expression: for genes that code for proteins, a collective term for transcription of the gene, translation of the resulting messenger ribonucleic acid (mRNA), and posttranslational modifications of the resulting protein, all of which determine the quantity and timing of appearance of the protein in the cell

histone proteins: proteins involved in forming histone octamers that package and compact chromosomal DNA

locus: physical region on a chromosome where a specific gene or genes reside

methyltransferase: a protein enzyme that catalyzes methylation, the addition of a methyl group (-CH₃) to a cytosine base of certain CpG dinucleotides in DNA

RNA polymerase: enzyme that synthesizes RNA from a DNA template in the process called transcription

Structure and Functions

In any given normal individual, the expression of most genes occurs from both of the alleles, the one inherited from the father and the one inherited from the mother. Expression of imprinted genes varies from this paradigm in that only one of the alleles is actively expressed. The active allele and the silent allele are determined during gametogenesis in the parents. At least 1 percent of mammalian genes are thought to be imprinted, and the purpose of this phenomenon is to fine-tune gene expression during differentiation and development. Mammals silence these genes and maintain this silencing through the attachment of -CH₃ or methyl groups (methylation) to cytosine bases in DNA at CpG dinucleotides. During DNA replication, enzymes called maintenance methyltransferases attach methyl groups to cytosine bases in the newly formed strand of DNA in order to match the methylation pattern found on the parental DNA strand. During meiosis, a special type of cell division used to produce gametes (eggs and sperm), the DNA is reactivated (the methylated groups are removed), and then a different set of enzymes called de novo methyltransferases establish the gender-specific imprinting pattern (sex-specific pattern of base methylation in the DNA). This mechanism is used for imprinting genes on both X chromosomes and autosomes.

Genetic imprinting can be illustrated by describing gene expression from the first chromosome locus where imprinting was observed. This locus is on human chromosome 15 and contains the gene for insulin-like growth factor 2 (Igf2) as well as a gene named H19, which encodes a regulatory RNA thought to be involved in the suppression of tumors. The Igf2 gene is silenced or imprinted on the maternal chromosome but actively expressed from the chromosome contributed by the male. The opposite imprinting pattern applies to the H19 gene. H19 is imprinted on the paternal chromosome but actively expressed from the maternal chromosome. As a result maternal Igf2 and paternal H19 gene expression is silenced while maternal H19 and paternal Igf2 gene expression is active. Normal development requires this gene expression pattern, and severe abnormalities occur in individuals who inherit disruptions of this pattern.

The details of the imprinting mechanism of the Igf2 and H19 genes are complex but provide a good example of common molecular aspects of many imprinted gene clusters. Along the Igf2/H19 locus is a region of DNA called an enhancer, which is bound by a protein factor called an activator. The activator typically recruits RNA polymerase and its associated protein transcription factors to the locus for transcription of these genes. Another DNA sequence known as an insulator is located nearby and lies between the Igf2 and H19 genes. The insulator is bound by a protein called the CCCTC-binding factor (CTCF), and CTCF binding prevents transcription of the Igf2 gene by shielding the Igf2 gene from the activator. Specifically CTCF attracts a complex of proteins that contain a histone deacetylase. Histone deacetylase catalyzes the “deacetylation” of histone proteins (the removal of acetyl groups), thus tightening the histones' grip on the DNA. DNA in the tightened grip of histones is less accessible to RNA polymerase and transcriptional activators; consequently, that DNA is not transcribed and is said to be silenced. On the maternal chromosome, CTCF binds to the insulator sequence, effectively turning off Igf2 gene transcription; however, the activator is still able to stimulate H19 gene transcription nearby. On the paternal chromosome, the H19 gene and the insulator sequences are methylated, preventing the activator from turning on H19 gene transcription and preventing the binding of CTCF to the insulator sequence. Without CTCF binding to the insulator sequence, the activator is free to stimulate Igf2 gene transcription.

Disorders and Diseases

Prader-Willi syndrome (PWS) occurs in 1 out of every 25,000 births, affecting 350,000-400,000 people across the world, and is the most common genetic cause of life-threatening obesity. Pedigree and molecular genetic analyses reveal that roughly 80 percent of cases involve deletion of a gene or genes on the long arm of chromosome 15 in the father that is exacerbated by genetic imprinting of the maternal chromosome 15 in the same region of the paternal deletion. Affected individuals are small at birth with feeding difficulties and retarded development, both physically and mentally. Children often exhibit self-injurious behavior such as skin picking. At six months of age feeding difficulties improve but transition to uncontrolled eating habits as an adolescent and adult, leading to obesity and diabetes. The major treatment is weight control through calorie restriction and the administration of recombinant human growth hormone to decrease body fat while increasing muscle mass.

A closely related disorder is Angelman syndrome (AS) in which affected individuals have seizures, jerky limb movements, marked mental retardation, a small head, and periods of inappropriate laughter. The estimated prevalence for AS is one in fifteen thousand. In 50 percent of AS patients, the same region of chromosome 15 involved in PWS, which is imprinted (methylated) from the male, is deleted from the corresponding maternal chromosome. The critical gene in this region required for early brain development is the ubiquitin ligase gene, UBE3A. Ubiquitin ligase enzymes are indispensable in cells because they catalyze the attachment of the small protein named ubiquitin onto proteins that are improperly folded or worn out, thus marking them for destruction.

Silver-Russell syndrome (SRS) occurs about once in every seventy-five thousand births. These individuals have stunted growth with asymmetry of the limbs and immature bone development, especially prevalent in the head and upper trunk. Characteristically a small, triangular face with frontal bone prominence is observed. SRS is thought to be the first human pathology caused by imprinting disruptions of genetic loci on two different chromosomes, chromosomes 7 and 11.

Beckwith-Wiedemann syndrome (BWS) is characterized by several clinical features. Some of those features include craniofacial development anomalies, hypoglycemia, enlargement of the kidneys, liver, and spleen, and abdominal tumors. Consequently, regular tumor monitoring through abdominal sonograms and analysis of urine and blood tumor markers is a critical aspect of care. Hypomethylation of an imprinted region of chromosome 11 appears to be involved in 40–60 percent of BWS cases. The estimated incidence is 1 in 13,700.

Albright hereditary osteodystrophy (AHO) is due to mutation in an imprinted gene that encodes the alpha subunit of the membrane-associated trimeric G protein (GNAS). Considered a rare disorder, some estimates place the incidence at one in roughly 7 million. As a result of maternal gene disruption, those affected are not responsive to the parathyroid hormone or other hormones, especially the thyroid-stimulating hormone. Because of the parathyroid hormone insensitivity, the kidneys respond as if the parathyroid hormone is deficient; hence, the disorder is also called pseudohypoparathyroidism (PHP). The clinical features include short build, short metacarpals with a rounded face, and short neck. It is possible to observe mineralization in subcutaneous tissue and AHO patients also show low blood calcium levels (hypocalcemia) with excessively high blood levels of phosphate (hyperphosphatemia). Dental characteristics include delayed eruption of teeth and lack of tooth enamel formation. Those individuals who have these features and hormone resistance are said to have PHP type Ia, and those who lack the clinical features but still have hormone resistance are said to express the type Ib subtype. Treatment for these patients includes calcium and vitamin D doses to help maintain normal calcium and parathyroid hormone levels in the bloodstream. Individuals with the clinical features but normal hormone responsiveness are said to display pseudopseudohypoparathyroidism (pseudoPHP) resulting from disruption of the paternal copy of the GNAS gene.

Perspective and Prospects

The disorders resulting from genetic imprinting defects were studied clinically and reported beginning in the 1940s. The molecular mechanisms of genetic imprinting were approached once the advent of recombinant DNA technologies occurred in the 1980s. Scientists began to use the mouse as a model to better understand imprinting in humans. The Igf2/H19 locus imprinting phenomenon was the first elucidated, in part through studies of an Igf2 knockout mouse strain (mouse in which the Igf2 gene was removed through recombinant DNA techniques). Progeny that inherited the deletion from the female parent were normal sized, but those mice that received the deletion from the father were small. As a result it was understood that the Igf2 gene is only expressed from the paternal chromosome and hence is an imprinted gene. Genetic engineering techniques are used to create mouse strains that model imprinting disorders, like PWS. Scientists have developed some mouse strains in which genes are introduced (transgenes) to alter the dosage or expression level of those genes to mimic imprinting phenomena. Recent publication and annotation of the complete mouse genome sequence will aid scientists in their efforts to further understand imprinting.

Through computational approaches and microarray (known DNA sequences affixed to a microchip) technology, researchers have identified imprinted genes. In yet another method, scientists have extended DNA sequencing to sequencing RNA in such a way that all of the RNAs in a given cell, tissue, or organ can be sequenced and quantitated at a given time. This allows for the identification of genes that undergo tissue-specific and time-specific expression as a result of imprinting. Using an RNA sequencing approach, a group recently identified over 347 imprinted autosomal genes in the mouse cerebral cortex and hypothalamus.

Studies of the epigenome (the chemical modifications to DNA bases and histone proteins that package the DNA of a genome) are accelerating as advances in molecular biology techniques have made it possible to investigate how genes are silenced. The National Institutes of Health (NIH) initiated the Roadmap Epigenomics Program in 2008 and, as of May 2012, had compiled over sixty-one complete epigenomes from different cell types. These studies are also adding to the knowledge of imprinting.

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