Genomic imprinting refers to a genetic phenomenon whereby there is preferential expression of a gene from only one of the two parental alleles. This phenomenon of allele-specific expression results from allele-specific epigenetic modifications such as CpG dinucleotide methylation or histone methylation or histone acetylation. These modifications are referred to as epigenetic modifications (also referred to as epigenetic "marks"). In non-imprinted regions of the chromosomes, the parental epigenetic marks are erased in the germ cells only to be newly established in a parental-specific manner. Once the parental-specific epigenetic marks are established, they are maintained following fertilization. In contrast, imprinted genes exhibit what are referred to as differentially methylated regions (DMRs) and these DMRs escape the genome-wide demethylation that takes place during the earliest cleavage events of embryonic development. In addition, these DMRs escape the global de novo methylation that normally occurs when the embryo undergoes implantation. Two distinct types of DMRs have been found: those that are formed following fertilization and those that are formed in the germ cells and maintained throughout development. The latter DMRs are associated with chromosomal regions termed imprinting control centers, ICRs.
The deregulation of imprinted genes has been associated with several diseases in humans. A characteristic feature of all of these diseases is that they do not exhibit normal Mendelian patterns of inheritance as well as showing parental origin effects. The normal role of imprinting seems to have evolved to fine-tune the growth and development of the fetus. Studies have shown that for the most part paternally expressed genes are associated with enhanced growth and maternally expressed genes lead to suppressed growth. In analysis of human imprinted genes and their counterparts in mice it has been shown that imprinted genes play important roles in the regulation of growth during embryonic and post-natal development. In addition, imprinted genes are often found misexpressed in cancers.
Classic human disorders related to genomic imprinting are Prader-Willi syndrome (PWS), Angelman syndrome (AS), Beckwith-Wiedemann syndrome (BWS), Russell-Silver syndrome (RSS), and Albright hereditary osteodystrophy. Given that the same chromosomal locus is involved in the genesis of PWS and AS these disorders are discussed together as a pair of syndromes.
|Syndromes Involving Imprinted Genes||Chromosomal Location|
|Beckwith-Wiedemann syndrome, BWS||11p15|
|Prader-Willi syndrome, PWS||15q11.2–q12|
|Angelman syndrome, AS||15q11.2–q12|
|Russell-Silver syndrome, RSS||7p11–p13, 7q31–qter|
|Transient neonatal diabetes mellitus, TNDM||6q24|
|Albright hereditary osteodystrophy, McCune-Albright syndrome, PHP1b||20q13|
|Familial nonchromaffin paraganglioma||11q13|
|Maternal and paternal UPD14 syndromes||14|
In addition to the syndromes listed in the Table above several diseases that are the result of complex genetic involvement have been shown to exhibit parent-of-origin effects. These disorders include autism, Hirschsprung disease, Alzheimer disease, schizophrenia, bipolar affective disorder, and type 1 and type 2 diabetes.
Prader-Willi and Angelman syndromes were the first diseases associated with genomic imprinting. Prader-Willi syndrome (PWS) was first described in 1887 by John Langdon Down who also identified Down syndrome. The full spectrum of PWS was reported in 1956 by Andrea Prader, Alexis Labhart, and Heinrich Willi, hence the current name of the disorder.
Angelman syndrome (AS) is named after the English physician Harry Angelman who first described the disorder in 1965. He observed three children with a similar constellation of symptoms and he referred to these symptoms as the "happy puppet syndrome" because of their smiling and laughing demeanor and jerky gait. The disease is now known to occur with a frequency of 1 in 15,000 to 20,000 persons worldwide.
Although the symptoms of these two disorders are quite different it was shown in 1989 that both are caused by indistinguishable deletions on chromosome 15. However, the distinct clinical spectrum of PWS and AS results as a consequence of the parental origin of the chromosomal deletion. PWS results from the loss of a group of paternally inherited genes in the deleted region of chromosome 15, whereas, AS results from loss of a maternally inherited gene in the same chromosomal region. The imprinted region of chromosome 15 that comprises the domain responsible for manifestation of PWS and AS spans from 15q11.2–q13.
In 70% of PWS cases there is a 4 megabase (Mb) de novo deletion of the paternal chromosome 15 domain (identified genetically as [del(15)(q11q13)pat]. This region contains several imprinted and several non-imprinted genes. In another ~29% of PWS cases there is maternal uniparental disomy of chromosome 15 (genetically identified as updmat). Uniparental disomy (UPD) refers to the presence of two copies of a chromosome (or part of a chromosome) from one parent and none from the other. This maternal UPD most often arises as a result of meiotic nondisjunction followed by loss of the paternal chromosome 15 following fertilization. A final small percentage (~1%) of PWS cases are patients with apparently normal chromosome 15 inheritance but there is an imprinting defect such that the paternal chromosome 15 carries a maternal imprint. Analysis of this region of chromosome 15 has identified several genes but the contribution of any of the genes to the development of PWS is still unknown. The genes in this region of chromosome 15 include SNURF/SNRPN (SNURF=SNRPN upstream reading frame: SNRPN=small nuclear ribonucleoprotein N), UBE3A (ubiquitin ligase E3A), ATP10C (aminophosphoplipid-transporting ATPase), MKRN3 (makorin ring finger protein 3; member of a protein family that function as ubiquitin ligases), NDN (necdin; a growth suppressor expressed predominantly in postmitotic neurons), MAGEL2 (MAGE-like protein 2 where MAGE family are melanoma antigen proteins), and over seventy C/D box snoRNA genes (snoRNAs are small nucleolar RNAs that guide methylation or pseudouridylation of rRNAs and other small nuclear RNAs).
At least four known genetic mechanisms can result in AS. The vast majority of cases (70%) result from de novo maternal deletions encompassing the chromosome 15q11.2–q13 region. Approximately 2% of AS cases involve paternal UPD. Genomic imprinting defects lead to an additional 2%–3% of AS cases. The remaining approximately 25% of AS patients will harbor mutations in the UBE3A gene. This latter gene is located at chromosome 15q11–q13 spanning 120kbp and composed of 16 exons, including 6 exons that comprise the 5'-untranslated region of the mRNA. The finding that point mutations in UBE3A were associated with AS led to the identification that all chromosomal defects found in AS patients encompass this gene. Of particular significance to the clinical manifestation of AS is the fact that imprinted UBE3A expression is restricted to the brain.
Whereas all PWS patients harbor some chromosome 15 event, there is a small percentage (15%–20%) of individuals suspected of having AS that harbor a genetic defect of unknown origin.
PWS is characterized a failure to thrive in the neonatal period accompanied by muscular hypotonia. During early childhood PWS patients exhibit hyperphagia (excessive hunger and abnormally large intake of solid foods), obesity, hypogonadism, sleep apnea, behavior problems and mild to moderate mental retardation. Additionally, PWS children have small hands and feet. In prepubertal males the hypogonadism results in sparse body hair, poor development of skeletal muscles, and delay in epiphyseal closure which resulting in long arms and legs. In prepubertal females the hypogonadism results in failure to progress through puberty or leads to primary amenorrhea (lack of menses).
AS is characterized by severe mental retardation, the smiling and laughing demeanor mentioned above, ataxia, absence of speech and microcephalus (head circumference that is at least 2 standard deviations smaller than normal).
BWS is the most well characterized disorder affecting growth that results from defects in imprinting. The overall frequency of BWS is 1 in 13,700. The disorder is found with equal distribution between males and females and has been identified in numerous ethnic populations. BWS is caused by alterations (both genetic and epigenetic) in a 1Mb region of chromosome 11 (11p15.5) that encompasses at least 15 genes many of which are imprinted. The most prominent genetic alterations found in BWS patients are paternal UPDs. There are two imprinted domains (differentially methylated regionas, DMR) within the 1 Mb region of chromosome 11. Alterations in two genes [one in domain 1 (DMR1) and one in domain 2 (DMR2)] are considered key events in the genesis of BWS. These two genes are IGF2 and CDKN1C. The IGF2 gene encodes the growth factor insulin-like growth factor 2 and the CDKN1C gene encodes the cell cycle regulator p57KIP2.
The IGF2 gene is normally only expressed from the paternal chromosome and this parental-specific expression pattern is controlled by an imprinting control element that lies close to the maternally imprinted neighboring gene identified as H19. The H19 gene encodes long non-coding RNA (lncRNA) that has been suspected to act as a tumor suppressor. The H19 promoter as well the imprinting center, DMR1, located several kb upstream are differentially methylated. The paternal allele is methylated whereas, the maternal allele is not. Expression of IGF2 and H19 is coordinated by DMR1 such that on the maternal chromosome only H19 is expressed and on the paternal chromosome only IGF2 is expressed. The CDKN1C gene resides approximately 700 kb from both IGF2 and H19 and it too is maternally expressed.
The CDKN1C gene is located in domain 2 which reside centromeric to domain 1 on chromosome 11. There are several other imprinted genes in the region of CDKN1C but mutations in CDKN1C are most associated with BWS relative to any of the other genes in domain 2. Since the CDKN1C gene encodes a cyclin-dependent kinase inhibitor it is involved in negative regulation of cell proliferation. It functions as both a tumor suppressor and as a potential negative regulator of fetal growth. Expression of the genes in domain 2 are regulated by the imprinting center called DMR2. Normally the maternal allele of DMR2 is methylated. Loss of maternal methylation of DMR2 is seen in 50%-60% of patients with sporadic BWS.
Other potentially important genes in domain 2 of chromosome 11 that are implicated in BWS and/or growth regulation are KCNQ1 (encodes a subunit of a voltage-gated potassium channel, was previously called KvLQT1), KCNQ1OT1 (this gene, present in intron 10 of the KCNQ1 gene, encodes a non-coding RNA expressed in the antisense direction relative to KCNQ1), PHLDA2 (plekstrin homology-like domain, family A, member 2), and SLC22A18 [solute carrier family 22 (organic cation transporter), member 18].
The cardinal features of BWS are exomphalos (an umbilical hernia at birth in which some abdominal organs push into the umbilical cord), macroglossia (an enlarged tongue), and gigantism (specifically embryonic and placental overgrowth). These three cardinal symptoms lead to an original designation of this disorder as EMG syndrome. In addition, individuals with BWS have a predisposition to childhood cancers. These cancers include Wilms tumor (a kidney cancer), adrenocortical cancer, hepatoblastoma, and rhabdomyosarcoma.