Histone Controls: Histone Modification Quiz

Genomic imprinting is an epigenetic mechanism that results in parent-of-origin-specific gene expression. For imprinted genes, only the allele inherited from one specific parent is expressed while the allele from the other parent is epigenetically silenced, typically through differential DNA methylation. Imprinting violates the standard rules of diploid genetics where both alleles contribute equally to expression. Approximately 100 to 200 genes in the human genome are imprinted, and many cluster in chromosomal regions regulated by shared imprinting control regions.

Imprinting marks must be erased in primordial germ cells and then re-established according to the sex of the developing organism. This ensures that eggs carry maternal imprinting marks and sperm carry paternal imprinting marks regardless of the imprinting status of the alleles inherited from the previous generation. If imprinting marks were not reset, a daughter who inherited a paternally imprinted allele from her father would pass on a paternal rather than maternal imprint to her children, disrupting the parent-of-origin specificity that defines imprinting.

Prader-Willi syndrome is caused by the loss of function of paternally expressed genes in the chromosomal region 15q11 to q13. In most cases this results from a deletion of the paternal chromosome 15 copy in this region. In the maternal copy of this region, the same genes are normally silenced by maternal imprinting. When the paternal copy is lost through deletion, maternal uniparental disomy, or an imprinting center defect, no functional copy of these paternally expressed genes remains, producing the Prader-Willi phenotype.

Prader-Willi and Angelman syndromes are caused by disruptions affecting the same chromosomal region but on opposite parental chromosomes. A deletion of the paternal 15q11 to q13 region causes Prader-Willi syndrome, while a deletion or mutation of the maternal copy causes Angelman syndrome. This striking contrast in clinical phenotype from the same genomic region powerfully demonstrates that the two parental copies of this locus carry different functional information encoded by differential imprinting rather than by differences in DNA sequence.

Prader-Willi syndrome requires absence of functional paternally expressed genes in 15q11 to q13. This can result from a deletion of the paternal chromosomal region, from maternal uniparental disomy where the child inherits both chromosome 15 copies from the mother leaving no paternal copy, or from an imprinting control center defect that prevents the paternal alleles from being expressed even when present. A point mutation in the maternal UBE3A gene causes Angelman syndrome, not Prader-Willi syndrome.

Uniparental disomy describes the inheritance of both copies of a chromosome from a single parent, leaving no contribution from the other parent for that chromosome. It can arise from errors in meiosis combined with subsequent correction during early development. For non-imprinted chromosomes, uniparental disomy may have no phenotypic effect if no recessive variants are present. For chromosomes containing imprinted genes, such as chromosome 15, uniparental disomy disrupts the normal balance of maternally and paternally expressed imprinted genes, potentially causing disease.

Imprinting control regions are cis-acting regulatory elements that carry parent-of-origin-specific DNA methylation marks established in the germline. They coordinate the expression of multiple imprinted genes in a cluster through two main mechanisms. First, as insulators, a differentially methylated imprinting control region can block enhancer-promoter interactions on one parental allele. Second, they can regulate the expression of imprinted non-coding RNAs such as AIRN or H19, which in turn silence neighboring genes in an allele-specific manner across the imprinted domain.

At the H19 and IGF2 locus, differential methylation of the imprinting control region determines reciprocal expression. On the maternal chromosome, the imprinting control region is unmethylated and bound by the CTCF insulator protein, which blocks the downstream shared enhancers from activating IGF2, so only H19 is expressed. On the paternal chromosome, the imprinting control region is methylated, CTCF cannot bind, the insulator is inactive, and the enhancers freely activate IGF2. H19 is also silenced on the paternal allele by spreading methylation.

Beckwith-Wiedemann syndrome is an overgrowth disorder caused by dysregulation of imprinted genes at chromosome 11p15. One common molecular cause is loss of imprinting at the H19/IGF2 locus, where both alleles express IGF2 instead of the normal monoallelic paternal expression. This biallelic overexpression of the growth-promoting IGF2 gene leads to excessive fetal and postnatal growth. Other causes include hypermethylation of the KCNQ1OT1 imprinting control region, each producing overlapping but distinct phenotypic presentations within the syndrome.

Mendelian inheritance assumes that the two alleles of a gene contribute equally to phenotype depending only on their dominant or recessive nature. Imprinted genes violate this principle because their expression depends entirely on which parent contributed the allele. A loss-of-function mutation in a maternally imprinted gene causes disease only when inherited from the father, while the same mutation inherited from the mother has no phenotypic effect because the maternal allele is already silenced by imprinting. This parent-of-origin effect is a defining characteristic of imprinted loci.

Genomic imprinting is distinguished from standard recessive inheritance in several ways. Expression of imprinted genes depends on parental origin, not allele dosage. Both parental alleles carry identical DNA sequences but differ in epigenetic marks such as DNA methylation. Imprinting marks are reset each generation in the germline to reflect the sex of the transmitting parent. In standard recessive inheritance, phenotype depends only on genotype, with both parental copies contributing equally regardless of which parent they came from.

Prader-Willi syndrome is characterized by severe hypotonia and poor feeding in infancy, followed by hyperphagia leading to obesity in childhood, mild to moderate intellectual disability, behavioral problems, and hypogonadism with incomplete pubertal development. These features collectively suggest that the paternally expressed genes in 15q11 to q13 normally regulate hypothalamic pathways controlling appetite, metabolic rate, muscle tone, and reproductive hormone signaling. Seizures and inappropriate laughter are features of Angelman syndrome, while accelerated growth suggests excess IGF2, a different imprinted gene locus.

The SNRPN gene encodes a protein involved in mRNA splicing, and the SNURF-SNRPN locus also encodes multiple small nucleolar RNAs including the SNORD116 and SNORD115 clusters. These are expressed exclusively from the paternal chromosome and are silenced on the maternal chromosome by imprinting. Loss of the SNORD116 cluster in particular has been strongly linked to the hyperphagia and hypothalamic dysregulation seen in Prader-Willi syndrome. These non-coding RNA genes illustrate that genomic imprinting affects non-protein-coding functional elements as well as protein-coding genes.

The parental conflict hypothesis proposes that imprinting evolved because paternal and maternal genomes have different evolutionary interests in resource transfer to offspring. Paternal genes maximize resources obtained from the mother to benefit offspring bearing paternal alleles, while maternal genes limit resource transfer to preserve maternal fitness across multiple offspring. The reciprocal imprinting of IGF2, a growth-promoting factor expressed only from the paternal allele, and IGF2R, a growth-suppressing receptor expressed from the maternal allele, is the most cited evidence supporting this evolutionary model of imprinting origins.

Differential DNA methylation at imprinting control regions is the primary molecular mechanism distinguishing parental alleles at imprinted loci. Imprinted non-coding RNAs including AIRN and H19 contribute to allele-specific silencing of neighboring genes in cis. Imprinting control regions coordinate the expression of entire gene clusters. Imprinting marks involve both DNA methylation and histone modifications working together; the claim in option C that imprinting involves only histone modifications is incorrect, as DNA methylation is central and often the primary heritable mark at most characterized imprinting control regions.