DNA Imprinting (Genomic Imprinting): What It Is and How It Is Tested

Short answer

DNA imprinting, usually called genomic imprinting, is the process by which only one copy of a gene is expressed while the other copy, inherited from the other parent, is suppressed. It works through chemical tags on the DNA rather than a change in the DNA sequence. In the laboratory, the practical question is how a disrupted imprint is detected: methylation testing of the imprinting control region is the first-line screen.

What DNA imprinting (genomic imprinting) means

Most genes are expressed from both the maternal and the paternal copy. An imprinted gene is an exception: a maternal or paternal allele is selectively silenced, so the gene is expressed from one parental copy only. The NHS England Genomics Education Programme states that more than 40 different regions of the genome are subject to imprinting, and describes the pattern as parent-specific, mono-allelic expression.

The NHGRI Talking Glossary stresses that imprinting does not change the DNA sequence. Chemical tags added to the DNA during egg or sperm formation silence one parental copy, which makes imprinting a form of non-sequence-based inheritance. For the wider field, see what epigenetics is, and for how it differs from sequence-based inheritance, genetics vs epigenetics.

How imprinting works: what is gene imprinting at the molecular level?

In an imprinted gene, one copy is epigenetically marked, or imprinted, in either the egg or the sperm. Geneimprint, the catalogue of imprinted genes, notes that these modifications are erased and then reset during the creation of eggs and sperm, and that the mechanisms are still incompletely defined. Two timescales are involved:

• Within one individual: the NHGRI states that epigenetic tags on imprinted genes usually stay in place for the life of the individual.
• Across generations: the tags are erased and reset when eggs and sperm are made, so the mark a person carries reflects the parent the gene came from, not a fixed property of the gene.

Imprinting in genetics: how imprinted loci fail

The NHS England Genomics Education Programme lists four ways an imprinted locus can be disrupted. They matter because each one changes how many working copies of the gene are active.

1. A pathogenic variant in the expressed imprinted gene.
2. A deletion or duplication involving one imprinted gene or several within a larger copy number variant.
3. Uniparental disomy (UPD), where both chromosome homologues come from a single parent.
4. An imprinting centre error that causes mis-expression of neighbouring imprinted genes, which can be genetic or epigenetic.

The same programme page lists the genes and syndromes below. The paired Prader-Willi and Angelman rows show the principle clearly: both sit at 15q11-q13, but the expressed copy is paternal in one and maternal in the other.

Region	Gene	Normally expressed allele	Associated condition	Active copies in the disorder
15q11-q13	SNRPN	Paternal	Prader-Willi syndrome	No active copies
15q11-q13	UBE3A	Maternal	Angelman syndrome	No active copies
11p15.5	CDKN1C	Maternal	Beckwith-Wiedemann syndrome	No functional copies
14q32	MEG3	Maternal	Temple syndrome	Two active copies
14q32	DLK1	Paternal	Paternal UPD14 or Kagami-Ogata syndrome	Two active copies
6q24.2	ZAC/PLAG1	Paternal	Transient neonatal diabetes	Two active copies
20q13.32	GNAS	Maternal	Pseudohypoparathyroidism type 1B	No active copies

These are selected rows; the programme page lists further genes and syndromes.

Where imprinting matters for labs and clinics: how disruption is detected

According to the NHS England Genomics Education Programme, methylation testing of the imprinting control region (ICR) is the initial screening test when an imprinting disorder is suspected clinically. The interpretation follows from the biology:

• In healthy individuals, one copy of the ICR is methylated and the other is unmethylated, so the average methylation level is around 50%.
• UPD, a deletion or duplication affecting the ICR, or an epigenetic switch at one ICR copy gives methylation levels of either 0% or 100%.
• Where more than one ICR is altered at once, the finding is called multi-locus imprinting disturbance.
• Further testing is needed to identify the specific mechanism, because the mechanism may inform the recurrence risk.

For laboratory and clinic staff, the useful consequence is that a methylation result alone does not name the cause. A 0% or 100% value is consistent with several of the mechanisms above, which is why a second-stage test follows. For background on how genetic results are discussed with families, see genetic counseling. This page gives general information only and is not individual medical advice. For the broader subject areas, see what genetics is and what genomics is.

Common misunderstandings

• Imprinting is a change in the DNA sequence. It is not. The NHGRI describes chemical tags that silence one parental copy while the sequence itself is unchanged.
• Imprints are permanent across generations. They are not. Geneimprint notes that the modifications are erased and reset when eggs and sperm are made, even though the NHGRI notes the tags usually remain for the life of the individual.
• Imprinting means a gene is switched off. Only one parental copy is silenced. The other copy is the one that is expressed.
• Every imprinting disorder is a sequence error. The mechanisms above include UPD and imprinting centre errors, some of them epigenetic, with no variant in the gene itself.

FAQ

What is gene imprinting?

Gene imprinting is the epigenetic marking of one parental copy of a gene, in the egg or the sperm, so that only the other copy is expressed in the offspring.

What is imprinting in genetics?

In genetics, imprinting is a parent-of-origin effect: whether an imprinted gene is active depends on whether it came from the mother or the father, not on its sequence. It is a form of non-sequence-based inheritance.

How many regions of the genome are imprinted?

The NHS England Genomics Education Programme states that more than 40 different regions in the genome are subject to imprinting.

How are imprinting disorders screened for in the laboratory?

Methylation testing of the imprinting control region is the initial screen. About 50% methylation is the expected average in healthy individuals, and 0% or 100% points to an altered imprint that needs further testing to find the mechanism.

Sources

• NHGRI Talking Glossary, Genetic Imprinting: genome.gov/genetics-glossary/Genetic-Imprinting (checked 2026-10-29).
• NHS England Genomics Education Programme, Genomic imprinting: genomicseducation.hee.nhs.uk/genotes/knowledge-hub/genomic-imprinting (checked 2026-10-29).
• Geneimprint, What is imprinting: geneimprint.com/site/what-is-imprinting (checked 2026-10-29).