Epigenetics & Imprinting
Learning objectives
- LO 1Define epigenetics, name its main mechanisms and explain how environment changes gene expression without changing DNA sequence.
- LO 2Explain genomic imprinting and the four ways an imprinted region can fail.
- LO 3Compare Prader-Willi and Angelman syndromes by parent of origin, mechanism and presentation.
- LO 4Describe Beckwith-Wiedemann (and its mirror, Silver-Russell) and why assisted reproduction raises its risk.
- LO 5Sort disorders of the epigenetic machinery into writers, erasers, remodelers and readers, and recognize each syndrome.
- LO 6Choose the right test for a suspected imprinting disorder and outline future epigenetic therapies.
MAPBig picture: two kinds of epigenetic disease
LO 1What is epigenetics?
Q1. How is epigenetics defined?
- Modifications of the DNA or associated proteins, other than the sequence itself, that are heritable through cell division
- Three properties:
- Reversible
- Affected by environment
- Reset in germ cells
- Explains why genetically identical MZ twins drift apart in phenotype over time
Analogy — the conductor's notes
DNA is the musical score. Epigenetic marks are the conductor's pencil notes ("skip this part," "play loudly"). Same score, very different performance, and the notes can be erased.
Q2. What are the main epigenetic mechanisms?
| Mechanism | What happens | Effect |
|---|---|---|
| DNA methylation | DNMT adds CH₃ (from SAM) to cytosine at CpG → 5-methylcytosine | Gene OFF (main mechanism in lecture) |
| Histone acetylation | Acetyl groups loosen chromatin; HDAC removes them | Acetylation ON; deacetylation OFF |
| Histone methylation | Methyl on lysine/arginine | ON or OFF depending on residue |
| Noncoding RNA | XIST, H19, KCNQ1OT1 | Silence genes in cis |
| Chromatin remodeling | Repositions nucleosomes (e.g., CHD7) | Changes DNA access |
DNA methylation
- Cytosine + CH₃ (SAM, DNMT) → 5-methylcytosine → OFF
Memory tool
"Methylation mutes, acetylation activates."
Step 1
Normal uses of methylation: X-inactivation (XIST → Barr body), imprinting, tissue-specific silencing. Fragile X: CGG expansion → hypermethylation → FMR1 silenced. HDAC inhibitors include valproate.
Q3. What does the agouti mouse show?
Same genes, different coats
- Yellow (unmethylated) → brown pseudo-agouti (methylated)
- Genetically identical mice
- Mothers fed methyl donors (folate, B12, choline, betaine) → pups with more methylation of the agouti gene → brown, lean
- Without them → yellow, obese, diabetic
- Lesson: environment changed phenotype without changing genotype
In-house exam
Expect: identical genotype + different diet/exposure + different phenotype → epigenetics (agouti mouse, MZ twins).
ApplyLO 1 application question
A1MZ twins share a genome, but at 50 only one has a methylation-silenced tumor suppressor gene. What explains this?
LO 2Genomic imprinting
Q1. What is imprinting, and when are imprints reset?
- Imprinting = parent-of-origin gene expression: one allele is silenced, the other expressed, depending on which parent it came from
- Marks sit at CpG-rich differentially methylated regions (DMRs), run by imprint control regions (ICRs); ~100 imprinted genes
- In gametogenesis:
- Old imprints are erased
- A new imprint is set by the person's own sex: sperm get a paternal pattern, eggs a maternal pattern
Erase → reset by sex
- A man passes only paternal imprints; a woman only maternal
High yield — the silent-copy rule
Disease can occur even with a normal copy on the other chromosome, because that copy is normally silenced. A mutation on the silent allele does nothing; pass it through the other parent and it becomes the active copy → disease.
Step 1
Parental conflict: the father's genes push growth (IGF2); the mother's restrain it. All-paternal genome (46,XX androgenote) → complete hydatidiform mole.
Q2. What are the four ways an imprinted region fails?
| Mechanism | What happens | Detect with |
|---|---|---|
| 1 · Deletion | The active parent's region is missing | FISH, microarray, methylation |
| 2 · Uniparental disomy (UPD) | Both copies come from one parent; the other parent's active copy is missing | Methylation, SNP array, microsatellites |
| 3 · Gene mutation | Point mutation in the active allele (UBE3A, CDKN1C) | Sequencing |
| 4 · Imprinting defect | ICR gains or loses methylation; no DNA change | Methylation only |
Trap
A normal karyotype, microarray and exome do not rule out an imprinting disorder: UPD and imprinting defects are invisible to them. Methylation analysis is the first test.
Q3. Why don't imprinting disorders follow Mendelian rules?
- Penetrance depends on the sex of the transmitting parent
- Mosaicism (marks set after fertilization) → blood can look normal
- MZ twins can be discordant
ApplyLO 2 application question
A1A healthy woman inherited a CDKN1C mutation from her father. Her son has Beckwith-Wiedemann. Why is she healthy?
LO 3Prader-Willi and Angelman (15q11–q13)
Q1. What goes wrong in each, and how often by each mechanism?
Top PWS · bottom AS
- Blue = paternal · red = maternal
| Mechanism | Prader-Willi | Angelman |
|---|---|---|
| Missing | Paternal 15q11–q13 (SNRPN, NDN, MAGEL2, snoRNAs) | Maternal UBE3A |
| Deletion | 70% (paternal) | 70% (maternal) |
| UPD | 25% (maternal UPD) | 2% (paternal UPD) |
| Gene mutation | 0% | 20% (UBE3A) |
| Imprinting defect | ≤5% | ≤5% |
Memory tool
Prader-Willi = missing Papa. Angelman = missing "Angel mom" (maternal UBE3A). UPD is big in PWS (25%) and tiny in AS (2%); gene mutation only in AS.
Q2. How do they present?
Prader-Willi
- Neonatal hypotonia, poor suck
- → hyperphagia, unsafe eating, obesity
- Moderate ID
- Hypogenitalism
- Short stature, small hands/feet
- Characteristic facies
Angelman
- Severe ID
- Minimal–absent speech
- Stiff, ataxic gait ("happy puppet")
- Paroxysms of laughter, happy affect
- Microcephaly, seizures
- Feeding problems, drooling; sleep disturbance
Step 1
Floppy newborn who becomes a hyperphagic, obese child → PWS. Happy, laughing, ataxic child with seizures → AS. Both: 15q11–q13 deletion on FISH in ~70%.
In-house exam
Know the percentages for each mechanism and which parent is missing. PWS is never caused by a single-gene mutation.
ApplyLO 3 application question
A1A child with PWS features has a normal FISH for 15q11–q13. Most likely mechanism and test?
LO 4Beckwith-Wiedemann, Silver-Russell and assisted reproduction
Q1. What does BWS look like?
- Large for gestational age (macrosomia)
- Macroglossia
- Ear pits/creases
- Omphalocele
- Hemihypertrophy (one side larger)
- Neonatal hypoglycemia
- Cancer risk: Wilms, hepatoblastoma
Memory tool — BWS = "Big"
Big baby, Big tongue, Belly-wall defect, Bigger on one side, Blood sugar low, Bad tumors.
Step 1
Screen for tumors through early childhood: abdominal ultrasound (Wilms) + AFP (hepatoblastoma). WAGR and Denys-Drash are the other Wilms syndromes.
Q2. How does 11p15 control growth?
IC2 (left) and IC1 (right)
- Orange dot = methylation · blue = CTCF insulator
| Center | Paternal (normal) | Maternal (normal) |
|---|---|---|
| IC1 (H19 / IGF2) | Methylated → H19 off → IGF2 on (growth ↑) | Unmethylated → H19 on, IGF2 off |
| IC2 (KCNQ1OT1 / CDKN1C) | Unmethylated → KCNQ1OT1 on → CDKN1C off | Methylated → CDKN1C on (p57, growth ↓) |
Q3. What causes BWS?
Causes of BWS
- Half = maternal IC2 loses methylation
| Mechanism | % |
|---|---|
| Loss of methylation at IC2 (maternal) | ~50% |
| Paternal UPD 11p15.5 | ~20% |
| Unknown | ~20% |
| Gain of methylation at IC1 (maternal) | ~5% |
| Maternal CDKN1C mutation | ~5% |
| Deletion / duplication / translocation | <1% each |
In-house exam
Most common cause of BWS = loss of methylation of imprinting center 2 on the maternal chromosome 11 (~50%).
Q4. What is Silver-Russell, the mirror of BWS?
- IUGR/SGA, postnatal growth failure, relatively normal head size
- Body asymmetry, triangular face, 5th-finger clinodactyly, feeding problems
- Causes: loss of methylation at IC1 (paternal) (most common); maternal UPD7 (~10%)
Q5. Why does assisted reproduction raise BWS risk?
ART hits the imprint window
- Ovulation induction and embryo culture overlap imprint setting/maintenance
- BWS risk after ART: 1 in 4,000 vs 1 in 13,700 in the general population (~3×)
- Imprints are set during gametogenesis and maintained in the early embryo: exactly when ART manipulates them (ovulation induction, in-vitro culture)
- Most post-ART BWS = loss of methylation at IC2
- An example of environment changing epigenetics without changing DNA
In-house exam
IVF baby + LGA + macroglossia + omphalocele + hypoglycemia → BWS; know the 1:4,000 vs 1:13,700 numbers.
ApplyLO 4 application questions
A1A newborn conceived by IVF has a large tongue, omphalocele and a glucose of 30 mg/dL. Most likely mechanism, and what follow-up?
A2An SGA infant has a triangular face, normal head size and limb asymmetry. Test shows maternal UPD7. Diagnosis?
LO 5Disorders of the epigenetic machinery
Q1. What are writers, erasers, remodelers and readers?
| Class | Job | Example genes | Syndromes |
|---|---|---|---|
| Writers | Put marks on chromatin | CREBBP, EP300, NSD1, EZH2, KMT2D | Sotos, Weaver, Rubinstein-Taybi, Kabuki |
| Erasers | Remove marks | HDAC4, HDAC8 | Townes-Brocks |
| Remodelers | Reorganize chromatin → change DNA access | SRCAP, CHD7 | CHARGE |
| Readers | Recognize marks → downstream effects | RPS6KA3, MECP2 | Smith-Magenis, Rett |
The epigenetic toolkit
- Pens write · erasers erase · bulldozer remodels · glasses read
Analogy — editing a manuscript
Writers add sticky notes, erasers peel them off, the remodeler rearranges the pages, and the reader acts on what the notes say.
Trap — terminology
The lecture calls these "imprinting control disorders," but they are Mendelian mutations (mostly de novo AD; Rett XLD) in genome-wide machinery, not parent-of-origin imprinting defects.
Q2. How do I recognize the writer syndromes?
| Syndrome | Key features | Gene |
|---|---|---|
| Sotos | Overgrowth (large head, baby, hands); low tone; developmental delay; abnormal teeth; facies; behavioral differences | NSD1 |
| Weaver | Overgrowth (large baby, tall); low or high tone; mild ID; joint contractures; kyphoscoliosis; abnormal MRI | EZH2 |
| Rubinstein-Taybi | Broad thumbs and great toes; dislocated patellas, scoliosis; strabismus, cataracts, glaucoma; ear infections; high palate, talon cusps; heart defects 35–40%; undescended testes; constipation | CREBBP, EP300 |
| Kabuki | "Kabuki" facies (long eyelids, arched eyebrows), persistent fetal finger pads, IQ <80, joint laxity, hypotonia, short stature, heart defects, cleft lip/palate, renal anomalies, hearing loss | KMT2D, KDM6A |
Rubinstein-Taybi
- Broad great toe (and thumb)
In-house exam
Broad thumbs and great toes + heart defect → Rubinstein-Taybi, a writer disorder. Gene names are low yield in lecture; the class is what's tested.
Q3. How do I recognize the eraser and remodeler syndromes?
Townes-Brocks (eraser)
- Imperforate anus
- Abnormal ear shape
- Thumb malformation
- Rarely: kidney, hearing, heart, genital, learning problems
- Gene: SALL1
CHARGE (remodeler)
- Need 4 of 7:
- Coloboma
- Heart (conotruncal, arch)
- choanal Atresia
- growth/mental Retardation
- Genitourinary (microphallus)
- Ear (ossicles, Mondini cochlea, deafness)
- Gene: CHD7
CHARGE ears
- Cup-shaped, malformed pinnae
Townes-Brocks thumbs
- Triphalangeal / malformed thumbs
Memory tool
The eraser "rubs out" the anus (Townes-Brocks: anus, ears, thumbs). The bulldozer remodels a whole CHARGE (spell out the letters).
Trap — look-alikes
Imperforate anus + thumb anomaly also fits VACTERL. Townes-Brocks adds the ear malformation; VACTERL adds vertebral, TE fistula, cardiac and limb defects.
Q4. How do I recognize the reader syndromes?
Smith-Magenis
- Hypotonia, failure to thrive, small
- Early speech delay; peripheral neuropathy
- Severe sleep problems
- Self-injury, impulsivity, "self-hug," "lick and flip"
- Features coarsen over time
- Gene: RAI1 (17p11.2 deletion)
Rett
- Girls: X-linked dominant
- Normal early development → regression, especially language loss and hand use
- Hand-wringing; acquired microcephaly
- Hyperventilation, bruxism, paroxysmal laughing
- Prolonged QT; scoliosis
- Gene: MECP2
Step 1
Rett: girl normal until ~6–18 months → regression, hand-wringing, acquired microcephaly, breathing irregularities; MECP2 (methyl-CpG binding reader); usually lethal in males.
In-house exam
Rett and Smith-Magenis are readers; know that Rett is X-linked dominant and affects girls.
Memory tool — sort them
Writers make things big or broad (Sotos, Weaver, RTS thumbs, Kabuki). Readers lose behavior and language (Smith-Magenis self-hug, Rett regression).
ApplyLO 5 application questions
A1A newborn has bilateral coloboma, tetralogy of Fallot, choanal atresia and cup-shaped ears. Which class of epigenetic defect?
A2An 8-year-old hugs herself repeatedly, wakes many times a night and bites her hands. Diagnosis and class?
LO 6Diagnosis and future therapy
Q1. How are imprinting disorders diagnosed?
- Start with methylation at the DMR/ICR: catches deletion, UPD and imprinting defects in one test
- Tools: methylation-specific MLPA (copy number + methylation together), bisulfite sequencing, methylation-sensitive PCR or restriction enzymes
- SNP array / microsatellites → distinguishes UPD from deletion; shows parent of origin
- Sequencing if methylation is normal (UBE3A in AS, CDKN1C in BWS)
- Multilocus panels: several imprints can be disturbed at once
- Mosaicism → test another tissue (buccal, skin) if blood is normal
High yield
Order: methylation → (if abnormal) SNP array / FISH to find the mechanism → (if normal and AS suspected) UBE3A sequencing. Mechanism matters for recurrence risk: deletion/UPD <1%; UBE3A mutation in the mother → up to 50%.
Q2. What therapies might come from epigenetics?
- The "missing" gene is often present but silenced → unsilencing could treat disease
- Topoisomerase inhibitors unsilenced paternal Ube3a in Angelman mice
- HDAC inhibitors (valproate, phenylbutyrate, SAHA)
- Antisense RNAs / microRNAs; CRISPR epigenome editing; patient iPSCs for drug screening
Analogy — the dimmer switch
In Angelman, the paternal UBE3A bulb works; it's just switched off in neurons. Therapy aims to flip the switch rather than replace the bulb.
IDImage ID
Image 1 — mice
Image 2 — chromosomes
Image 3 — pie chart
Image 4 — foot
Image 5 — ears
Image 6 — hands
MCQExam-style questions
1Genetically identical mice born to mothers fed folate, B12 and choline are brown and lean; those born to unsupplemented mothers are yellow and obese. What best explains the difference?
2A hypotonic newborn with poor suck becomes an obese, constantly hungry toddler with small hands and hypogonadism. FISH for 15q11–q13 is normal. Most likely mechanism?
3A 4-year-old with severe ID, no words, seizures, a jerky ataxic gait and frequent laughter has normal methylation at 15q11–q13. Next best test?
4Which is the most common cause of Beckwith-Wiedemann syndrome?
5A newborn conceived by in-vitro fertilization weighs 4.9 kg and has macroglossia, an omphalocele and ear creases. Which surveillance is indicated?
6The increased risk of Beckwith-Wiedemann after assisted reproduction is best explained by:
7An SGA infant has postnatal growth failure, a triangular face, relatively large head and body asymmetry. Which finding is most likely?
8A child has broad thumbs and great toes, a congenital heart defect, glaucoma and undescended testes. The defective protein is best classified as an epigenetic:
9A newborn has an imperforate anus, malformed ears and a triphalangeal thumb. Which category of epigenetic disorder?
10An infant has coloboma, a conotruncal heart defect, bilateral choanal atresia, microphallus and a Mondini cochlea. The mutated gene encodes a:
11An 18-month-old girl stops using words she had learned, loses purposeful hand use and repeatedly wrings her hands. Head growth has slowed. ECG shows a long QT. Inheritance?
12A child's karyotype, chromosomal microarray and exome are all normal, but an imprinting disorder is suspected. Best next test?
!Source notes
| Item | Lecture | Step 1 / other lectures |
|---|---|---|
| Angelman mechanisms | 70% deletion, 2% UPD, 20% UBE3A, ≤5% imprinting | HEM15: 68%, 7%, 11%, 3% (+10% unknown). PWS numbers agree. Use this lecture's numbers on the HEM18 exam |
| BWS location | Written "11q15.5" in some notes | 11p15.5 |
| "Imprinting control disorders" | Label for writer/eraser/remodeler/reader syndromes | These are Mendelian machinery disorders, not parent-of-origin imprinting defects |
| PWS cause | Sometimes summarized as "methylation of the paternal chromosome" | The defect is loss of paternal expression by any of 3 mechanisms (deletion, maternal UPD, imprinting defect) |
| Gene names | Shown only on the overview slide (low yield in house) | Step 1 expects MECP2 (Rett), UBE3A (AS), CDKN1C/IGF2 (BWS) |