BIOL-S402F Medical Genetics and Immunology

(Part B: Medical Genetics)

Lecture 10

By Dr. Andy YY CHEUNG

cheungyy@hkmu.edu.hk
Epigenetics and Development
• Embryonic stem cells
• Pluripotent
• Can become any cell that is needed for development
• Key event in early embryogenesis
• Differential epigenetic modification (including extensive
methylation) of specific DNA nucleotide sequences
• Ensures that specific genes are expressed only in the cells and
tissue types in which their gene products are needed
• Helps determine the fate of each cell; that is, the type of cell it
becomes, such as a myocyte, neuron, or fibroblast
Twin studies provide insights
on epigenetic modification
• Are a powerful means for testing epigenetic effects
• Compare methylation and other signatures of epigenetic
modification in identical (monozygotic) twin pairs, because
their DNA sequences are essentially the same
• As twins age, differences increase in methylation patterns of
the DNA sequences of somatic cells
Twin Studies Provide Insights
on Epigenetic Modification (cont’d)
• Twins with significant lifestyle differences (e.g., smoking
versus non-smoking)
• Accumulated larger numbers of differences in their methylation
patterns
• Became more different as a result of epigenetic changes, which
in turn affected the expression of genes
• These results, along with findings generated in animal studies,
suggest that changes in epigenetic patterns may be an
important part of the aging process
Course outline:
4. Molecular Basis of Genetic Diseases
a. Gregor Mendel and the Laws of Inheritance Lectures 7
b. DNA as the Basis of Inheritance
c. Common monogenic genetic diseases Lectures 8
d. Complex diseases

5. Genetics in Diseases and Development

a. Cytogenetics Lectures 9
b. Common chromosomal abnormalities
c. Epigenetics Lectures 10
d. Mitochondrial DNA inheritance
e. Development and sex determination Lectures 11
f. Clinical genetics and ethical issues
6. Cancer Genetics
a. Genetic factors and environmental factors in cancers
b. Mutations in cell cycle regulatory genes Lectures 12
c. Mutations in the DNA repair system
d. Epigenetics in cancer
Genetics vs. epigenetics
• Genetics is the study of genes,
genetic variation, and heredity in
organisms
• Epigenetics is the study of
changes in cell function that do
not involve alterations in the DNA
sequence
• The Greek prefix epi- (“above") in
epigenetics implies features that
are "on top of" or "in addition to"
the traditional genetic basis for
inheritance
Epigenetics

• Epigenetics is the modifications on the DNA of genome, DNA

binding proteins such as histones in nucleosome and/or RNA
molecules that regulating mRNA stability and post-transcriptional
activities
• In other words, modifications except DNA sequences on genome
• alter the expression of genes, resulting in disease and
phenotypic variations (upon genetics)
• Types of epigenetic modifications
• DNA methylation
• Histone modification
• RNA-based mechanisms e.g. microribonucleic acids (miRNAs)
• Specific environmental or nongenetic factors, such as diet
and exposure to certain chemicals, can affect epigenetics
Epigenetics (cont’d)
DNA Methylation
• Is the attachment of a methyl group to a cytosine base that is
followed by a guanine base; also known as CpG dinucleotide
(CpG site)
• CpG is shorthand for 5'—C—phosphate—G—3' , that is,
cytosine and guanine separated by only one phosphate group;
phosphate links any two nucleosides together in DNA
• In humans, about 70% of promoters located near the
transcription start site of a gene (proximal promoters) contain
a CpG island
• CpG islands are regions with a high frequency of CpG sites
DNA Methylation (cont’d)
• Process
DNA Methylation
Methylation of CpG islands stably silences genes
• In humans, DNA methylation occurs at the 5 position of the
pyrimidine ring of the cytosine residues within CpG sites to
form 5-methylcytosines
• The presence of multiple methylated CpG sites in CpG islands
of promoters and enhancer regions causes stable silencing of
genes
• Causes a gene to become transcriptionally inactive or silent
• When DNA sequence in the promoter / enhancer region of a
gene becomes heavily methylated, DNA is less likely to be
transcribed into messenger RNA
DNA Methylation suppresses gene
expression
• DNA methylation is a biological process by which
methyl groups are added to the DNA molecule

• Methylation can change the activity of a DNA

segment without changing the sequence

• When located in a gene promoter, DNA methylation

typically acts to repress gene transcription
DNA Methylation alters gene package and transcriptional
factor accessibility
• DNA methylation regulates
gene expression by recruiting
proteins involved in gene
repression or by inhibiting
the binding of transcription
factor(s) to DNA.
• DNA is highly condensed
• Human DNA (2 m) is packaged in 10-5 m
• The DNA-protein complex forms chromatin, a highly dynamic structure
Histone octamer

• A histone octamer is the eight

protein complex found at the
center of a nucleosome core
particle

• A histone is a protein that

provides structural support to a
chromosome

• plays a key role in the

transcription of the DNA
surrounding it
Histones are basic proteins enriched in lysine and arginine (>1/5), highly conserved in sequence
5 main types of histones: H1, H2A, H2B, H3, H4
Histone octamer : H2A, H2B, H3, H4
146 bp of DNA are wrapped around the histone octamer
142 hydrogen bonds between DNA and histone core + hydrophobic interaction

Importantly the positive charge of the histones neutralize the negative charge of the DNA

Any DNA sequence can be bound by the histones

30 milions of nucleosomes in one human cell

Only 30% of the chromatin is DNA

Beads on a string form (10nm)

• The DNA linker separates nucleosomes (20-60 bp)
• H1 Histone allows nucleosomes to approach each others: linker histone
• H1 is half in quantity respect the others histones because one H1 is associated to a single
nucleosome
• Histone tails (25 aa all’N-terminus) interact with other nucleosomes
Histone Modification

Post-translational modifications of histones, including acetylation and

methylation of conserved lysine residues on the amino-terminal tail
domains
• Histone acetylation and deacetylation: the acetylation of histones marks
active, transcriptionally competent regions, whereas hypoacetylated
histones are found in transcriptionally inactive euchromatic or
heterochromatic regions
Accessibility of transcription factor(s) in the gene
region

Transcription factors are proteins that

bind to DNA-regulatory sequences
(enhancers and silencers), usually
localized in the 5’-upstream region
of target genes, to modulate the rate
of gene transcription.
Acetylated histones allow transcription to begin

• the acetylation of H3
histones activates gene
transcription by attracting other
transcription related complexes

• the addition of the acetyl group

neutralizes this positive charge
and hence reduces the binding
between histones and DNA,
leading to a more open structure
which is more accessible to the
transcriptional machinery
Heterochromatin that corresponds to the highly condensed form in which the DNA is not accessible and
euchromatin that is relaxed form and the DNA can be transcribed.

The chromatin structure can be inherited and this is called epigenetic inheritance because is linked to the structure of the
chromatin rather than the sequence of the DNA
Histones N-term tail is not associated to the nucleosome and can host PMTs
Basically, PTMs modulate all processes involving DNA access (transcription, replication, recombination, repair ...)

PTMs:

They depend on specific enzymes

They are reversible

Histonemodifications

Histones modification have two main functions:

1. to create global chromatin environment: by partitioning the genome in euchromatin and
heterochromatin; Changing histone modifications can shift compact chromatin to the loose chromatin.
2. to orchestrate DNA-base biological tasks such as DNA transcription; Histone modifications can orchestrate
the ordered recruitment of transcriptional machinery to the DNA sites and regulate gene transcription
Histone Modification

Post-translational modifications of histones, including acetylation and

methylation of conserved lysine residues on the amino-terminal tail
domains
• Results of Histone acetylation and deacetylation
• Alterations in chromatin
• Chromatin compaction and organization normally help regulate
gene expression to maintain cell identity
• Chromatin structure must be controlled in self-renewing and
differentiated cells in cell-renewal systems
• Histone hypoacetylation, condensation of chromatin, and methylation
interactions
• Inhibit the binding of proteins that promote transcription; the gene
becomes transcriptionally inactive
Histone acetyltransferases

histone deacetylases
 Reduced association between adjacent nucleosomes

Facilitated access to
Transcription Factors
(TFs)

Displacement of nucleosomes
by chromatin remodeling factors

Facilitated access to TFs

Histone Modification

Post-translational modifications of histones, including acetylation and

methylation of conserved lysine residues on the amino-terminal tail
domains
Histone methylation can be a marker for both active and inactive regions of
chromatin
• Methylation of lysine 9 on the N terminus of histone H3 (H3-K9) is a
hallmark of silent DNA and is globally distributed throughout
heterochromatic regions such as centromeres and telomeres
• In contrast, methylation of lysine 4 of histone H3 (H3-K4) denotes activity
and is found predominantly at promoters of active genes
 Histone methyltransferase
Heterochromatin Protein 1
PTMs of histones not only change per se chromatin conformation but also they are responsable for the
recruitment of complexes and proteins
 acetylation ad methylation can modify the same lysine residues

Acetylation and methylation are mutually exclusive

One modification can influence the others

Disorders of chromatin remodeling
Only 1.5% human genome is coding region
Non-coding RNA
• A non-coding RNA (ncRNA) is a functional RNA molecule that is not
translated into a protein
• Abundant and functionally important types of non-coding RNAs
include transfer RNAs (tRNAs) and ribosomal RNAs (rRNAs), as well as
small RNAs such as microRNAs, siRNAs, piRNAs, snoRNAs, snRNAs,
exRNAs, scaRNAs and the long ncRNAs such as Xist
Small interfering RNA
• Small interfering RNA (siRNA), sometimes known as short interfering
RNA or silencing RNA, is a class of double-stranded RNA at first non-
coding RNA molecules, typically 20-24 (normally 21) base pairs in
length, similar to miRNA, and operating within the RNA interference
(RNAi) pathway
• originate from regions of double-stranded RNA molecules (dsRNA)
• It interferes with the expression of specific genes with
complementary nucleotide sequences by degrading mRNA after
transcription, preventing translation
Mechanism of Small interfering RNA
1.Long dsRNA is cleaved by an endo-ribonuclease called Dicer; Dicer cuts the long dsRNA to
form short interfering RNA or siRNA; this is what enables the molecules to form the RNA-
Induced Silencing Complex (RISC)
2.Once siRNA enters the cell it gets incorporated into other proteins to form the RISC
3.Once the siRNA is part of the RISC complex, the siRNA is unwound to form single
stranded siRNA
4.The single stranded siRNA which is part of the RISC complex now can scan and find a
complementary mRNA
5.Once the single stranded siRNA (part of the RISC complex) binds to its target mRNA, it
induces mRNA cleavage
6.The mRNA is now cut and recognized as abnormal by the cell
7.This causes degradation of the mRNA and in turn no translation of the mRNA into amino
acids and then proteins -> silencing the gene that encodes that mRNA
Microribonucleic Acids (MicroRNA or
miRNA)
• small, single-stranded, non-coding RNA molecules containing 21 to 23 nucleotides
• involved in RNA silencing and post-transcriptional regulation of gene expression
• miRNAs base-pair to complementary sequences in mRNA molecules, then gene
silence said mRNA molecules
• miRNAs resemble the small interfering RNAs (siRNAs) of the RNA interference
(RNAi) pathway, except
• miRNA originate from self-folding regions of RNA transcripts forming short hairpins
• an interaction with target mRNAs in a perfect complementary base sequence that
results in mRNA cleavage
• an interaction in an imperfect base sequence causes a translational inhibition
miRNA vs siRNA
• First, miRNAs were viewed as endogenous and purposefully expressed products of
an organism's own genome, whereas siRNAs were thought to be primarily
exogenous in origin, derived directly from the virus, transposon, or transgene trigger
• Second, miRNAs appeared to be processed from stem-loop precursors with
incomplete double-stranded character, whereas siRNAs were found to be excised
from long, fully complementary double-stranded RNAs (dsRNAs)
• Despite these differences, the size similarities and sequence-specific inhibitory
functions of miRNAs and siRNAs immediately suggested relatedness in biogenesis
and mechanism
• Both classes depend upon the same two families of proteins: Dicer enzymes to
excise them from their precursors, and Ago proteins to support their silencing
effector functions
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2675692/
RNA interference (RNAi) experiment
• RNA interference (RNAi) is the biological process
of mRNA degradation induced by complementary
sequences double-stranded (ds) small interfering
RNAs (siRNA) and suppression of target gene
expression.
Peng, Y., & Croce, C. M. (2016). The role of MicroRNAs in human cancer. Signal transduction and targeted therapy, 1(1), 1-9.
https://www.youtube.com/watch?v=cK-OGB1_ELE
https://www.youtube.com/watch?v=j-zTy6vOP3M
RNA interference (RNAi) & microRNA (miRNA)
Long non-coding RNA
• Long non-coding RNAs (long ncRNAs, lncRNA) are a type of RNA,
generally defined as transcripts more than 200 nucleotides that are not
translated into protein
• This arbitrary limit distinguishes long ncRNAs from small non-coding
RNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and
other short RNAs
• Long intervening/intergenic noncoding RNAs (lincRNAs) are sequences
of lncRNA which do not overlap protein-coding genes
• Long non-coding RNAs include intergenic lincRNAs, intronic ncRNAs, and
sense and antisense lncRNAs, each type showing different genomic
positions in relation to genes and exons
• >= 200 nt
• Not encoding any
protein
• Sharing similar
structure with
mRNA
• Playing regulatory
roles
Does the
chromatin
randomly sit
inside the
nucleus?
Chromatin in the
mammalian cell
nucleus is
organized into
chromosome
territories
Different
chromosome
regions will
reside on
different
regions of the
nuclear
membrane
Topologically
associating
domain (TAD)
• A topologically
associating domain
(TAD) is a self-
interacting genomic
region, meaning that
DNA sequences within
a TAD physically
interact with each other
more frequently than
with sequences outside
the TAD
Chromatin architecture: different levels of
chromatin complexity
1. Nucleosome
2. Histone modifications
3. Histone modifiers
4. Chromatin arrangement (eu/hetero)
5. DNA looping
6. TADs, LADs
7. Chromosome territories

Topological Associated Domains (TADs)

Lamin Associated Domains (LADs)
Nucleolar Associated Domains (NADs)
A further level of chromatin organization: TADs (topological associated domains) and chromosomal territories

Within chromosomal territories the gene-rich regions are

separated from heterochromatin and generally are
positioned at the periphery of chromosome territories
while gene poor regions are at the interior of
chromosome territories.

Each chromosome is subdivided into topological

associated domains (TAD).
TADs are characterized by a central region of high
chromatin interactions where reside the tissue-specific
genes, surrounded by less-interacting boundary regions
enriched of housekeeping genes.

TADs with repressed transcriptional activity tend to be

associated with the nuclear lamina, while active TADs
tend to reside more in the nuclear interior.

TAD boundaries are suggested to have low interaction

frequencies and barrier activity, which can stop
heterochromatin spreading from neighboring domains.
• Nuclear lamina interacts with the genome at specific DNA sequences called Lamina
Associated Domains (LADs)
• LADs correlate with low gene expression by creating an environment of gene
repression (K9me2, K9me3, K27me3)
Fragile X-Associated Disorders
• Symptoms:
• • Chromosome instability
• • Intellectual disabilities such
as ADHD aetiology:
• • Expansion and methylation
of CGG repeat in FMR1 5’
UTR, promoter methylation
Fragile X-Associated Disorders
• caused by changes in the Fragile X Messenger Ribonucleoprotein 1
(FMR1) gene
• In addition to FXS, there are other fragile X-associated disorders that are
caused by changes in FMR1
• The FMR1 gene usually makes a protein called FMRP that is needed for brain
development
• Changes in the gene determine whether someone makes less or none of this
protein, depending on how much the gene is changed
Fragile X-associated disorders include:
• Fragile X-associated primary ovarian insufficiency
• Fragile X-associated tremor/ataxia syndrome
• Fragile X syndrome
Fragile X–Associated Tremor/Ataxia
Syndrome (FXTAS)
PREMUTATION OF THE FMR1 GENE (55–200 CGG REPEATS)
• Fragile X–associated tremor/ataxia syndrome is an “adult onset” neurodegenerative disorder, usually affecting
males over 50 years of age
• Females comprise only a small part of the FXTAS population, and their symptoms tend to be less severe
• FXTAS affects the neurologic system and progresses at varying rates in different individuals
• All individuals with FXTAS are premutation carriers of the FMR1 (Fragile X) gene (CGG repeats 55-200)
• The job of the FMR1 gene is to make protein (FMRP) that is important in brain development
• The premutation leads to the overproduction of FMR1 mRNA (which contains the expanded repeats)
• High levels of mRNA are what cause the signs and symptoms of FXTAS, but more research is needed
Note: Not all premutation carriers will develop FXTAS, but all individuals with FXTAS have an FMR1 premutation.
Researchers are investigating what other factors might contribute to FXTAS in FMR1 premutation carriers.
• In its “full mutation” form the FMR1 gene causes Fragile X syndrome, a different, but genetically related disorder
that is present from birth but is often undiagnosed or misdiagnosed for many years
• Female premutation carriers can also be affected by Fragile X-associated primary ovarian insufficiency (or FXPOI),
another of the conditions associated with the change in the FMR1 gene
Fragile X–Associated Tremor/Ataxia
Syndrome (FXTAS)
Major Signs & Symptoms
1. Intention tremor: A tremor of the hand when using utensils, writing instruments, reaching for or pouring something. The
tremor is not as apparent at rest.
2. Gait ataxias: Balance problems which may include falling, needed support when walking or going up/down stairs, trouble
stepping on/off curbs, generalized instability, or display of a wide-based gait.
3. MRI findings strongly associated with (but not unique to) FXTAS. These findings include white matter lesions involving
middle cerebellar peduncles (MCP) signs.
4. Neuropathology findings called “FXTAS inclusions” within brain cells.
Fragile X-Associated Primary Ovarian
Insufficiency (FXPOI)
PREMUTATION OF THE FMR1 GENE (55–200 CGG REPEATS)
• Fragile X-associated primary ovarian insufficiency, one of three known
Fragile X-associated disorders caused by changes in the FMR1 gene, is
a condition in which the ovaries are not functioning at full capacity in
an FMR1 premutation carrier
• The ovaries in women with FXPOI do not function to full capacity and
may resemble ovaries of an older woman, both in the number and
quality of available eggs
Fragile X-Associated Primary Ovarian
Insufficiency (FXPOI)
Signs & Symptoms
• Common symptoms of FXPOI (ovarian insufficiency) include absent or irregular cycles,
“sub-fertility” or infertility, hot flashes, and premature ovarian failure (POF), which is the
complete cessation of menstrual periods before the age of 40
• FMR1 premutation carriers can have normal ovarian function, but can still go through
early menopause, which is menopause occurring between 40 and 45 years of age
(menopause normally occurs between 45 and 55 years old)
• Even though women with FXPOI may develop symptoms similar to those of menopause,
such as hot flashes and vaginal dryness, FXPOI differs from menopause in some important
ways:with FXPOI
Women Women who have completed menopause
• Can still get pregnant in some cases because their
ovaries may occasionally function to release viable • Cannot get pregnant because their ovaries no
longer release eggs
eggs
• Can experience a return of menstrual periods • Cannot have menstrual periods again
Fragile X syndrome (FXS)
• FULL MUTATION OF THE FMR1 GENE (> 200 CGG REPEATS)
• is characterized by moderately to severely impaired intellectual
development, macroorchidism (an increase of testicular volume at
least twice the norm for age), and distinct facial features, including
long face, large ears, and prominent jaw
• In most cases, the disorder is caused by the unstable expansion of a
CGG repeat in the FMR1 gene and abnormal methylation, which
results in suppression of FMR1 transcription and decreased protein
levels in the brain
Fragile X-Associated Disorders
• Video: https://www.youtube.com/watch?v=PrKAf2MgdlM&t=98s
Fragile X-Associated Disorders
Pathogenesis of FRAGILE X SYNDROME
• Colak et al. (2014) demonstrated that FMR1 silencing is mediated by
the FMR1 mRNA
• The FMR1 mRNA contains the transcribed CGG-repeat tract as part of
the 5-prime untranslated region, which hybridizes to the
complementary CGG-repeat portion of the FMR1 gene to form an
RNA/DNA duplex
• Colak et al. (2014) concluded that their data linked trinucleotide
repeat expansion to a form of RNA-directed gene silencing mediated
by direct interactions of the trinucleotide repeat RNA and DNA
Pathogenesis of FRAGILE X
TREMOR/ATAXIA SYNDROME; FXTAS
• In patients with FXTAS, Berry-Kravis et al. (2003) found that the
premutation was associated with increased levels of CGG repeat-
containing FMR1 mRNA, which may interfere with nuclear function and
lead to neurodegenerative symptoms
• Arocena et al. (2005) noted that FXTAS appears to affect only carriers of
premutation alleles, who have normal or near-normal FMR1 protein
levels in both peripheral blood leukocytes and brain tissue, suggesting
that FXTAS may result from a toxic gain-of-function of the FMR1 mRNA
itself
• Handa et al. (2005) found that transcribed but untranslated expanded
CGG premutation alleles were toxic to human cells
Any problem for female to carry 2 X chromosomes comparing to male?

TED-Ed video:
https://www.youtube.com/watch?v=veB31XmUQm8
X-reactivation and inaction in human development and reprogramming
X-inactivation of gene regions in random manner
XIST
• Xist (X-inactive specific transcript) is a non-coding RNA on the X chromosome
of the placental mammals that acts as a major effector of the X-inactivation
process
• It is a component of the Xic – X-chromosome inactivation centre
• The Xist RNA, a large (17 kb in humans) transcript, is expressed on the
inactive chromosome and not on the active one
• It is processed in a similar way to mRNAs, through splicing and
polyadenylation
• However, it remains untranslated
• The inactive X chromosome is coated with this transcript, which is essential
for the inactivation
Stages of X inactivation counting and
control of Xist expression
• 3. 1 History and background of X chromosome inactivation
• https://www.youtube.com/watch?v=k0wBwlwfBFU&list=PL6urLi_ZNS-ufvGPC
zAEoA49vUq5ldNuK&index=13
• 3. 2 Timing of random and imprinted X chromosome inactivation
• https://www.youtube.com/watch?v=fjpOLNIEfpg&list=PL6urLi_ZNS-ufvGPCzA
EoA49vUq5ldNuK&index=11
• 3. 3 Stages of X inactivation counting and control of Xist expression
• https://www.youtube.com/watch?v=4SN2Sh6W_L0&list=PL6urLi_ZNS-ufvGP
CzAEoA49vUq5ldNuK&index=10
• 3. 4 Control of Xist expression by pluripotency factors
• https://www.youtube.com/watch?v=nwc4E6jfEC4&list=PL6urLi_ZNS-ufvGPCz
AEoA49vUq5ldNuK&index=9
Stages of X inactivation counting and
control of Xist expression
• 3. 6 Stages of X inactivation initiation and spreading of silencing
• https://www.youtube.com/watch?v=mbTbaHVKuic&list=PL6urLi_ZNS-ufvGPC
zAEoA49vUq5ldNuK&index=8
• 3. 7 Stages of X inactivation establishment of silencing
• https://www.youtube.com/watch?v=o-pVoF7DQ54&list=PL6urLi_ZNS-ufvGPC
zAEoA49vUq5ldNuK&index=6
• 3. 8 Stages of X inactivation maintenance of silencing e g Dnmt1
• https://www.youtube.com/watch?v=vB3Sxv2Znoc&list=PL6urLi_ZNS-ufvGPCz
AEoA49vUq5ldNuK&index=5
• 3. 9 Stages of X inactivation maintenance of silencing e g Smchd1
• https://www.youtube.com/watch?v=WUshhRtVY0A&list=PL6urLi_ZNS-ufvGPC
zAEoA49vUq5ldNuK&index=4
•
Two chromosomal changes of X chromosome
after inactivation:
• Inactivated X chromosome is compacted to make a small, dense
structure called a Barr body
• final DNA methylation is established at the promoters of genes on
the inactive X chromosome after several steps of epigenetic marking
during cell differentiation
Polycomb protein

• What do Polycomb proteins do?

• Polycomb (PcG) proteins play roles

in gene silencing through different
mechanisms
Polycomb complexes silence gene
transcription via chromatin structure
modulation.
• These proteins act in complexes
and govern the histone
methylation profiles of a large
number of genes that regulate
various cellular pathways
PcG complexes in mammalian: PRC1 & PRC2
Mechanisms of PcG recruitment to chromatin
• Three major mechanisms of recruitment
of PcG complexes

(A) a DNA-based mechanism

• PcG complexes are targeted to defined

DNA sequences

• DNA binding domains (DBD) present in

different PcG complexes
• (B) histone modifications can also
mediate the recruitment of PcG by its
interaction with chromatin "readers"
present in the PcG complexes

• (C) ncRNAs also interact with PcG

complexes and are required for their
recruitment to chromatin
Mechanisms of PcG-mediated transcriptional
regulation
PcG complex can
• compact chromatin
prevent RNAPII
processivity during
transcription
elongation
• triggers the
recruitment of the
acetyltransferase,
which acetylates
histone tails and
enhances
transcription
Genomic Imprinting

• Is the process of gene silencing, in which genes are predictably silenced,

depending on which parent transmits them.
• Transcriptionally silenced genes: Imprinted
• Are usually heavily methylated
• Diseases from abnormal imprinting patterns
• Prader-Willi and Angelman syndromes
• Beckwith-Wiedemann syndrome
• Russell-Silver syndrome
 Prader-Willi and Angelman Syndromes

Prader-Willi Syndrome: https://www.youtube.com/watch?

Angelman syndrome: https://www.youtube.com/watch?
v=8CKN6idlE80 v=O1mSJeDfdh4
Prader-Willi and Angelman Syndromes
• Prader-Willi syndrome
• Genes deletion on the long arm of
chromosome 15
• Most cases: inherited from the father
(paternal deletion)
• Small number of case: a child gets 2
inactive copies of the gene from their
mother, rather than 1 from each
parent
• Clinical manifestations
• Short stature
• Hypotonia
• Small hands and feet
• Obesity
• Mild-to-moderate mental retardation
• Hypogonadism
• Angelman syndrome
• Ubiquitin protein ligase E3A (UBE3A)
gene on the long arm of chromosome
15
• Most cases: child not getting a copy of
the UBE3A gene from its mother, or
the gene not working
• Small number of case: a child gets 2
inactive copies of the gene from their
father, rather than 1 from each parent
• Clinical manifestations
• Severe mental retardation
• Seizures
• Ataxic gait (awkward, uncoordinated
walking)
Prader-Willi and Angelman Syndromes
(cont’d)
Prader-Willi Syndrome
• Several genes in the critical region
are transcribed only on the
chromosome transmitted by the
father
• Genes are silenced/imprinted on
the chromosome transmitted by
the mother
• A paternally transmitted deletion
removes the only active copies of
these genes, producing the
features of this syndrome
Angelman Syndrome
• UBE3A gene encodes a ligase for
protein degradation during brain
development, thus resulting in
mental retardation and ataxia
• UBE3A gene is silenced/imprinted
on the chromosome transmitted
by the father
• In brain tissue, genes are active
only on the chromosome
inherited from mother;
maternally transmitted deletion
removes the single active copy
Future Directions
• Experimental observations are clarifying the roles of
epigenetic states in determining cell fates and disease
phenotypes
• Possibilities for reversing the epigenetic abnormalities and
preventing their establishment in utero are being identified
Summary (I)

• Epigenetics is regulating gene expressions in additional to DNA

sequences;
• The modifications include: (i) methylations on CpG islands of
DNA molecules, and (ii) acetylation or phosphorylation on
histone proteins of nucleosomes;
• The modifications control the packaging of DNA/histone
complex and accessibilities of transcript factors;
• In additional, non-coding RNAs including miRNAs and long
non-coding RNAs (lncRNAs) control stability and post-
transcriptional capacity of mRNA molecules
Course outline:
4. Molecular Basis of Genetic Diseases
a. Gregor Mendel and the Laws of Inheritance Lectures 7
b. DNA as the Basis of Inheritance
c. Common monogenic genetic diseases Lectures 8
d. Complex diseases

5. Genetics in Diseases and Development

a. Cytogenetics Lectures 9
b. Common chromosomal abnormalities
c. Epigenetics Lectures 10
d. Mitochondrial DNA inheritance
e. Development and sex determination Lectures 11
f. Clinical genetics and ethical issues
6. Cancer Genetics
a. Genetic factors and environmental factors in cancers
b. Mutations in cell cycle regulatory genes Lectures 12
c. Mutations in the DNA repair system
d. Epigenetics in cancer
In human cells, which organelles contain DNA
materials?
Mitochondrion is the ATP energy production factory
Mitochondrial DNA
https://www.youtube.com/watch?v=IwYOnxMfRD4
Mitochondrial DNA codons have different to nuclear DNA

The dissimilarity of the nuclear and mitochondrial codon table, and the codons in the blue boxes are
interpreted differently in both cases, while the mitochondrial version was proposed in blue.
Alternation of nucleotide sequence may
change amino acid(s) of a protein
Non-Mendelian inheritance: mitochondrial inheritance
Non-Mendelian inheritance: Inheritance pattern associate
with mitochondrial genes
Videos: mitochondrial disease

• Introduction to mitochondrial disease

• https://www.youtube.com/watch?v=k-8MBHzuKdo

• Mitochondrial diseases
• https://www.youtube.com/watch?v=66Tjk8wtJYY
Tissues/organs affected by mitochondrial dysfunctions
Leigh syndrome
• Mutations in mitochondrial DNA
(mtDNA) and over 30 genes in
nuclear DNA such as SURF1;
• The syndrome are described as
beginning in infancy and leading to
death within a span of several years; Leigh syndrome inheritance
• Respiratory failure is the most patterns:
• Maternal inheritance;
common cause of death in Leigh
• Autosomal recessive;
syndrome;
• X-linked.
• Neurological symptoms include
peripheral neuropathy (a result of
damage to the nerves located
outside of the brain and spinal cord)
Disorders involving mitochondria
Summary (II)
• Mitochondrial DNA, unlike nuclear DNA, is inherited
from the mother, while nuclear DNA is inherited from
both parents

• Non-Mendelian inheritance: mitochondrial inheritance

95