Epigenetic Regulation in Health and Disease Flashcards
Heritable changes in gene function that occurs without a change in the DNA sequence
Epigenetics
What are some common modifications to the genome?
DNA methylation, Histone Modification, Non-coding RNA
All of the epigenetic phenomena are characterized by chemical modifications to
DNA itself (DNA Methylation), or to Histones (The proteins around which DNA is wound)
In humans, DNA methylation typically occurs at the
Cytosine bases of DNA within CpG dinucleotides
Associated with the 5’-end regulatory regions of almost all housekeeping genes, as well as with half of the tissue specific genes
CpG rich regions (“CpG Islands”)
When these promoter CpG Islands are methylated, the associated genes tend to be
Transcriptionally inactive
The correct expression of many tissue-specific, germline-specific, imprinted, and X-chromosome inactivated (in females) genes, as well as that of repetitive genomic sequences, relies largely on
DNA Methylation
Play key roles in the erasure, establishment, and maintenance of DNA methylation patterns through development
Epigenetic modifications
The extent of DNA methylation changes in an orchestrated way during mammalian development, starting with a
Wave of demethylation during cleavage
However, after implantation, there is
Genome-wide methlyation
An active process that strips the male genome of methylation within hours of fertilization
Demethylation
In contrast, the maternal genome is passively demethylated during subsequent
Cleavage divisions
The extent of methylation in the genome of gastrulating embryo is high, owing to de novo methylation, but it tends to decrease in specific tissues during
Differentiation
Occurs rarely after gastrulation, but this phenomenon is seen frequently in cancer
De novo Methylation
Which enzyme removes methyl groups?
Demethylase (dMTase)
Which enzyme adds methyl groups
DNA methyl transferase (DNMT)
Replication of somatic cells results in hemimethylated DNA, which is then fully methylated by
DNMT
Negatively regulates transcriptional output
Transcription factor binding to methylated DNA sequence motifs
DNA methylation is important in
- ) Regulation of gene expression (i.e. tissue specific transcription)
- ) Genomic imprinting
An autism spectrum disorder with a monogenic origin
Rett Syndrome
A progressive neurological disorder that is one of the most common causes of mental retardation in females
Rett syndrome
What type of trait is Rett Syndrome?
X-linked dominant
Children affected by Rett syndrome have a period of apparently normal development lasting
6-18 months
What is the cause of most cases of Rett Syndrome
MECP2 gene mutations
Capable of binding specifically to methylated DNA and represses transcription from methylated gene promoters
MECP2
MECP2 is ubiquitously present, but is most abundantly expressed in the
Brain
Los of function of MeCP2 in differentiated post-mitotic neurons likely results in the inappropriate overexpression of genes with potentially damaging effects during
Nervous system maturation
The unequal expression of the maternal or paternal alleles of a gene
Genomic Imprinting
The epigenetic tags on imprinted genes usually stay put for the life of the organism, but they are reset during
Egg and sperm formation (Thus why they are not passed to offspring)
Imprinted genes play vital roles in
- ) Embryonic growth
- ) Neonatal behavior
- ) Tissue or developmental stage-specific monoallelic expression patterns
The SNRPN gene, producing small nuclear ribonucleoprotein N, being methylated during oogenesis but not spermatogenesis is an example of
Genomic imprinting
An example of genomic imprinting because it is methylated during spermatogenesis but not oogenesis
The UBE3A gene
Region that contains at least two imprinted genes, one maternally imprinted and one paternally imprinted
Chromosome 15
If a child receives a chromosome 15 in which a large deletion removed the function of these genes from their father, and an (inactive) maternally imprinted gene from their mother, they will have
Prader-Willi Syndrome
If a child receives the deleted chromosome 15 from their mother, and an (inactive) copy of the paternally imprinted gene from their father, they will have
Angelman syndrome
Prader-Willi syndrome is indicated by
Mental retardation and Hyperphagia
Angelman Syndrome is indicated by
Excessive laughter, seizures, and mental retardation
In Prader-Willi syndrome, the maternal allele is imprinted by
-No SNRPN protein is expressed from the imprinted maternal chromosome 15 SNRPN allele
Methylation
In Angelman syndrome, the paternal allele is imprinted by methylation resulting in
-Why a deletion in the mothers gene causes the syndrome
No expression of UBE3A protein by the UBE3A allele
Histones can be reversibly modified in their amino-terminal tails, which protrude from the nucleosome core particle, by
- ) acetylation of lysine
- ) phosphorylation of serine
- ) methylation of lysine and arginine residues
- ) sumoylation
The N termini of core histone proteins contain many lysine residues that impart a highly positive charge. These positively charged domains can bind tightly to
the negatively charged DNA through
Electrostatic Interactions
Tight binding between DNA and histones is associated with
Gene inactivity
Neutralizes the positively charged histone tails, weakening their interaction with DNA (forming euchromatin) and allowing active transcription
Acetylation of Histone tails
Which enzyme acetylates histone tails?
Histone acetyltransferase (HATs)
A functional RNA molecule that is transcribed from DNA but is not translated into proteins
non-coding RNA
-includes: miRNA, siRNA, piRNA, and IncRNA (long non-coding RNA)
Long non-coding RNAs regulate epigenetics by
Chromatin remodeling, transcriptional regulation, post-transcriptional regulation, and as precursors for siRNAs
What is an example of epigenetic regulation by long non-coding RNAs (ncRNAs)?
X-chromosome inactivation
X-chromosome inactivation involves which two IncRNAs?
- ) Xist (of X-inactive specific transcript)
2. ) Tsix (its antisense transcript, a negative regulator of Xist)
Transcribed from the X-inactivation center (XIC) of the inactive X chromosome (Xi)
The lncRNA Xist
What does the Xist RNA do?
Covers the entire chromosome and silences gene expression through epigenetic modifications of histones and DNA (thus inactivating the X chromosome)
Can bind to the X-inactive specific transcript (Xist) and inhibit its action, thus preventing X-inactivation
-antisense to Xist RNA
Tsix
Both chromosomes will express Xist in low concentrations, but then one chromosome will start to express high levels of Tsix, which dratically reduces the concentration of Xist on that chromosome and thus, that chromosome become the
Active X-chromosome
The ability of one genotype to produce more than one phenotype when exposed to different environements
Phenotypic plasticity
Environmental effects (such as diet or stress) on a phenotype may involve
Epigenetic changes in gene function
Changes in chromatin marks and transcriptional networks associated with sustained neuronal activity, mood disorders, and addiciton
Adult Neuronal plasticity and neurogenesis
Methylation of the agouti gene results inthe agouti mRNA being made briefly during development, before the agouti gene is then silenced for the remainder of the mouses life. This leads to a
Healthy brown mouse
Non-methylation of the agouti gene results in the agouti gene being continually active, producing mRNA across the mouse’s lifespan. This leads to a
Yellow mouse that develops obesity and diabetes during adulthood
When a female yellow mouse (agouti gene unmethylated) was given a diet supplement during pregnancy and nursing with additional methyl groups, her offspring were
Mostly brown and healthy (agouti gene methylated and silenced)
When a female yellow mouse (agouti gene unmethylated) was given no dietary supplements during pregnancy, her offspring were
Mostly yellow and unhealthy (agouti gene unmethylated and active)
What are two methods to study changes in the epigenome?
- ) Bisulfite conversion of DNA
2. ) Methylation-sensitive restriction enzymes
Converts cytidine to uridine if the citidine is NOT methylated
Bisulfite
Following bisulfite conversion, the DNA strands are no longer complementary and a PCR primer is generated by a reverse transcriptase. Next we perform
PCR, DNA sequencing, or Methylation specific restriction enzyme digestion
The C’s that are not methylated are converted toU’s. Then they are replicated by DNA polymerase and become
T’s
We can ditect DNA methylation using methylation-sensitive restriction enzymes. The methylation incensitive restriction enzymes will
Cut DNA next to a methylated C
Functionally relevant changes to the genome that do not involve a change in nucleotide sequence
Epigenetics
Epigenetics are cellular and physiological traits that ARE heritable by daughter cells and not cause by changes in
DNA sequence
Epigenetics describes the study of stable, usually long-term alterations in the
Transcriptional potential of a cell
These covalent modifications alter how genes are expressed without altering the underlying DNA sequence
-an example of epigenetics
- ) DNA methylation
2. ) Histone modifications
Attach to silencer regions of the DNA and remain associated with the silencer regions subsequent to DNA replication and cell division
Repressor proteins
Epigenetics may last through cell divisions for the duration of a cell’s lie and may also last for multiple generations. These non-genetic factors cause the organisms genes to
Behave (or “express themselves”) differently
Methylation of Cytosine can turn off
Gene expression
Methylation of CpG in 98% of the genome does not matter. But methylation of the CpG stretches before transcriptional start site,
Inactivates transcription
If there is an MeCP2 mutation in a boy, they will likely die as a fetus girls survive due to the fact that they have
Two X-Chromosomes
Inactivation of one of the X-chromosomes is called
Lyonization
Once you use a methylation-sensitive restriction enzyme technique, you can study the results with
Southern-blot hybridization
