Epigenetics
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What is epigenetics?
The inheritance of variation that occurs without differences in DNA sequence.
What are epigenetic marks?
Heritable changes in DNA or chromatin structure that alter gene expression.
What three molecular mechanisms can alter chromatin structure?
DNA methylation, chemical modifications to histones, and RNA molecules that alter chromatin structure.
What is DNA methylation?
The addition of methyl groups (–CH3) to nucleotide bases.
What is the most common methylated base in eukaryotes?
5-methylcytosine.
Where does DNA methylation most often occur?
At CpG dinucleotides.
What is a CpG dinucleotide?
A cytosine followed by a guanine on the same DNA strand, connected by a phosphate.
How does methylation near a promoter usually affect transcription?
It inhibits transcription.
What enzyme adds methyl groups to cytosines?
DNA methyltransferase.
What is hemimethylated DNA?
DNA in which only one of the two strands is methylated.
How are DNA methylation patterns maintained after replication?
Maintenance DNA methyltransferase recognizes hemimethylated CpG sites and methylates the newly synthesized strand.
Where does a methyl group attached to cytosine project in DNA?
Into the major groove, where many DNA-binding proteins interact with DNA.
What enzymes can DNA methylation help recruit?
Histone deacetylases, which remove acetyl groups from histones.
What causes female honeybee larvae to develop into queens?
Being fed royal jelly.
How does royal jelly affect DNA methylation in honeybees?
It silences Dnmt3, a gene encoding a DNA methyltransferase.
How can restriction enzymes help detect DNA methylation?
Some restriction enzymes cut methylated and unmethylated DNA differently.
What is bisulfite sequencing used for?
Detecting DNA methylation at specific cytosines.
What does sodium bisulfite do to unmethylated cytosine?
It converts unmethylated cytosine to uracil.
How does bisulfite sequencing distinguish methylated and unmethylated cytosines?
Unmethylated cytosines convert to uracil and are read as thymine after amplification, while methylated cytosines remain cytosine.
What chemical groups can be added to histones?
Phosphate groups, methyl groups, acetyl groups, and ubiquitin.
Where do histone modifications commonly occur?
On positively charged amino acids in histone tails.
How do histone modifications affect gene expression?
They alter chromatin structure and can increase or decrease transcription.
How does histone acetylation affect chromatin?
It promotes a more open chromatin structure.
How does histone acetylation usually affect transcription?
It increases transcription.
Does histone methylation always repress transcription?
No. Its effect depends on which amino acid is methylated.
What does H3K4me3 mean?
Trimethylation of lysine 4 on histone H3.
How does H3K4me3 affect transcription?
It promotes transcription.
How does trimethylation of lysine 9 on histone H3 affect transcription?
It inhibits transcription.
How does trimethylation of lysine 20 on histone H4 affect transcription?
It inhibits transcription.
What are Polycomb group proteins?
Proteins that form complexes that modify histones and repress transcription.
What does Polycomb repressive complex 2 (PRC2) do?
It adds two or three methyl groups to lysine 27 on histone H3.
Why is inheritance of histone modifications more complicated than inheritance of DNA methylation?
Histones are randomly distributed during replication, and some modifications may be lost.
How may histone modifications be restored after DNA replication?
Histone-modifying enzymes that remain associated with chromatin can help restore the modifications.
What are stem cells?
Undifferentiated cells that can self-renew and develop into specialized cell types.
What does pluripotent mean?
Able to develop into nearly any cell type in the body.
What are induced pluripotent stem cells (iPSCs)?
Somatic cells artificially reprogrammed into a pluripotent state.
How do epigenetic processes contribute to cell differentiation?
They establish different patterns of gene expression in cells with the same DNA sequence.
What is a paramutation?
An interaction between two alleles that causes a heritable epigenetic change in the expression of one allele.
What does the b1 locus control in corn?
The amount of purple anthocyanin pigment produced.
What phenotype is associated with the B-I epiallele in corn?
Dark purple pigmentation and high b1 expression.
What phenotype is associated with the B′ epiallele in corn?
Light pigmentation and low b1 expression.
How do B-I and B′ differ in DNA sequence?
They have identical DNA sequences.
What are epialleles?
Forms of a gene with identical DNA sequences but different heritable epigenetic states.
What happens when B-I and B′ occur together in a corn plant?
B′ converts B-I into a low-expression state called B′*, producing a lightly pigmented plant.
What DNA region is required for paramutation at the corn b1 locus?
Tandem repeats of an 853-base-pair sequence upstream of b1.
How does chromatin structure differ between B-I and B′?
B-I has more open chromatin, while B′ has more closed chromatin.
What role do siRNAs play in corn paramutation?
siRNAs produced from tandem repeats help convert B-I into the repressed B′* state.
What is the X-inactivation center?
A region of the X chromosome that controls X inactivation.
What does the Xist gene encode?
A long noncoding RNA approximately 17,000 nucleotides long.
How does Xist promote X inactivation?
It recruits Polycomb complexes, including PRC2 and PRC1, that establish repressive epigenetic marks.
What does Tsix encode?
A long noncoding RNA complementary to Xist RNA.
On which X chromosome is Tsix expressed?
The active X chromosome.
What is the role of Jpx?
It produces a long noncoding RNA that stimulates Xist transcription.
What is the role of Xite?
It helps sustain Tsix expression.
What is genomic imprinting?
An epigenetic process in which expression of a gene depends on whether the allele was inherited from the mother or father.
How can DNA methylation produce genomic imprinting?
Different methylation patterns can silence one parental allele while allowing the other to be expressed.
What does the genetic conflict hypothesis propose?
Maternal and paternal alleles can experience conflicting evolutionary pressures over offspring growth and resource use.
What is behavioral epigenetics?
The study of how epigenetic changes relate to behavior and experiences.
How can early life experiences affect later behavior?
They can produce lasting epigenetic changes that influence gene expression.
What maternal behavior was associated with offspring stress responses in rats?
Maternal licking behavior.
What methylation pattern was associated with childhood abuse in the studies described?
Increased DNA methylation at certain sites in the brain.
How did a low-protein paternal diet affect offspring in the studies described?
It altered lipid and cholesterol metabolism and decreased offspring cholesterol levels.
How did a high-fat paternal diet affect daughters in the studies described?
It impaired glucose tolerance and insulin secretion.
What epigenetic differences accompanied the paternal diet effects?
Differences in DNA methylation patterns.
What is the epigenome?
The complete collection of epigenetic modifications within an individual's genome.
What is an epigenome-wide association study (EWAS)?
A study that looks for associations between epigenetic changes at specific genomic locations and particular phenotypes.
Do different cell types have the same epigenetic patterns?
No. Different cell types have different epigenetic patterns associated with their specialized functions.
What is epigenetic editing?
Deliberately changing epigenetic modifications to alter gene expression.
How can modified CRISPR-Cas9 be used for epigenetic editing?
A guide RNA directs an inactive Cas9 fused to a DNA- or histone-modifying enzyme to a specific DNA region.
Why use nuclease-inactive Cas9 for epigenetic editing?
It targets a DNA sequence without cutting the DNA.
How does unmethylated cytosine decay in ancient DNA?
It can convert to uracil.
How does methylated cytosine decay in ancient DNA?
It can convert to thymine.
How can ancient DNA reveal past methylation patterns?
Different decay products of methylated and unmethylated cytosines allow researchers to infer methylation patterns.
How similar were ancient hominid and modern human methylation patterns in the slides?
Approximately 99% similar.
Where were methylation differences found between ancient hominids and modern humans?
In HOXD genes and disease-related genes.