Chapter 21 - Epigenetics Flashcards
What is epigenetics?
Change in gene expression or phenotype that are potentially heritable but that do not alter the underlying DNA base sequences
Typically, very stable from generation to generation, but can be induced by environmental factors
What are the 3 mechanisms leading to epigenetic changes?
DNA methylation
Histone modification
RNA molecules
What is DNA methylation?
Always on cytosine in eukaryotes - 5-methylcytosine
Associated with repression of transcription
- Methyl groups typically sit in major grooves of DNA where DNA binding proteins sit
- When methylation occurs, it becomes difficult for these proteins to bind in and control regulation
- Can also block transcription factors and polymerases from binding
Typically adjacent to guanines - forms CPG dinucleotides
Regions with many CPG nucleotides - CPG islands
- Typically located on or near promoters (affect gene regulation)
Can repress or activate genes by methylating or demethylating cytosines in genes
What is methyltransferase and how does it work?
Enzyme that methylates DNA
Come in and recognize hemi-methylated DNA (one strand is methylated, other isn’t)
Will add methyl groups to unmethylated cytosines
In this way, methylation is maintained across cell divisions and future generations
What is the royal jelly example with DNA methylation?
Royal jelly silences the Dnmt3 gene, which regulates DNA methylation
Typically, the gene is active in bees, which methylates their DNA, resulting in a worker phenotype
In royal jelly, the gene is shut down, which causes no methylation of the DNA, resulting in a queen phenotype
How is DNA methylation traditionally detected?
Some restriction endonucleases are sensitive to methylation and will not cut a sequence that contains a methylated cytosine, while other restriction enzymes are insensitive
Can use a combo of sensitive and insensitive to cut up the DNA and then run it on a gel to see the patterns of unmethylated and methylated
How is bisulfate sequencing used to detect DNA methylation?
Can treat unmethylated cytosines with sodium bisulfate, which converts them to uracil
Can sequence pretreated and treated to see where unmethylated cytosines are in DNA sequences
Cytosines that come up as thymine indicate that they were unmethylated
Cytosines that are unchanged indicate methylation
What are histone modifications?
Typically occur on the tails of histone proteins
Include additions of phosphates, methyl groups, acetyl groups, and ubiquitin
Can occur at different amino acids on different histones leading to 100+ unique potential changes to the histone itself
Can either increase or decrease rate of transcription of a gene
- Do this by altering chromatin structure – more open or closed structure
- Open – increase rate of transcription
- Closed – decrease rate of transcription
What is the effect of histone acetylation on gene expression?
Increases gene expression
Addition of acetyl groups on histones opens chromatin structure
What is the effect of histone methylation on gene expression?
Decreases or increases gene expression
Depends on amino acid it binds to - can open or close structure
What are polycomb groups and what do they do?
Large group of proteins that represses transcription by modifying histones
Often responsible for adding or removing modifications
Bind in to where histones are and make it more difficult for the enzymes/proteins that are necessary for transcription to bind into DNA
Proteins are recruited to specific targets on the DNA by transcription factors, chromatin markers, or other noncoding components
What are the 2 hypotheses for how histone modifications are passed down through generations?
When old histones are distributed after replication and new histones are added, epigenetic marks in old histones recruit enzymes to make similar changes in new histones
Epigenetic marks are all lost during replication but modifying enzymes remain attached to histones and reestablish marks on both old and new histones after replication
How are histone modifications detected?
Chromatin immunoprecipitation (ChIP)
Fragment the chromatin and apply a specific antibody that binds to histone probes
- Probes cause modification to chromatin itself and histones are removed
- DNA is precipitated out, and you can determine genetic location of where these histone modifications were
Long and drawn out process – now use ChIP-seq
- Can sequence fragments that are marked, so you can determine locations where modifications are occurring
What are the 5 mechanisms in which RNA molecules lead to epigenetic changes?
X inactivation
- Xist - encodes a long noncoding RNA that suppresses transcription through histone methylation
Paramutation
- siRNA epigenetically alter allele that induces a change in another allele
siRNAs silence genes and transposable elements by directing DNA methylation
Methylation and histone modifications influence the expression of microRNAs
MicroRNAs control the expression of genes that produce epigenetic effects
What are the 5 epigenetic effects and developments?
Cell differentiation
Paramutation
X-inactivation
Genomic imprinting
Monozygotic twins
What is cell differentiation?
All cells are genetically identical in an organism, yet these cells exhibit a vast array of phenotypes
- Differences between cells are very stable and are passed on from generation to generation (cellular level) even though DNA sequence is the same
As stem cells divide and give rise to different specialized cells, the gene expression programming of the cell becomes progressively fixed
- Each cell is only expressing genes that are necessary to be an epithelial cell
Changes in DNA methylation and chromatin structure that play a role in both silencing and activation of genes that are necessary for cell-specific expression
What is paramutation?
Type of transgenerational epigenetic effect in which one allele of a genotype alters the expression of another allele
- This alteration persists for several generations
- Persistence can occur even after allele is taken out of gene pool
No change in DNA sequence itself
Altered allele is able to convert another allele to new phenotype
How is mutation seen in corn at the b1 locus?
Helps determine amount of purple pigment that is produced by the corn
B’ is altering allele – alters B-I allele so it is regulated/silenced
- Both alleles at DNA sequence level are identical – called epialleles
Heterozygote plant will produce light pigmentation, but it will convert B-I allele to B’*
B’* will be passed on to future generations and will be able to convert other alleles to the B’* allele just as the B’ did
How does paramutation work at the molecular level for corn?
B-I locus has 7 tandem repeats upstream of coding sequence that don’t encode a protein but could act like an enhancer for transcription
Both B-I and B’ alleles have tandem repeats upstream, but chromatin structure between them is different
At B-I, chromatin structure is more open at tandem repeats/coding region
- Most likely allowing transcription to occur more regularly
At B’, chromatin structure is more closed, causing transcription to be reduced
Most likely occurs because of an siRNA that binds near tandem repeats to cause chromatin structure to close up more
What is X-inactivation?
Random inactivation of one of the X chromosomes in females to provide equal expression of genes in males and females – form of dosage compensation
Once a particular X chromosome is inactivated, it will remain inactivated when DNA is replicated, and epigenetic mark on inactivated X is passed on to future generations of cells
Controlled by a segment of X chromosome called X-inactivation center
Key player is the Xist protein – encodes for long noncoding RNA
- Long noncoding RNA is transcribed by one of the X chromosomes, and it coats the X chromosome in itself
- Recruits the polycomb recessive complex I, which produces epigenetic marks (typically histone modifications) along X chromosomes that will become inactive
- Marks change configuration of chromatin structure on chromosome to repress transcription of all of the genes on the X chromosome, thereby rendering it inactive
How does the other X chromosome not become inactive in X-inactivation?
Other genes at X-inactivation center play a role in not allowing the other chromosome to also be inactivated
Tsix is an antisense (opposite direction to Xist) long noncoding RNA to Xist
- Represses Xist on the X chromosome that is going to stay active
Jpx stimulates expression of Xist on the inactive X chromosome
Xite is another long noncoding RNA that stimulates the expression of Tsix on the active chromosome
What is genomic imprinting?
Sex of the parent that transmits a certain allele determines the expression of an allele in its progeny
Thought to be due to methylation of alleles in the parents
Imprinted genes in mammals typically affect early embryonic development and fetal growth - Leads to genetic conflict hypothesis
What is the genetic conflict hypothesis?
Suggests that there are different and conflicting evolutionary pressures acting on maternal and paternal alleles that affect fetal growth
There are paternal alleles that tend to maximize the size of the offspring, and these alleles are favored evolutionarily – associated with infant survival and adult health
Conversely, maternal alleles tend to limit/reduce fetal growth to allow for less strain on the mother to carry the progeny and allow her to reproduce again
Predicts that genomic imprinting evolves in this way
What occurs with monozygotic twins and epigenetic effects?
Because monozygotic twins develop from the same egg, they’re genetically identical, however we often see variation between identical twins in terms of appearance, health, behavior, etc.
Variation isn’t well understood, but it is believed to come from epigenetics
- Could be environmental epigenetic factors or be present in one twin but not the other or can change in individual over time
