Week 9 Flashcards
Overkalix Epigenetics
Region in sweden that is prone to famines
Descendants of those who suffered from famines (granddaughters) had poor health outcomes
Overkalix Epigenetics
Region in sweden that is prone to famines
Descendants of those who suffered from famines (granddaughters) had poor health outcomes
Dutch Hunger winter 1944-1945
Children conceived during this winter had poor health outcomes. Obesity and other long-term health issues
Epigenetics
Above the genome
Changes in gene expression or phnotype that are potentially heritable but that do not alter the underlying DNA base sequence
An epigenetic mark is inherited
Transmission genetics
the two alleles have different DNA seuqences and you are following the inhertiance of these two different sequences. This is not epigenetic inheritance.
vertical transmission genetics
Why is epigenetics so eukaryotic focused
In prokaryotes DNA is loose and free within the nucleus of the cell, no higher order packing if associated with it.
In eukaryotes there is higher order packing, during DNA replication the DNA is packed into chromatin
Packing of eukaryotic DNA (lowest order)
DNA is wrapped around four subunit proteins called histones, DNA is (-)vely charged and histones are (+)ve increasing the interaction
Eight histones wrap around 150 nucleotides of DNA form a nucleuosome
Euchromatin
Loose slightly unpacked DNA
Heterochromatin
Tightly packed DNA
Highest order of packing
Nucleosomes are packed against one another to form a sollonoid
looping the fiber around a scaffold forms the metaphase chromosome
Packing of Inactive/Active chromatin
DNA was not methylated in genes that were expressed and was methylated in genes that were not expressed
DNA was more sensitive to nucleases in genes that were expressed and was less sensitive to nucleases when not expressed
Methylation
Occurs at CpG islands on the fifth carbon of the pyrimidine ring, some are methylated and some aren’t
Heritability of gene expression patterns
CpG sites are palindromes
some sites on the genome will be methylated while others will not be.
DNA methyltransfererases recognize hemimethylated sites on the template strand and will methylate the other strand
Methylation Function
Methylation can inhibit some TFs from binding an promote the binding of factors that recognize methylated Cs and silence gene expression
Histone modification
Histone acetylases can add acetyl to the lysine residue on the arm of the histone protein removing the (+)ve charge, this weakens the electrostatic interactions between DNA and the histone resulting in euchromatin.
Histone arms that are acetylated always lead to euchromatin and gene expression, however methylation can lead to an increase or decrease of expression.
Histone modification
Histone acetylases can add acetyl to the lysine residue on the arm of the histone protein removing the (+)ve charge, this weakens the electrostatic interactions between DNA and the histone resulting in euchromatin.
Histone arms that are acetylated always lead to euchromatin and gene expression, however methylation can lead to an increase or decrease of expression.
Histone modification proteins
Activation
HATs
KMT H3K4
Repression
HDACs
DNMT
KMT H3K9
X-inativation
The X chromosome had different doses in males and females
Females having a different dose of chromosome can be lethal because the genes on the X would be expressed to two times the levels in males
Calico Cats
Only females have the patchy colouring
In each cell in a rapidly dividing embryo (blastoderm stage) one X chromosome is randomly inactivated.
The cell that has one X inactived will divide and give rise to identical daughter cells with the same colouring
X inativation: epigenetics
Once the X-chromosome is inactivated, it is inherited mitotic after mitotic division as inactive, clone of cells.
The inactive X-chromosome is a whole chromosome composed of heterochromatin
Regulating X-inactivation
Occurs only in females cells; therefore, there must be a mechanism that counts the number of X chromosomes in a cell to make sure that one X remains active
What is necessary for X-inactivation
X-inactivation center on each x chromosome.
necessary for the inactivation the chromosome it is on.
we find random inactivation of the chromosome (active in one cell, not in another)
The inactivation of the X chromosome is not always random, due to the mutation in the XIC only the WT can be inactivated
XIC
Is sufficient for inactivation, works in cis
when translocation between the x chromosome and an autosome occurs, the XIC is moved onto the autosome and it will be inactivated
XIC
Is sufficient for inactivation, works in cis
when translocation between the x chromosome and an autosome occurs, the XIC is moved onto the autosome and it will be inactivated
XIC Function
XIC encodes XIST and TSIX
Both are non-coding RNAs and are antisense to each other
XIST coats the X-chromosome during X-inactivation
TSIX is a regulatory RNA
Expression of XIC gene
both x chromosomes are active
one of these chromosome doesn’t express very much XIST RNA, the other expresses more, the XIST-protein complex forms and begins to coat the chromosome that expresses more of it at the beginning of inactivation.
inactivation occurs due to overexpression of RNA, cis-interaction
X-inactivation in the autosome
XIST forms a complex with other proteins and migrates down from the X portion of the chromosome to the autosome, silencing all the DNA
Xist-associated comples
Recruits other proteins, like DNA methylases and histone modification enzymes that create the inactive chromatin
Imprinting
Expression of the gene is dependent on from which parent the gene came from
lgf2
Igf2 (lf in the mother) and Igf2 (+ in the father) lgf2 is expressed and you get WT mice.
Igf2 (lf in the father) and lgf2 (+ in the mother) Igf2 is not expressed and you get small dwarfed mice
Eukaryotic enhancers
Act a great distance on genes to increase expression
how are genes on the same chromosome (cis) independently regulated when enhancer work at such great distances.
Insulators
seperate genes and there regulatory sequences
stop the enhancers from acting on neighboring genes. CTC binding factor (CTCF) is a factor important for insulator function
Order of Igf2 gene
Igf2 insulator H9 enhancer (insulator and H9 are unmethylated from mother and methylated from the father)
Maternal Igf2
CTCF will bind to the unmethylated insulator
the enhancer can only activate transcription of HO and not Igf2
Paternal Igf2
CTCF cannot bind to the methylated insulator and the enhancer can activate Igf2 gene expression
RNAe
RNA epigentics involves the use of mi/siRNAs to recruit proteins involved in modification of chromatin to specific genes/regulatory sequence
RNAe mechanism
Active state chromatin can be transcribed to produce short pieces of RNA that can bind to AGO and bind to DNA and recruit proteins responsible for repressing gene expression
RNAe and B-I/B-1, B’/B’ corn
heterozygote hybrid of B-I/B-I and B’/B’ is yellow when we cross the hybrid with purple B-I/B-I corn we don’t get 1/2 purple corn as expected. We get yellow corn forever.
Tandem repeats are an enhancer for b1 locus, in purple corn b1 transcription is increased. In yellow corn the tandem repeat enhancer is silent chromatin so less b1 is produced.
in B’ corn the siRNA produced from the tandem repeats bind AGO and surpress the activity of the tandem repeats, repression enzymes bind.
in B’/B-I corn the AGO siRNA complex acts in trans and surpresses tandem repeats on both B’ and B-I alleles reuslting in now b1 and yellow corn.
Mutation rate in Humans vs Bacteria
Humans: 1 x 10^-8/bp gamete
Bacteria: 1x10^-10/bp division
Bacteria respond to conditions via acquisition of mutations whereas we respond via other mechanisms.
Even with a higher mutation rate, humans can not outpace the rate of change observed in the bacterial genome. Mutation is a major mechanism of adaption used by bacteria. Another is horizontal gene transfer.
Mechanisms of Horizontal Gene Transfer
Conjuagtion
Transformation
Transduciton: infection via phage
Conjugation
Bacteria have a fertility factor plasmid (F) that encodes a sex pillus, a single strand of plasmid DNA can be transfered via the sex pilus to another bacteria, the plasmid is replicated in the bacteria.
The f factor can recombine with the bacterial plasmid, a fragment of the plasmid will be transfered to the recipient bacteria and recombine with the recipient plasmid
antiobiotic resistance is passed on this way
Transformation
Treat the cells to make them competent to take up DNA.
Donor plasmid is extracted and fragmented (genes closer together on the plasmid will be on the same fragments and taken up)
fragments recombine and are inserted into the plasmid
way of mapping genes on a chromosome
Transduction
Bacteriophage are a vector for moving bacteria genetic information between species
when the bacteria genome gets fragmented it can accidentally become packaged in a viral shell
the phage containing bacterial DNA fragment can transfect another bacteria and that DNA fragment can be recombined into the recipient DNA plasmid
only genes close together can be transduced
