Physiology 3140A Lecture Notes - Lecture 5: Histone Methylation, Sumo Protein, Cytosine
22 May 2018
School
Department
Course
Professor
Physiology 3140
Dr.Pin
Epigenetics II
EPIGENETICS
- Heritable changes in gene expression that do not involve any change in DNA sequence but
modifications in the chromatin.
Three general types:
1. Modification of histone core proteins
o could be phosphorylation, ubiquination, methylation, sumoylation and acetylation
o can be associated with repression or activation
o includes chromatin remodeling proteins
2. DNA methylations
o generally at cytosines
o usually associated with gene repression
3. microRNA
o affect transcription, silence genomic regions or alter RNA processing all leading to
changes in RNA accumulation and expression
DNA Methylation
Roles for DNA methylation:
- Recruitment of factors that allow for inheritance of histone modifications (so they can be the
targets for the epigenetic readers)
- Include interacting with histone modifying enzymes or preventing binding of transcription
factors
- Inactivation of the X chromosome in females
- Imprinting- monoallelic gene expression of maternal or paternal genes
- Repression of DNA translocation
o Within the genome, there are retrotransposons – area where genes will jump from one
place to another in the genome if it is not protected against
o Evolutionarily inserted in the genome
- Repression of gene expression
- DNA can be modified by methylation of cytosines
o primary human fibroblast cell line demonstrated that 4.25% of total cytosines in
genomic DNA are methylated
o However, 67.7% of CpGs are methylated, with 99.98% of DNA methylation occurring in
CpG dinucleotides
o You see most of these islands in the beginning of the gene (another layer of being able to
repress gene expression)
- Functional relevance of non cytosine methylation is still unclear
CpG islands:
- Compose 1% of the genome
- have ~ 10-fold higher frequency of the CpG dinucleotide than the rest of the genome
o this is why they are called islands
o they are highly enriched for cytosines and guanines
- originally defined as genomic regions ∼200 base pairs in size with a C+G content of 50% and an
observed CpG/expected CpG >0.6
o basically you are going to see a lot more Cs and Gs than you would expect to see
randomly
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- often (but not always) is associated with the promoter regions of genes; >50% of all mammalian
genes are associated with CpG islands
- Generally thought to be actively protected from DNA methylation to allow for appropriate
regulation of transcription
- Can have 2 diff types of CpG islands:
o Associated with promoter
▪ Either going to be methylated or not
▪ In the image, they are not methylated – so this is an active gene
▪ This lack of methylation is consistant with the ability of TFs that come in, bind
the DNA and to be able to cause expression
o Non associated with the promoter
▪ These regions are almost always methylated
- This type of methylation would be consistent with active or potentially active genes
- Hypomethylated = less methylation than expected (area associated with the promoter)
How does DNA methylation occur?
2 classes of DNA methylation promoting enzymes:
1. DNA methyltransferase 1 (DMNT1)
o Maintains the methyls that are put on
o The genome is mostly free of DNA methylation bc you want there to be access to all the
genes to allow for differentiation and activation of genes to go along diff developmental
pathwyas
o You don’t want to be restricting the ability of genes in embryonic stem cells or germ
cells to be turned on
o Once you have put the methylation on, there has to be a way to maintain that
methylation from generation to generation (bc epigenetics is heritable)
o There is a way for cells to get rid of their methylation
▪ (ave this passive effect where you have this cell division, but you just don’t add
the mark
▪ In doing so, you are repressing this enzyme – bc this enzyme is constitutively
active, especially in cells that have already determined their fate
o So this DMNT1 comes in and ensures that this cytosine that is going to be brought in
during DNA replication is going to be methylated too
o DMNT1 is just reading what is already there and remaking it (copying out the
methylation pattern)
o Maintains previously methylated DNA
o primary role is to copy DNA methylation patterns during DNA synthesis as well as
repair of DNA methylation patterns
o During cell replication, DNMT1 replicates the methylation patterns to the new strand
o So you have these cytosines that are methylated and unless you have some type of
enzyme that maintains that methylation, those strands are going to lose the methylation
as they go through DNA replication
o 5-azacytidine inhibits DMNT activity
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▪ this is a pharmacological molecule
▪ ppl use this to prevent this kind of methylation to activate genes
▪ cancer treatment: to prevent the methylation →you are going to have proteins
that will be silenced and so preventing cell division
▪ so in cancer, you have promotion of cell division, but you also have repression of
a number of genes that would be nice to have to prevent that abnormal growth
▪ so by putting 5-azacytidine, you may activate those genes that may be anti-cell
cycle or proapoptotic
o DMNT1/3 is not used to go from heterochromatin →euchromtin
2. DNA methyltransferase 3A (DMNT3A) and DMNT3B
o De Novo Methyltransferases
o These put the methyl groups on CpG islands on genes that are currently not being
repressed
o These are really active during post differentiation
o Ex: if you have a cell type that gives rise to 3 other cells types
▪ In one cell, you want to maintain all the potential genes that are going to be
active here, but once you get to a stage where they are already differentiating,
this is when you want to close down the genome
▪ This is where you start to see DMNT3A and DMNT3B take over
o establish the patterns of methylation during development
o capable of methylating native DNA, regardless of whether the DNA is in a replicative
state or not they don’t need to be divided
o **- DNMT3L is a DNMT3A and B regulatory factor
2 Types of DNA Demethylation:
1. Passive
o Based on cell division and inhibition of DNMT1
o The cell is dividing and you just prevent it from adding DNA methylations
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Heritable changes in gene expression that do not involve any change in dna sequence but modifications in the chromatin. Recruitment of factors that allow for inheritance of histone modifications (so they can be the. Repression of dna translocation targets for the epigenetic readers) Include interacting with histone modifying enzymes or preventing binding of transcription factors. Dna can be modified by methylation of cytosines: primary human fibroblast cell line demonstrated that 4. 25% of total cytosines in genomic dna are methylated, however, 67. 7% of cpgs are methylated, with 99. 98% of dna methylation occurring in. Cpg dinucleotides: you see most of these islands in the beginning of the gene (another layer of being able to repress gene expression) Functional relevance of non cytosine methylation is still unclear. Generally thought to be actively protected from dna methylation to allow for appropriate regulation of transcription.
