Physiology 3140A Lecture Notes - Lecture 29: Histone Acetyltransferase, Cpg Site, Histone Methylation
2 May 2018
School
Department
Course
Professor
Cell Physiology Lecture 29
Epigenetics 2
- Heterochromatin:
o Histone methylation
▪ H3K9 TRIMETHYLATION
▪ H3K27 METHYLATION
o HP1 – heterochromatin protein 1
o DNA methylation
- These things are consistent with having compact chromatin
- Euchromatin:
o Histone acetylation:
▪ H3K27 ACETYLATION
o Histone methylation:
▪ H3K4 METHYLATION – 3,2,1
▪ H3K36 TRIMETHYLATION
o RNA polymerase, Transcription factor, promotion factors
Heterochromatin Euchromatin;
1. Remove repressive marks
o Marks that are consistent with heterochromatin
o NEED: Lysine demethylase (eraser- remove the mark)
▪ 2 types of lysine demethylase:
• 1) LSP-1; Lysine specific demethylase 1
o Target = H3K9 trimethylation
• 2) Jmjol3
o Target = H3K27 trimethylation
2. Add active marks
o Need: HAT – histone acetyl transferase(Writers)
o Need: HMT – histone methyl transferase
▪ MLL/KMT – lysine methyl transferase
3. Recruiting Transcription Factors
o Read the marks
o Chromo and bromo domain proteins
o Can have TF that has the ability to bind the DNA sequence and has a DNA binding site, and
transcriptional activation site BUT it may also have these chromo and bromo domain
proteins
▪ Depending on where it is going to bind and what it is going to bind to, these factors
can either unwind the DNA or involved in the interaction in the euchromatin
causing expression
o READERS
4. Make room between nucleosomes
o Need to open up the heterochromatin
o NEED: Pioneer factors
▪ 1) Forkhead proteins
▪ 2) GANA factors
▪ Transcription factor that has ability to bind to the heterochromatin and unwind it
Note: every time you have something that adds marks, you have something that takes away marks
find more resources at oneclass.com
find more resources at oneclass.com
NEED:
- Reader in BOTH heterochromatin and euchromatin
- Writer in: euchromatin
- Eraser in: heterochromatin
Euchromatin Heterochromatin
- Writers in heterochromatin
- Erasers in euchromatin
DNA Methylation
- DNA methylation generally associated with DNA repression, at cytosine
o Different mechanisms methylation works to drive the repression
Roles for DNA methylation:
Recruitment of factors that allow for inheritance of histone modifications
o Methylation is a target for epigenetic readers
Include interacting with histone modifying enzymes or preventing binding of transcription factors
o Can not look at an individual modification, have to look at it at the background of all the
other epigenetic modifications that occur
Inactivation of the X chromosome in females
o Females have two X chromosomes. Most of the X chromosomes is inactivated – methylation
plays big role
Imprinting- monoallelic gene expression of maternal or paternal genes
o Same idea as inactivation
o Locus to locus basis
Repression of DNA translocation
o Within genome, there are retrotransposon elements
o Retrotransposon: gene jumps from one place to another in the genome if it is not protected
against
▪ Evolutionary inserted into the genome
Repression of gene expression
DNA methylation:
- 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
o CpG site has multiple cytosines and guanines
o If you look at the CpG areas in the genome, 2/3of CpG islands are methylated
▪ Inactive areas!
o Within the island, 99.8% of them are methylated
o Note: see the islands in the beginning of the genome
▪ Another layer of being able to repress gene expression or activate gene expression
- Individual cytosines are not being methylated – groups with guanines are
find more resources at oneclass.com
find more resources at oneclass.com
- 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 In the CpG island, have 10x more CpG than you would expect
o Highly enriched for cytosines and guanines
- Originally defined as genomic regions:
o 200 base pairs in size
o C+G content of 50%
o Observed CpG/expected CpG >0.6
▪ See more C+G than expected randomly
- 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
- This type of methylation would be consistent with active or potentially active genes
- Gene: all of the areas are CpG dinucleotides
- Can have two different types of CpG island
o 1) Associated with the promoter
▪ HYPOMETHYLATED
▪ METHYLATED – INACTIVE
▪ NON-METHYALTED – ACTIVE
o 2) Not associated with the promoter
▪ MYPERMETHYLATED: ALMOST ALWAYS METHYLATED
- Lack of methylation (hypomethylation) is consistent with the ability of the TF to come in, bind to the
DNA & cause expression
To go from one DNA state to another (euchromatin, heterochromatin), you have to have enzymes that add or
take away methyl groups
- Two types of DNA methylation enzymes
o 1. DNA methyl transferase – 1
o 2. DNA methyl transferase – 3A and 3B
1. DNA methyltransferase 1 (DMNT1)
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
H3k27 methylation: hp1 heterochromatin protein 1, dna methylation. These things are consistent with having compact chromatin. Euchromatin: histone acetylation, histone methylation, h3k27 acetylation, h3k4 methylation 3,2,1, h3k36 trimethylation, rna polymerase, transcription factor, promotion factors. Remove repressive marks: marks that are consistent with heterochromatin, need: lysine demethylase (eraser- remove the mark, 2 types of lysine demethylase, 1) lsp-1; lysine specific demethylase 1, target = h3k9 trimethylation, 2) jmjol3. Make room between nucleosomes: need to open up the heterochromatin, need: pioneer factors, 1) forkhead proteins, 2) gana factors, transcription factor that has ability to bind to the heterochromatin and unwind it. Note: every time you have something that adds marks, you have something that takes away marks. Dna methylation generally associated with dna repression, at cytosine: different mechanisms methylation works to drive the repression. Recruitment of factors that allow for inheritance of histone modifications: methylation is a target for epigenetic readers.
