W13L2 Flashcards
Histone methylation
Histone methyltransferases (HMTs) methylate arginine or lysine; transfer a methyl group from the donor S-adenosylmethionine (SAM); carried out by the SET domain regions within the HMT
Unlike acetylation, methylation can be both an active or repressive mark depending on the residue marked
H3K4me3
considered an active mark
Mixed Lineage Leukemia proteins (MLLs) catalyze methylation of H3K4 (also known as lysine methyltransferases – KMTs)
Most methylation is trimethylation (me3), but mono (me1) and di (me2) methylation also occur
H3K4me1
associated with transcriptional silencing in myoblasts, macrophages, and human embryonic stem cells
Establishes boundaries
that restrict the recruitment of
chromatin-modifying enzymes
to defined regions within
promoters
H3K4me2
marks enhancers where transcription factors bind
H3K27me3
associated with genomic regions that are weakly transcribed
or silent
Polycomb Repressor Complex 2 (PRC2)
promotes H3K27me3
Enhancer of
Zeste Homologue 2 (EZH2)
carries SET domain
upregulated in breast,
pancreatic, and prostate cancer
Somatic LOF mutations in various leukemias
Methylation marks of H3 are the most studied
Interplay between acetylation (active) and methylation (repressed) for H3K27 and H3K9
H3K36me3
associated with gene transcription – active mark
H3K9me2/3
-associated with heterochromatin; define LADs –lamin-associated domains)
Interplay between acetylation (active) and methylation (repressed) for H3K27 and H3K9
What happens when you get both active and repressor marks?
Exists on developmentally important genes or immediate response genes
Maintains the possibility for transcription to occur
Genes are “primed” or ”poised”
- poised not quite open or closed - has methylation of K4 and K27
Why this level of control?
- Allows a specific type of gene expression to be “fixed in”
– most genes start off as open and generally become active (euchromatin) or inactive (heterochromatin)
- Prevent improper activation of genes
– limits the effects of activators and repressors
- Can keep genes in a “ready” state
– genes are inactive but primed, containing both active and repressive marks
– These genes can be rapidly activated
- Provides a link between environment and gene regulation
Specific histone covalent modifications recruit effector proteins that have a variety of functions for modifying chromatin
Bromodomains- binds acetylated lysines
Chromodomains- binds methylated lysines
SANT domains- binds unmodified histones
Are readers of the epigenetic code
BRG1/Baf60c has a SANT domain – required for “opening” up DNA
DNA methylation
DNA can be modified by methylation of cytosines
Functional relevance of non cytosine methylation is still unclear
primary human fibroblast cell line demonstrated that 4.25% of total cytosines in genomic DNA are methylated
However, 99.98% of DNA methylation occurs in CpG dinucleotides and ~75% of these CpGs are methylated
CpG islands
Compose 1% of the genome; ~25,000 in the genome
have ~ 10-fold higher frequency of the CpG dinucleotide than the rest of the genome
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
Two classes of DNA methylation promoting enzymes
Two classes of DNA methylation promoting enzymes:
- DNA methyltransferase 1 (DMNT1)
- Maintenance methyltransferases
- Maintains previously methylated DNA
- primary role is to copy DNA methylation patterns during DNA synthesis as well as repair of DNA methylation patterns
- During cell replication, DNMT1 replicates the methylation patterns to the new strand
- 5-azacytidine inhibits DMNT activity - DNA methyltransferase 3A (DMNT3A) and DMNT3B
- De novo methyltransferases
- patterns of methylation are established during development
- capable of methylating native DNA, regardless of whether the DNA is in a replicative state or not
- DNMT3L regulates DNMT3A and B function
Two types of DNA demethylation
Passive – based on cell division and inhibition of DNMT1
Active - this can occur through the removal or conversion of methylcytosine and usually involved either base excision repair or nucleotide excision, such as via Tet1
Roles for DNA methylation
Recruitment of factors that allow for inheritance of histone modifications
Include interacting with histone modifying enzymes or preventing binding of transcription factors
Methylcytosine binding proteins (MBD2 & MECP2) can recruit HDACs by recruiting to the methylated CpG islands and then deacetylate nearby histones
- proteins like MBD2 or MECP2 can then recruit H3K9 HMTs to methylate the histone nearby
- DNA methylation can precede histone acetylation and methylation
Inactivation of the X chromosome in females
Imprinting- monoallelic gene expression of maternal or paternal genes
Repression of DNA translocation
Repression of gene expression
X inactivation
The X-chromosome that makes more Xist becomes the Xi chromosome; this chromosome is silenced
Xa chromosome is shown
How does DNA methylation contribute to X inactivation?
- CpG methylation for the Xist repressed —> stable Xist repression
- hyperacetylation for the Xist upregulated –> stable Xist expression
