Lecture 12: epigenetic mechanism of gene regulation

in eukaryontes (mammals) most methyl groups ar efound in?

"CpG" dinucleotides (not CG base pairings)

Mechanisms of X chromosome inactivation:

-Random inactivation of one X chromosome is brought about by "coating" of the chromosome by the untranslated XIST (X-inactive specific transcript, long non-coding RNA; lncRNA) transcript. -The inactive X chromosome is coated by Xist RNA. -XIST expression is repressed by the antisense transcript Tsix on the active X. -Xi (inactive X chromosome): high levels of DNA methylation, low levels of histone acetylation, low levels of histone H3K4me3, and high levels of histone H3K27me3, all of which are associated with gene silencing. -A histone variant called macroH2A (H2AFY) is exclusively found on nucleosomes along the Xi Xist recruits proteins (PRC2) that turn X into heterochromatin = silenced

Monoallelic gene expression: three mechanisms

1. Altered structure in the gene promoter (ICR) 2. Differential expression of an antisense RNA transcript 3. Blocking of an enhancer by an insulator (and CTCF)

Epigenetic markers

1. DNA methylation 2. chromatin modification

C. elgans, Drosophila and yeast contain little or no what?

5-methyl cytosine

What are found in human cancer cells?

Aberrant DNA methylation patterns and aberrant histone modifications

Genomic Imprinting: basic concepts continued

An imprinted gene is expressed from only one of the two parental chromosomes (nonrandom) differential methylation of imprinting control region (ICRs) imprinting occurs in mammals, but no other vertebrate looked at so far <100 different genes currently known to be imprinted important roles in development imprinted genes are organized in clusters

Genomic imprinting: basic concept

Cell have two alleles (copies) of autosomal genes both alleles are expressed, for most genes small class of genes shows "monoallelic expression," where a single allele in a cell is preferentially expressed In most cases of monoallelic gene expression, cells randomly select only one allele to encode RNA and protein for that gene An exception is "genomic imprinting," where selection of the active allele is nonrandom and based on the parent of origin

in plant DNA, cytosine methylation occurs at ?

EITHER CG or CNG, where N can be any base

CpG islands were first detected by their sensitivties to the ?

Hpall which cuts only methylated CpG regions

Imprinting: establishing and maintaining

Imprinting is reset in the germline by erasure of the DNA methylation marks in the primordial germ cells involves an active demethylation process by unknown enzymatic activities The de novo methyltransferase DNMT3a and cofactor DNMT3L are required to reeestablish imprinting

Random X chromosome inactivation in mammals

Marsupials (kangaroos, koalas) -The paternal X chromosome undergoes preferential inactivation around 2-4 cell stage and remains inactive in all tissues (placental mammals) -the paternal mark is erased in cells of the blastocyst -random inactivation of either the paternal or maternal X chromosome

Genomic Imprinting

The nonrandom expression of a gene from only one of the two parental chromosomes regulated by differential methylation

What are CpG islands?

There are regions of the genome that have a higher concentration of CpG sites

What is X chromosome inactivation?

X-inactivation is a process by which one of the two copies of the X chromsome present in female mammals in inactivated

DNA methylation controls and represses ?

chromatin and txn

CpG islands are usually unmethylated and ?

chromatin open

Cytosine DNA methylation

covalent modification of DNA methyl group is transferred from S-adenosylmethionine (SAM) to the carbon-5 position of cytosine by a family of cytosine by a family of cytosine DNA methytransferases (DNMTs)

MspI

cuts both unmethylated and methylated CpG regions

FRM1 gene

encodes the fragile X mental retardation protein (FMRP) that protein is a cytoplasmic RNA-binding protein that is involved in neuronal maturation and/or development

C. elegans dosage compensation

expression of genes on the female X chromosome is reduced by half compared with the male X

CpG islands are found near?

gene promoters

Hypomethylated (under)

genes are active

Hypermethylated (over)

genes are inactive

Drosophila dosage compensation

genes on the male X chromosome are expressed at twice the level of the female X

Fragile X mental retardation and aberrant DNA methylation patients

have a trinucleotide repeat expansion (>200 repeats of CGG, normal 6~50 repeats) within the 5'-UTR of the FMR1 gene located on the X-chromosome -hypermethylation of DNA and hypoacetylation of histones in the promoter region of the FMR1 gene lead to loss of FMR1 gene expression

After replication, the DNA double helix is?

hemimethylated

SILENCING

long term repression through chromatin

Methylation of CpG islands results in binding of repressors called ?

methy-CpG-binding proteins

Hypomethylation (under) of DNA may stimulate ?

oncogene expression

Maintenance DNMT (DNMT1) recognizes?

only hemimethylated sites and methylates the new strand of DNA appropriately

CpG island is used to help in the ?

prediction and annotation of genes

Genes in mammalian genomes have CpG islands associated with ?

promoter regions

methylation is maintained during DNA replication by ?

semiconservative process

DNA methylation marks genes for?

silencing

CpG islands are ?

small regions of DNA (1-2 kb in size) that are CpG-rich but normally unmethylated

Epigenetics

study of heritable changes in gene expression that occur without a change in the primary DNA sequence (old definition) changes arise from modifications of both the DNA and protein components of chromatin chromatin marks result from DNA sequence-specific interactions of proteins that recruit modifying enzymes to specific targets

CpG islands are associated with?

the promoters of ~40-50% of "house keeping genes"

Hypermethylation (over) of DNA may silence ?

tumor suppressor genes