L. 24; EPIGENETICS (Ch.16)

Affect of methylation not occurring during oogenesis

CTC-binding factor binds to DNA found on both ICR and DMR. CTCFs then bind to each other forming a loop in DNA. Loop prevents enhancer from stimulating Igf2. = maternal allele of Igf2 is TURNED OFF.

Epigenetic changes associated with cancer

DNA methylation (hypermethylation may promote cancer by inhibiting tumor suppressor genes. Hypomethylation may activate oncogenes or affect genomic imprinting). Covalent Histone modifications (such changes could increase the expression of oncogenes or inhibit the expression of tumor suppressor genes). Chromatin remodeling (depending on how the nucleosomes are changed, it could increase the expression of oncogenes or inhibit the expression of tumor suppressor genes).

Molecular changes that underlie epigenetic gene regulation:

DNA methylation. Chromatin remodeling. Covalent Histone modification. Localization of Histone variants. Feedback loop.

Epigenetics and development

Development involves a series of genetically programmed stages in which a fertilized egg becomes an embryo and eventually an adult. Many changes that occur during development are maintained by epigenetic regulation. 3 examples: 1. Genomic imprinting 2. X-chromosome inactivation 3. Formation of specific cell types and tissues

Covalent Histone modification

Histone variants may become localized to specific locations and affect transcription.

Affect of methylation

ICR and DMR are methylated. CTCFs are unable to bind to these sites which prevents loop formation, which allows the enhancer to stimulated the Igf2 gene. = paternally inherited Igf2 allele is transcriptionally active. Methylation of the paternal H19 gene and ICR insulator allow the enhancer to stimulate expression of the Igf2 gene instead of the H19 gene.

Methylation during oogenesis and spermatogenesis

Igf2 gene is de novo methylated (methylation of a completely unmethylated site) during sperm formation but not during egg formation.

Epigenetic inheritance

Involves Epigenetic changes that are passed from parent to offspring. Ex: genomic imprinting.

1. Genomic imprinting

Is a form of gene regulation in which an offspring expresses the copy of a gene from one parents but not both; in mammals, only the Igf2 gene inherited from the father is expressed

Epigenetics

Is the study of mechanisms that lead to changes in gene expression that can be passed from cell to cell and are reversible, but do not involve a change in the sequence of DNA.

Epigenetics and environmental agents

Many environmental agents have been shown to cause epigenetic changes. These include dietary effects as well as toxins in the environment Examples: Dietary effects on the Agouti gene in mince Toxins that contribute to cancer

Switching a gene off through DNA methylation + Histone modification

Normally gene expression is leaky. To shut it of completely the DNA is methylated, which blocks activator binding and recruits DNA binding proteins and chromatin remodeling complexes to insure no transcription activity occurs.

Chromatin remodeling

Nucleosomes may be moved to new locations or evicted. Level of transcription may be altered when occurs near promoter. Large scale changes may occur as is what happens during x-chromosome inactivation.

Avy allele

Strains of mice carrying this allele show a range of coat colors from yellow to pseudo-agouti

Feedback loop

The activation of a gene that encodes a transcription factor may result in a feedback loop in which that transcription factor continues to stimulate its own expression.

Epigenetics and diet

The agouti gene is mice promotes synthesis of yellow fur pigment. In one strain of mice, s transposable element carrying a promotor is inserted upstream from the agouti gene; this is called the Avy allele.

Methylation occurs at two sites

The imprinting control region (ICR) and a differently methylated region (DMR).

DNA methylation can be maintained

Through cell divisions. Methylated CpG sites are recognized on one strand and the corresponding CpG on the other strand is methylated to maintain the parental state of DNA.

Effects of diet on pregnant mice

When pregnant mice where fed a diet that contained chemicals that tend to increase DNA methylation, the offspring tended to have darker fur.

3. Development of specific cell types

With regard to the poly comb group complex, there are two types: PRC1 and PRC2. Repression may begin by the binding of PRC2 to a polycomb response element. This leads to trimethylation of lysine 27 on Histone 3. PRC1 is then recruited to the gene and may inhibit transcription in three ways: 1. Chromatin compaction 2. Covalent modification of Histones 3. Direct interaction with a transcription factor

2. X-chromosome inactivation

XCI occurs during embryogenesis in female mammals. A portion of the X chromosome called the x inactivation center (XIC) plays a key role. Prior to XCI, the Tsix gene is expressed on both X chromosomes.

XIC encodes two genes

Xist and Tsix, which are transcribed in opposite directions. Xist is expressed from the inactivated X chromosome. Tsix is expressed from the active X chromosome. The Xist RNA involved in X chromosome inactivation is expressed from one X chromosome and then coats that X chromosome. Xist RNA then recruits Histone deacetylases that silence gene expression from that X chromosome, leading to its inactivation.

DNA methylation

attachment of methyl groups to cytosine bases. When occurs near promotors, transcription is often inhibited.