Chapter 12 : Epigenetics

X-Chromosome inactivation : Calico Cat example?

- A classic example of X-inactivation is seen in cats. If a female cat is heterozygous for black and tan alleles of a coat color gene found on the X, she will inactivate her two Xs (and thus, the two alleles of the coat color gene) at random in different cells during development. - The result of is a tortoise shell coat pattern, made up of alternating patches of black and tan fur. - The black patches come from groups of cells in which the X with the black allele is active, while the tan patches come from cells in which the X with the tan allele is active.

Role of DNA Methylation in Cancer

- Aberrant DNA hypermethylation contributes to gene silencing, including that of tumor suppressor genes, which may promote development and progression of certain cancers - Aberrant DNA methylation has been observed in correlative studies in a number of malignancies acute myeloid leukemia (AML), breast cancer, and lung cancer.

The mammalian DNA methylation machinery is composed of two components :

- DNA methyltransferases (DNMTs) : which establish and maintain DNA methylation patterns - Methyl-CpG binding proteins (MBDs) : which are involved in reading methylation marks

DNA Methyl Transferases examples?

- DNMT1 maintains DNA-methylation pattern during replication. - DNMT2 has very weak methylation activity. - DNMT3A and DNMT3B - involved in de novo acquisition of DNA-methylation. - DNMT3L - involved in maternal genomic imprinting affects activity of DNMT3A and 3B.

Prader-willi syndrome (PWS)

- Deletion of about 4 Mb of the long arm of chromosome 15 - When this deletion is inherited from the father, the child manifests a disease known as prader-willi syndrome (PWS)

What does epigenetic enable a cell to do. Changes in the genome?

- Enables a cell/organism to respond to its dynamic external environment during development and throughout life - Epigenetic changes to the genome can be inherited if these changes occur in cells giving rise to gametes

Role of DNA Methylation examples?

- Long term gene silencing - X-chromosome inactivation - Maintenance of imprinted genes - In carcinogenesis

Model for the inheritance of DNA methylation simple steps?

- Methylated - DNA replication - DNA methyltransferase

Triple X syndrome

- Triple X syndrome, in which a woman has an XXX genotype. - Women with an XXX genotype have female sex characteristics and are fertile (able to have children).

Mechanism of X chromosome involves :

- XIC : X chromosome inactivation center - XIC controls expression of the XIST - XIST : X-inactive-specific transcript - XIST produces a non-coding 17 kb RNA molecule - "Coats" the entire local X chromosome - cis-acting

Structure of chromatin?

- short region of DNA double helix - Nucleosomes : basic unit of chromatin - Chromatin fiber of packed nucleosomes

Two Epigenetic Mechanisms

1. DNA methylation (DNA modification) 2. Histone modifications (protein modifications)

Such remodeling is carried out by ?

1. PTMs on histones by specific enzymes (histone acetyltransferases (HATs), deacetylases, methyltransferases, and kinases) 2. ATP-dependent chromatin remodeling complexes which wither move, eject, restructure nucleosomes

The attachment of methyl groups to ___________ of genes, along with histone hypoacetylation and condensation of chromatin, inhibit what?

5' regions - inhibit the binding of proteins that promote transcription.

Most cytosine methylation occurs in the sequence ....

5'-C G-3'

Histone modification

A histone modification is a covalent post-translational modifications (PTM) to histone proteins which includes methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation.

Acetylation targets ...

Acetylation targets Lys residues in the amino-terminal tails of core histone proteins - HATS or Histone acetylases/Writer add acetylation on histones

Are Barr bodies found in males and females?

Barr bodies are generally not found in males because their single X chromosome is still active.

How XIST silences the future inactive X chromosome? The key player is the X-linked gene XIST - X(inactive)-specific transcript :

Chromosome Xq13.2.

DNA methylation? Most common DNA Methylation in mammalian cells?

DNA methylation is a covalent modification of DNA that doesn't change the DNA sequence but has an influence on gene activity. - Most common DNA Methylation in mammalian cells is 5-methylcytosine.

What does epigenetic cover?

Epigenetics covers all phenomena without affecting the DNA sequence of interest itself, can somehow produce heritable changes - on the level of how genes are expressed and how chromosome functions work

So in cancer cells?

In cancer cells, the promoters of TSG genes lose the 'active' histone marks and gain repressive methylation marks, such as lysine 9 or 27 on histone H3. - DMNT inhibitors and HDAC inhibitors are effectively used against cancer cells by inhibiting components of the epigenetic machineries leading to reactivation of critical genes.

In the 1960s, Mary Lyon hypothesized what? Result?

In the 1960s, Mary Lyon hypothesized that one X chromosome in each somatic cell of the female is inactivated. - This would result in dosage compensation, an equalization of the amount of X-linked gene products in males and females.

Klinefelter syndrome

Klinefelter syndrome, in which males have an extra X chromosome, leading to a genotype of XXY. - Affected men may be infertile or develop less dense body and facial hair than other men.

What does cytosine methylation most exclusively occur at?

Occurs most exclusively at cytosines that are immediately followed by Guanine - Known as CpG dinucleotides

SWI-SNF makes what accessible to what?

SWI-SNF makes the TATA box accessible to the TATA-binding protein and allowing transcription to be initiated

CpG Island

The CG island is a short stretch of DNA in which the frequency of the CG sequence is higher than other regions. - It is also called the CpG island, where "p" simply indicates that "C" and "G" are connected by a phosphodiester bond.

The Lyon hypothesis stated what?

The Lyon hypothesis stated that X inactivation occurs early in female embryonic development and that the X chromosome contributed by the father is inactivated in some cells, whereas in other cells the X chromosome contributed by the mother is inactivated

The PTMs on histones can impact what?

The PTMs on histones can impact gene expression by altering chromatin structure or recruiting histone modifiers.

The enhanceosome is surrounded by what? Structure and position?

The enhanceosome is surrounded by two nucleosomes, called nuc 1 and nuc 2. - One of them, nuc 2, is strategically positioned over the TATA box and transcription start site. GCN5, another co-activator, binds and acetylates the two nucleosomes.

Barr Bodies In female cells, one X chromosome is randomly switched off. What does this chromosome do?

This chromosome forms a dense region in the nucleus known as a Barr body.

Sex chromosome aneuploidies : What is an Aneuploid?

When an organism has an extra or missing copy of a chromosome, it is said to be aneuploid.

Angelman Syndrome

When the same deletion is inherited from the mother, the child develops Angelman Syndrome, which is characterized by severe mental retardation, seizures, and an ataxic gait

XIST is transcribed to produce what? Other facts?

XIST is transcribed to produce a non-coding RNA that "coats" the X-chromosome and inactivates it. - XIST is uniquely expressed from the inactive X. - XIST RNA does not travel over to any other X chromosome in the nucleus (i.e., cis action). - Barr bodies are inactive X chromosomes "painted" with XIST RNA.

The histone code

a hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends. - Together with similar modifications such as DNA methylation it is part of the epigenetic code.

Thus, histone tail acetylation results in what?

chromatin decondensation, thereby allowing access to transcription factors and other transcription - HDACs or Histone deacetylates/Eraser remove acetylation from histones

in eukaryotes, transcription levels are made finely adjustable in a chromatin environment by ......

clustering binding sites into enhancers.

In normal cells, the promoters of active tumor-suppressor genes (TSG) are enriched with what?

combinatorial histone modification markers including acetylation of histone tails, methylation of lysine 4 on histone H3 (H3K4).

DNA methylation is most commonly found in .....

fungi, plants, invertebrates and vertebrates. - No methylation in many insects and single celled organisms

if the way that DNA is wrapped around the histone changes, what also changes?

gene expression can change as well

Imprinted alleles tend to be what?

heavily methylated.

Barr Bodies Once an X chromosome is inactivated in a cell .....

it will remain inactive in all descendants of that cell. X inactivation is therefore a randomly determined, but fixed (or permanent), process.

DNA methylation are what?

methyl marks added to DNA bases that repress gene activity

Barr Bodies Because they have two populations of cells, females are what?

mosaics for X chromosome activity.

Enhanceosome acts to do what?

move nucleosomes by recruiting the SWI-SNF complex

The features of PWS include what?

short stature, hypotonia (poor muscle tone), small hands and feet, obesity, mild to moderate mental retardation, and hypogonadism

Aneuploidies of X chromosomes tend to be what?

tend to be much less harmful, despite the fact that the X is a large chromosome. This is mostly due to X inactivation.

After acetylation, the activating transcription factors recruit ________. And then what?

the co-activator CBP, the RNA pol II holoenzyme, and the SWI-SNF chromatin-remodeling complex - SWI-SNF is then positioned to nudge the nucleosome 37 bp off the TATA box

Chromatin remodeling

the dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression.

Acetylation of the tail domains inhibits what?

the folding of nucleosome arrays into secondary and tertiary chromatin structures

The binding of multiple regulatory proteins to the multiple binding sites in an enhancer can catalyze what?

the formation of an enhanceosome, a large protein complex that acts synergistically to activate transcription.

Purpose of X-inactivation?

the purpose of the X-inactivation system is to shut down the second X of an XX female, but it can also shut down more X chromosomes if they are present.

Genomic Imprinting In some human genes, one of the alleles is ______________ depending upon the parent from whom the allele was received Example?

transcriptionally inactive (no mRNA is produced) - For example, an allele transmitted by the mother would be inactive, and the same allele transmitted by the father would be active. -The normal individual would have only one transcriptionally active copy of the gene. This process of gene silencing is known as imprinting, and the transcriptionally silenced genes are said to be imprinted.