Genetics 16

The methylation of a previously unmethylated site is called ______.

de novo methylation

Mechanisms of Epigenetic regulation

•DNA methylation •Chromatin remodeling •Covalent histone modification •Localization of histone variants •Feedback loops

Epigenetics And Environmental Agents examples

•Dietary effects on the Agouti gene in mice •Toxins that contribute to cancer

What can effect development

•Genomic imprinting •X-chromosome inactivation •Formation of specific cell types and tissues

2 types of competing protein complex are key

•Polycomb group (PcG)- involved with gene repression •Trithorax group (TrxG)- involved with gene activation

changes caused by environmental agents

•Temperature •Diet •Toxins

The weaker expression of a paramutagenic allele is due to epigenetic changes that decrease or silence its transcription

•These epigenetic changes can be transferred to a paramutable allele

PRC1 inhibits transcription

1.Chromatin compaction 2.Covalent modification of histones 3.Direct interaction with a transcription factor

Epigenetic silencing: Chromatin compaction

1.PRC1 may cause nucleosomes in the target gene to form a knot-like structure.

Epigenetic silencing: Covalent modification of histones

1.PRC1 may covalently modify histone H2A by attaching ubiquitin molecules.

The formation of heterochromatin begins at a ---- site, continues by----- in both directions, and stops when a ----- site is reached

Blank 1: nucleation Blank 2: spreading Blank 3: barrier

This shows that the B' allele is ------, and the B-I allele is --------

Blank 1: paramutagenic Blank 2: paramutable

Identify proteins involved in forming loop domains in heterochromatin.

CCCTC-binding protein condensin

VIN3 protein complexes with PRC2, PRC2 binds to

COLDAIR RNA during transcription, winding up at FLC gene

Which of the following are features associated with constitutive heterochromatin in yeast and animal cells?

Composed of many, short tandemly repeated sequences Trimethylation of a lysine at the ninth position in histone H3 DNA is highly methylated on cytosines Located at telomeres and close to centromeres

M phase through interphase in two daughter cells

Constitutive and facultative heterochromatin regions retain the same pattern observed in mother cell.

Which of the following are true regarding epigenetics?

Epigenetic changes are transmissible from cell to cell Variations of gene expression are unrelated to variations in the DNA base sequence Epigenetic changes may be transmitted to offspring Variations are reversible from one generation to the next

Identify changes that can occur during embryonic development that will lead to a pattern of differential gene expression unique to a specific cell type.

Epigenetic changes that cause specific genes to be permanently repressed Epigenetic changes that enable specific genes to be transcribed

Expression pattern is maintained after cell fusion

Expected results following cell fusion for a cis-epigenetic mechanism

Due to the presence of a transcription factor, both copies of gene B are expressed in the fused cell. Expression pattern is maintained after cell division

Expected results following cell fusion for a trans-epigenetic mechanism

True or false: Because epigenetics refers to heritable changes in gene expression, all epigenetic changes are examples of transgenerational epigenetic inheritance.

False

When binding to chromatin, where would a dimer of heterochromatin protein 1 (HP1) be found?

In the linker region between nucleosomes

Which of the following is an example of epigenetic inheritance?

Methylation of DNA that occurs in an oocyte

Epigenetic silencing: Direct interaction with a transcription factor

PRC1 may directly inhibit proteins involved with transcription, like TFIID.

Which molecular processes will enhance the formation of higher-order structure in heterochromatin?

Posttranslational modifications of histones Binding of proteins to nucleosomes DNA methylation

The Xist RNA binds to XIC and then spreads to both ends of the X chromosome (1)

The Xist RNA recruits proteins to this X chromosome that cause it to become more compact and be inactive with regard to the expression of most genes (2)

Prolonged cold temperatures activate

VIN3 and COLDAIR genes

Example of trans-epigenetic change

affects both copies of a gene -maintained by diffusible factors, such as transcription factors

Larvae injected with a DNA methyltransferase inhibitor

became queen bees

FLC repressed

both FT and SOC1

Vernalization refers to the phenomenon that

certain species of plants must be exposed to the cold before they can undergo flowering

Overview of epigenetics

changes in gene expression that can be passed from cell to cell reversible does not involve a change in the sequence of DNA

Lamina-associated domains (LADs) are regions of ______ found in close contact with the nuclear lamina in eukaryotic cells.

chromosomes

If an epigenetic change is maintained only at a given site and does not affect the expression of a gene elsewhere in the nucleus, it is a ______ mechanism.

cis-epigenetic

DNA methylation, chromatin remodeling, covalent histone modification, and localization of histone variants are all examples of molecular mechanisms that are involved in

epigenetics or epigenetic

Genomic imprinting

expressed the copy of gene from 1 parent but not both ex: Mammals Igf2 gee is only from father

A functional mop1 gene (mediator of paramutation 1 gene), an RNA-dependent RNA polymerase, is required

for paramutation

Igf2 Gene

is de novo methylated (during sperm formation) •The methylation occurs at two sites: the imprinting control region (ICR) and a differentially methylated region (DMR)

Condensin and CCCTC-binding factor (CTCF) are involved in forming ----- domains in heterochromatin.

loop

Example of cis-epigenetic change

may affect only one copy of gene but not the other copy

Result is consistent with the idea that DNA methylation inhibits the Agouti gene

pregnant mice were fed a diet that contained chemicals that tend to increase DNA methylation(of CpG islands), the offspring tended to be have darker fur

FT and SOC1 activate Several genes

promote flower development

The Agouti gene in mice promotes: (this is called the Avy allele)

the synthesis of yellow fur pigment.

With regard to the polycomb 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 H3.

Multiple tandem repeat sequences are located close to the coding sequences of paramutagenic and paramutable alleles and may be used

to make siRNAs

In eukaryotic cells, which processes are prevented by heterochromatin?

transcription viral proliferation transposable element movement

the CTC-binding factor binds to the unmethylated gene and inhibits

transcription by forming a loop

Interaction between two alleles at a single locus where one allele induces a change in the other allele

•Allele that has this capacity is said to be paramutagenic •Allele that has been altered is said to be paramutable

Methylation inhibits the binding of a protein called

•CTC-binding factor, which allows the Igf2 gene to be stimulated by a nearly enhancer.

example of epigenetic changes during embryonic development

•For example, an embryonic cell may undergo epigenetic changes that will cause its future daughter cells to become muscle cells

programmed developmental change

•Genomic Imprinting •X chromosome Inactivation •Cell differentiation

X-chromosome inactivation (XCI)

during embryogenesis in female mammals

paramutation

occurs when one allele of a gene induces a heritable change in the other allele without altering the DNA sequence.

Chromatin modification, methylation, caused by complex causes repression

of FLC gene repression of FLC so that early flower buds forms

Regions of the chromatin containing numerous, short, tandemly repeated sequences that are located near the centromeres and at the telomeres of eukaryotic chromosomes are called ______ heterochromatin.

constitutive

Regions of heterochromatin that are seen in the same location in all cell types are called -----

constitutive heterochromatin

An RNA that does not encode a polypeptide is a(n) ______ RNA.

non-coding

A fibrous layer of proteins lining the inner nuclear membrane of eukaryotic cells is called the ______.

nuclear lamina

basic unit of chromatin ---- composed of ----- wrapped in ---- proteins

nucleosomes DNA Histones