Chapter 17: Control of Gene Expression in Eukaryotes

Provide 2 ways that histones can be modified and describe the effects of these modifications as well as the enzymes involved (Fig 17.2).

1. Methylation of histones 2. Acetylation of histones

At least three different processes affect gene regulation by altering chromatin structure:

1. chromatin remodeling 2. the modification of histone proteins 3. DNA methylation

List a few differences between prokaryotic and eukaryotic gene regulation

1. many bacterial genes are organized into operons and are transcribed into a single RNA molecules --> most eukaryotic genes have their own promoters and are transcribed separately 2. chromatin structure affects gene expression in eukaryotic cells (DNA must unwind from the histone proteins before transcription can take place) 3. presence of nuclear membrane in eukaryotic cells separates transcription and translation in space and time --> therefore, regulation of gene expression in eukaryotic cells is characterized by a greater diversity of mechanisms that act at different points in the transfer of information from DNDA to protein

What is CpG methylation associated with?

CpG methylation is associated with long-term gene repression (EX: inactivated X chromosome of females)

Define CpG islands

DNA methylation is most common on cytosine bases adjacent to guanine nucleotides (CpG where p=phoshpate group in DNA backbone)

List a few differences between prokaryotic and eukaryotic gene regulation Similarities

DNA-binding proteins influence the ability of RNA polymerase to initiate transcription

Define DNase I hypersensitive sites. Are these regions where transcription occurs or not?

DNase I hypersensitive sites: as genes become transcriptionally active, regions around the genes become highly sensitive to the action of DNase I chromatin in these regions adopt a more open configuration during transcription --> the relaxation of chromatin allows regulatory proteins access to binding sites on DNA

2. Acetylation of histones What enzymes are used?

acetyltransferase enzymes add acetyl groups deacetylases strip acetyl groups from histones and restore chromatin structure (represses transcription)

some TFs are ________ (stimulate transcription) and others are ________ (inhibit transcription)

activators, repressors

1. Methylation of histones

addition of methyl groups to histone proteins --> can either activate/repress transcription depending on which histone is modified and which particular AA in the histone tail is methylated

Describe how DNA methylation is associated with gene regulation. What gets methylated and how does this result in gene regulation?

another change in chromatin structure associated with transcription is the methylation of cytosine bases

__________ binds to the core promoter and is capable of minimal levels of transcription

basal transcription apparatus

Where do chromatin-remodeling complexes bind?

chromatin-remodeling complexes bind directly to particular sites on DNA and reposition the nucleosomes, allowing other transcription factors and RNA polymerase to bind to promoters and initiate transcription

Know that RNAi is an important tool for ________ gene regulation

eukaryotic

Explain the relationship between how tightly packaged DNA is and whether transcription occurs or not What must bind to DNA for a gene to be transcribed? How can these proteins bind with DNA wrapped tightly around histone proteins?

for a gene to be transcribed, proteins called transcription factors must bind to the DNA (and regulator proteins and RNA polymerase must also bind) Q: how can these proteins bind with DNA wrapped tightly around histone proteins? A: before transcription, chromatin structure changes so that the DNA becomes more accessible to the transcription machinery

________ are required for the initiation of transcription

general transcription factors

Define general transcription factors, other transcription factors, basal transcription apparatus, core promoter, and regulatory promoter. General transcription factors, core promoter, and basal transcription apparatus

general transcription factors bind to the core promoter and are part of the basal transcription apparatus: the complex of RNA polymerase, transcription factors, and other proteins that assemble to carry out transcription

How is the methylation of cytosine in DNA different from methylation of histone proteins?

heavily methylated DNA associated with the repression of transcription (transcriptionally active DNA is usually unmethylated)

1. Methylation of histones What enzymes are used?

histone methyltransferases add methyl groups histone demethylases remove methyl groups from histones

Explain the relationship between how tightly packaged DNA is and whether transcription occurs or not Do chromatin structures repress or activate gene expression?

in the nucleus, histone proteins form octamers around which DNA tightly coils to create chromatin chromatin structure represses gene expression

Most enhancers are capable of stimulating any promoter in the vicinity but their effects are limited by ______

insulators

Explain the purpose of an insulator and how they work (Fig 17.8)

insulators: DNA sequences that block the effects of enhancers in a position-dependent manner if an insulator lies between an enhancer and promoter, it blocks the action of the enhancer if an insulator lies outside the region between an enhancer and promoter, it has no effect

Where are DNA regions with many CpG sequences commonly found?

near transcription start sites while genes are not being transcribed, these CpG islands are often methylated, but the methyl groups are removed before the initiation of transcription

Describe how regulatory promoters and mediators are associated with eukaryotic gene regulation. Where are these located with respect to a gene (Fig 17.5) mediator

one of the components of the basal transcription apparatus is a complex of proteins called the mediator which interacts with RNA polymerase

Differentiate between enhancers and silencers. What type of transcription factors bind to these? Where are enhancers and silencers located with respect to a gene? (Fig 17.5) Enhancers

other TFs bind to regulatory promoter and to enhancers (located some distance from the gene) enhancers are regulatory elements that affect the transcription of distant genes

Differentiate between enhancers and silencers. What type of transcription factors bind to these? Where are enhancers and silencers located with respect to a gene? (Fig 17.5) Silencers

other sequences, called silencers, have an inhibitory effect on the transcription of distant genes like enhancers, silencers are position and orientation independent, and they contain binding sites for transcription factors that decrease transcription

_________ bind to a regulatory promoter and to enhancers

other transcription factors

Explain how the stability of mRNA is a means of regulating eukaryotic gene expression

posttranscriptional gene regulation assumes an important role in eukaryotic cells gene regulation in eukaryotes often takes place during RNA processing and degradation

Describe how regulatory promoters and mediators are associated with eukaryotic gene regulation. Where are these located with respect to a gene (Fig 17.5) Regulatory promoter

regulatory promoters typically contain several different consensus sequences to which different transcription factors can bind

Define chromatin remodeling

some transcription factors and other regulatory proteins alter chromatin structure without altering the chemical structure of the histones directly

2. Acetylation of histones

the addition of acetyl groups (CH3CO) to histone proteins acetylation usually stimulates transcription in general, acetyl groups destabilize chromatin structure, allowing transcription to take place acetylation specifically neutralizes histones which are positively charged so DNA is less tightly bound (and therefore can be transcribed)

Explain how the stability of mRNA is a means of regulating eukaryotic gene expression The amount of protein synthesized depends on what?

the amount of corresponding mRNA that is available for translation the amount of available mRNA depends on both the rate of mRNA synthesis and rate of mRNA degradation

how can an enhancer affect the initiation of transcription at a promoter that is far away?

the binding of TFs to the enhancer causes the DNA between the enhancer and the promoter to loop out bringing the promoter and enhancer close to each other so transcription factors are able to interact directly with the basal transcription apparatus at the core promoter

TFs that bind to sequences in the regulatory promoter (or enhancer) make contact with the mediator and affect what?

the rate at which transcription is initiated

Explain how the stability of mRNA is a means of regulating eukaryotic gene expression in eukaryotes, transcription takes place in the nucleus and the pre-mRNAs undergo processing before being moved to the cytoplasm for translation, which allows opportunities for gene control after _________

transcription

Define general transcription factors, other transcription factors, basal transcription apparatus, core promoter, and regulatory promoter. Transcription factors

transcription in eukaryotes is regulated by proteins called transcription factors that bind to specific DNA sequences many transcription factors regulate by recruiting other proteins