Ch 15

How is the Gal4 protein inactivated? By binding to the Gal80 protein By binding to glucose-1-phosphate By binding to galactose By binding to the UASG

By binding to the Gal80 protein

What general role does acetylation of histone protein amino acids play in the transcription of eukaryotic genes?

Histone acetylation events are most often associated with transcription activation.

Which amino acid in histone tails is the most frequent target for acetylation?

Lysine

Where are CpG islands clustered in mammalian genomes? Centromere Promoters Introns Heterochromatin

Promoters

In the GAL gene system, ________ are cis-acting regulatory elements.

UAS

Nucleosome-depleted Region (NDR)

a 150-100 bp region containing few nucleosomes that lies immediately upstream of the start of transcription.

If a mouse inherits a deletion in the SHH enhancer, what effect would you expect to see?

abnormal limb development

Open chromatin is ___ to regulatory proteins, but DNA tightly bound to nucleosomes is _____.

accessible, inaccessible

What do Histone methyltransferases do? What do histone demethylases do?

add methyl groups to lysines at the N terminus of histones. remove methyl groups.

enhancesomes

are protein complexes that assemble at enhancers to facilitate transcription.

What does the RNA-induced silencing complex (RISC) do?

binds these small RNA molecules and denatures them. One strand becomes degraded (the passenger strand) while one becomes the guide strand to silence gene expression by one of three ways.

What role do insulator sequences play in the regulation of eukaryotic transcription?

block communication between enhancers and nontargeted promoters.

How do Chromatin remodelers reorganize nucleosomes? What do Chromatin modifiers add?

by sliding, moving, or modding their protein composition. acetyl or methyl groups to histones to activate or repress gene activity, respectively

What occurs when CpG islands are unmethylated?

chromatin in promoter region open, allowing access by TF and RNA pol.

Sequences rich in CpG ("CpG islands") are targeted for methylation. What does this cause?

chromatin to condense and represses transcription

Which regulatory sequences act only on one copy of the chromosome?

cis-acting regulatory sequences

What are Insulator sequences? What do they do?

cis-acting, protein-binding sequences; prevent enhancers from turning on the wrong genes at the wrong time.

Methylated histones ___ chromatin, while unmethylated histones tends to ___ chromatin.

close, open

What are structural motif? What do these structures allow?

common structures in reg proteins. amino acid/nucleotides interactions in major and minor grooves

You have identified a mutation in a gene which also seems to decrease transcription of another gene 2000 bp away from the mutation site. What regulatory sequence, which may be found within another gene, has likely been mutated in this instance? homeodomain motif proximal elements enhancer sequence core promoter upstream activator sequence

enhancer sequence

Each cell has the same genome, but not necessarily the same ____.

epigenome

Prader-Willi syndrome is a genetic disorder involving a partial deletion of chromosome 15q on the paternal chromosome. When both copies of a gene (or chromosome) are functional but only one is expressed, this is an example of chromatin modifications. histone acetylation. position effect variegation. genomic imprinting. X inactivation.

genomic imprinting

How do different silencers play a role in cell identity and development?

have different sites for different regulatory proteins for action in different tissues

The imprinting control region (ICR) involved in genomic imprinting on chromosome 15 is what type of sequence?

insulator

If you want to affect chromatin packaging, which amino acid could you mutate to affect both histone acetylation and methylation patterns?

lysine

Where are CpG islands clustered in mammalian genomes?

promoters

Regulation of gene activity requires interaction between what?

protein and DNA

Enhanceosomes

protein complexes that assemble at enhancers to facilitate transcription

Reduced rate of evolution of enhancers at regions that bind protein is due to which process?

strong purifying selection, which prevents evolutionary change

What do Epigenetic maintainers ensure?

that epigenetic mods are passed on to daughter cells (the exact mechanism that allows this is not entirely clear)

What does a gap indicate? What the continuous banding in other samples indicate?

that some parts of the upstream region were not cut by DNaseI. DNase I hypersensitivity.

post-translational polypeptide processing forms

the mature protein product. An enzyme cleaves the starting amino acid and may replace it with a phosphate. acetate, amide or a methyl group. Although phosphorylation is the most common out of the list of modifications.

RNA interference

the post-transcriptional regulation of mRNAs by regulatory RNA molecules

In yeast, if you want to prevent the Gal4 regulatory protein from binding near each of the GAL genes, which sequence element would you target? homeodomain motif enhancer sequence core promoter proximal elements upstream activator sequence

upstream activator sequence.

What is meant by the term chromatin remodeling?

Chromatin remodeling includes altering chromatin structure by altering the composition of histones within nucleosomes. Chromatin remodeling includes altering chromatin structure by altering the positioning of nucleosomes with respect to specific DNA sequences.

Silencer

DNA sequence that binds regulatory proteins that inhibit transcription

Enhancer

DNA sequence that binds regulatory proteins that interact with promoter-bound proteins to activate transcription

Promoter

DNA sequence where RNA polymerase binds and begins the process of transcription

What is Closed chromatin?

DNA-histone interactions are strong and regulatory sequences are not accessible; transcription is silent.

What causes variegated forms of petunia?

RNAi

Which of the following is characteristic of open promoters?

They are constitutively expressed/transcribed, they do not generally contain a TATA box and instead use a poly A/T tract located near the NDR near the transcription site.

What does DNase I hypersensitivity allow?

identification of open and closed chromatin

What happens to microRNA (miRNA)?

transcribed with RNA Pol II but folds on itself to form double-stranded RNA (dsRNA)

What does the binding of transcription activators (ACT) allow?

transcription of a gene occurring immediately upstream of the NDR (+1 nucleosome).

(true or false) Alternative splicing is an example of gene regulation that occurs after the synthesis of mRNA.

true

promoter sequence is likely to be:

upstream of the gene it controls

enhancer sequence is likely to be located where? Is its function depended on its orientation?

upstream of the gene it controls. no

What causes open chromatin?

DNA-histone interactions are weak and regulatory sequences are accessible; transcription proceeds.

Molecular biologists can determine experimentally whether a region of DNA contains closed chromatin or open chromatin by assessing the sensitivity of the region to ___

DNAse

Which enzyme cuts double-stranded RNAi precursors to 21-25 base-pair segments?

Dicer

Which enzyme cuts double-stranded RNAi precursors to 21-25 base-pair segments? RISC Argonaute Dicer Drosha

Dicer

Which of the following may be located tens of kilobases away from the transcriptional start site? Enhancer sequence. TATA box. Proximal promoter elements. The core promoter.

Enhancer sequence

What may be located tens of kilobases away from the transcriptional start site?

Enhancer sequence.

Which of the following may be located tens of kilobases away from the transcriptional start site?

Enhancer sequences

In the GAL gene system, the ________ protein is a trans-acting regulatory protein.

Gal4

Galactose is absent, but you find active transcription of the GAL genes. Which protein is likely mutated or absent to allow for constitutive transcription of the GAL genes? Gal10 Gal80 Gal2 Gal4 Mig1

Gal80

The +1 nucleosome has a modified what? What does this mod allow?

H-2A. to be easily removed; loosen the DNA-histone interactions, allowing transcription to proceed.

Which pattern of chromatin mod would activate transcription to the greatest extent?

Increased acetylation and decreased methylation of histones

DNA Binding Domain

Is an independent folding protein domain that contains at least one motif that recognizes single or double-stranded DNA.

What normally removes epigenetic modifications? What is an exception to this removal?

Meiosis, sex-specific processes in primordial germ cells that re-establishes the methylation patterns for genomic imprinting

what are transcription factors?

Proteins that bind to promoters and are functional in transcription.

What is RNAi?

RNA interference; injecting double stranded RNA into a cell turns off expression of a gene with the same sequence as the RNA

Many types of cancer are known to overexpress the receptor protein tyrosine kinase. Which molecular technique can be used to reduce expression of an oncogene in vitro? Southern blotting PCR western blotting RNAi DNAse sensitivity assay

RNAi

Which statements about the modification of chromatin structure in eukaryotes are true? Select all that apply. Some forms of chromatin modification can be passed on to future generations of cells. Deacetylation of histone tails in chromatin loosens the association between nucleosomes and DNA. Acetylation of histone tails is a reversible process. DNA is not transcribed when chromatin is packaged tightly in a condensed form. Methylation of histone tails in chromatin can promote condensation of the chromatin. Acetylation of histone tails in chromatin allows access to DNA for transcription.

Some forms of chromatin modification can be passed on to future generations of cells. Acetylation of histone tails is a reversible process. DNA is not transcribed when chromatin is packaged tightly in a condensed form. Methylation of histone tails in chromatin can promote condensation of the chromatin. Acetylation of histone tails in chromatin allows access to DNA for transcription. One of the mechanisms by which eukaryotes regulate gene expression is through modifications to chromatin structure. When chromatin is condensed, DNA is not accessible for transcription. Acetylation of histone tails reduces the attraction between neighboring nucleosomes, causing chromatin to assume a looser structure and allowing access to the DNA for transcription. If the histone tails undergo deacetylation, chromatin can recondense, once again making DNA inaccessible for transcription. Recent evidence suggests that methylation of histone tails can promote either the condensation or the decondensation of chromatin, depending on where the methyl groups are located on the histones. Thus, methylation can either inactivate or activate transcription, and demethylation can reverse the effect of methylation. Changes in chromatin structure may be passed on to future generations of cells in a type of inheritance called epigenetic inheritance.

Describe the importance of the chromatin remodeling process to transcription.

These alterations can be used to activate transcription of a gene by opening its promoter sequences. These alterations can be used to repress transcription of a gene by hiding its promoter sequences. These alterations can be used to repress transcription of a gene by hiding its enhancer sequences. These alterations can be used to activate transcription of a gene by opening its enhancer sequences.

Which of the following is characteristic of open promoters? They tend to contain a TATA box. Their expression is regulated by transcription factors and transcription is blocked until nucleosomes are removed. They are constitutively expressed. They are relatively insensitive to DNase I cleavage.

They are constitutively expressed

What role do insulator sequences play in the regulation of eukaryotic transcription?

They block communication between enhancers and nontargeted promoters.

What role do insulator sequences play in the regulation of eukaryotic transcription? They block binding of transcription repressors to cis-acting promoter elements. They block binding of transcription factors to enhancers. They block communication between enhancers and nontargeted promoters. They block binding of transcription factors to cis-acting promoter elements.

They block communication between enhancers and nontargeted promoters.

What does competition among acetyltransferases and methyltransferases cause?

complex chromatin states beyond the simple "open" and "closed.

Are Open promoters active or inactive? Where are they located?

constitutively active; in nucleosomedepleted regions. which can bind transcription activators (ACT)

Name a major characteristic of open promoters.

constitutively expressed.

What do dicer do?

cuts the dsRNA into smaller molecules.

Why are enhancers and silencers important?

determine cell identity

How do different enhancers play a role in cell identity and development?

different enhancers (that bind different regulatory proteins) activate gene expression in different tissues.

Define epigenetics.

heritable changes in phenotype or gene expression with no alteration of DNA sequence

A region of chromatin has recently become DNAse I hypersensitive. Which enzyme has been activated to cause this change in chromatin structure?

histone acetylase

What is Sonic hedgehog (SHH)?

important reg in several developmental pathways, including limb development

What causes Chromatin packaging?

interactions between DNA and histones, forming nucleosomes.

Upstream activator sequence

is an enhancer-like DNA sequence that binds regulatory proteins that interact with promoter-bound proteins to activate transcription

upstream activator sequence

is an enhancer-like DNA sequence that binds regulatory proteins that interact with promoter-bound proteins to activate transcription.

Dicer

is the enzyme complex that is active in RNAi, where it cuts double-stranded regulatory RNAs into 21-bp to 26-bp segments that are subsequently denatured by RISC.

RNA interference

is the posttranscriptional regulation of mRNAs by regulatory RNA molecules.

enhancer sequence is likely to be: Check all that apply. located upstream of the gene it controls orientation independent located either nearby or at great distance from the gene it controls located whitin a few dozens nucleotides of the gene it controls located downstream of the gene it controls orientation dependent

located upstream of the gene it controls orientation independent located either nearby or at great distance from the gene it controls located downstream of the gene it controls

promoter sequence is likely to be: Check all that apply. orientation independent located downstream of the gene it controls located within a few dozens nucleotides of the gene it controls located either nearby or at great distance from the gene it controls orientation dependent located upstream of the gene it controls

located within a few dozens nucleotides of the gene it controls orientation dependent located upstream of the gene it controls

Which amino acid in histone tails is the most frequent target for acetylation?

lysine

During RNAi, what do miRNAs target for destruction?

mRNAs

What does "Cis acting" mean?

mutations that only influence transcription on *same chromosome*

What is Nucleotide Methylation? Where and where does this occur?

occurs on DNA, not histones; uses DNA methyltransferases. on C at CpG dinucleotides methylation. occurs in genomic imprinting.

What is Genomic Imprinting?

phenomenon in which expression of an allele in offspring depends on whether the allele is inherited from the male or female parent

What do cis-regulatory sequences do? Name at least two examples.

regulate genes on the same chromosome. promoter, enhancers

In general, what do enhancers do?

regulate the timing/spatial patterns of gene expression

What do covered promoters characterize?

regulated genes that require the remodeling/movement of nucleosomes to allow transcription activators to bind.

Silencer sequence

represses transcription by binding proteins that block enhancer mediated transcription

silencer sequence

represses transcription by binding proteins that block enhancer mediated transcription.

insulator sequence

shields genes from enhancer effects by promoting the formation of specific DNA loops that protect particular genes from enhancers.

insulator sequence

shields genes from enhancer effects by promoting the formation of the specific DNA loops that protect particular genes from enhancers

RISC

the protein complex that is part of the RNA interference (RNAi) mechnaism. It denatures short double-stranded RNAs to single strands that carry out RNAi.

What is the primary function of the SWI/SNF complex?

to open chromatin structure by displacing or ejecting nucleosomes.

A muscle enzyme called ME1 is produced by transcription and translation of the ME1 gene in several muscles during mouse development, including heart muscle, in a highly regulated manner. Production of ME1 appears to be turned on and turned off at different times during development. To test the possible role of enhancers and silencers in ME1 transcription, a biologist creates a recombinant genetic system that fuses the ME1 promoter, along with DNA that is upstream of the promoter, to the bacterial lacZ(β-galactosidase) gene. The lacZ gene is chosen for the ease and simplicity of assaying production of the encoded enzyme. The diagram shows the structure of the recombinant, as well as bars that indicate the extent of six deletions the biologist makes to the ME1 promoter and upstream sequences. The table displays the percentage of β-galactosidase activity in each deletion mutant in comparison to the recombinant gene system without any deletions. Part A Does this information indicate the presence of enhancer and/or silencer sequences in the ME1 upstream sequence? yes no

yes