Chapter 15 - Gene Regulation in Eukaryotes

What are three common ways that the function of regulatory transcription factors can be affected?

1) Binding of a small effector molecule such as a hormone, 2) protein-protein interaction, and 3) covalent modification such as phosphorylation.

What are two common ways in which chromatin structure is altered?

1) Covalent modification of histones, and 2) ATP-dependent chromatin remodeling

Changes in chromatin structure can involve changes in the structure of DNA and/or changes in chromosomal compaction. These changes include what four processes? Which are most common?

1) Gene amplification, 2) gene rearrangement, 3) DNA methylation, and 4) chromatin compaction. DNA methylation and chromatin compaction are most common.

What are three mechanism of action in DNA methylation?

1) Histone methylation, 2) blocking DNA binding proteins (like activators or transcription factors), 3) allowing for the binding of methyl-CpG-binding protein recruits histone deacetylase.

The stability of eukaryotic mRNA varies considerably (several minutes to several days); its half-life can be shortened or lengthened. What two factors can affect mRNA stability?

1) Length of the polyA tail, and 2) destabilizing elements

Identify two common protein complexes that communicate the effects of regulatory transcription factors.

1) TFIID (first of the general transcription factors that will recruit RNA polymerase; binds to TATA box), and 2) mediator (controls RNA-polymerase's ability to enter elongation phase of transcription).

The polyA-binding protein can no longer bind is the polyA tail is less than _____ adenosines long. The mRNA will then be rapidly degraded by exo- and endonucleases.

10 to 30

In humans, approximately _____ miRNAs have been identified.

200

Most newly made mRNA have a polyA tail that is about _____ nucleotides long.

200

It is estimated that _____ of human mRNAs are alternatively spliced, as opposed to _____ in baker's yeast.

70%; 5%

What is RISC?

A multiprotein complex that incorporates one strand of a micro RNA (miRNA). RISC uses the miRNA as a template for recognizing complementary mRNA. When it finds a complementary strand, it activates RNase and cleaves the RNA. This process is important both in gene regulation by microRNAs.

Destabilizing elements are especially found in mRNAs that have short half-lives. These elements can be found anywhere on the mRNA, but are most common where?

At the 3' end between the stop codon and the polyA tail (in the 3' untranslated region (UTR).

What is guide RNA?

Can direct the addition or deletion of one or more uracils into an RNA.

Chromatin is a very dynamic structure that can alternate between what two conformations?

Closed and open

In vertebrates and plants, many genes contain _____ near their promoters; these are 1,000 to 2,000 nucleotides long.

CpG islands

DNA methylation is a change in chromatin structure that silences gene expression carried out by the enzyme _____.

DNA methyltransferase

What what conditions is it advantageous for a cell to stop synthesizing proteins?

During viral infection (to prevent the virus from manufacturing viral proteins) and starvation (so that the cell can conserve resources).

T/F: DNA methylation always inhibits the transcription of eukaryotic genes.

False; it USUALLY does, especially when it occurs in the vicinity of the promoter

T/F: All response elements are located within a few hundred nucleotides upstream of the promoter.

False; most are located within a few hundred nucleotides upstream of the promoter, but some are found at various other sites (several thousand nucleotides away, downstream from the promoter, within introns).

T/F: Most regulatory transcription factors bind directly to RNA polymerase.

False; most do not bind directly to RNA polymerase.

T/F: Alternative splicing is a random event.

False; the specific pattern of splicing is regulated in a given cell.

T/F: DNA methylation is common in all eukaryotic species.

False; while vertebrates and plants have abundant DNA methylation (~2-7% in mammals), yeast and _Drosophila_ have little DNA methylation.

What are two types of steroid hormones? What are their function?

Glucocorticoids (influence nutrient metabolism in most cells, including glucose utilization, fat mobilization, and protein breakdown) and gonadocorticoids (include estrogen and testosterone, influencing the growth and function of the gonads).

This motif can mediate protein dimerization.

Helix-loop-helix

What is the difference in CpG islands between housekeeping genes and tissue-specific genes?

In housekeeping genes, the CpG islands are unmethylated; genes tend to be expressed in most cell types. In tissue-specific genes, the expression of these genes may be silenced by the methylation of CpG islands; methylation may change binding of transcription factors (inhibit binding of an activator protein). Methyl-CpG-binding proteins may recruit factors that lead to compaction of the chromatin.

What effects can RNA editing have on mRNAs?

It can generate start or stop codons or change the coding sequence of a polypeptide.

The function of eIF2 and eIF4F are modulated by phosphorylation in what two ways?

Phosphorylation of eIF2alpha inhibits translation, while the phosphorylation of eIF4F increases the rate of translation.

What are examples of proteins involved in ATP-dependent chromatin remodeling?

Proteins in the SWI/SNF (SWItch/Sucrose Non-Fermenters) family. Acronyms refer to the effects on yeast when these enzymes are defective.

What is RNA editing?

Refers to a change in the nucleotide sequence of an RNA molecule. It involves additions or deletions of particular bases, or a conversion of one type of base to another.

What is alternative splicing?

Refers to the phenomenon that pre-mRNA can be spliced in more than one way. In most cases, large sections of the coding regions are the same resulting in two alternative versions of a protein that have similar functions; nevertheless, there will be enough differences in amino acid sequences to provide each protein with its own unique characteristics.

What is an ARE?

The AU-rich element is recognized and bound by cellular proteins; these proteins influence mRNA degradation.

In what ways are histones modified covalently?

The amino terminals of histones are modified via acetylation, phosphorylation, and methylation.

What are two benefits of gene regulation in eukaryotes?

They can responds to changes in nutrient availability and respond to environmental stresses.

_____ are proteins that influence the ability of RNA polymerase to transcribe a given gene. What are two main types?

Transcription factors: general transcription factors (necessary for basal transcription) and regulatory transcription factors (serve to regulate the rate of transcription of nearby genes).

Identify methods of regulation of gene expression during transcription, RNA processing, translation, and postranslational modifications in eukaryotes.

Transcription: regulatory transcription factors, compaction of chromatin, DNA methylation RNA processing: alternative splicing, RNA editing Translation: miRNAs, phosphorylation, proteins that influence RNA stability, RNA binding proteins Posttranslational modification: feedback inhibition, covalent modifications

T/F: DNA methylation is heritable and usually results in down regulation of genes.

True

T/F: Many response elements are orientation independent or bidirectional.

True; they can function in the forward or reverse orientation.

T/F: The position of nucleosomes are not always positioned at regular intervals along the DNA.

True; while they are usually positioned at regular intervals, they have been shown to change positions in cells that normally express a particular gene (but not in cells where the gene is inactive).

Regulatory transcription factors recognize _____ regulatory elements located near the core promoter. What are these sequences known as?

_cis_; response elements, control elements, or regulatory elements

A regulatory protein that increases the rate of transcription is termed a(n) _____; the sequence it binds is called a(n) _____.

activator; enhancer

Most eukaryotic genes are regulated by many factors; this is known as _____. What are these factors?

combinatorial control; the combination of activators, silencers, their modulation, the chromatin structure, and DNA methylation determine whether RNA polymerase may transcribe a gene.

A more widespread mechanism for RNA editing involves changes of one type of base to another. This involves _____ of bases.

deamination

Transcription factor proteins contain regions called _____ that have specific functions. What are some of these functions?

domains; one domain could be for DNA-binding, while another could provide a binding site for effector molecules.

What two initiation factors appear to play a central role in controlling the initiation of translation?

eIF2 and eIF4F

Homodimers are formed by two _____ transcription factors; heterodimers are formed by two _____ transcription factors.

identical; different

What do miRNAs encode?

miRNA genes do not encode a protein. They give rise to small RNA molecules, typically 21 to 23 nucleotides. They silence expression of specific mRNAs.

What are miRNAs? In what types of organisms are they found?

microRNAs cause RNA interference, encoded by genes in eukaryotic organisms but also found in prokaryotes where they are called small non-coding RNAs or sRNA.

A(n) _____ is a domain or portion of it that has a very similar structure in many proteins. Name two.

motif; zinc finger motifs and leucine zipper motifs (result in protein dimerization) are two examples.

As an mRNA ages, its polyA tail is shortened by the action of cellular _____.

nucleases

The polyA tail is recognized by _____ which binds to the polyA tail and enhances stability.

polyA-binding protein

A regulatory protein that decreases the rate of transcription is termed a(n) _____; the sequence it binds is called a(n) _____.

repressor; silencer

Alternative splicing involves proteins known as _____ that play a key role in the choice of splice sites.

splicing factors

Regulatory transcription factors that respond to steroid hormones are termed _____. The hormone actually binds to the transcription factor.

steroid receptors

RNA editing was first discovered in _____, the protozoa that causes sleeping sickness.

trypanosomes

The binding of a transcription factor to an enhancer increases the rate of transcription 10- to 1,000-fold; this is called _____. The binding of a transcription factor to a silencer decreases the rate of transcription; this is called _____.

up-regulation; down-regulation