chapter 17: gene regulation in eukaryotes

In which ways do histone modifications affect the level of transcription?

-By changing the histone modification patterns that are recognized by other proteins -By influencing interactions between DNA and histones within nucleosomes

Which are the most common ways that the functions of regulatory transcription factors are controlled?

-Covalent modifications -The binding of a small effector molecule -Protein-protein interactions

What are molecular mechanisms that underlie epigenetic control of gene expression?

-Localization of histone variants -Covalent histone modification -DNA methylation -Chromatin remodeling

Transcription factors that affect the ability of RNA polymerase to begin the transcription process may work by ______.

-regulating the binding of the transcriptional complex to the core promoter -controlling the switch from the initiation to the elongation stage of transcription

In somatic cells of female mammals, one of the two X chromosomes becomes a condensed _______ body, where the genes are inactivated.

Barr

What effect can ATP-dependent chromatin remodeling have on transcription?

Both activation and repression.

Stretches of DNA of 1000-2000 bp in length containing a high number of methylation sites and found near gene promoters are called ______.

CpG islands

5-methylcytosine is formed by ______.

DNA methyltransferase

What environmental factors promote epigenetic changes?

Diet Temperature Toxins

Nucleosomes containing the histone variant ______, which are usually found at the +1 nucleosome, are thought to be more easily removed from the DNA than those containing the standard histone ______

H2AZ, H2A

Variants have been identified for which of the following histones?

H2B H3 H1 H2A

TFIID binds to the _________ box and helps recruit RNA polymerase II to the core __________.

TATA, Promoter

The function of TFIID is to ______.

bind to the TATA box and recruit RNA polymerase II to the core promoter

A protein that increases the rate of transcription but does not directly bind to the DNA is called a(n) ______

coactivator

A protein that increases the rate of transcription but does not directly bind to the DNA is called a(n) _______

coactivator

Activator proteins often increase transcription through an interaction with ______.

coactivators

DNA sequences in eukaryotes that can be bound by regulatory transcription factors, which then affect the ability of RNA polymerase to transcribe a particular gene are called:

control elements, regulatory elements, regulatory sequences

DNA methylation is the _____ attachment of methyl groups to DNA

covalent

The binding of a regulatory transcription factor to a(n) ________ can stimulate transcription 10- to 1000-fold, which is called _________ regulation.

enhancer, up

DNA methylation, chromatin remodeling, covalent histone modification, and localization of histone variants are all molecular mechanisms that contribute to _________ gene regulation.

epigenetic

During embryonic development, many genes undergo _______ changes that enable them to be transcribed or cause them to be permanently repressed.

epigenetic

Variation of gene expression that is transmissible and reversible but not related to the variation in the DNA is called ___________.

epigenetic

Fill in the blank question. The Igf2 gene in mammals is only expressed from the paternal chromosome. This is due to different patterns of DNA methylation during oogenesis and spermatogenesis. Methylation can occur at two different sites: the _______ ________ region (ICR), and the _______ _______ region (DMR).

imprinting control, differentially methylated

Proteins called ________-CpG-________ proteins bind methylated sequences and recruit other proteins to the region to ________ transcription.

methyl, binding, inhibit

If fully methylated DNA is introduced into a plant or animal cell, in subsequent generations the DNA will be _______. If the same sequence of nonmethylated DNA is introduced into a cell, it will be __________ in daughter cells.

methylated, nonmethylated

The covalent attachment of a -CH3 group to DNA is known as DNA ______.

methylation

The core promoter of active genes is found in a(n) _________-free _________, which is a segment of DNA that is missing histones.

nucleosome, region

A change in chromatin confirmation from closed to open often involves the movement of ______.

nucleosomes

The function of a regulatory transcription factor can be modulated by covalent modifications, such as the attachment of a __________ group.

phosphate

The phenomenon where gene expression is controlled so that genes can be expressed at high or low levels is called gene ________

regulation

DNA sequences that are analogous to the operator sites found near bacterial promoters are called ________ elements or __________ elements.

regulatory, control

X-chromosome inactivation occurs in ______ cells of ______ mammals.

somatic; female

A protein that influences the ability of RNA polymerase to transcribe a given gene is a(n) _______ _________

transcription factor

True or false: The methylation state of DNA is inherited during cell division

true

In general ________ CpG islands correlate with active genes, and ________ CpG islands correlate with suppressed genes.

unmethylated, methylated

An enhancer is a DNA element that is bound by a regulatory transcription factor, which leads to ______.

up regulation

Gene regulation means that ______.

gene expression can be controlled so that genes can be expressed at high or low levels

In eukaryotes, DNA methyltransferase is an enzyme that attaches a methyl group to ______ the position of the ___________ base.

5, cytosine

What type of mechanism is responsible for enabling the transcription of muscle-specific genes in an embryonic cell that will eventually give rise to muscle tissue?

epigenetic changes

Histone modifications can affect transcription levels by directly influencing interactions within ________, and also by altering the ________ code.

nucleosomes, histone

Most histone genes encode standard histone proteins, but some have accumulated mutations that change the amino acid sequence of the histone proteins. These proteins are called histone _________.

variants

In which ways can methylation affect transcription?

-The methylation of CpG islands may prevent or enhance the binding of regulatory transcription factors to the promoter region. -Methyl-CpG binding proteins recruit other proteins that inhibit transcription.

ATP-_______ ________ remodeling uses the energy of ATP hydrolysis to change the position or composition of nucleosomes.

dependent chromatin

The placement of ________ at or near promoters often plays a key role in whether a gene is active or inactive.

nucleosomes

examples of how environmental factors may function as epigenetic regulators:

-Flowering and/or seed germination occurs when certain flowering plants are exposed to colder temperatures during the previous winter. -Body differences between queen bees and worker bees are caused by dietary differences. -Exposure to tobacco smoke has been shown to alter DNA methylation and covalent modifications of specific genes in lung cells.

What is 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.

What is the size of the nucleosome-free region found at the core promoter of active genes?

150 bp