chapter 15

Select the strategies used by ENCODE investigators to identify functionl elements in the human genome

* map DNA methylation sites *identify DNA binding sites for transcription factors *isolate and sequence RNA molecules transcribed by the human genome * identify sites where DNAsel can cleave the DNA * identify sites of histone modifications

The function of regulatory transcription factors must be modulated to ensure that the genes are turned on

* under the appropriate environmental conditions * at the proper time * in the correct cell type

Select the roles commonly played by insulators

*acting as a barrir to chromatin- remodeling or histone-modifying enzymes *blocking the effects of enhancers that exert their effects on neighboring gens

Place the steps leading to the activation of the CREB in order from first to last. putting the first step at the yop

1. an extracellular signaling , 2. a G protein is activated 3. adenylyl cyclase 4. cAMP binds to protein kinase A 5. protein kinase A travels 6. The CREB protein binds

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

150 bp

THE SWI/SNF FAMILY, THE ISWI FAMILY , THE IN080 FAMILY AND THE MI2 FAMILY ARE FAMILIES OF

CHROMATIN REMODELING COMPLEXES

which enzyme catalyzes the formation of 5-methylytosine

DNA methyltransferase

whihc histone variant is. usually fiound in nucleosomes that flank the transcriptional start site of promoters

H2A.Z

enzymes that carry out what functions travel along wiht RNA polymerase 11

H3, Histone acetylation, h2b

According to the __ huypothesis, the patern of __ modification acts like a language or code in specifying alterations in chromtin structure

Histone Code, histone

varition in __ __ orientation and location makes it difficult to study all the regions of DNA that affect the the expression of a given gene

Regulatory Element

What would happen if nucleosomes did not re-form behindRNA polymerase II

Transcriptional initiation might occur at multiple points ina. gene

similarily to a a-helix , a __ finger motif can also recognize the __ groove of DNA

Zinc, Major

The binding of glucocorticold receptor homodimer to a glucocorticold response element __ the transcription of the nearby gene

activates

steroid hormones bind regulatory transcription factor called steroids receptors in order to __

affect gee transction

in helix turn helix and helix loop helix motifs___ __ side chains of the a helix form ___ bond with nucleoide bases

amino acid, hydrogen

how can gene regulation mechanisms be limited to only a particular gene and not its neighbors

because of insulators between genes

a regulatory element that functions in the forward or reverse direction is said to be

bidirectional

Select wats in which chromatin remodelers change chromatin structure

change in nucleosome position * change in the composition of nucleosomes due to exchange of histones * removal of histones from the DNA creating nucleosome free gaps

histone __ are proteins that bind histones and aid in the assembly of histone octamers

chaperones

DNA methylation is the __ attachemenet of methyl groups to DNA

covalent

Select the most common ways that the fuctions of regulatory transcription factors are controlled

covalent modifications, protein protein interactions, the binding of a small effector molecule

As RNA polumerase II progresses over the DNAhistone __ removes acetyl groups behind it, fovoring the binding of histones to the __ to form nucleosomes

deacetylase, DNA

plants and animals require a greater level of gene regulation than single- celled eukaryotes because of

different tissue types, differnet developmental stages, more complex cell structure , multicellularity

steroid hormones are synthesized by _ glands and secreted into the bloodstream unltimately affecting the transcription or expression of genes in target cells

endocrine

a glucocorticoid response element functions as a

enhancer

Select motifs that promote proteins dimerization

helix-loop-helix motif, Leucine zipper motif

core __ proteins contain a globular domain and a flexible amino-terminal tail. DNA wraps around the globular domains and the amino terminal tails protrude from the chromatin

histone

The central goal of the encylopedia of DNA elements (ENCODE) onsortium is to make a comprehensive list of functional elements in the __ __ including those that control gene expression

human genome

in genomic __ specific genes are __ during oogenesis or spermatogenesis but not both

imprinting, methylated

repressors inhibit TFIID by

inhibiting the ability of TFIID to recruit DNA polymerase II to the core promoter, Preventing the binding of TFIDD to the TATA box

a segment of DNA that acts as a boundary between two genes is called a

insulator

positively charged __ within core histones proteins can be acetylated by histone __

lysines, acetyltransferases

select the common types of covalent modifications made to the amino terminal talls of histones

methylation, phosphorylation,acetylation

The encode project mapped more than 4__ regulatory regions where __ specifically interact with the DNA

million, proteins

The placement of __ at or near promoters often plays a key roole in whether a gene in active or inactive

nucelosomes

The core promoter of active genes is found in a __-free region, which is a segment of a dna with missing histones

nucleosome , region

transcription can occur more easily when chromatin is in a __ conformation

open

the function of a regulatory transcription factor can be modulated by covalent modifications such as the attachement of a __ group

phosphate

The pattern of covalent modification to histone talls provides binding site for proteins that affect the dregree of transcription. Certain patterns can either __ or __ transcription

promote , inhibit

the phenomenon where the level of gene exression is coontrolled so that genes can be expressed at high or low levels is called gene __

regulation

the pheonomenon where the level of gene expression is controlled so that genes can be expressed at high or low levels is called gene __

regulation

you are studying a region of DNA near a gene promoter, you notice that in some cases there is a nucleosome very close to the promoter but in other cases, the nucelosome is gone. this move is mst likely the result of chromatin __

remodelers

The CREB protein binds to DNA at a sequence called the cAMP __ __.

response element

Binding of the IRP to the iron response element (IRE)3'UTR

stablizes the transferrin receptor mRNA

Regulatory trancription factors that respond to steroid hormones are called

steriod receptors

A repressor interacting with mediator prevents

the phosphorylation of RNA

what is the purpose of histone variants

to create functionally speialized regions of chromatin

The cAMP response element contains __ of a consensus sequence bound by CREB protein which has

two copies ; two identical subunits

when a fully methylated DNA segment of DNA is replicated, the newly made daughter strand contains __ cytosines. This DNA is said to be __

unmethylated, hemimethylated

in general __ CpG islands correlate with active genes and __ CpG islands correlate withsuppressed genes

unmethylated, methylated

Leucine __ motifs mediate dimerization between two __

zipper, proteins

The cAMP __ element binding protein (__ protein) is a regulatory transcription factor that is activated in response to signaling molecules that incrase cytoplamic cAMP

repsonse, CREB

which histone variant is abundant on the inactivated x chromosome in female mammals

macroH2A

mapping the locations of nucleosomes in the genomes allows for the determination of

*where histone variants are found *where nucleosomes are located *where covalent modification of histones occur

which of the following regulates iton assimilation in mammalian cells

rna binding proteins

Select the locations where cis regulatory elements can be found relative to the gene of interest

close, upstream,downstream,far,within