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