31 Eukaryotic Regulation and Epigenetics Flashcards
1
Q
classes of gene regulation in eukaryotes
A
- changes in chromatin
- initiation of transcription
- RNA processing and stability
- protein modification
2
Q
changes in chromatin include…
A
- histone modification
- chromatin remodeling
- DNA methylation
3
Q
initiation of transcription includes…
A
- presence and action of transcription factors such as activators and repressors
- transcription factor binding sites
- DNA sequences such as enhancers and insulators
4
Q
RNA processing and stability includes…
A
- RNA splicing
- RNA degradation
- RNA interfence
5
Q
polytene chromosomes
A
found in the salivary glands of drosophila larvae
6
Q
puffs
A
expanded areas along the arms of chromosome
areas where gene expression is occurring - transcription is occurring
7
Q
Balbiani rings
A
larger regions of expanded areas along chromosomes where transcription is occurring
8
Q
Transcriptionally active DNA is….coiled
A
loosely
9
Q
DNasel sensitive
A
areas where chomatin is decondensed
they are more easily cut by DNAse
10
Q
DNasel hypersensitive sites
A
- small regions upstream from start of transcription
- nucleosome is missing
- binding sites for regulatory proteins
11
Q
2 domains of histones
A
globular
positively charged tailes
12
Q
globular domain of histones interacts with…
A
other histones and the DNA
13
Q
positively charged tails of histones interact with…
A
negatively charged phosphate groups n the DNA
14
Q
histone tails are modified by…
A
methylation
acetylation
15
Q
Methylation of histone tails ___ transcription depending on…
A
increases or decreases
which amino acids are methylated
16
Q
acetylation of histone tails…
A
weakens the interaction between DNA and histones allowing TF to bind the DNA and increase transcription
17
Q
amino acid on histones that is acethylated
A
lysine
18
Q
Histone deacetylase
A
tightens association between histones and DNA
19
Q
histone acetyl transferase
A
loosens DNA-histone association by neutralizing the positive charge on the histones
20
Q
DNA is more ___ wound around histones when lysine is acetylated
A
loosely
21
Q
histone code
A
combination of modifications present that help regulate chromatin structure and regulate transcription
22
Q
most histone modification occurs…
A
in the tails
23
Q
FLC gene
A
suppresses flowing in Arabidopsis when it is turned on by acetylation
deacetylase enzyme removes acetyl group allowing flowering
24
Q
2 ways of chromatin remodeling
A
- positioning the nucleosomes along the DNA
- conformational changes in the DNA and the nucleosomes
25
repositioning of the nucleosomes along the DNA allows...
the promotor to be exposed in the area between the nucleosomes and not part of the DNA bound in the nucleosome structure
26
describe reposition of the nucleosomes
chromatin remodeling complex binds to the DNA and repositions the nucleosome
this exposes the binding site allowing TFs and RNA polymerase to bind to the DNA and initiate transcription
27
conformational changes in the DNA or nucleosomes allows...
DNA to bind more tightly or loosely to the histones
looser binding allows more gene expression
lysine residues are acetylated to loosen the binding with DNA
28
FLD gene
produces a deacetylase that removesthe acetyl group from the FLC gene in arabidopsis
29
Histone methylation can ___ expression of a gene.
activate or repress
| usually represses
30
DNA methyl transferases
cause DNA methylation that usually causes genes to be turned off
31
The base methylated to alter gene expression
cytosine
forms 5 methyl cytosine
32
what results in gene silencing
heavy methylation of cytosine
33
CpG island
5-CG-3' sequence found near the start of transcription
they are methylated in silenced genes
the methylation is removed prior to transcription when the gene needs to be turned on
34
CpG islands will have...
methylated cytosines diagonally opposite of each other which attract deactylases which remove acetyl group form histone tails further repressing transcription
35
methylated CpG island will be found in
- silenced genes
| - long-term repressed regions of DNA such as X chromosome in barr bodies
36
In general an increase in methylation leads to...
a decrease in transcription of DNA
37
There is an association between increased DNA methylation and...
deacetylation of histones in areas where there is little transcription
38
epigenetics
heritable changes in gene expression that occur without changing the DNA sequence
39
Epigenetic changes include...
modifications to histones such as acetylation, methylation, phosphorylation
inherited patterns of DNA methylation
40
honeybee and epigentics
the development of honeybee larvae into the queen vs a worker bee is an example of a phenotype that is due to epigenetic effects
41
how does epigenetics cause female honeybee to become queen
- a female larvae is fed extra royal jelly
- royal jelly suppresses Dnmt3
- Dnmt3 normally adds methyl groups to DNA
- genes that are normally silenced are now expressed
42
induced pluripotent cells
adult cells that are treated with a mixture of transcription factors resulting in dedifferentiation of the cells
can become pluripotent but not totipotent
43
totipotent
can become any cell in the body and divide an infinite number of times
44
pluripotent
can be almost anything except placenta or umbilical cord cells
45
imprinting
offspring gets a gene from each parent but only one is expressed or one is expressed more than the other
46
biased expression
one gene copy is expressed more than the other
47
imprinting is highly...
variable and occurs only in certain tissues or time of development
48
basal transcription apparatus
the assembly of RNA polymerase and transcription factors that bind at the aukarytoic core promotor
transcription factors bind to the core promoter and recruit RNA polymerase II
49
the core promoter is required for...
transcription of nearly all RNA polymerase II genes
50
transcription factors binding to the regulatory promoter act by...
stimulating or stabilizing the assembly of the basal transcription apparatus
51
transcription factors binding to the regulatory promoter are...
specific to individual genes or suites of genes and regulate the timing of gene transcription
52
Where is the TATA box?
core promoter
53
where are the octamer, GC, and CAAT boxes?
regulatory promoter
54
Where does the basal transcription apparatus bind?
the core promoter
55
enhancers interact with...
proteins associated with the transcription apparatus
56
enhancers are...
DNA sequences that can be upstream or downstream from the start of transcription
play an important role in transcription regulation
57
transcription factors bind to...
DNA at transcription factor binding sites and interact with the transcription apparatus
they can be activators or repressors
they also bind to other transcription factors and polymerase to regulate transcription
58
common binding domains for transcription factors
- helix turn helix
- zinc finger
- leucine zipper structure
59
one gene can have many...
enhancers
60
a typical enhancer is about ___ bp lang and has about __ binding sites for proteins
500 bp
| 10 binding sites
61
enhancers can act ___ and are ___
at a distance
independent of orientation
62
insulators
cis DNA elements that block enhancers form interacting with the wrong gene
63
Are enhancers or insulators....
cis acting
both
64
Are enhancers or insulators....
regulator of transcription from nearby promoters
enhancers
65
Are enhancers or insulators....
regulators of more than one gene
enhancers
66
Are enhancers or insulators....
working at a distance from the promotor
enhancers
67
Are enhancers or insulators....
bound by transcription factors which may be activators or repressors
enhancers
68
Are enhancers or insulators....
| boundary elements that function to insulate the effects of enhancers
insulator
69
Are enhancers or insulators....
functioning in a position dependent manner to block enhancers from enhancing genes that shouldn't affect
insulators
70
Are enhancers or insulators....
bound by insulator bind proteins
insulators
71
heat shock genes
turn on when there is a sudden increase in temp
72
environmental factors that may induce transcription
- temperature
- light
- hormones such as progesterone, estrogen, testosterone, insulin, prolactin
73
impact of light on transcription in RBC
light stimulates transcription
important for photosynthesis
74
northern blot
shows relative amount of RNA present
75
steroids bind...
to cytoplasmic receptors and then this complex binds to the DNA to regulate gene expression
76
insulin acts...
at the cell surface and signals transcription factors
77
In regulation that alters gene expression, transcription factors can...
- interact with other proteins
- be modified
- be localized
- be degraded
78
modification of transcription factors results in
altered action
79
localization of transcription factors can result in
different gene expression in different cells or tissues
80
Which eukaryotic RNA polymerase transcribe pre-MRN
RNA polyermase II
81
What are the types of processing tht occur to form mature mRNA
- 5'GTP cap
- cleavage and polyadenylation of 3' end
- removal of introns and joining of exons
82
How can different proteins can be produced from the same gene?
- different cleavage sites for polyadenylation of mRNA
| - alternative splicing of introns
83
IgM
- example of how different sites may be cleaved and polyadenylated
- early in life, A2 cleavage site is used making longer protein
- later in life, A1 cleavage site is used making a shorter protein that is secreted
84
Calcitonin
- show how different tissues can have different cleavage site for polyadenylation and splicing
- in thyroid on exons 1-4 are included
- in brain, exons 1,2,3,5,6 are included
85
splicing isoforms
different sets of exons ae used in different cells
they have different roles in different cells
86
alternative splice sites in mRNA processing allow...
different mature mRNA and therefore different proteins to be produced from the same primary transcript
87
alternative splice sites can result in...
different proteins in different tissues or different times in development
88
Regulation of splicing is probably and important mechanism for...
controlling eukaryotic gene expression
89
Drosophila sex determination
- depends on alternative splicing
- sex determined by ratio of X chromosomes to autosomal sets of chromosomes
- if ratio = 1, Sxl produced, female - does not contain exon 3 leading to functional protein
- if ratio = 0.5, Sxl not produced, male - contains exon 3 leading to nonfunctional protein
90
tra gene in drosophila
- presence or absence of Sxl protein causing alternate splicing in the tra gene
in males, Sxl protein is absent and upstream 3' splice site is used including exon B which has stop codon to produce premature stop codon
in females, Sxl protein causes downstream 3' splice site to be used, not including B exon. Therefore no stop codon until D
91
tra means
transformed
92
Dsx
double sex gene
if transformer gene product is functional, female Dsx protein is produced
if transformer gene not function, male Dsx protein formed
93
Male drosophila
- ratio of 0.5 leads to no Sxl protein production
- the upstream 3' splice site is used for the tra gene including the exon B which leads to early stop codon producing nonfunction tra protein
- nonfunction tra gene leads to male Dsx protein being formed
94
Female drosophila
- ratio of 1 produces functional Sxl gene not containing exon 3
- Sxl gene causes downstream 3' splice site to be used in tra pre-mRNA producing functional tra protein
- function tra protein leads to female Dsx protein being produced
95
the amount of protein synthesized depends on...
the availability of mRNA for translation
96
the amount of mRNA depends on...
the rates of synthesis and degradation
97
what leads to mRNA degradation
ribonucleases and RNA interference
98
RNA stability is influenced by...
length of polyA tail
99
mechanism for mRNA degradation by ribonucleases
- poly a tail is shorted by RNases
- once tail at critical length, 5' cap is removed
- RNA is degraded from 5' end
100
how many types of ribonucleases are there?
10 or more
101
Other nontypical mechanisms for mRNA degradation by ribonucleases
- internal cleavage sites
| - 5' and 3' UTR can contribute to stability
102
How many human genes are regulated by RNA interference?
as much as 30%
103
general process of RNAi
- dsRNA is cleaved by dicer to form micro or small interfering RNAthat is about 24 nts long
- these small RNAs bind with argonaute proteins to form RISC
- RISC moves to the mRNA where small RNA base pairs to the mRNA and either inhibits translation or degrades the mRNA
104
micro mRNA
inhibits translation
105
small interfering RNA
degrades mRNA
106
miRNA is transcribe from...
a distant gene and targets other genes for regulation
107
siRNA comes from...
mRNA, transposons, or viral RNA and targets genes that it comes from
108
RISC
formed by miRNA and siRNA binding with argonaute proteins
109
mechanisms of gene regulation by RNAi
- mRNA cleavage
- inhibition of translation
- transcriptional silencing
110
RNAi mRNA cleavage
siRNA combines with proteins and bind mRNA and then cleaves the mRNA (slicer activity). mRNA then degrades
111
RNAi inhibition of translation
pairing of miRNA with mRNA can decrease translation of the mRNA
112
RNAi transcriptional silencing
- siRNA alters chromatin structure by binding to chromatin, attracting ezymes that methylate the tails of histones
- DNA binds to histone more tightly decreasing transcription
- direct methylation of DNA by miRNA also decreases transcription
