Chapter 17: Control of Gene Expression in Eukaryotes Flashcards
1
Q
What are transcription factors?
A
Regulatory proteins that bind to specific DNA sequences
Transcription factors are proteins that bind to specific DNA recognition sequences in the promoter or enhancer elements of a gene.
2
Q
Which of the following elements is not a DNA binding domain?
Leucine zipper
Zinc finger
Helix-turn-helix
Gal4p
A
Gal4p
Gal4p is a yeast protein that contains a DNA binding domain.
3
Q
True or False?
Alternative splicing is an example of gene regulation that occurs after the synthesis of mRNA.
A
True
Alternative splicing is a form of mRNA processing and occurs after mRNA synthesis.
4
Q
True or False?
Transcription and translation are not coupled in eukaryotic cells, although both processes take place in the cytoplasm.
A
False
In eukaryotes, transcription and translation are not coupled because transcription occurs in the nucleus and translation in the cytoplasm.
5
Q
True or False?
In general, one could say that fewer levels of regulation are possible in prokaryotes than in eukaryotes.
A
True
6
Q
How does DNA methylation regulate gene activity?
A
by adding methyl groups to the cytosine of CG doublets in DNA
Methylation of 5-methyl-CpG DNA sequences appears to inactivate transcription of the sequences.
7
Q
Which process seems to be the most similar between eukaryotic and prokaryotic genetic regulation?
A
transcriptional regulation
8
Q
DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to ________.
A
addition of methyl groups to the cytosine of CG doublets
9
Q
Which of the following elements function specifically in eukaryotic transcription and gene expression?
A
promoters and enhancers
Promoters are the sites of assembly of the basic transcription complex, and along with enhancers, control transcription in eukaryotes.
10
Q
Which of the following clusters of terms applies when addressing enhancers or silencers as elements associated with eukaryotic genetic regulation?
A
cis-acting, variable orientation, variable position
11
Q
Mutations in the promoter region of the β-globin gene indicate that some areas are more sensitive than others. When mutations occur in consensus sequences (modular elements such as GC box, CAAT box, TATA box), does transcription usually increase or decrease?
A
decrease
12
Q
True or False?
Transcription in eukaryotes is generally influenced by enhancers just as in prokaryotes.
A
False
13
Q
Which of the following best describes the mechanism by which steroid hormones control gene expression?
A
Steroid hormones that enter the cell activate receptors. These hormone-receptor complexes then bind HREs and influence gene expression.
14
Q
The reason some cells respond to the presence of a steroid hormone while others do not is that _______.
A
the receptors necessary for regulation differ among cells of various types
The specificity of steroid hormone regulation is due to the presence or absence of the receptor in different cell types.
15
Q
Which of the following best describes the role of chaperone proteins in the regulation of gene expression by steroid hormones?
A
Chaperone proteins maintain functionality of the receptor.
Chaperone proteins maintain the functionality of the receptor prior to binding of the steroid hormone to the receptor.
16
Q
What are transcription factors?
A
regulatory proteins that bind to specific DNA sequences
Transcription factors are proteins that bind to specific DNA recognition sequences in the promoter or enhancer elements of a gene.
17
Q
Which of the following statements about transcription factors is true?
A
Transcription factors bind DNA sequences present in the enhancer and activate transcription via protein-protein interactions with RNA polymerase.
Transcription factors carry out two functions: they bind to DNA sequences in the enhancer, and they activate transcription via their interactions with RNA polymerase.
18
Q
When transcription factors interact with DNA, is the resulting genetic control typically positive or negative?
A
positive
19
Q
Transcription factors are proteins with at least two functional domains–one that binds to DNA and one that binds to RNA polymerase or to other transcription factors.
A
True
20
Q
What is the function of an activator?
A
It physically makes contact with some element of the transcription complex and activates transcription.
Activators stimulate transcription by RNA polymerase II.
21
Q
In the galactose utilization system of yeast, the GAL4 protein is a(n) ______.
A
activator
GAL4 contains a transcription-activating domain, which, when exposed, activates transcription of GAL7, GAL10, and GAL1.
22
Q
In what way do upstream activator sequences (UASs), regulatory sequences in yeast, differ from enhancers and silencers?
A
UASs function only upstream.
23
Q
Which processes are examples of posttranscriptional regulation in eukaryotes?
A
alternative splicing of single mRNA transcripts to give rise to multiple mRNAs and increased stability of the mRNA
Alternative splicing of mRNA transcripts and increased mRNA stability are two processes used to regulate gene expression posttranscriptionally.
24
Q
True or False?
Alternative RNA processing can result in different mRNAs that start with different exons.
A
True
25
True or False?
The term spliceopathy is often used to signify a genetic condition caused by a defect in the regulation of RNA splicing.
True
26
What is the role of Dicer in RNA-induced gene silencing?
cleaves longer RNAs into short, regulatory RNA molecules
The regulatory siRNAs and miRNAs are involved in suppression of gene expression.
27
Many promoter regions contain CAAT boxes containing consensus sequences CAAT or CCAAT approximately 70 to 80 bases upstream from the transcription start site.
How might one determine the influence of CAAT boxes on the transcription rate of a given gene?
Delete the CAAT box sequence and measure the transcription rate.
Make mutations in the CAAT box sequence and measure the transcription rate.
Introduce extra CAAT box sequences and measure the transcription rate.
28
A deletion within the GAL4 gene that removes the region encoding amino acids 1 to 100.
A deletion within the GAL4 gene that removes amino acids 1-100 would remove the DNA-binding section and not allow transcriptional activation.
29
A deletion of the entire GAL3 gene.
Without the product of the GAL3 gene, there would be no disruption of the Gal4p/Gal80p complex and therefore no transcription of the GAL1 gene.
30
A mutation within the GAL80 gene that blocks the ability of Gal80 protein to interact with Gal3p.
If the GAL80 gene product can’t interact with Gal3p, there can be no interaction with the Gal4p/Gal80p complex and therefore no GAL1 transcription.
31
A deletion of one of the four UASG elements upstream from the GAL1 gene.
A deletion of one of the four UASG elements would reduce transcription of the GAL1 gene.
32
A point mutation in the GAL1 core promoter that alters the sequence of the TATA box.
Generally, mutations in the TATA box of a promoter reduce transcription of the relevant gene.
33
Which statements about the modification of chromatin structure in eukaryotes are true?
DNA is not transcribed when chromatin is packaged tightly in a condensed form.
Some forms of chromatin modification can be passed on to future generations of cells.
Acetylation of histone tails is a reversible process.
Acetylation of histone tails in chromatin allows access to DNA for transcription.
Methylation of histone tails in chromatin can promote condensation of the chromatin.
34
One of the mechanisms by which eukaryotes regulate gene expression is through modifications to chromatin structure. When chromatin is condensed, DNA is not accessible for transcription. Acetylation of histone tails reduces the attraction between neighboring nucleosomes, causing chromatin to assume a looser structure and allowing access to the DNA for transcription. If the histone tails undergo deacetylation, chromatin can recondense, once again making DNA inaccessible for transcription.
Recent evidence suggests that methylation of histone tails can promote either the condensation or the decondensation of chromatin, depending on where the methyl groups are located on the histones.
Thus, methylation can either inactivate or activate transcription, and demethylation can reverse the effect of methylation.
Changes in chromatin structure may be passed on to future generations of cells in a type of inheritance called epigenetic inheritance.
35
A number of experiments have demonstrated that areas of the genome that are relatively inert transcriptionally are resistant to DNase I digestion; however, those areas that are transcriptionally active are DNase I sensitive.
Describe how DNase I resistance or sensitivity might indicate transcriptional activity.
When DNA is transcriptionally active, it is in a less condensed state and as such, more open to DNase digestion.
36
Which statements about the regulation of transcription initiation in these genes are true?
Both the fantasin gene and the imaginin gene will be transcribed at high levels when activators specific for control elements A, B, C, D, and E are present in the cell.
The fantasin gene will be transcribed at a high level when activators specific for control elements A, B, and C are present in the cell.
Control elements C, D, and E are distal control elements for the imaginin gene.
37
Only certain genes are transcribed in a eukaryotic cell at any particular time. The regulation of transcription initiation depends on the interaction of specific transcription factors with specific control elements in enhancers.
In the eukaryotic cell used as an example, the enhancers for the fantasin gene and imaginin gene are unique because they contain different sets of control elements (A, B, and C for the fantasin gene; C, D, and E for the imaginin gene). Each gene will be transcribed at a high level when activators specific for all of the control elements in its enhancer are present in the cell.
38
Alternative RNA splicing produces different mRNA molecules from the same primary RNA transcript.
During alternative RNA splicing, all introns are removed, and some exons may also be removed.
The removal of different exons produces different mRNA molecules, which are then translated into different proteins.
Alternative RNA splicing can greatly expand the number of proteins produced from the same gene.
39
Characteristics of Promoters
Required for basal-level transcription
TATA, CAAT, and GC boxes
Always located upstream of the gene within 100 bases of the transcription initiation site
40
Characteristics of Enhancers
NOT required for basal-level transcription
Responsible for tissue-specific and time-specific gene expression
May influence the expression of more than one gene
May be located upstream, downstream, or within the gene.
41
Chromatin Remodeling Complexes
Repositions Histones
42
Decreases Gene Expression
Histone Deacetylaces (HDACs)
Deacetylation
Increased attraction between DNA and histones
43
Increases Gene Expression
Histone Acetyltransferases (HATs)
Acetylation
Decreased attraction between DNA and histones
44
Refers to changes in DNA/chromosomes structure that can influence overall gene output.
Chromatin remodeling
45
Sequences in the DNA to which transcription factors and RNA polymerase bind to initiate transcription.
Promoters
46
Cis-acting DAN sequences to which transcription factors bind to regulate transcription.
Enhancers
47
They can act over distances of thousands of base pairs and can be upstream, downstream, or internal, to the gene they affect.
Enhancers
48
Bind DNA and regulate transcription.
Transcription Factors
49
The addition of a 5' cap and a poly-A tail, and removal of introns are all steps in ____.
RNA Processing and Transport
50
RNA processing contributes to ___, which regulate translation.
mRNA stabililty
51
Eukaryotic regulation is more complex than it is in prokaryotes because of:
(4 reasons)
larger amount of DNA
larger number of chromosomes
spatial separation of transcription and translation
mRNA processing, RNA stability, and cellular differentiation in eukaryotes
52
Chromosome Organization in the ___ Influences _____ .
Chromosome Organization in the Nucleus Influences Gene Expression
53
Chromosomes occupy a discrete territory in the nucleus
gene-poor chromosomes are located peripherally
gene-rich chromosomes are located more internally
54
6 Levels of Eukaryotic Gene Regulation
1. Regulation of Transcription
2. Regulation of Splicing and Processing.
3. Regulation of Transport
4. Degradation of mRNA
5. Regulation of Translation
6. Modification and Activity of Protein
55
Channels between chromosomes are called ____ .
interchromosomal compartments.
56
In the nucleus, each chromosome occupies a discrete territory, and is separated from other chromosomes by an interchromosomal domain, where mRNA transcription and processing is thought to occur.
In the _____, each chromosome occupies a discrete territory, and is separated from other chromosomes by an _____, where ______ is thought to occur.
57
FISH probes hybridized to human chromsome 7.
Hybridization to metaphase chromosomes. In the nucleus (right) the probes reveal the location of the territories occupied by chromosome 7.
58
Chromosome structure is continuously rearranged so that ______are cycled to the edges of chromosome territories.
Chromosome structure is continuously rearranged so that transcriptionally active genes are cycled to the edges of chromosome territories.
59
Transcription Initiation Is a Major Form of Gene Regulation
Promoters contain several elements.
The TATA box is the region to which RNA polymerase II binds.
60
Transcription Factor Binding Sites
The CAAT box and GC box are elements that bind transcription factors.
61
Transcription ____ Is a Major Form of Gene Regulation
Transcription Initiation Is a Major Form of Gene Regulation
62
Transcription Enhancers
Enhancers are modular and contain several short DNA sequences.
Enhancers often include binding sites for positive and negative regulatory factors.
63
Yeast Regulatory Sequences
In yeast, regulatory sequences similar to enhancers, called upstream activator sequences (UAS), can function upstream at variable distances and in either orientation.
They differ from enhancers in that they cannot function downstream of the transcription start point.
64
Transcription in Eukaryotes Requires Several Steps
Eukaryotic chromosomal DNA is complexed with histones to form chromatin.
Nucleosomes in the chromatin can inhibit transcription.
Chromatin remodeling is required for transcription to occur.
65
Nucleosomes can inhibit multiple steps required for gene transcription.
The binding of enhancer transcription factors requires accessing nucleosomal DNA and may result in displacement of the nucleosome.
Similarly, the formation of the basal transcription complex at the TATA box, other upstream elements (USEs) and the core promoter site is also suppressed by nucleosomes.
RNA polymerase II is slowed by the presence of nucleosomes.
66
_______ is slowed by the presence of nucleosomes.
RNA polymerase II is slowed by the presence of nucleosomes.
67
Chromatin Remodeling
The SWI/SNF complex is a chromatin remodeling complex that can be directed to specific DNA sites by:
1. transcription factors,
2. by acetylation of histones,
3. by binding to methylated DNA.
68
The SWI/SNF nucleosome remodeling complexes can be directed to specific DNA sites in several ways
(a) Transcription factors, including those with leucine zipper domains can target binding.
(b) Histone components of nucleosomes modified by acetylation can serve as SWI/SNF targets.
(c) Methlyated DNA regions can also be target sites for nucleosome remodeling complexes.
69
3 mechanisms that might be used to alter nucleosome structure by the ATP hydrolysis-dependent remodeling complex SWI/SNF.
(a) DNA–histone contacts may be loosened.
(b) The path of the DNA around an unaltered nucleosome core particle may be altered.
(c) The conformation of the nucleosome core particle may be altered.
70
chromatin remodeling
A process in which the structure of chromatin is altered by a protein complex,resulting in changes in the transcriptional state of genes in the altered region.
71
Nucleosome remodeling complexes may alter nucleosome structure in several ways:
1. Altering the contacts between DNA and histones
2. Alternating the path of the DNA around the nucleosome
3. Altering the structure of the nucleosome core itself
72
Histone Modification
Histone modification by histone acetyltransferase (HAT) lessens the attraction between histones and DNA
73
histones
Positively charged proteins complexed with DNA in the nucleus. They are rich in the basic amino acids arginine and lysine,and function in coiling DNA to form nucleosomes.
74
nucleosome
In eukaryotes, a nuclear complex consisting of 4 pairs of histone molecules wrapped by two turns of a DNA molecule.
The major structure associated with the organization of chromatin in the nucleus.
75
____ added to specific basic amino acids on ____ tails results in lessening of attraction between ___ charged DNA and basic amino acids of histones.
Acetyl groups added to specific basic amino acids on histone tails results in lessening of attraction between negatively charged DNA and basic amino acids of histones.
76
Positively charged tails of nucleosomal histone proteins probably interact with the negatively charged phosphate groups of DNA.
Acetylation of the tails weakens their interaction with DNA and may permit some transcriptional factors to bind to DNA.
77
HDACs
Histone deacetylases (HDACs) reverse this remodeling.
78
HAT
Histone modification by histone acetyltransferase (HAT) lessens the attraction between histones and DNA
79
HAT
Histone modification by histone acetyltransferase (HAT) lessens the attraction between histones and DNA
Specific transcription factors target HATs to genes.
80
Assembly of the Basal ____ Complex Occurs at the ____
Assembly of the Basal Transcription Complex Occurs at the Promoter
81
Eukaryotic Transcription
Eukaryotes have 3 RNA polymerases that recognize different types of promoters to transcribe certain sets of genes.
RNA polymerase II transcribes mRNAs.
82
Eukaryotic Transcription
Eukaryotes have 3 RNA polymerases that recognize different types of promoters to transcribe certain sets of genes.
RNA polymerase II transcribes mRNAs.
Basal (general) transcription factors are required for the binding of RNA polymerase II to the promoter.
Activators have a DNA-binding domain that binds the enhancer sequence and…
…a trans-activating domain that activates transcription through protein-protein interactions with the factors in the transcription complex.
83
RNA polymerase II transcribes ____.
RNA polymerase II transcribes mRNAs.
Basal (general) transcription factors are required for the binding of RNA polymerase II to the promoter.
TFIID, the first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP).
84
the first general transcription factor to bind the promoter:
TFIID
TFIID, the first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein (TBP).
85
Formation of _____ allows factors that bind to ____ at a distance from the ____ to interact with regulatory proteins in the transcription complex and to _____ transcription.
Formation of DNA loops allows factors that bind to enhancers at a distance from the promoter to interact with regulatory proteins in the transcription complex and to maximize transcription.
86
Activators have...
Activators have a DNA-binding domain that binds the Enhancer sequence and…
…a Trans-activating domain that activates transcription through protein-protein interactions with the factors in the transcription complex.
87
Transcription Activators
The DNA-binding domain of an activator typically has a at least one of the following:
helix-turn-helix motif
zinc finger
a leucine zipper
Many transcription factors also contain domains that bind coactivators, such as hormones or small metabolites, that regulate their activity.
88
helix–turn–helix
(a) three planes of the -helix of the protein are established, and
(b) these domains bind in the grooves of the DNA molecule.
89
zinc finger
Cysteine and Histidine residues bind to a atom. This loops the amino acid chain out into a fingerlike configuration.
90
leucine zipper
the result of dimers from leucine residue at every other turn of the helix in facing stretches of 2 polypeptide chains.
(b) When the helical regions form a leucine zipper, the regions beyond the zipper form a Y-shaped region that grips the DNA in a scissorlike configuration.
91
DNA Methylation and Regulation of Gene Expression
The methylation state of a gene can be determined by restriction enzyme analysis with HpaII and MspI.
Both recognize same restriction enzyme site: CCGG
Methylation most often occurs at C of CG doublets
92
Methylation most often occurs at ___
C of CG doublets
93
Both recognize same restriction enzyme site:
CCGG
94
The methylation state of a gene can be determined by restriction enzyme analysis with ___ and ___.
HpaII and MspI
95
Methylated DNA
CH3
96
HpaII does NOT cut methylated sites
MspI DOES cut methylated sites
97
The restriction enzymes HpaII and MspI recognize and cut at CCGG sequences.
(a) If the second cytosine is methylated, HpaII will not cut.
(b) The enzyme MspI cuts at all CCGG sites, whether or not the second cytosine is methylated. Thus, the state of methylation of a given gene in a given tissue can be determined by cutting DNA extracted from that tissue with HpaII and MspI.
98
Regulation by methylated sites
An inverse relationship exists between the degree of methylation and the degree of gene expression
Methylation patterns are tissue specific and heritable for all cells in that tissue…
And incorporation of 5-azacytidine causes undermethylation of sites of incorporation and changes in the pattern of gene expression.
99
An _____ relationship exists between the degree of methylation and the degree of gene expression
An inverse relationship exists between the degree of methylation and the degree of gene expression
100
Methylation patterns are ____ and ____ for all cells in that tissue.
Methylation patterns are tissue specific and heritable for all cells in that tissue.
101
Incorporation of _____ causes _____ of sites of incorporation and changes in the pattern of gene expression.
Incorporation of 5-azacytidine causes undermethylation of sites of incorporation and changes in the pattern of gene expression.
102
The base 5-azacytosine has a ___ at the 5 position and can be incorporated into DNA in place of deoxycytidine during DNA synthesis.
The base 5-azacytosine cannot be _____, causing undermethylation of the _____ wherever it has been incorporated.
The base 5-azacytosine has a nitrogen at the 5 position and can be incorporated into DNA in place of deoxycytidine during DNA synthesis.
The base 5-azacytosine cannot be methylated, causing undermethylation of the CpG dinucleotide wherever it has been incorporated.
103
DNA methylation is an example of _____ inheritance
DNA methylation is an example of EPIGENETIC inheritance
104
Epigenetic inheritance and gene regulation
Heritable alterations in gene expression in which DNA sequence is unchanged
Paramutation in plants
Parental imprinting:
- genes rendered inactive depending upon parental source
- imprinted genes usually methylated by special methylases, demethylated by demethylases
active genes are less methylated (hypomethylated)
X-chromosome inactivation
- random X chromosome inactivation in placental females
- inactivation hereditary through cell division
105
Parental imprinting
genes rendered inactive depending upon parental source
imprinted genes usually methylated by special methylases, demethylated by demethylases
active genes less methylated (hypomethylated)
Type of Epigenetic inheritance and gene regulation
106
X-chromosome inactivation
random X chromosome inactivation in placental females
inactivation hereditary through cell division
Type of Epigenetic inheritance and gene regulation
107
epigenesis
The idea that an organism or organ arises through the sequential appearance and development of new structures.
In contrast to preformationism, which holds that development is the result of the assembly of structures already present in the egg.
108
epigenetics
The study of modifications in an organism’s gene function or phenotypic expression that are not attributable to alterations in the nucleotide sequence (mutations) of the organism’s DNA.
109
Developmental Genetics and gene regulation
Cytoplasmic localization: cytoplasm exerts influence
Cell-cell interaction: as development proceeds cells influence other cells
Signaling Pathways: regulate development, coordinate transcription, direct differentiation of tissues and organs: Notch is an example.
Transcriptional Networks: control of gene expression
110
Notch Signaling Pathway
Binding of Delta by Notch leads to proteolytic cleavage of cytoplasmic end of Notch
This cleaved cytoplasmic tail of Notch protein moves to nucleus activating transcription of a gene set directing developmental pathway that determines cell fate.
111
Numerous Signaling Pathways used in Early Vertebrate Development Have Been Identified
Notch/ Delta Pathway
- Blood Cell Development
- Neurogenesis
- Retina Development
TGF-ß Pathway
- Mesoderm induction
- Left-right asymmetry
- Bone development
112
Numerous Signaling Pathways used in Early Vertebrate Development Have Been Identified
Notch/ Delta Pathway
- Blood Cell Development
- Neurogenesis
- Retina Development
TGF-ß Pathway
- Mesoderm induction
- Left-right asymmetry
- Bone development
Hedgehog Pathway
- Notochord induction
- Somitogenesis
- Gut/visceral mesoderm
Receptor Tyrosine Kinase Pathway
-Mesoderm maintenance
Wnt Pathway
- Dorsalization of Body
- Female reproductive development
- Dorsal-ventral differences
113
Notch/ Delta Pathway
- Blood Cell Development
- Neurogenesis
- Retina Development
Signaling Pathway used in Early Vertebrate Development
114
Hedgehog Pathway
- Notochord induction
- Somitogenesis
- Gut/visceral mesoderm
Signaling Pathway used in Early Vertebrate Development
115
Receptor Tyrosine Kinase Pathway
-Mesoderm maintenance
Signaling Pathway used in Early Vertebrate Development
116
Wnt Pathway
- Dorsalization of Body
- Female reproductive development
- Dorsal-ventral differences
Signaling Pathway used in Early Vertebrate Development
117
Wnt Pathway
- Dorsalization of Body
- Female reproductive development
- Dorsal-ventral differences
Signaling Pathway used in Early Vertebrate Development
Normal roles in control of cell proliferation, differentiation, and movements
Wnt signaling altered in cancer, bone density diseases, and other conditions
Active target of new and novel therapies
118
Salamander Rejuvination
Wnt pathway involved in tissue regeneration
zebrafish tail example
This regeneration in mammals is limited, why?
119
Wnt Pathway
More Details.....
Critical for correct early development
Overexpression in early development leads to serious developmental problems
“Ectopic expression of the proto-oncogene int-1(this is the wnt gene in frog) Xenopus embryos leads to duplication of the embryonic axis”
120
Transcriptional Network Importance
Understanding the many genes involved in development and how they interact with one another at the molecular level...
---Allows us to begin to unravel how development proceeds in space and time in a highly coordinated manner
121
Posttranscriptional Regulation of Gene Expression
Although Transcriptional Control is the major type of regulation in eukaryotes, Posttranscriptional Regulation also occurs in many organisms.
Therefore, the number of proteins that a cell can make (its proteome) is NOT directly related to the number of genes in the genome.
122
posttranscriptional modification
Changes made to pre-mRNA molecules during conversion to mature mRNA.
These include the addition of a methylated cap at the 5' end and a poly-A tail at the 3' end, excision of introns,and exon splicing.
123
The number of proteins that a cell can make (its ____) is NOT directly related to the number of ____ in the ____.
The number of proteins that a cell can make (its proteome) is NOT directly related to the number of genes in the genome.
124
Posttranscriptional Regulation of Gene Expression
Alternative Splicing
| .....38016 different versions possible example
125
Two important type of small RNAs involved in gene regulation
Small Interfering RNAs (siRNA)
Micro RNAs (miRNA)
126
MicroRNA history
First demonstrated in C.elegans by Victor Ambros and colleagues.
Showed that lin-4 does not encode protein, but instead a pair of small RNAs (22nt & 61nt)
61nt RNA was predicted to form stem-loop structure and serve as precursor for 22nt RNA
Ambros & Ruvken labs noticed complementarity sequences of these RNA to 3’UTR sequences in lin-14 transcript.
Lin-14 3’UTR had been shown to mediate translational repression of lin-14
Complementary sequences to lin-4 RNA in Lin-14 3’UTR was shown to be critical for translational repression
These observations provided first evidence for miRNA functionality!
It took 7 years to discover examples in other systems!
By 2007, a miRNA database at the Sanger Institute contained over 4500 entries, of which ~500 were human
127
MicroRNA characteristics
miRNAs can be highly abundant in cells
(e.g. 50,000molecules/cell for miR-2 or miR-58)
- many miRNAs are transcribed by RNA pol lI
- miRNA can have highly defined expression patterns
approx. 25% (human) are in the introns of pre-mRNAs
- miRNA genes are frequently clustered in genome
- high levels of conservation between miRNAs are observed in animals
128
Yet Another Role for Dicer
RITS (RNA-induced initiation of transcriptional silencing) complex
In this pathway short RNAs can also mediate RNA-directed DNA methylation (RdDM).
129
dicer
An enzyme (a ribonuclease) that cleaves double-stranded RNA (dsRNA) and pre-micro RNA (miRNA) to form small interfering RNA (siRNA) molecules about 20–25 nucleotides long that serve as guide molecules for the degradation of mRNA molecules with sequences complementary to the siRNA.
130
microRNA
Single-stranded RNA molecules approximately 20–23 nucleotides in length that regulate gene expression by participating in the degradation of mRNA.
131
Mechanisms of gene regulation by RNA gene silencing.
In the cytoplasm, two systems operate to silence genes.
In siRNA mediated silencing, a precursor RNA molecule is processed by Dicer, a protein with RNAse activity to form an antisense single-stranded RNA that combines with a protein complex with endonuclease activity.
siRNA/RISC (RNA-induced silencing complex) binds to mRNAs with complementary sequences, and cuts the mRNA into fragments that are degraded. T
his process is called RNAi in animal cells, and posttranslational gene silencing (PTGS) in plants.
A partially double-stranded precursor is processed by Dicer to yield microRNA (miRNA) that binds to complementary -untranslated regions (UTRs) of mRNA, inhibiting translation. In plants, miRNAs cause arrest of translation.
Small RNAs, processed by Dicer, play a role in RNA-directed DNA methylation (RdDM).
These RNAs combine with DNA methyl transferases (DMTases) to methylate cytosine residues in promoter regions, silencing genes.
132
DNA methylation result:
downregulation of transcription of methylated genes
133
siRNAs:
| Origin, Cleavage, Action, Target
Origin: mRNA, transposon, or virus
Cleavage of: RNA duplex or single-stranded RNA that forms long HairPins
Action: Some trigger degradation of mRNA, others inhibit transcription
Target: Genes from which they were subscribed.
134
miRNAs:
| Origin, Cleavage, Action, Target
Origin: RNA transcribed from a distinct gene.
Cleavage of: single-stranded RNA that forms short HairPins
Action: Some trigger degradation of mRNA, others inhibit translation
Target: Genes other than those from which they were subscribed.
