This document provides an overview of RNA interference (RNAi) including its mechanism, applications, and methods for delivering small interfering RNA (siRNA). It discusses how dsRNA is processed by the enzyme Dicer into siRNAs which are incorporated into the RISC complex to degrade complementary mRNA. Viral vectors, liposomes, nanoparticles, and chemical modifications are described as methods used to deliver exogenous siRNAs. The document outlines both the therapeutic potential of RNAi and challenges associated with effective siRNA delivery.
3. O u t lin e s
Introduction
RNA silencing
Definition of RNA interference
Discovery of RNAi
Mechanism of RNA interference
Generation of small interfering RNA
Small interfering RNA delivery methods
Applications of RNA interference
Therapeutic applications
Other applications
Conclusion
4. In t r o d u c t io n
RN A i
(R N A In t e r f e r e n c e )
5. RNA silencing
Several terms are used to described RNA silencing;
usually there are three phenotypically different but
mechanistically similar phenomena:
3. Cosuppression or post-trascriptional gene silencing
(PTGS) in plants
5. Quelling in fungi
7. RNA interference in animal kingdom
6. Quelling:
The silencing in fungal system
Quelling came to light during attempts
to boost the production of an orange
pigment made by the gene al1 of the
fungus Neurospora crassa
N. crassa (al1+) transformed with
plasmid+al1
few transformants show albino
phenotype
al1-quelled strain had similar level of
unspliced al1 mRNA to wilde-type.
Native al1 mRNA was highly reduced
indicating that quelling and NOT the
rate of transcription affected the level
of mature mRNA in a homology-
dependent manner
7. RNAi:
Silencing in Cenorhabditis elegans
dsRNA administrated to
worms can permeate and
affect the entire body causing
a systemic RNA-interference
RNAi studies represents a
means of identifying partial or
complete loss-of-function
phenotypes, possibly leading
to the identification of gene
function.
8. Definition
RNA interference (RNAi) is a mechanism that inhibits
gene expression at the stage of translation or by
hindering the transcription of specific genes.
RNAi targets include RNA from viruses and
transposons.
9. Need for interference
Defense Mechanism
Defense against Infection by viruses, etc
As a defense mechanism to protect against transposons and
other insertional elements
Genome Wide Regulation
RNAi plays a role in regulating development and genome
maintenance.
30% of human genome regulated
10. PTGS in plants:
The discovery of Jorgensen and Napoli in
1990
They were trying to make petunias more purple
Overexpression of petunia gene
Entered homologous RNA
Expected:more pigments
Observed:white sectors
Cosuppression:
• Loss of mRNAs of both endo-and transgene
12. Cenorhabditis elegans
RNAi can be induced in C. elegans in three simple ways:
Injection of dsRNA into the worm gonads
Soaking the worms in dsRNA solution
Feeding the worms engineered bacteria producing dsRNA
13. Discovery
Inject worms with dsRNA
corresponding to a gene
(important for muscle function)
involved in wiggling (unc-22)
14. Discovery
Inject worms with dsRNA
corresponding to a gene
(important for muscle function)
involved in wiggling (unc-22)
Conclusion: dsRNA triggers potent and specific gene silencing
15. RNAi vs Antisense
Effects of mex-3 RNA interference on
levels of the endogenous mRNA.
• Negative control showing lack of
staining in the absence of the
hybridization probe.
• Embryo from uninjected parent
showing normal pattern of
endogenous mex-3 RNA (purple
staining).
• Embryo from parent injected with
purified mex-3 antisense RNA.
• Embryo from a parent injected with
dsRNA corresponding to mex-3.
Injected antisense or dsRNA into C. elegans
dsRNA was more effective than ssRNA (antisense)
Effective even in tiny amounts
Inactivation was due to degradation of target mRNA
16. What is the secret of this little worms
success?
Simple organism
Similarity to other complicated animals
It has neurons,muscles, gut, …
Simple life cycle
Rapid growth
Produce about 300 progeny in 6 days
Eat bacteria
Suitable for genetic investigation
17. What is the secret of this little worms
success?
18. Nobel prize winners in the C. elegans
field Sidney Brenner
John Sulston
Robert Horvitz
Andrew Fire
Craig Mello
19.
20. Happy ending
These results were thoroughly reproducible
RNAi was found to work in many species
RNAi became a powerful method that is changing the face of
biology
MicroRNAs were discovered (the next topic)
Andy and Craig win the 2006 Nobel Prize in Physiology or
Medicine!
22. RNAi was found to work in many
diverse species
Fungi
Trypanosomes
Insects
Zebrafish
Mice
23. M e c h a n is m o f R N Ai
RN A i
(R N A In t e r f e r e n c e )
24.
25. RNAi Overview
During RNAi Double-stranded RNAs cut into short
double-stranded RNAs, s(small) i(interfering) RNA's,
by an enzyme called Dicer. These then base pair to an
mRNA through a dsRNA-enzyme complex. This will
either lead to degradation of the mRNA strand
Highly specific process
Very potent activity
So far only been seen in eukaryotes
Evidence 30% of genome is regulated by RNAi
26. The Players In Interference
RNA
siRNA: dsRNA 21-22 nt.
miRNA: ssRNA 19-25nt. Encoded by non protein coding
genome
RISC:
RNA induced Silencing Complex, that cleaves mRNA
Enzymes
Dicer : produces 20-21 nt cleavages that initiate RNAi
Drosha : cleaves base hairpin in to form pre miRNA; which is
later processed by Dicer
27. siRNAs
Small interfering RNAs that have an integral role in the
phenomenon of RNA interference (RNAi), a form of post-
transcriptional gene silencing
RNAi: 21-25 nt fragments, which bind to the complementary
portion of the target mRNA and tag it for degradation
A single base pair difference between the siRNA template
and the target mRNA is enough to block the process.
Each strand of siRNA has:
a. 5’-phosphate termini
b. 3’-hydroxyl termini
c. 2/3-nucleotide 3’ overhangs
28. miRNA
Originate from capped & polyadenylated full length precursors
(pri-miRNA)
Hairpin precursor ~70 nt (pre-miRNA) Mature miRNA ~22 nt
(miRNA)
29. Difference between miRNA and siRNA
Function of both species is regulation of gene expression.
Difference is in where they originate.
siRNA originates with dsRNA.
siRNA is most commonly a response to foreign RNA (usually
viral) and is often 100% complementary to the target.
miRNA originates with ssRNA that forms a hairpin secondary
structure.
miRNA regulates post-transcriptional gene expression and is
often not 100% complementary to the target.
And also miRNA help to regulate gene expression, particularly
during induction of heterochromatin formation serves to
downregulate genes pre- transcriptionally (RNA induced
transcriptional silencing or RITS)
RITS
30. Dicer
RNase III-like dsRNA-specific ribonuclease
• Enzyme involved in the initiation of RNAi.
• It is able to digest dsRNA into uniformly
sized small RNAs (siRNA)
Dicer family proteins are ATP-
dependent nucleases.
Rnase III enzyme acts as a dimer
Loss of dicer→loss of silencing processing
in vitro
Dicer homologs exist in many organisms
including C.elegans, Drosphila, yeast and
humans (Dicer is a conserved protein)
31. Dicer’s domains
Dicer is a ribonuclease (Rnase III family) with 4 distinct domains:
domains
1 4 2 2 3
1. Amino-terminal helicase domain
2. Dual Rnase III motifs in the carboxy terminal segment
3. dsRNA binding domain
4. PAZ domain (110-130 amino-acid domain present in protein like
Argo, Piwi..);it is thought to be important for protein-protein
interaction
32. RISC
RISC is a large (~500-kDa)
RNA-multiprotein complex,
which triggers mRNA
degradation in response to
siRNA
Unwinding of double-
stranded siRNA by ATP
independent helicase.
The active components of an
RISC are endonucleases
called argonaute proteins
which cleave the target
mRNA strand.
33. Mechanism of RNA interference
• dsRNA are chopped into short
interfering RNAs (siRNA) by Dicer.
siRNA Dicer
2. The siRNA-Dicer complex recruits
additional components to form an
RNA-Induced Silencing Complex
(RISC). The siRNA unwinds.
RISC
3. The unwound siRNA base pairs with
complementary mRNA, thus
guiding the RNAi machinery to the
target mRNA.
4. The target mRNA is effectively
cleaved and subsequently
degraded – resulting in gene
silencing.
silencing
34. Exogenous dsRNA is detected and bound by an
effector protein, known as RDE-4 in C. elegans and
R2D2 in Drosophila, that stimulate dicer activity.This
protein only binds long dsRNAs.
These RNA-binding proteins then facilitate transfer of
cleaved siRNA to the RISC complex.
40. Summary of Players
Drosha and Pasha are part of the “Microprocessor”
protein complex (~600-650kDa)
Drosha and Dicer are RNase III enzymes
Pasha is a dsRNA binding protein
Exportin 5 is a member of the karyopherin
nucleocytoplasmic transport factors that requires Ran
and GTP
Argonautes are RNase H enzymes
41.
42. G e n e r a t io n o f
s iR N A
RN A i
(R N A In t e r f e r e n c e )
45. siRNA design
21-23nt
2-nt 3' overhangs ( UU overhangs )
G/C content: 30-50%.
No basepair mismatch
Synthesised siRNA should not target introns, the 5′and 3′-end
untranslated regions (UTR), and sequences within 75 bases of
the start codon (ATG).
BLAST : eliminate any target sequences with significant
homology to other coding sequences.
46. s iR N A d e l iv e r y
method s
RN A i
(R N A In t e r f e r e n c e )
47. Effective methods for the delivery of small RNA to allow a
sufficient silencing effect in the target organ(s) and/or cells are
yet to be developed.
In particular, toxicity and side effects of RNAi must be well
characterized and limited.
Therefore, careful design and selection of target sequence and
quantification of the effect on the expression of target protein and
mRNA are essential for success of gene interfering approaches.
48. High-pressure injection
“High-pressure injection” was the first strategy to demonstrate
injection
successful delivery of siRNA in vivo.
A large volume (1–2mL) of saline containing unmodified siRNA is
injected intravenously into the tail vein of mice within very short
time (in less than 7 sec), which presumably results in the siRNA
molecules being forced into several organs mainly the liver,
kidney and to a lesser degree the lung.
Certainly, such an approach seems to be impossible in human
subjects (1000 mL saline solution containing siRNA per 10 kg of
weight).
49. Electroporation
• Electroporation of small
RNA directly into target
tissues and organs has
also been developed to
successfully silence gene
function.
50. Problem
Delivery of siRNA to tissue is a problem both because:
The material must reach the target organ
And must also enter the cytoplasm of target cells.
RNA cannot penetrate cellular membranes, so systemic delivery
of siRNA is unlikely to be successful.
RNA is quickly degraded by RNAse activity in serum and even
siRNA chemically modified to be more stable has a half-life of
only a few hours at most.
51. Solution
For these reasons, other mechanisms to deliver siRNA to target
cells has been devised. These methods include:
Viral delivery
The use of liposomes or nanoparticles
Bacterial delivery
Chemical modification of siRNA to improve stability
52. Viral delivery
Viral delivery has been used extensively in gene therapy to
deliver DNA to target cells.
There are 5 main classes of viruses used in the delivery of
nucleotides to cells:
Retrovirus
Adenovirus
Lentivirus
Baculovirus
Adeno-associated-virus (AAV).
53. Retroviruses
Retroviruses were one of the first vectors used to transduct cells
with plasmids expressing hairpin-RNA constructs. Despite the
relative ease of use in vitro, use of the retrovirus in vivo has
safety concerns and significant limitations.
Retroviruses integrate their DNA into the host.s genomic DNA,
bringing with it, the risk of mutagenesis and carcinogenesis.
carcinogenesis
Another problem is that retroviral transduction is limited to
actively dividing cells, which means that the majority of
mammalian cells will not receive the siRNA.
54. Adenovirus
Adenoviral vectors are commonly used in gene therapy trials.
Since the adenovirus does not integrate DNA into the host.s
genome, the effects are short-lived, usually lost after several
cell divisions. For this reason, the adenovirus is used when a
short duration of action is sufficient or desirable, such as
tumor-targeting therapy.
Despite the lowered risk of insertional mutagenesis, the
adenovirus is associated with significant dose-dependent liver
toxicity that can severely limit therapy.
Another major disadvantage of adenoviral vectors is the
dependence on specific surface receptors on the target cell
which are often absent, rendering transduction impossible in
many cases.
55. Lentivirus
Lentiviral vectors are a subclass of retroviruses that lack the risk
of insertional mutagenesis and are able to transducer primary
and non-dividing cells.
Several studies have demonstrated the use of lentiviral vectors to
deliver RNAi to target cells.
56. Baculoviruses
Baculoviruses are insect viruses that can carry large quantities
of genetic information.
This may allow their use for combined RNAi therapy and gene
therapy.
Safety concerns are less prominent with these vectors since
the virus is unable to replicate or express proteins in
mammalian cells.
57. Adeno-associated viruses (AAV)
Adeno-associated viruses (AAV) are another possible vector for
siRNA.
These viruses do not appear to be pathogenic and can
transducer non-dividing cells.
58. Liposomes and nanoparticles
Liposomes and nanoparticles have been known as an alternative to
viral delivery systems.
Unmodified siRNA has a half-life of less than 1 hour in human plasma
and siRNA is rapidly excreted by the kidneys.
Liposomes and nanoparticles can act as envelopes to protect the
siRNA from metabolism and excretion, but can also carry specific
molecules designed to target the siRNA to specific tissue types.
Liposomes such as Lipofectamine, cationic DOTAP, neutral DOPC
have been used to carry siRNA into cells.
Nanoparticles such as the cationic polymer, polyethyleneimine (PEI)
have also been used to successfully deliver siRNA to target cells.
59. Bacterial delivery
Bacterial delivery using nonpathogenic bacteria has been used
to silence genes in a process known as transkingdom RNA
interference (tkRNAi).
Generally, the shRNA is produced in bacteria that invade and
release the RNA into eukaryotic cells (hence the term
transkingdom).
The bacteria can also be engineered to carry shRNA encoding
DNA plasmids.
The advantages of this system include:
Safety
Ability to control the vector using antibiotics
60. Chemical modification
Finally, chemical modification of siRNA has been used to
improve stability and prevent degradation by serum RNAase.
Importantly, these modifications must obviously not affect the
RNA interference activity of the siRNA.
One of the most common modifications is the use of locked
nucleic acid residues (LNA).
A methylene bridge connects the 4.C with the 2.O in LNA
residues. This modification increases the stability of
oligonucleotides in serum, without reducing the gene
silencing effect.
61. Side effects of gene silencing by small
RNA molecules
Unspecific silencing
Caused by the failure to identify similar sequences with only
few nt difference in other genes.
Activation of intracellular PKR and immune pathways that are
linked to toll-like receptor activation.
PKR ( protein kinase R) is activated by dsRNA longer than
30 nt, which subsequently induces the production of cytokines
of the IFN family. These IFNs ultimately promote inflammatory
responses.
62. Side effects of gene silencing…
High pressure injection” and electroporation can cause significant
injection
damage to the integrity of the normal tissues and organs and thus
preclude the utilisation in a clinical set-up.
Liposomes/cationic encapsulated siRNA may also be toxic to the
host and may cause severe host immune responses.
Other emerging strategies includes chemical modification of
siRNA molecules and encapsulated with different molecules are
still in their infancy and need to be thoroughly investigated before
used in therapeutic applications.
63. Ap p l ic a t io n s o f
R N Ai
RN A i
(R N A In t e r f e r e n c e )
65. Hematology (blood)
Hematologic disorders result from
Loss of gene function
Mutant gene function
Absent gene function
RNAi
May be used to create models of disease processes
Could help to develop pharmacologic and genetic therapeutic
targets
66. Oncology (cancer)
Targeting of oncogenes
Dominant mutant oncogenes, amplified oncogenes, viral
oncogenes
Define role of signaling molecules in tumor-creation
Improvement efficacy of chemotherapy and
radiotherapy
Tumor regression through creation of potentially new
mode of chemotherapy
67. Stem cell biology
Mouse research
Knock out tumor-suppression gene in mouse embryonic
stem cell
Observe tumor phenotype
Positive correlation between extent of Trp 53
(suppression gene) inhibition and severity of disease
68. Infectious Diseases
Virus targeting
RNAi – inhibit cellular and viral factors of disease
RNA transcriptase is RNAi target
Inhibition of replication
Main goal
Render cells resistant to infectious organisms
69. Hepatitis C
Infects ~200 million people worldwide
Often fatal
2002, Anton McCaffrey and Mark Kay at Stanford
University
Injected "naked" RNA strands into the tail veins of
mice
RNAi treatment controlled the virus in mice
70. Silencing genes in HIV
AIM:
Silence the main structural protein in the virus, p24,
and the human protein CD4.
Hit the virus where it counts by eliminating a protein it
needs to reproduce or cause infections.
71. Respiratory infections
RSV, infects almost every child by the age of two
2005, Sailen Barik University of South Alabama
Short strands of "naked" RNA
Controlled the virus in mice
Clinical trials are ongoing
72. Macular degeneration
Macular degeneration is the leading
cause of adult blindness
Excess VEGF which leads to
sprouting of excess blood vessels
behind the retina & obscuring vision.
The new RNAi drugs shut down
genes that produce VEGF. The drug
can be injected directly into the eye
First clinical trial: 24 patients,
launched in 2004.
Two months after being injected with
the drug, 6 of the patients had
significantly clearer vision
Other patients' vision had at least
stabilized
More extensive trials are ongoing
73. Huntington’s disease
Ideal candidate for RNAi therapy
Disease caused by protein, that
affects more than 30,000 people
in the U.S. alone.
We would want to shut down the
expression of the gene coding for
the abberant protein
2004, Beverly Davidson and
colleagues at the University of
Iowa
Davidson treated mice with
Huntington's
74. Other uses of RNAi
Studying cell division
Testing Hypotheses of Gene Function
Target Validation
Pathway Analysis
• Gene Redundancy
Functional Screening
75. Studying cell division using RNAi
Genes involved in cell division identified by using RNAi
RNA interference (RNAi) used to assign functions of
genes involved in C. elegans cell division
133 genes identified. Only 11 previously identified
76. Testing Hypotheses of Gene Function
Array analysis and other methods for identifying differentially
expressed genes have created an enormous database of genes
and associated phenotypes.
In many cases, scientists make predictions about gene function
based on expression patterns in different samples. Other
predictions of mammalian gene function are developed using
homology searches with genes whose functions are known in
model organisms like Drosophila, C. elegans, and S. cerevisiae.
In many cases, testing the accuracy of these predictions can be
accomplished using siRNAs.
77. Testing Hypotheses of Gene Function:
……… still working
Al-Khalili et al treated myotubes with serum and showed that
increased glucose uptake correlated with increased cell-surface
content of glucose transporter (GLUT1). To confirm that glucose
transport depends on GLUT1 expression, cells were treated with
GLUT1 siRNA and were shown to have reduced levels of serum-
stimulated glucose transport.
Chen and Barritt used siRNAs to study the transient receptor
potential canonical 1 (TRPC1) gene. The TRPC1 gene was
thought to encode a non-selective cation channel activated by
depletion of cellular storage and/or an intracellular messenger.
When liver cells were treated with the TRPC1 siRNA, they
exhibited increased cell volume and decreased inflow of Ca2+,
Mn2+.
78. Target Validation
In its simplest form, drug development follows the path
of target identification → target validation →
therapeutic compound development → compound
testing in model systems → clinical trials.
siRNA are easy to use and highly specific, they
provide the ultimate tool for validation studies.
Reducing the expression of a potential therapeutic
target and determining if the desired phenotype results
provides confidence that an inhibitor of the same
target gene should have therapeutic value.
79. Target Validation:
… an interesting example
Filleur et al showed that the antiangiogenic molecule
thrombospondin-1 (TSP-1) could reduce vascularization and
delay tumor onset.
Over time, tumor cells producing active TSP1 began to form
exponentially growing tumors.
These tumors were composed of cells secreting unusually high
amounts of the angiogenic stimulator, vascular endothelial growth
factor (VEGF), which were sufficient to overcome the inhibitory
TSP1.
Treating tumor cells with a combination of TSP1 and a VEGF-
specific siRNA caused a striking reduction in cell proliferation.
This result suggested that using a combination of TSP1 and an
anti-VEGF compound would slow or eliminate tumor growth
80. Pathway Analysis
Reducing the expression of a single gene has implications on the
expression and activities of genes that are in the same
pathway(s).
Treating cells with an siRNA targeting a given gene and then
monitoring the expression of other genes using a microarray will
make it possible to identify genes that are associated with the
target gene.
Furthermore, a specific pathway can be dissected by treating
cells sequentially with siRNAs targeting the various genes in the
pathway and assaying which genes are affected. This will make it
possible to assign a position in the pathway for each gene.
81. Gene Redundancy
In many cases, eliminating the expression of a single gene in
higher eukaryotes can be tolerated even if that gene product
functions in a critical pathway. This is because many critical cell
functions are accomplished by more than one gene product.
When one gene product is eliminated, the redundant gene
product compensates to allow the cell or animal to survive.
Identifying redundant genes could be achieved by co-transfecting
siRNAs and assaying for a given phenotype.
Evaluating each of the candidate genes alone to ensure that they
only cause the cell cycle defect when reduced in combination
with the target gene would help pinpoint the most likely redundant
gene
82. Functional Screening
Libraries of siRNAs targeting broad collections of genes will
enable screening experiments to tie genes to cellular function.
To date, libraries with more than a couple of hundred siRNAs
have been limited to a few large research organizations.
Recognizing the benefits of siRNA libraries, Ambion is preparing
a collection of more than 1800 siRNAs targeting the known
human kinases.
There have been no published reports on the application of
siRNA libraries in screening experiments, but screens in
Drosophila and C. elegans using dsRNA libraries exemplify the
opportunities.
83. Biotechnology & Agriculture
RNA interference has been used for applications in
biotechnology, particularly in the engineering of food plants that
produce lower levels of natural plant toxins. Such techniques take
advantage of the stable and heritable RNAi phenotype in plant
stocks.
For example, cotton seeds are rich in dietary protein but naturally
contain the toxic terpenoid product gossypol, making them
unsuitable for human consumption.
RNAi has been used to produce cotton stocks whose seeds
contain reduced levels of delta-cadinene synthase, a key enzyme
in gossypol production, without affecting the enzyme's production
in other parts of the plant, where gossypol is important in
preventing damage from plant pests.
84. Biotechnology & Agriculture…
Similar efforts have been directed toward the reduction of the
cyanogenic natural product linamarin in cassava plants.
Although no plant products that use RNAi-based genetic
engineering have yet passed the experimental stage,
development efforts have successfully reduced the levels of
allergens in tomato plants and decreased the precursors of likely
carcinogens in tobacco plants.
Other plant traits that have been engineered in the laboratory
include the production of non-narcotic natural products by the
opium poppy, resistance to common plant viruses, and
fortification of plants such as tomatoes with dietary antioxidants.
85. C o n c l u s io n
RN A i
(R N A In t e r f e r e n c e )
90. RNA interference characteristics
dsRNA needs to be directed against an exon, not an
intron in order to be effective
Homology of the dsRNA and the target gene/mRNA is
required
Targeted mRNA is lost (degraded) after RNAi
The effect is non-stoichiometric; small amounts of
dsRNA can wipe out an excess of mRNA (pointing to
an enzymatic mechanism)
ssRNA does not work as well as dsRNA
91. Advantage of RNAi
Downregulation of gene expression simplifies "knockout"
analysis.
Easier than use of antisense oligonucleotides. siRNA more
effective and sensitive at lower concentration.
Cost effective
High Specifity
middle region 9-14 are most sensitive
With siRNA, the researcher can simultaneously perform
experiments in any cell type of interest
Can be labelled
Ease of transfection by use of vector
92. Importance of RNAi
Powerful for analyzing unknown genes in sequenced genomes.
⇒ efforts are being undertaken to target every human gene via
siRNAs
Faster identification of gene function
Gene therapy: down-regulation of certain genes/ mutated alleles
Cancer treatments
knock-out of genes required for cell proliferation
knock-out of genes encoding key structural proteins
Agriculture
Biochemistry of RNA interference Numerous studies have investigated the biochemical mechanisms that underpin RNAi induced gene silencing (Tabara et al., 1999; Mourrain et al., 2000; Sijen et al., 2001). These studies have revealed that RNAi suppresses gene function by promoting degradation of specific mRNA involving highly specific and complex protein–protein interactions that occur in the RNA-induced silencing complex (RISC). Depending on the thermodynamic stability of the 5′-end, both the sense and antisense regions of a given siRNA can enter the RISC complex. However, the antisense strand of the siRNA, which is complementary to the target mRNA, serves to accurately identify the target mRNA and induces sequence-specific degradation in association with other components of RISC at the relatively thermodynamically unstable 5′-end. A key component of RISC is the protein argonaute-2 that binds to a single strand of siRNA. Argonaute-2 and the 5′ strand of the siRNA mediate the recognition of the target mRNA and, with other components of RISC, induce mRNA cleavage with consecutive suppression of protein translation
siRNA (small interfering RNA) http://en.wikipedia.org/wiki/Small_interfering_RNA Small interfering RNA (siRNA), sometimes known as short interfering RNA, are a class of 20-25 nucleotide-long RNA molecules that interfere with the expression of genes. They are naturally produced as part of the RNA interference (RNAi) pathway by the enzyme Dice r. They can also be exogenously (artificially) introduced by investigators to bring about th knockdown of a particular gene. siRNA's have a well defined structure. Briefly, this is a short (usually 21-nt) double-strand of RNA (dsRNA) with 2-nt overhangs on either end, including a 5' phosphate group and a 3' hydroxy (-OH) group. Transfection of an exogenous siRNA is problematic, since it is only transient, and the dsRNA structure cannot easily be permanently maintained. One way of overcoming these problems is to modify the siRNA in such a way as to allow it to be expressed by an appropriate vector, e.g. a plasmid. This is done by the introduction of a loop between the two strands, thus producing a single transcript, which can be processed into a functional siRNA. This transcription cassette usually uses an RNA polymerase III promoter, which direct the transcription of small nuclear RNA's, such as U6 or H1. It is assumed (although not known for certain) that the resulting short hairpin RNA (shRNA) transcript is processed by Dicer. Introduction of too much siRNA can result in non-specific events due to activation of the interferon pathway. Most papers suggest that this is probably due to activation of the dsRNA sensor PKR, although retinoic acid inducible Gene I (RIG-I may also be involved One method of reducing the non-specific effects is by turning the shRNA into a micro RNA. Micro RNA's are naturally occurring, and, as such, tolerated better by the cell. By engineering an siRNA sequence into an miRNA structure, non-specific effects can potentially be eliminated.
miRNA (micro-RNA) http://en.wikipedia.org/wiki/MiRNA A miRNA (micro-RNA) is a form of single-stranded RNA which is typically 20-25 nucleotide long. It is thought to regulate the expression of other genes. miRNAs are RNA genes which are transcribed from DNA, but are not translated into protein. The DNA sequence that codes for an miRNA gene is longer than the miRNA itself. This DNA sequence includes the miRNA sequence and an approximate reverse complement. When this DNA sequence is transcribed into a single-stranded RNA molecule, the miRNA sequence and its reverse-complement base pair to form a double stranded RNA hairpin loop; this forms a primary miRNA structure (pri-miRNA). In animals, the nuclear enzyme Drosha cleaves the base of the hairpin to form pre-miRNA. The pre-miRNA molecule is then actively transported out of the nucleus into the cytoplasm by Exportin 5, a carrier protein. The Dicer enzyme then cuts 20-25 nucleotides from the base of the hairpin to release the mature miRNA. In plants, which lack Drosha homologues, pri- and pre-miRNA processing by Dicer probably takes place in the nucleus, and mature miRNA duplexes are exported to the cytosol by Exportin 5.
Double-stranded RNA triggers processed into siRNAs by enzyme RNAseIII family, specifically the Dicer family Processive enzyme - no larger intermediates. Dicer family proteins are ATP-dependent nucleases. These proteins contain an amino-terminal helicase domain, dual RNAseIII domains in the carboxy- terminal segment, and dsRNA-binding motifs They can also contain a PAZ domain, which is thought to be important for protein-protein interaction. Dicer homologs exist in many organisms including C. elegans , Drosphila , yeast and humans Loss of dicer: loss of silencing, processing in vitro Developmental consequence in Drosophila and C. elegans Dicer is a conserved protein
The initiation pathway may be amplified by the cell through the synthesis of a population of secondary siRNAs using the dicer-produced initiating or primary siRNAs as templates. These siRNAs are structurally distinct from dicer-produced siRNAs and appear to be produced by an RNA-dependent RNA polymerase (RdRP).
Generation of siRNA for silencing of gene expression. (A) From top to below, chemically synthesized siRNA, long dsRNA that can be cleaved by Dicer to form siRNA, and shRNA that can be cleaved by Dicer to form siRNA. (B) From top to below, sense and antisense strands are expressed by RNA polymerase III promoter (e.g., U6 promoter) separately and form a double-stranded siRNA molecule, shRNA are expressed by RNA polymerase III promoter (e.g., U6 promoter) first and then cleaved by Dicer to form mature siRNA. Chemically synthesized siRNA, shRNA, and long dsRNA have been used to generate siRNA by introducing these molecules into cells. After entry into the cytoplasm, shRNA and long dsRNA are cleaved into 21-nt long mature siRNA by a RNase III (Dicer), which is an end-recognition endonuclease). These methods generally result in temporary silencing effects. However, long dsRNA can also elicit responses of the innate immune system such as interferon (IFN) release. To obtain stable and inducible RNAi, researchers have recently developed shRNA structures driven by U6 or H1 promoters (RNase III promoters), wherein the shRNA has 2 short duplex stems: one stem connected to a loop sequence, and the other ending with 6 or more thymidines (T) as the termination signal.
RNA polymerase III (pol III) : human U6 promoters mouse U6 promoters the human H1 promoter RNA pol III was chosen to drive siRNA expression because it naturally expresses relatively large amounts of small RNAs in mammalian cells and it terminates transcription upon incorporating a string of 3–6 uridines.
http://www.ambion.com/techlib/misc/siRNA_finder.html Target prediction The secondary structure of mRNA not only influences the maturation of pre-mRNA and the translation into protein (de Smit&van Duin, 1990; Balvay et al., 1993), it also determines the efficacy of a complimentary siRNA to access its mRNA target (Holen et al., 2002; Kretschmer-Kazemi Far & Sczakiel, 2003). Notably Heale and collegues have developed a secondary structure prediction model to identify nonaccessible mRNA sites for RNAi (Heale et al., 2005). For effective gene silencing engineering of 21-nt doublestranded siRNA with a 2-nt deoxythymideine (Ts) overhang at the 3′-end has been recommended by several groups (Chiu & Rana, 2002; Elbashir et al., 2002; Paddison et al., 2002; Khvorova et al., 2003; Reynolds et al., 2004; Ui-Tei et al., 2004), because a 3′-end overhang is more efficient in guiding dsRNA to unwind. Generally synthesised siRNA should not target introns, the 5′- and 3′-end untranslated regions (UTR), and sequences within 75 bases of the start codon (ATG). Furthermore, the guanine (G)–cytosine (C) content of the designed siRNA should be between 30% and 50% and the 5′-ends of antisense and sense strand should have high and low thermodynamic stability, respectively. Investigators should avoid internal repeats and palindromes of siRNA. At certain positions in the sense strand of the 21-nt siRNA, base preferences may be considered: an adenosine (A) at positions 3 and 19; absence of G or C at position 19; and a uracil (U) at position 10; and absence of G at position 13. Indeed, thermodynamic properties of siRNA are critical in determining its stability and gene silencing efficacy (Khvorova et al., 2003). Finally, a BLASTsearch of the appropriate genome database should be performed and low-stringency sequences should be avoided to ensure that no other unrelated genes are targeted to minimize off-target effects. Many effective and specific siRNA have been published already and can be found in the public domain.
“ High-pressure injection ” was the first strategy to demonstrate successful delivery of siRNA in vivo. A large volume (1–2mL) of saline containing unmodified siRNA is injected intravenously into the tail vein of mice within very short time (in less than 7 sec), which presumably results in the siRNA molecules being forced into several organs (mainly the liver, kidney and to a lesser degree the lung; Lewis et al., 2002). Certainly, such an approach seems to be impossible in human subjects (1000 mL saline solution containing siRNA per 10 kg of weight).
Electroporation of small RNA directly into target tissues and organs has also been developed to successfully silence gene function (Kishida et al., 2004). We and others have recently instilled siRNA directly into the airways, which was very effective in mediating gene silencing or inhibiting virus replication in the lung and thus modulating disease phenotype (Bitko et al., 2005; Li et al., 2005; Bhandari et al., 2006; Yang et al., 2006).
Viral delivery has been used extensively in gene therapy to deliver DNA to target cells. Viruses evolved to specialize in gene transduction and can also be used to ferry siRNA into cells. There are 5 main classes of viruses used in the delivery of nucleotides to cells, including the retrovirus , adenovirus , lentivirus , baculovirus , and adeno-associated-virus (AAV). Retroviruses were one of the first vectors used to transduct cells with plasmids expressing hairpin-RNA constructs. Despite the relative ease of use in vitro, use of the retrovirus in vivo has safety concerns and significant limitations. Retroviruses integrate their DNA into the host.s genomic DNA, bringing with it, the risk of mutagenesis and carcinogenesis. Two pediatric patients treated with gene therapy for x-linked severe immune deficiency syndrome (x-SCID) developed leukemia following the use of retroviral vectors. An equally daunting problem is that retroviral transduction is limited to actively dividing cells, which means that the majority of mammalian cells will not receive the siRNA.
Adenoviral vectors are commonly used in gene therapy trials. Since the adenovirus does not integrate DNA into the host.s genome, the effects are short-lived, usually lost after several cell divisions. For this reason, the adenovirus is used when a short duration of action is sufficient or desirable, such as tumor-targeting therapy. The lack of genomic integration also provides a clear safety advantage to adenoviral vectors. Despite the lowered risk of insertional mutagenesis , the adenovirus is associated with significant dose-dependent liver toxicity that can severely limit therapy. Another major disadvantage of adenoviral vectors is the dependence on specific surface receptors on the target cell which are often absent, rendering transduction impossible in many cases. Several studies have reported success in delivering siRNA to cells with an adenoviral vector using local injection. There are only a few reports of success in delivering siRNA to target cells using systemic therapy, and results were mixed.
Lentiviral vectors are a promising subclass of retroviruses that lack the risk of insertional mutagenesis and are able to transducer primary and non-dividing cells. Several studies have demonstrated the use of lentiviral vectors to deliver RNAi to target cells. There is also significant research into more accurate targeting of lentiviral vectors using envelope signals .
Baculoviruses are insect viruses that can carry large quantities of genetic information. This may allow their use for combined RNAi therapy and gene therapy. Safety concerns are less prominent with these vectors since the virus is unable to replicate or express proteins in mammalian cells. Adeno-associated viruses (AAV) are another possible vector for siRNA. These viruses do not appear to be pathogenic and can transducer non-dividing cells. Despite this, their use in in vivo delivery of siRNA is limited to stereotactic brain injections.
Liposomes and nanoparticles have been heralded as an alternative to viral delivery systems. Unmodified siRNA has a half-life of less than 1 hour in human plasma and siRNA is rapidly excreted by the kidneys. Liposomes and nanoparticles can act as envelopes to protect the siRNA from metabolism and excretion, but can also carry specific molecules designed to target the siRNA to specific tissue types. Liposomes such as Lipofectamine , cationic DOTAP , neutral DOPC have been used to carry siRNA into cells. Nanoparticles such as the cationic polymer, polyethyleneimine (PEI) have also been used to successfully deliver siRNA to target cells.
Bacterial delivery using nonpathogenic bacteria has been used to silence genes in a process known as transkingdom RNA interference ( tkRNAi ). Generally, the shRNA is produced in bacteria that invade and release the RNA into eukaryotic cells (hence the term transkingdom). The bacteria can also be engineered to carry shRNA encoding DNA plasmids. The advantages of this system include safety, trivial genetic engineering, and the ability to control the vector using antibiotics .
Finally, chemical modification of siRNA has been used to improve stability and prevent degradation by serum RNAses. Importantly, these modifications must obviously not affect the RNA interference activity of the siRNA. Chemical modifications are also being sought out that could improve upon silencing activity and/or result in better targeting to specific cell types. One of the most common modifications is the use of locked nucleic acid residues (LNA). A methylene bridge connects the 4.C with the 2.O in LNA residues. This modification increases the stability of oligonucleotides in serum, without reducing the gene silencing effect. No successful in vivo studies have been performed. A second chemical modification is the replacement of phosphodiester linkages using phosphor-sulfur connections ( phosphothioates ). This modification increases the half-life of oligonucleotides in vivo. There are several other chemical modifications that have been used to try to improve delivery of siRNA to cells. SiRNA Therapeutics has successfully used a synthetic RNA derivative with several chemical modifications against a mouse model of HBV. Clearly, research into the delivery of siRNA to target cells is still in its infancy. Until these issues are resolved, the brilliance of RNAi will be moot in the clinical arena. This realization can be tempered by the groundbreaking research being done at the bench.
Intrinsic off-target effects Although RNAi is highly specific in knocking down expression of genes, there are considerable issues rising in regards to off-target effects (Fig. 5). The most common intrinsic off-target effect induced by siRNAis caused by the failure to identify similar sequences with only few nt difference in other genes that induce unspecific silencing. Saxena et al. have shown that a 21-nt siRNA with 3 to 4 mismatched nt can still efficiently silence mRNA that are partially complimentary to the active siRNA strand (Saxena et al., 2003). Of particular significance is positions 2–8 in the mature antisense siRNAstrand, which may be strongly associated with off-targeting effects despitemismatches at other positions for respective mRNA (Birmingham et al., 2006). Therefore, the stringent design of siRNA and subsequent blast to known genomic data (e.g., NCBI gene bank) may reduce the possibility of targeting other non-specific genes. The complete experimental investigation of all possible off-target effects is difficult to achieve experimentally but employing computational analysis based on the genome and transcriptome sequence data that are available in the public domain is feasible and recommended (i.e., GenBank, Refseq, EMBL and DDBJ). Another common intrinsic off-target effect provoked by siRNA is the activation of intracellular PKR and immune pathways that are linked to toll-like receptor activation (Williams, 1997; Alexopoulou et al., 2001). PKR is activated by dsRNA longer than 30 nt, which subsequently induces the production of cytokines of the IFN family. These IFNs ultimately promote inflammatory responses and alter cell metabolism, which often results in apoptosis (Kim et al., 2004). Kim and colleagues, however, demonstrated that siRNA duplexes 27 nt in length or smaller may not induce PKR activation and subsequent IFN responses (Kim et al., 2005). Therefore, in vivo titration of effective siRNA together with employing siRNA that are less or equal to 27-nt in size may greatly minimize unwanted off-target effects. Other side-effects caused by delivery methods “ High pressure injection” and electroporation can cause significant damage to the integrity of the normal tissues and organs and thus preclude the utilisation in a clinical set-up. Liposomes/cationic encapsulated siRNA may also be toxic to the host and may cause severe host immune responses. Other emerging strategies have just recently developed, which includes chemical modification of siRNA molecules, encapsulated with different molecules (such as polyamine, basic complexes, atelocollagen, polyethylenimine and virosomes). These emerging methods are still in their infancy and need to be thoroughly investigated before used in therapeutic applications.
What good is RNAi for Us A Volume Knob for gene expression RNAi applied as an experimental technique to knockout genes Functional genomic studies Determining importance of a gene in a process (SRP54) Studies to identify genomic regulators (Read between lines in the Book of Life) Use as therapeutic tool Agriculture design of disease resistance improved nutritional and handling characteristics What can we do with this ?? RNAi is a ,powerful tool that can allow us to silence any gene. Knockout analysis; Fuctional genomic studies; Identification of regulator miRNA in cell- to be able to move towards a bettrer understanding of the book of life; Therapeutic Intervention; Agriculture; Wherever else our Imagination allows
Respiratory syncytial virus (RSV) is a major cause of respiratory illness in young children. RSV causes infection of the lungs and breathing passages. In adults, it may only produce symptoms of a common cold, such as a stuffy or runny nose, sore throat, mild headache, cough, fever, and a general feeling of being ill. But RSV infections can lead to other more serious illnesses in premature babies and kids with diseases that affect the lungs, heart, or immune system. RSV is highly contagious, and can be spread through droplets containing the virus when a person coughs or sneezes. The virus can also live on surfaces such as countertops or doorknobs, and on hands and clothing. RSV can be easily spread when a person touches an object or surface contaminated with the virus. The infection can spread rapidly through schools and child-care centers. Infants often get it when older kids carry the virus home from school and pass it to them. Almost all kids are infected with RSV at least once by the time they are 2 years old. RSV infections often occur in epidemics that last from late fall through early spring. Respiratory illness caused by RSV — such as bronchiolitis or pneumonia — usually lasts about a week, but some cases may last several weeks. Doctors typically diagnose RSV by taking a medical history and doing a physical exam. Generally, in healthy kids, it's not necessary to distinguish RSV from a common cold. But in cases where a child has other health conditions, a doctor might want to make a specific diagnosis. RSV is typically identified in nasal secretions, which can be collected either with a cotton swab or by suction through a bulb syringe. Human respiratory syncytial virus (RSV) is a negative-sense, single-stranded RNA virus of the family Paramyxoviridae , which includes common respiratory viruses such as those causing measles and mumps . RSV is a member of the paramyxovirus subfamily Pneumovirinae . RSV causes respiratory tract infections in patients of all ages. It is the major cause of lower respiratory tract infection during infancy and childhood. In temperate climates there is an annual epidemic during the winter months. In tropical climates, infection is most common during the rainy season. In the United States, 60% of infants are infected during their first RSV season [1] , and nearly all children will have been infected with the virus by 2-3 years of age [1] . Natural infection with RSV does not induce protective immunity, and thus people can be infected multiple times. Sometimes an infant can become symptomatically infected more than once even within a single RSV season. More recently, severe RSV infections have increasingly been found among elderly patients as well.
Macular Degeneration or Macular Disease is an eye disease of the retina that is associated in which the central portion of the retina becomes damaged. Central vision is the sharpest or clearest area of your vision and is required for activities such as reading, driving and anything that is visually demanding, whether far or near. Macular Disease is quite common and affects more people in the United States than either cataracts or glaucoma. In fact, Macular Disease is the most frequent cause of blindness for patients aged 55 and above in the United States and is estimated to affect over 10 million Americans ( http://www.macular.org/disease.html ) in some fashion. As the name implies, Macular Disease affects the Macula. The Macula is the area of the retina that allows us to see fine detail and is responsible for central or “straight ahead” vision as well as the ability to see the detail of faces, reading material, colors and precise vision required for driving a car. Age Related Macular Degeneration (ARMD) is the most common type of macular degeneration. Your chances of developing Age Related Macular Degeneration (ARMD) are directly related to you age. The older you are, the greater the chance that you will be affected by Macular Degeneration. Age Related Macular Degeneration (ARMD) is a degenerative condition of the macula that results from hardening of the very fine arteries of the retina that carry oxygen and nutrients to the retina. Depriving the macula of oxygen and nutrition cause a gradual and progressive loss of function. The visual effects of macular degeneration can be relatively minimal with a mild “dimming” or “distortion” of your central vision, or very profound resulting in a complete loss of your central vision. However, macular degeneration DOES NOT cause total blindness. Since the effect of Macular Degeneration is limited to the central retina, its effects are limited to central vision without causing any disturbance of your affecting peripheral vision.
RNA interference has been used for applications in biotechnology , particularly in the engineering of food plants that produce lower levels of natural plant toxins. Such techniques take advantage of the stable and heritable RNAi phenotype in plant stocks. For example, cotton seeds are rich in dietary protein but naturally contain the toxic terpenoid product gossypol , making them unsuitable for human consumption. RNAi has been used to produce cotton stocks whose seeds contain reduced levels of delta-cadinene synthase , a key enzyme in gossypol production, without affecting the enzyme's production in other parts of the plant, where gossypol is important in preventing damage from plant pests. [124] Similar efforts have been directed toward the reduction of the cyanogenic natural product linamarin in cassava plants. [125] Although no plant products that use RNAi-based genetic engineering have yet passed the experimental stage, development efforts have successfully reduced the levels of allergens in tomato plants [126] and decreased the precursors of likely carcinogens in tobacco plants. [127] Other plant traits that have been engineered in the laboratory include the production of non- narcotic natural products by the opium poppy , [128] resistance to common plant viruses, [129] and fortification of plants such as tomatoes with dietary antioxidants . [130] Previous commercial products, including the Flavr Savr tomato and two cultivars of ringspot -resistant papaya , were originally developed using antisense technology but likely exploited the RNAi pathway.