Transcript Proteomics: High-throughput Analysis

The discovery of RNA interference
• An Unexpected Result…
• petunias surprisingly developed
areas of hypopigmentation
when transduced with the gene
encoding an enzyme required
for pigment synthesis.
– The phenomena was called
Co-suppression
– Similar effects seen in fungi.
called “Quelling”
• Later, in the C. elegans Camp...
• Antisense RNA injection method
for gene inactivation
• Sense RNA injections gave same
result!
– Remained a mystery...
“The basis for the sense effect is
under investigation ...”
[Guo and Kemphues, 1995]
• Some Sharp Reasoning
• Both sense and antisense RNAs sufficient for silencing
• Silencing can persist, even though RNA is easily degraded
• Could dsRNA be mediating a new silencing mechanism?
• The RNAi revolution begins…
– Fire and colleagues found that introducing long
double-stranded RNA (dsRNA) into C. elegans led to
the targeted degradation of homologous mRNA.
– Coined the term “RNA interference” - RNAi
• RNAi in C. elegans
– Silencing of a green fluorescent
protein (GFP) reporter in C. elegans
occurs when animals feed on
bacteria expressing GFP dsRNA (a)
but not in animals that are defective
for RNAi (b).
• Note that silencing occurs throughout
the body of the animal, with the
exception of a few cells in the tail that
express some residual GFP.
• The lack of GFP-positive embryos in a
(bracketed region) demonstrates the
systemic spread and inheritance of
silencing.
RNAi Timeline
– 1990
• co-suppression of purple color in plants.
– 1995 Guo S, and Kemphues KJ.
• First noticed that sense RNA was as effective as antisense RNA for suppressing gene expression in
worm C. elegans
– 1998 Fire et al.
• First described RNAi phenomenon in C. elegans by injecting dsRNA into C. elegans which led to an
efficient sequence-specific silencing and coined the term "RNA Interference".
– 2000 Zamone et al.
• Reported processing of long dsRNA by Rnase III (Dicer) into shorter fragments of 21-23-nt intervals in
Drosophila extracts
– 2001 Bernstein et al.
• Cloned Dicer, the RNase III enzyme that is evolutionarily conserved and contains helicase and PAZ
domains, as well as two dsRNA-binding domains.
– 2002 Tuschl T and colleagues
• First described RNAi in mammalian cells
– 2003 Paddison et al. Sui et al. Paul et al.
• Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells.
– 2003 Song et al.
• First reported that siRNAs can be used therapeutically in whole animals
– 2004 Kawasaki and Taira Morris et al.
• First observed that siRNA silences gene at transcriptional level possibly through directing de novo DNA
methylation.
–
Dicer –
•
–
RNAi triggers are double-stranded RNAs containing 21-23 nt sense and antisens strands hybridized to have 2 nt overhangs at both 3'
ends.
Small Interfering RNA –
•
–
RNA-induced silencing complex (RISC) is an siRNA-directed endonuclease, catalyzing cleavage of a single phosphodiester bond on
the RNA target.
RNAi Trigger –
•
–
RNA-directed DNA methylation (RdDM) is an RNA directed silencing mechanism found in plants. Similar to RNA interference
(RNAi), RdDM requires a double-strand RNA that is cut into short 21-26-nt fragments. DNA sequences homologous to these short
RNAs are then methylated and silenced.
RNA-Induced Silencing Complex –
•
–
RNA Interference (RNAi), a term coined by Fire et al in 1998, is a phenomenon that small double-stranded RNA (referred as small
interference RNA or siRNA) can induce efficient sequence-specific silence of gene expression.
RNA-Directed DNA Methylation –
•
–
Ribozymes are RNA molecules that act as enzymes in the absence of proteins.
RNA Interference –
•
–
Post-transcriptional gene silencing (PTGS) is a sequence-specific RNA degradation system designed to act as an anti-viral defense
mechanism. A form of PTGS triggered by transgenic DNA, called co-suppression, was initially described in plants and a related
phenomenon, termed quelling, was later observed in the filamentous fungus Neurospora crassa
Ribozyme –
•
–
Micro-RNAs (miRNA) are single-stranded RNAs of 22-nt that are processed from ~70-nt hairpin RNA precursors by Rnase III nuclease
Dicer. Similar to siRNAs, miRNAs can silence gene activity via destruction of homologous mRNA in plants or blocking its translation
in plants and animals.
Post-Transcriptional Gene Silencing –
•
–
A small and highly potent molecule that functions in an autocrine and paracrine manner, and that induces cells to resist viral replication.
This term is related to RNAi because in mammals introduction of dsRNA longer than 30 nt induces a sequence-nonspecific interferon
response.
Micro-RNA –
•
–
Dicer is a member of the RNase III family of nucleases that specifically cleave double-stranded RNAs. Dicer processes long dsRNA into
siRNA of 21-23 nt.
Interferon –
•
–
RNAi Glossary
Small Interfering RNA (siRNA) is 21-23-nt double-strand RNA. It guides the cleavage and degradation of its cognate RNA.
Helicase –
•
Enzyme responsible for unwinding double stranded molecule
What is RNAi?
– RNA interference (RNAi) is an evolutionally highly
conserved process of post-transcriptional gene
silencing (PTGS) by which double stranded RNA
(dsRNA) causes sequence-specific degradation of
mRNA sequences.
– It was first discovered in 1998 by Andrew Fire and
Craig Mello in the nematode worm Caenorhabditis
elegans and later found in a wide variety of organisms,
including mammals.
RNAi is a conserved mechanism
– RNAi is a universal, omnipresent conserved
mechanism in eukaryotic cells.
– The cellular mechanism of RNAi Predates
evolutionary divergence of plants and worms.
– key proteins involved in RNAi in disparate organisms
are highly conserved.
THE SILENCING MECHANISM
• Two-step model to explain RNAi.
– I. dsRNA is diced by an ATPdependent ribonuclease (Dicer) into
short interfering RNAs (siRNAs).
• duplexes of 21 23 nucleotides bearing twonucleotide 3' overhanging ends.
– II. siRNAs are transferred to a second
enzyme complex, designated RISC for
RNAi-induced silencing complex.
The siRNA guides RISC to the target
mRNA, leading to its destruction.
• the antisense strand of the siRNA is
perfectly complementary
• The classical RNA interference
(RNAi) pathway in Drosophila
– Long double-stranded RNAs
(dsRNAs) are processed by the
R2D2/Dicer heterodimer into small
interfering RNAs (siRNAs).
– The duplexed siRNA is unwound in
an ATP-dependent manner*.
• *starting at the 5' terminus that has
the lowest relative free energy of base
pairing.
– This strand of the siRNA, the guide
strand, is also preferentially taken up
by the RNA-induced silencing
complex (RISC).
– The single-stranded siRNA guides the
endonuclease activity of the activated
RISC ("holoRISC") to the
homologous site on the mRNA,
cleaving the mRNA.
RNAi Amplification
– A small amount of dsRNA can silence a vast amount
of target mRNA in C. elegans.
– Mechanistic explanations for this observations:
• Each siRNA fragment can target the homologous mRNA
• Catalytic mechanism: each siRNA fragment can be used
several times.
• RNA directed RNA synthesis
• RNA Dependent RNA Polymerase (RdRP)
– RdRP activity found in plants and C. elegans
– Required for RNAi?
• Not found in mammals or drosophila
• RdRP deficient plants and worms... Results not decisive
– Proposed mechanism: Random degenerative PCR [Lipardi et al., 2001]
• siRNA acts as primer for elongation on target mRNA
Immunity via RNAi
– RNAi is used as a form of primitive immunity to
protect the genome from invasion by exogenous
nucleic acids introduced by mobile genetic elements,
such as viruses and transposons.
Putting a stop to the promiscuous
Duplication Fodder…
Richard Dawkins
• Cellular machinery is extremely good at copying
DNA.
• The cell nucleus is a paradise for DNA, humming
with sophisticated, fast, and accurate duplicating
machinery.
• Cellular machinery is so friendly towards DNA
duplication that it is small wonder cells play host
to DNA parasites --- viruses, viroids, plasmids and
a riff-raff of other genetic fellow travelers.
The plot thickens… The Discovery of
Endogenous Effectors for RNAi
– Discovery of the first naturally occurring small RNA specie , lin-4
• Non-coding, 22nt RNA
– Identified in screen for defects in timing of larval development
– lin-4 partially complementary to conserved sites in lin-14 3’UTR [Lee et al.,
1993]
• lin-4 binds these sites
• lin-4 negatively regulates lin-14 translation
– The naturally occurring small RNA designated microRNAs (miRNAs) (only
later)
– No other miRNAs found for 7 years!
– Second miRNA – let-7 [Reinhart et al., 2000]
• Non coding, 21nt RNA
• Regulates lin-14 in same way as lin-4
– Note: Homologues of lin-4 escaped bioinformatics
Let-7 Homologs were easily detected [Pasquinelli et al., 2000]
• Drosophila, sea urchins, mice, humans...
Endogenous RNAi:
miRNA in the Genome
• Characteristic Properties
– Highly conserved, particularly 5’ end
– All from hairpin precursors
• Genome Wide miRNA Identification
– Most has been done experimentally (Cloning and sequencing)
• Over 100 novel miRNAs identified from C. elegans, Drosophila, and mammals
– Expected to represent ~1% of predicted genes [Lim et al., 2003]
• Same as other gene families with regulatory roles
• 200-255 miRNAs in humans
• >175 have now been experimentally confirmed [Griffiths-Jones, 2004]
• Functional Characterization
–
–
–
–
Lewis et al., (2003) estimate average of five mRNA targets per miRNA
Many targets are transcription factors - miRNAs regulate the regulators
Suggests major role in highly regulated processes
Thousands of proteins may be regulated by miRNA
miRNA vs. siRNA
– miRNA: microRNA.
• Encoded by endogenous genes.
• Hairpin precursors - pre-miRNAs
– The pre-miRNAs are hairpins with imperfect complementarity in their stems and
frequent bulges, mismatches and G:U wobble base pairings.
• Recognize multiple targets.
– siRNA: short-interfering RNA.
• Mostly exogenous origin.
• dsRNA precursors
• May be target specific
–
–
–
–
Discovered in different ways
Similar biogenesis
Share common pathway components and outcomes
Understanding of miRNA comes from research on siRNA and vice versa
• Maybe current understanding does not allow us to distinguish them
MULTIPLE MECHANISMS OF
SMALL-RNA-MEDIATED GENE
SILENCING
• The endogenous RNAi pathway contributes significantly
to regulating cellular gene expression.
– Silencing of endogenous genes regulates basic biological
processes, including the transition from one developmental
stage to the next.
• the archetype miRNAs, let-7 and lin-4, regulate C. elegans larval
development
• miRNAs are expressed in a specific spatial and temporal pattern during
development in D. melanogaster or differentiation of mouse embryonic
stem cells
• The function of most miRNAs remains unknown…
• miRNA Biogenesis
– Transcribed from endogenous gene as pri-miRNA
• Primary miRNA: long with multiple hairpins
• Imperfect internal sequence complementarity
– It is processed into 70-nt hairpins by the RNase III family member Drosha to
become the pre-miRNA.
• Note: How does it identify pri-miRNA?
– Hairpin terminal loop size
– Stem structure
– Hairpin flanking sequences
– The pre-miRNA is exported to the cytoplasm by Exportin 5.
– It is cleaved by the R2D2/Dicer heterodimer into the mature miRNA.
• Symmetric 2nt 3’ overhangs, 5’ phosphate groups
• The miRNA pathway
– pri-miRNA
– processed by Drosha to become the premiRNA.
– exported to the cytoplasm by Exportin 5.
– cleaved by the R2D2/Dicer heterodimer
into the mature miRNA.
– The miRNA is loaded into RISC and
guides it to sites on the mRNA that have
only partial sequence complementarity to
the miRNA, leading to repression of
translation.
• Intermediate Summary:
– miRNA
vs. siRNA
– mRNA cleavage
vs. Translational Repression
Initiation
Execution
An additional mechanism:
Heterochromatin formation
• The repeat-associated siRNA (rasiRNA)
pathway
– Transcription from opposing promoters
found in repetitive DNA elements, such as
centromeric repeats and satellite DNA,
leads to the formation of long dsRNAs.
– These long dsRNAs are cleaved by
Dicer, presumably the R2D2/Dicer
heterodimer, into siRNAs.
– These are unwound and taken up by the
RNA-induced transcriptional silencing
complex (RITS)
– RITS directs the establishment of
silenced chromatin over the region of
DNA homologous to the siRNAs.
– This silenced chromatin is characterized
by sequence-specific DNA methylation
and histone methylation and by recruiting
heterochromatin-associated proteins.
•
A model for the mechanism
of RNAi
– Silencing triggers in the form
of double-stranded RNA may
be presented in the cell as
synthetic RNAs, replicating
viruses or may be transcribed
from nuclear genes.
– These are recognized and
processed into small
interfering RNAs by Dicer.
– The duplex siRNAs are
passed to RISC (RNAinduced silencing complex)
– The complex becomes
activated by unwinding of the
duplex.
– Activated RISC complexes
can regulate gene expression
at many levels:
• promoting RNA degradation
• translational inhibition
• chromatin remodelling
– Amplification of the
silencing signal in plants may
be accomplished by siRNAs
priming RNA-directed RNA
polymerase (RdRP)dependent synthesis of new
dsRNA.
RNAi movie http://www.nature.com//focus/rnai/animations/index.html
Presenting the cast:
RNAi applications
• Genome-wide RNAi screening
– Done in C. elegans
• 19 757 protein coding genes (predicted)
• 16 757 inactivated using RNAi
– New standard for systematic genome wide functional
studies
• RNAi as a solution for mammalian genetics
• Potential therapeutic use
•
Double-stranded RNA can be introduced
experimentally to silence target genes of
interest
– silencing is systemic and spreads throughout the
organism.
– a, A silencing signal moves from the veins into
leaf tissue. red is chlorophyll fluorescence that is
seen upon silencing of the GFP transgene.
– b, C. elegans engineered to express GFP in
nuclei. Animals on the right have been treated
with a control dsRNA, whereas those on the left
have been exposed to GFP dsRNA.
• Some neuronal nuclei remain florescent,
correlating with low expression of a protein
required for systemic RNAi59.
– c, HeLa cells treated with an ORC6 siRNA and
stained for tubulin (green) and DNA (red).
Depletion of ORC6 results in accumulation of
multinucleated cells.
• Stable silencing can also be induced by expression
of dsRNA as hairpins or snap-back RNAs.
– d, Adult Drosophila express a hairpin
homologous to the white gene (left), which
results in unpigmented eyes compared with wild
type (right).
New Frontiers for RNA…
• Small RNAs likely to have bigger impact on gene and
protein regulation
• New classes of small RNAs:
– Tiny non-coding RNA [Ambros et al., 2003]
•
•
•
•
•
•
tncRNA – 20-22nt
Discovered in C. elegans
Not likely generated from hairpin loops
Not conserved among species
Many complementary to mRNAs
Function unknown
– RNA as a Molecular Switch: Small Modulatory RNA –
smRNA [Kuwabara et al., 2004]
•
•
•
•
Discovered in mice
Conserved in vertebrates
Interacts with regulatory protein
Turns transcriptional repressor into activator
Just Scratching the Surface…
• New roles for RNA added to our current paradigm
for gene and protein regulation.
• A new buzz word?
“Regulomics”
• The difficulties in STP research fundamentally owe their
complexity to the designer – natural selection.
The reason lies in the profound difference between systems
“designed” by natural selection and those designed by intelligent
engineers (Langton 1989).
For instance, human designers being farsighted but blinkered, tend
to find their designs thwarted by unforeseen side effects and
interactions, so they try to guard against them by giving each
element a single function insulating it from other elements and
allowing the minimally required interconnections. In contrast
natural selection is ultimately myopic and having no foresight the
process tries out designs in which many side effects occur; most
such designs are terrible, but every now and then there is a
serendipitous side effect: few unrelated functional systems interact
to produce a bonus. This “design” process ultimately produced the
biological systems we investigate; system which operate with an
outrageously complex weave of interconnections.