Advantages of C' elegans:

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• Advantages of C. elegans
• 1. rapid life cycle
• 2. hermaphrodite
• 3. prolific reproduction
• 4. transparent
• 5. only 1000 cells
• 6. laser ablation
• 7. complete cell lineage map
• 8. genetics

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RNA interference A type of gene regulation
Involving small RNA molecules and induced by
double stranded RNA
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Adding a Chalcone synthase gene from Petunia
fused to a strong viral promoter to transgenic
Petunia interfered with expression of the native
homologous gene. Gene Silencing
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Gene Silencing

• More common from strong promoters.
• 2. More common from inverted repeat inserts
• (could make a double stranded RNA).
• 3. Induced by RNA viruses
• (have double stranded RNA replication
• intermediates).

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RNA viruses can block expression of a transgene
if a copy of the transgene has been added
Tobacco plant expressing GFP protein Infected
with RNA virus with GFP gene Virus infection
travels through veins GFP expression inhibited
starting at veins.
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Double stranded RNA is common to Viruses that
can silence host gene expression And to
transgenes that can silence host gene expression
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Transgenes insert into chromosomal DNA randomly
or
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Transgenes often integrate in complexes
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Gene silencing and RNA viruses share potential
to produce dsRNA
Fire and Mello (1998, Nature) used C. elegans to
prove that dsRNA inhibits expression of
endogenous genes homologous to that dsRNA
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Double stranded GFP RNA interferes with
expression of GFP in transgenic C. elegans
GFP expressed in nuclei After adding dsRNA for
GFP
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Features of RNAi
Induced by dsRNA with homology to exons Small
RNAs produced Target sequence specific Catalytic
very small amounts of ds RNA are
sufficient Spreads injection into gut silences
genes in embryos Lasts Silencing continues as
the embryo matures
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Mechanism of RNAi
Dicer binds dsRNA and cleaves making siRNA
siRNAs direct ARGONAUTE to bind homologous mRNA
and cleave it, or prevent translation
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Gene regulation by small RNAs
SiRNAs degrade mRNA to stop gene expression
quickly
StRNAs prevent translation to stop gene
expression quickly
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Catalysis RDRP copies mRNA making more ds RNA.
Dicer cuts that generating more siRNA More
RDRP is activated and more dsRNA is made.
Spread dsRNA transported to other cells.
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Transcriptional gene silencing is initiated by
RNA directed methylation of promoter
regions dsRNA homologous to promoters leads to
methylation and inactivation by recruitment of
chromatin remodeling enzymes.
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Transcriptional Gene silencing requires dsRNA,
DNA methyltransferases, histone methylation and
histone deacetylation.
RNA directed DNA methylation
Histone methylation
DNA methylases associate with histone
modification enzymes leading to changes in
histone methlyation patterns and histone
deacetylation. Condensed chromatin results.
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Chromatin remodeling initiation and maintenance
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Centromeres are transcriptionally inactive. They
have condensed chromatin Repeated sequences lead
to production of double stranded RNAs The dsRNAs
maintain the condensed state of the centromeres
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Pol II does not transcribe methylated DNA
well Pol IV transcribes methylated DNA
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Small RNAs direct sequence-specific chromatin
remodeling in the nucleus leading to long term
block to transcription Methylation markers on
DNA maintain dense chromatin state Copied when
DNA replicated PolIV copies marked DNA to
maintain supply of sequence-related small RNAs
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What is the function of RNAi mechanism in
non-transgenic organisms?
Protection against viruses Keep transposable
elements inactive Gene regulation
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MIRNA genes are PolII genes that encode a
hairpin shaped mRNA. Dicer cleaves the double
stranded portion to make a short dsRNA. That
combines with the RISC complex and directs
cleavage of a specific target mRNA
MIRNA gene
Pol II
AAA
DCL1
HYL1
200 MIRNA genes
HEN1, HYL1
DCL1
57 unique miRNAs from 26 families
HASTY
AGO1
RISC components
miRNA Precursor Transcript
miRNA
AGO1
RISCmiRNA
Target
AAA
..... .............
AGO1
Cumulative data from Bartels, Carrington, Chen,
Weigel, Zhu, others
Cleaved target
AAA
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miRNAs and Targets in Animals
Registered miRNAs
C. elegans 114 Drosophila 78 Zebrafish 362 Mouse
245 Human 321
Herpesviruses SV40
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Overlapping transcripts on opposite strands can
generate small RNAs Controlled expression of
the opposing transcripts lead to RNA mediated
silencing Regulate protein levels
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Small RNA regulation of salt stress response
Salt stress induces ROS and increases in
proline. High proline protects cells against
water loss. Increased ROS leads to induction
of an SRO5 transcript that overlaps the P5CDH
transcript As a result, RNAi is
initiated against P5CDH transcripts. P5CDH
protein levels drop and proline accumulates
Borsani et al 2005 Cell 123, 1279
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Centromeres have condensed chromatin and highly
methylated DNA. Pol IV is recruited to transcribe
repeated sequences in centromeres. The production
of double stranded RNAs maintains the condensed
state of the centromeres.
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Summary
Small double stranded RNAs regulate gene
expression by directing degradation of specific
transcripts preventing translation of specific
transcripts promoting chromatin condensation of
specific target genes
Double stranded RNA can be used to mimic
mutations in C. elegans and in other
organisms. Sequence-specific targets Effect
will be carried on in the progeny of treated
animals
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Double stranded GFP RNA interferes with
expression of GFP in transgenic C. elegans
GFP expressed in nuclei After adding dsRNA for
GFP
How would you design a genetic screen to identify
the genes involved in the RNAi mechanism?
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How would you set up a genetic screen to
investigate the mechanism of RNAi?
Design a screen for mutants in genes required for
RNAi
Easy to induce RNAi in C. elegans by feeding them
E. coli engineered to express a transgene in
both directions sense and antisense
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A real genetic screen for C. elegans genes
essential for RNAi
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A real genetic screen for C. elegans genes
essential for RNAi
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Candidate mutants isolated after feeding E. coli
producing double stranded RNA How could double
stranded RNA be made in E. coli? Checked
candidate mutants by microinjection into gut The
listed mutants passed the secondary test
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Different mutants had specific phenotypes for
activation of transposable elements and
silencing of transgenes
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Functions of genes in RNAi decifered
Rde4 Initiating RNA binding protein Rde1
Argonaut Rde2 ? Mut7 endonuclease
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RNA is a gene regulator as well as a carrier
of information