Part I: Ribozymes

Part II: SELEX(RNA in-vitro evolution)

Part III: RNAiRNA inhibition and silencing

Prof. F.Allain 2/2/2004

The RNA world hypothesis

Part I: Ribozymes

A brief History

How many ribozyme ? Why ?

Catalytic efficiency, condition

3D structure of ribozyme:And a mechanism of catalysis

Biological application ?

A brief History

1982:Self-splicing in Tetrahymena pre-rRNA (group I intron)

Kruger et al, and Cech, Cell 31, 147-157 (1982)

1983:RNAse P is a ribozyme

Guerrier-Takada et al, and Altman, Cell, 35, 849-857 (1983)

How many ribozyme ? Why ?- the hammerhead ribozyme (plant virus)

- the hairpin ribozyme (plan virus)

- hepatitis delta ribozyme (human virus)

- neurospora VS ribozyme (mitochondrial RNA)

- group I and group II intron ribozyme (rRNA and mt RNA)

- RNAse P (tRNA maturation)

- Ribosome (translation)

- Spliceosome ?? (splicing)

One main reaction: Nucleolytic cleavageTransesterification (SN2)

From Lilley TIBS (2003)

HammerheadHaipinHepatitis deltaVS ribozyme

The hammerhead ribozyme (plant virus)

- discovered in small RNA satellites of small viruses (1986)

- replication by rolling circle mechanism

Secondary structure

The hammerhead ribozyme (plant virus)

- tertiary structure

Scott et al and Klug, Science 1996

The hairpin ribozyme (plant virus)

From Lilley TIBS (2003)

The hepatitis delta ribozyme (human virus)

From Lilley TIBS (2003)

Group I &II intron ribozyme (rRNA and mt RNA)

Doudna and CechNature, 2002

Group I intron ribozyme (rRNA and mt RNA)

Golden et al, and cechScience (1998)

Catalytic efficiency, condition

- ribozyme follows a Michaelis-Menten kinetics

E + S ES E + P k1 k2

k-1

- all ribozyme need cations for activity (Mg2+ ,Mn2+)

Km= k-1+ k2

k1

= 10-5-10-7 M kcat= 0.5-2 min-1

kcat/ Km= 103-106 M-1.min-1 Good catalytic efficiency!!

3D structure of ribozyme: mechanism of catalysis

hairpin ribozyme Hepatitis delta ribozyme

Ruppert et al, Nature 2001, Science 2002 Ferre d’Amare, Nature 1998

From Lilley TIBS (2003)

How to catalyse the reaction ?

Structure of the hairpin ribozyme

hairpin ribozyme

Ruppert et al, Nature 2001, Science 2002

hairpin ribozyme

Ruppert et al, Nature 2001 Ruppert et al, Science 2002

Transition stateGround state

hairpin ribozyme

Loop A

free

bound

Loop B

free bound

hairpin ribozyme

Ruppert et al, Science 2002

Transition state

Acid-Base catalysis ? (textbook Voet and Voet)

like with RNAse A

Acid-Base catalysis ?

G8 as abase

A38 as anacid

Bevilacqua, Biochemistry 2003

Hepatitis delta ribozyme

Ferre d’Amare, Nature 1998

Biological application ?

Tentative of gene therapy with the hairpin and the hammerhead ribozymeagainst viral RNA for example.

Reference:

Reviews: Lilley TIBS (2003)De Rose Chem & Biol (2002)Ferre d’Amare Biopolymer (2003)

Article: Kruger et al, and Cech, Cell (1982) Guerrier-Takada et al, and Altman, Cell (1983) Scott et al Nature (1995) Science (1996) Rupert et al Nature (2001), Science (2002)

Part II: SELEX

A brief History

The method ?

A few examples.

Biological application ?

SELEX :Systematic Evolution of Ligands by EXponential enrichment

A brief History

Ellington and Szostak, Nature (1990)

Tuerk and Gold , Science (1990)

In vitro selection of RNA molecules that bind specific ligands

Andrew D. Ellington & Jack W. Szostak

Subpopulations of RNA molecules that bind specifically to a variety of organic dyes have been isolated from a population of random sequence RNA molecules. Roughly one in 1010 random sequence RNA molecules folds in such a way as to create a specific binding site for small ligands.

Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase.

Tuerk C, Gold L.

High-affinity nucleic acid ligands for a protein were isolated by a procedure that depends on alternate cycles of ligand selection from pools of variant sequences and amplification of the bound species. Multiple rounds exponentially enrich the population for the highest affinity species that can be clonally isolated and characterized. In particular one eight-base region of an RNA that interacts with the T4 DNA polymerase was chosen and randomized. Two different sequences were selected by this procedure from the calculated pool of 65,536 species. One is the wild-type sequence found in the bacteriophage mRNA; one is varied from wild type at four positions. The binding constants of these two RNA's to T4 DNA polymerase are equivalent. These protocols with minimal modification can yield high-affinity ligands for any protein that binds nucleic acids as part of its function; high-affinity ligands could conceivably be developed for any target molecule.

Wilson and Szostak, Ann.Rev.Bioc. (1999)

- Selection against small molecules

- Selection against proteins

- Selection of new ribozymes (RNA world)

The ATP aptamer structure

Nucleolin RNA Targets

B110-50nM(5’ETS)Mouse

B250-100nM(5’ETS)Mouse

G-CA-UG-CG-CU-G5’ 3’

UC

C

C

A

G

AC

5’ 3’

C-GG-CU-AA-U

CU

C

CC

A

G

GU

Consensus NRE

5’ 3’

N-NN-NN-NN-N

NxU/G

C

C C

G/A

G

Ny

selex NRE5-20nM

5’ 3’

C

A•A•UG•AG-CG-C

G

AU

CC

A

G

A

RBD2-RNA-RBD1 “sandwich”

5’3’1

G16

22

F56

5’3’

RBD2

RBD1

linker

Allain et al, EMBOJ (2000)

In vitro selection of an enzyme

Reference:

Reviews: Wilson and Szostak Ann.Rev.Bioch.(1999)

Gold et al, Ann.Rev.Bioch.(1995)

Part III: Introduction to RNAi

A brief History

SiRNA and miRNA

RNAi Mechanism

A few very recent structures

Biological application

A practical example of siRNA

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

ANDREW FIRE*, SIQUN XU*, MARY K. MONTGOMERY*, STEVEN A. KOSTAS*†, SAMUEL E. DRIVER‡ & CRAIG C. MELLO‡

Experimental introduction of RNA into cells can be used in certain biological systems to interfere with the function of an endogenous gene,. Such effects have been proposed to result from a simple antisense mechanism that depends on hybridization between the injected RNA and endogenous messenger RNA transcripts. RNA interference has been used in the nematode Caenorhabditis elegans to manipulate gene expression,. Here we investigate the requirements for structure and delivery of the interfering RNA. To our surprise, we found that double-stranded RNA was substantially more effective at producing interference than was either strand individually. After injection into adult animals, purified single strands had at most a modest effect, whereas double-stranded mixtures caused potent and specific interference. The effects of this interference were evident in both the injected animals and their progeny. Only a few molecules of injected double-stranded RNA were required per affected cell, arguing against stochiometric interference with endogenous mRNA and suggesting that there could be a catalytic or amplification component in the interference process.

Nature V391 pp 806-811 (1998)

+ DS RNA against GFP

Fire at al, Nature V391 pp 806-811 (1998)

In situ mRNA hybridization of Mex3 RNA in Embryo

-C +C

From animal: with AntisensRNA with DS RNA

Fire at al, Nature V391 pp 806-811 (1998)

RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals.

Zamore PD, Tuschl T, Sharp PA, Bartel DP.

Double-stranded RNA (dsRNA) directs the sequence-specific degradation of mRNA through a process known as RNA interference (RNAi). Using a recently developed Drosophila in vitro system, we examined the molecular mechanism underlying RNAi. We find that RNAi is ATP dependent yet uncoupled from mRNA translation. During the RNAi reaction, both strands of the dsRNA are processed to RNA segments 21-23 nucleotides in length. Processing of the dsRNA to the small RNA fragments does not require the targeted mRNA. The mRNA is cleaved only within the region of identity with the dsRNA. Cleavage occurs at sites 21-23 nucleotides apart, the same interval observed for the dsRNA itself, suggesting that the 21-23 nucleotide fragments from the dsRNA are guiding mRNA cleavage

Cell, v101 pp25-33 (2000)

dsRNAi is cut in 21-23 nt fragments

Zamore et al, Cell, v101 pp25-33 (2000)

The mRNA is cut in 21-23 nt fragments by the siRNA

Zamore et al, Cell, v101 pp25-33 (2000)

A first model for the mechanism RNAi

Zamore et al, Cell, v101 pp25-33 (2000)

Role for a bidentate ribonuclease in the initiation step of RNA interference.

Bernstein E, Caudy AA, Hammond SM, Hannon GJ..

RNA interference (RNAi) is the mechanism through which double-stranded RNAs silence cognate genes. In plants, this can occur at both the transcriptional and the post-transcriptional levels; however, in animals, only post-transcriptional RNAi has been reported to date. In both plants and animals, RNAi is characterized by the presence of RNAs of about 22 nucleotides in length that are homologous to the gene that is being suppressed. These 22-nucleotide sequences serve as guide sequences that instruct a multicomponent nuclease, RISC, to destroy specific messenger RNAs. Here we identify an enzyme, Dicer, which can produce putative guide RNAs. Dicer is a member of the RNase III family of nucleases that specifically cleave double-stranded RNAs, and is evolutionarily conserved in worms, flies, plants, fungi and mammals. The enzyme has a distinctive structure, which includes a helicase domain and dual RNase III motifs. Dicer also contains a region of homology to the RDE1/QDE2/ARGONAUTE family that has been genetically linked to RNAi.

Nature v 409, pp 363-366 (2001)

22 ntRNA

Identification of DICER

Bernstein et al, Nature v 409, pp 363-366 (2001)

Elbashir et al, G&D, v18 pp188-200 (2001)

The RISC complex

SiRNA and miRNA

MicroRNAs. Genomics, Biogenesis, Mechanism, and Function.

Bartel DP.

MicroRNAs (miRNAs) are endogenous approximately 22 nt RNAs that can play important regulatory roles in animals and plants by targeting mRNAs for cleavage or translational repression. Although they escaped notice until relatively recently, miRNAs comprise one of the more abundant classes of gene regulatory molecules in multicellular organisms and likely influence the output of many protein-coding genes.

Cell, v116, pp 281-297 (2004) (review)

First miRNAin C.elegans

miRNAin C.eleganswith homologsIn flies and human

miRNA in Plants

A high number: about 1% of the genes

Human: 200-255 miRNA

C.elegans: 103-120 miRNA

Drosophila: 96-124 miRNA

Functions ??

miRNA siRNA

Post-transcriptionalCleavage of mRNA

Translational repressionof the mRNA

Transcriptional silencing

Structure of the PAZ domain

Lingel et al and Yan et al, Nature 426, pp 465-474 (2003)

Structure of an Viral siRNA suppressor

Vargason et al, Cell 115, pp 799-811 (2003)

Applications:

-Genome study (C-elegans)

-Gene knockout

Reference:

Reviews: Bartel Cell.(2004)

Hannon Nature (2002)

Article: Fire at al, Nature V391 pp 806-811 (1998)

Elbashir et al, G&D, v18 pp188-200 (2001)

Bernstein et al, Nature v 409, pp 363-366 (2001)

RNAi as a tool for knock down in mammalian cells

Why ?

Which is the right siRNA sequence ?

How do I get the “siRNA’s” into the cell ?

Practical aspects

RNAi vs Knock-Out

+ RNAi: relatively easy to perform

not so time consuming

no real transgenic cells or animals

- RNAi: its just a knock down

finding siRNA’s is not always easy

negative controls

Designing siRNA • The target sequence should be 50-100 bp downstream of start codon or in the

3’ UTR

• Search for a 23nt long sequence with a AA(N19)TT or NA(N21) motif

• Ensure that your target sequence is not homologous to any other genes

• Avoid more than three guanosines or three cytosines in a row

• avoid stretches of > 4 T's or A's

• secondary structure of the target mRNA does not appear to have a strong effect on silencing

• Designing several siRNA’s helps to find a highly efficient one

Lamin A/Ctargeted region (cDNA): 5' AACTGGACTTCCAGAAGAACATC

sense siRNA: 5' CUGGACUUCCAGAAGAACAdTdT

antisense siRNA: 5' UGUUCUUCUGGAAGUCCAGdTdT

Example for siRNA’s

GL2 Luciferasetargeted region (cDNA): 5' AACGTACGCGGAATACTTCGATT

sense siRNA: 5' CGUACGCGGAAUACUUCGAdTdT

antisense siRNA: 5' UCGAAGUAUUCCGCGUACGdTdT

Elbashir, Nature. 2001 May 24;411(6836):494-8.

Delivering Double Stranded RNA

Hannon, Nat Rev Genet. 2001 Feb;2(2):110-9

dsRNA Approach

• It is possible to get dsRNA commercially, either as two single stranded RNAs or already annealed

• Commercially available RNAs are produced by solid phase synthesis

• Another possibility is to get dsRNA by T7 in vitro transcription:

DNA oligos are the templatesAnnealing of antisense and sense product will give dsRNAAfter purification they are useable

• Normally the T7 procedure is cheaper and even faster (incl. oligo ordering)

• For one transfection reaction around 0.2 mM siRNA is necessary

• Transfections are carried out by cationic lipids

• Due to secondary structure dsRNA is rather stable, compared to ssRNA

EXAMPLE:combinatorial control of splicing in the c-src N1 exon

Black, Annu Rev Biochem. 2003;72:291-336

HeLa-cell-line

1775 or 1808 hPTB siRNA in 3’UTR

+

minigene

1. Transfection(Lipofectamin 2000)

2. Transfection 48 h(Lipofectamin 2000)

whole proteomisolation96 h

cytoplasmaticRNA isolation96 h

check proteinexpressionvia western

1775 or 1808 hPTB siRNAin 3’UTR

check alternativespliced exonvia RT-PCR

EXAMPLE:combinatorial control of splicing in the c-src N1 exon

Wagner, Mol Cell. 2002 Oct;10(4):943-9

Plasmid Approach

Ambion Inc. Austin, Texas, USA

Lentivirus-Based Approach:shRNA-expressing vector

Rubinson, Nat Genet. 2003 Mar;33(3):401-6

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Functional silencing of genes in miceby Lentivirus-infection

Generation of lentivirus infected zygotes

Silencing of p53:

Tissue was harvestedfrom 8-wk-old mices

SummaryPros Cons

•Fast

•Effective

•Works in many systems

•Non-inducible

•Most effective in embr. System

•Time dependent

•Stable

•Inducible

•Tissue specific

•Time consuming to generate

•Cloning can be problematic

•Stable

•Inducible

•Tissue specific

•Time consuming to generate

•Promotor can silence each other

•Most commen technique in plants

•Also in non cycling cells possible

•Therapeutically useful

•Resistance

•Not well established

•Difficult to work with