High throughput genetics & RNAi Screens

Luke Lopas

and

Mark Devries

RNAi history

http://www.invitrogen.com/site/us/en/home/Products-and-Services/Applications/RNAi-Epigenetics-and-Gene-Regulation/RNAi/RNA-Interference-Overview.html

Mechanisms of RNAi

http://www.nature.com/nrg/journal/v5/n8/pdf/nrg1415.pdf

C. elegans

• Why is it such a good models organism?. Grows fast. Shares similar cellular components. Transparent. All 959 somatic cells traced

Back ground• Development to adult in about 2.5 days• Life span 2-3 weeks• Either hermaphroditic or male

Different methods of RNAi

Microinjection

• Most potent method

• Difficult method

Soaking

• High throughput analysis

• Can conduct stage specific analysis

• Weaker effect

Feeding

• High throughput analysis

• Weak effect

Transgene

• Allows for inducible/ tissue specificity

• More effective method for some genes

Choosing a gene library• Genomic sequence information

• Predict wrong genes structure

• Only 9% of genome not covered

• cDNA

• Can have stronger effect

• Only represents genes being expressed

• Misses low expression genes

Functional genomic

• Aims to give in vivo function to every gene

• Uses all techniques of RNAi delivery

• Uses both types of RNAi libraries

• Requires a dissecting microscope

• Can use rrf-3 mutant

Functional genomic findings• Insight into genome organization in C.

elegans• Highly expressed genes show phenotype• Chromosomal regions have specialized

function

Short comings • Protocol difference• Inter experimental variability

Gene family. Specific gene family. Narrows choices

Transcriptome

.Expressed genes.Microarrays

Interactome. protein-protein. Yeast two hybrid

Use functional genomics

. Narrows choices. ‘in Silico’

Genome wide

. whole genome

RNAi gene screen

. Focus on specific process . Reverse genetics vs forward genetics

Functional genomic analysis of cell division in C. elegans

using RNAi of genes on chromosome III

Gonczy et al.

What did they want to do?

• “…apply RNAi on a genomic scale to identify genes required for cell division.”– Unbiased testing of each ORF…actually testing

96% of ORFs

• Use a functional genomic approach in early life cycle of C. elegans to identify genes necessary for cell-division– Specifically investigate genes on chromosome III

• Assign cellular functions to the multitude of genes coming out of sequencing projects.

Why RNAi?

• Easy experiment (relative)

• Can study cell division– No mitosis occurs

between dsRNA innoculation and fertilization

Picture from Ahringer Lab

How’d they do it?

Figure From Ben Schmidt’s 875 presentation

How’d they do it? Continued

Figure from Ben Schmidt’s 875 presentation

Data analysis

DIC microscopy used for first 24 hours

- requires transparent samples

Effects on progeny observed over 2-4 days

Micrasterias radiata as imaged by DIC microscopy, from Wikipedia

Controls

From Gonczy et al., 2000

Results

From Gonczy et al., 2000

More Results

From Gonczy et al., 2000

How does this tie into what we’ve done before?

Imagine the categories on the previous slide…do they remind you of anything?

How does this tie into what we’ve done before?

Imagine the categories on the previous slide…do they remind you of anything?

Gene Ontology Categories

Analysis of Chromosome III

• Tested 2,232 ORFs (96.4%)– 133 (6.1%) gave

detectable DIC phenotypes

• Found all previously known mutations from classical genetic studies

University of Edinburgh

Analysis of Chromosome III

• RNAi loses potency later in development

• In total: tested 12% of ORFs in genome, so if assume random genome-wide distribution, over 1,000 genes essential for first two cleavage divisions!!!

University of Edinburgh

Is RNAi an efficient tool for gene function discovery?

Pros- Can look at a ton of

genes- Can ascribe function to

genes w/o previously ascribed function

- Provides a source for investigation using classical genetic methods

Cons- Loss of sensitivity as

development proceeds

- Questions surrounding neuronal sensitivity

DIC images

From Gonczy et al., 2000

Guess the phenotype

• First video is wt

• All other videos have a developmental phenotype.

C. elegans movies

Answers

All are mutants in different alleles in the same gene. Defect involves cell division, more specifically spindle formation.

Can these results be translated to other organisms?The gene implicated in

cell division are more highly conserved among species

From Gonczy et al., 2000

What do results mean?

From Nature Networks

Take home messages

• Lots of genes are involved in early development!

• RNAi allows you to look at and assign putative function to A LOT of genes!

• RNAi is an efficient reverse genetic tool but is not perfect

Silencing Genomes

Phenobank

Phenobank

Phenobank

Phenobank

Movie Link

Other interesting websites

• Drosophila RNAi Screening Center– If you are at all interested in fly RNAi and

how these results translate to mammals, check it out!

Question from Class

• I have two general questions with regards to functional genomic screens and RNAi; first of all, we learnt from gene ontology that it encompasses three distinct processes - is RNAi used as a method to derive molecular function and/or biological processes information for gene ontology?

• Secondly, RNAi requires a gene to be knockout to identify the function of that particular gene; what about genes that have redundancy function, i.e. more than one gene performs the same function? The possibility of redundancy function or synergistic function (where function can be measured along a scale - the more genes that code for a function is present, the more gene phenotype is observed) seems to me that it renders incomprehensive screens of gene function.

– This was one stated advantage of using C. elegans, the fact that there is little redundancy in genome. But what do you think about studies in mammals?

Question from class

• ITs obvious that RNAi is becoming a powerful tool in worm research, but what are the implications to humans? I've read some papers on RNAi therapeutics, and was curious about your thoughts on that? Could ones' genome be sequenced, bad things identified, and then specific RNAs given to silence problematic genes? This is almost like gene therapy which could someday become more of a reality.