MSCI815 Module 6

 

Analysis of human disease genes in Drosophila.

 

Lawrence T. Reiter, Ph.D.

Department of Neurology

May 8th, 2008

 

The purpose of this module is to introduce the concept of cross species database searches to identify appropriate genetic model systems for the study of human disease genes.  We will discuss several entry points into the identification of homologues to human diseases genes, how to search human disease databases and also how to search several Drosophila specific databases to identify reagents and information on a particular homologue.

 

Genetic Model Organisms in the lab:

 

Organism

Transcriptome

(Genes)

Similarity to Human Genome

Cellular

Complexity

Organisms per

Genetic Screen

Generation

Time

Yeast

6,200

46%

1 cell

>109

2 hours

Nematode

18,300

43%

959 cells

106-107

3 days

Fly

14,400

61%

>106 cells

105-106

10 days

Mouse

>30,000

>95%

>109 cells

102-103

12 weeks

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Entry points to human fly and fly human comparisons:

 

1.     Do you know the name of the gene in humans?

a.     Homologene at NCBI

b.     Homophila

 

2.     Do you know the name of the disease?

a.     OMIM

b.     Homophila

 

3.     Do you know the name of the Drosophila gene?

a.     Flybase

b.     Homophila

 

What is Homophila and how do I use it?

 


 

 

The Homophila database was designed to help researches in human genetics investigate the fly homologues to human disease genes and to help investigators in fly genetics focus their research on particular genes that are relevant to human genetic disease.  Out of ~5000 human genes known to cause genetic disease 75% have homologues in flies @ an e-value of 10-10 or less.  These genes fall into most classes of human disease including neurological disorders, cancer, blood disorders, soft tissue disorders and, of course, developmental disorders.  For more details see:

 

L. Reiter, L. Potocki, M. Gribskov and E. Bier. 2001. A systematic analysis of human disease associated gene sequences in Drosophila melangaster. Genome Research 11:1114-1125.

 

Searching Homophila:

 

      Search by text keyword (human or fly text)

      Search by gene name (human or fly)

      Search by unique OMIM ID number

      Download complete precompiled list of homologues for a particular e-value cut off (1e-10 to 1e-300)

 

What makes a good candidate gene for study in the Drosophila system?

 

      Human disease gene function is poorly understood

      Fly counterpart highly related at the protein level to human gene (BLAST comparisons)

      Facility of genetic analysis in fly (why use a genetic model?)

      Reagents

o   Mutant alleles exist

o   P-elements in or nearby gene (P-screen database)

o   Mis-expression phenotype (GAL4/UAS)

      Identified loci subject to test in humans or mice – Closing the Loop!

 

Drosophila specific resources available online:

 

      Mutant alleles and UAS over-expression lines

Flybase

Bloomington Stock Center    

 

      UAS-RNAi lines

Vienna Stock Center

NIG Stock Center, Japan

 

      Deficiency lines and stocks to make new deletions in the region

DrosDel

 

      RNAi primers for knock down in S2 cells

RNAi amplicon primer sets

 

      Finding mutations on chromosomes

P-screen

Fly SNPs

 

Questions for Homophila Module:

 

1.     Identify a fly homologue to the human UBE3A gene, which causes Angelman syndrome. What reagents are available to study this gene in flies?

 

2.     How many human ataxias are caused by mutations in genes that have fly homologues?

 

3.     I work on embryo development in flies.  Are there any human diseases associated with mutations in Hedgehog?

 

4.     What kinds of experiments could I do in flies to understand dopa-responsive dystonia?

 

5.     What reagents are available to study the fly Pebble gene in vivo and in vitro?

 

For more information and for links to all the resources listed in this module see the Drosophila Transgenic Core website:

 

http://curlyo.utmem.edu