RNAi
C. elegans RNAi databases
I used the C. elegans BRCA1 homolog, brc-1, to search for phenotypes caused by RNAi knock-down of the gene. Two databases were used: Wormbase and the RNAi database.
Wormbase
Searching for a known homologous gene in C. elegans focused Wormbase results in a comprehensive entry for the gene. The information available ranges from RNAi phenotypes to gene ontology to homology. I will focus on the phenotype data provided, specifically RNAi phenotypes.
Below in Table 1 is a list of phenotypes found when BRCA1 is knocked down with RNAi, as well as through mutation analysis. Clicking on the phenotype link provides information about the experiments that found the phenotype, including links to publications. Many of the phenotypes listed make sense: tumor suppressor genes are commonly activated during cell stress for example. Many of these phenotypes also had connections to DNA damage repair problems, which increase evidence for BRCA1's role in sensing DNA damage.
Table 1. Phenotypes found by knocking down BRCA1 using RNAi. Click on the figure to link out to Wormbase entry.
Wormbase also includes a table of RNAi experiments that do not support a phenotype when knocking down BRCA1 (Table 2). It is important to note that some of these overlap with the phenotypes supported by other RNAi experiments.
Table 2. Phenotypes not found when knocking down BRCA1 using RNAi. Note that the phenotypes in purple were found above in Click on the figure to link out to Wormbase entry.
RNAi Database
RNAi Database gave fewer results than Wormbase, and annotated results were a little harder to follow. Four experiments knocking down BRCA1 resulted in wild-type phenotypes, whereas one resulted in a non-wild-type phenotype, though I was unable to determine from the entry what this phenotype was. RNAi Database also searches results from C. elegans.
Drosophila RNAi databases
I would have liked to use the Drosophila databases for RNAi experiments, but no homolog to BRCA1 is known in Drosophila melanogaster.
Analysis
Only Wormbase returned phenotypes from RNAi experiments knocking down brc-1. Some of the phenotypes listed in Table 1 above are associated with DNA damage. These results support the hypothesis that BRCA1 is involved in sensing DNA repair, as absence of the homologous gene in C. elegans due to RNAi knock-down results in DNA damage phenotypes. The protein aggregation phenotype may be due to the role of brc-1 in protein ubiquitination, assuming this function is conserved between humans and C. elegans. The high incidence of male progeny phenotype is often associated with stress on C. elegans, which is a hemaphroditic organism. Therefore, I propose that this phenotype may be due to a stress that triggers production of male progeny, and that this stress may have been DNA damage not repaired due to lack of brc-1.
Site created by Jessica D. Kueck
Genetics 677 Assignment, Spring 2009
University of Wisconsin-Madison
