Much of what we know about gene interactions in development has been learned using nematodes, yeast, flies, and bacteria. This is due, in part, to the relative ease of genetic manipulation of these well-characterized genomes. However, of great interest are gene interactions involving complex diseases in humans. Wang and White [(2011). Nature Methods 8(4):341–346] describe work using RNAi to examine the interactive proteome in mammalian cells. They mention that knockdown inefficiencies and off-target effects of introduced RNAi species are areas that need particular improvement if the methodology is to be fruitful.

Comment on how 'knockdown inefficiencies' and 'off-target effects' would influence the interpretation of results.

Key Concepts

Knockdown Inefficiencies

Knockdown inefficiencies refer to the incomplete reduction of target gene expression when using RNA interference (RNAi) techniques. This can lead to residual expression of the gene, which may obscure the true biological effects of the gene's silencing. Consequently, if the knockdown is not efficient, it can result in misleading interpretations of the gene's role in cellular processes or disease mechanisms.

Off-Target Effects

Off-target effects occur when RNAi molecules unintentionally silence genes other than the intended target. This can lead to unintended phenotypic changes and complicate the analysis of gene interactions. Understanding and controlling for off-target effects is crucial, as they can confound results and lead to erroneous conclusions about the specific roles of genes in development or disease.

Interactive Proteome

The interactive proteome refers to the complete set of protein interactions within a cell, which can influence various biological processes. Studying the interactive proteome helps researchers understand how proteins collaborate in pathways and networks. In the context of RNAi studies, accurately interpreting changes in the interactive proteome is essential, as knockdown inefficiencies and off-target effects can alter the dynamics of these interactions, leading to misinterpretations of cellular functions.