A database and cloning system for a genome-wide piRNA interference collection

A database and cloning system for a genome-wide piRNA interference collection

Internship Description

In C. elegans, genome-wide tools based on RNA interference (RNAi) have been used to do Systems Biology screens. The collection was based on the observation that bacteria expressing a double-stranded RNA (dsRNA) can elicit an RNAi response in C. elegans if the bacteria are ingested (Timmons and Fire, 1998). This lead to the creation of a genome-wide collection of bacteria expressing dsRNA against most of C. elegans genes (Ahringer and colleagues). This has been used a lot in the field but has some limitations. For example, in the germline, the phenotype from ingested dsRNA is considerably weaker than injected dsRNA. Also, ingested dsRNA is generally inefficient at knocking down genes in the male germline.

The germline is of particular interest because this tissue is widely used to study meiosis, early development, gene regulation, inheritance across generations, and stem cell biology. We are developing a novel method to silence genes using molecular machinery from the piRNA pathway (see Ozata et al 2018, Nature Reviews Genetics for an overview) which we are calling piRNA interference (piRNAi). To use this method on a genome-wide scale, we are looking for a motivated student to perform bioinformatics analysis of genome-wide targeting sequences that lead to minimal off-target effects. The project also has a wet lab experimental component, which aims to validate a large-scale cloning method (Golden Gate Cloning) that can be used to generate a genome-wide piRNAi library.​

Deliverables/Expectations

1. A database and web interface for pre-designed piRNAs for C. elegans and other nematode species.
2. A validated cloning method to generate piRNA interference constructs from oligos synthesized on a massively parallel scale.​ 

Faculty Name

Christian Froekjaer Jensen

Field of Study

Genetic engineering and bioinformatics