The C. elegans TransgeneOme

We have built a fosmid transgene resource covering 70% of the C. elegans proteome  as a platform for in vivo exploration of protein function. Combined with a robust transgenesis pipeline and generic, tag-based approaches for in vivo localization or affinity purification the resource can be used to study any protein of interest throughout development under endogenous cis regulatory control. The resource received its field test in the modENCODE project where we applied it to study transcription factor function in vivo through systematic ChIP/Seq and localization analysis. Through a focused effort on protein groups of interest and an open collaboration with the community we aim to systematically generate transgenic worm lines on a genome scale.

The Drosophila TransgeneOme

This project aims to provide a genome wide collection of engineered fosmid constructs for targeted low copy trans- genesis in Drosophila and to test their performance on a large set of proteins. It is a collaborative project (supported by the Max Planck Innovation funds) between us (generation of the constructs resource), Pavel Tomancak in the MPI-CBG (development of novel tagging cassettes), Frank Schnorrer at the MPI of Biochemistry and (fly transgenesis) and several research groups that are responsible for the testing of the resources in in vivo experiments (Kunst, Kühnlein, Vorbrüggen). The project builds up upon a fosmid library and a set of recombineering tools previously developed in collaboration with the Tomancak lab.

We have successfully completed the pilot phase including 10% of the genome and we are working on the genome wide collection.

The Hela TransgeneOme

This project (funded by the MPG initiative BAC TransgeneOmics) aims to describe the subcellular localization of all protein expressed in HeLa cells using BAC transgenics. We have engineered a resource of BAC transgenes for the expressed proteome of Hela. Using the automated cell culture robotics developed in the Hyman lab the constructs will be  transfected in HeLa cells and stable cell lines will be established for all tagged genes.

The C. briggsae TransgeneOme

Extending the TransgeneOme pipeline we have established in C. elegans to other nematode species would provide a platform for addressing a wide range of evo-devo problems. As a first step towards this goal we have generated a fosmid gDNA library for C. briggsae. With the help of Andreas Dahl at the CRTD we have developed a new deep sequencing based approach for clone mapping that significantly reduces the cost and effort required to map a large number of clones compared to the traditional end sequencing approach. The method can be easily extended to more nematode species. We have started to use the resource to compare orthologous groups of gene expression regulatory proteins (transcription factors and RNA binding proteins) in C. elegans and C. briggsae.

Mouse BAC transgenesis and gene Targeting

In collaboration with Francis Stewart the MPI-CBG we are developing tools and high throughput pipelines for protein tagging in mouse ES cells. These tools and the pilot resources we are generating are currently applied for systematic function exploration of disease related genes and genes involved in the maintenance of the stem cell state.