DECODERS platform: decoding locus-specific molecular interaction networks

Development and production of tools for molecular targeting and in situ biotinylation.

We use biotin ligase and peroxidase enzymes (TurboID or APEX2, respectively) targeted to individual loci to specifically label proximal interactants through in situ biotinylation. Targeting tools notably include CRISPR/dCas9 (CASPEX strategy), antibodies (AMAPEX strategy) or DNA probes (HYPRO strategy).

Design and implementation of experimental strategies

The DECODERS platform aims to support and assist with the design of appropriate experimental strategies for different research hypotheses and models. It implements biochemical and molecular approaches in close collaboration with the different teams and trains users in the experimental workflow.

High throughput data analysis

Mass spectrometry identification and differential quantitative analysis of interactants are performed in collaboration with the Proteomics platform of Institut Jacques Monod (ProteoSeine, Université Paris Cité).

Our services

• Collaboration with research teams for the design of proximity biotinylation projects on genomic regions.
• Realization of experimental procedures in molecular biology and biochemistry.
• Differential quantitative analysis of mass spectrometry data (in collaboration with ProteoSeine).

Scientific supervisor:

Benoit Palancade – Research Director, CNRS

Resources

The platform provides all the molecular and biochemical tools required to implement the different experimental approaches.

• Sharable database of in situ biotinylation protocols.
• Plasmid library (APEX2, TurboID, Split TurboID, dCas9…) and cloning tools.
• Recombinant proteins (APEX2-protein A; APEX2-protein A/G; APEX2-HYPRO).
• Biotinylation and biotin enrichment reagents.
• Digoxigenin labeling kits for DNA probes (HYPRO strategy).
• Antibodies for validation by immunofluorescence.