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Massively parallel CRISPR genome engineering in Drosophila

Massively parallel CRISPR genome engineering in Drosophila

By In Aiv Internship On April 16, 2019

Internship title: Massively parallel CRISPR genome engineering in Drosophila

Name: Synthetic Fly Lab
Affiliation: CRI Research
Address: 8-10 Rue Charles V
E-mail: radoslaw@ejsmont.net

LAB Director
Name: Ariel Lindner
Phone number: +33188328305
E-mail: ariel.lindner@cri-paris.org

Name: Radoslaw Ejsmont
Phone number: +33614751734
E-mail: radoslaw.ejsmont@cri-paris.org

Subject Keywords: CRISPR
Genome engineering
Cell culture
Tools and methodologies: CRISPR
Insect cell culture
Drosophila genetics
Gibson assembly

Summary of lab’s interests: Our team will develop a comprehensive set of synthetic biology tools to study and recreate gene regulatory networks in vivo, using Drosophila, a well-established model organism for studying animal development. These tools will enable researchers to bridge the gap between quantitative biology, that provides gene expression data, systems biology that aims to establish accurate models of gene regulatory network and synthetic biology that will be used to test these models. Data from the synthetic gene regulatory networks can also be used as the baseline, a reliable empirical dataset that can improve existing computational methods for network modeling.
Project summary: Transcriptional control of host genes using synthetic transcription factors requires placing synthetic enhancers, usually 100-200 bp in length, upstream of the target genes. The amount of target genes a transcription factor controls can vary from a few to even hundreds. Placing target genes under control of a synthetic transcription factor therefore requires large number of edits of the host genome. CRISPR is the current state-of-art technique for genome manipulation and performs excellently in insertion of short DNA sequences using non homologous end joining (NHEJ) or homologous recombination (HR). In this project we would like to explore the boundaries of CRISPR in Drosophila by inserting an increasing number of short (100-200 bp) fragments using either NHEJ or HR into various locations in the genome. We aim to develop a reliable system for assembly of self-processing arrays of guide RNAs and repair templates as well as transgenesis of these CRISPR constructs into Drosophila cell culture and flies. Finally, we aim to find an upper limit on the number of efficient insertions that can be performed in parallel.
Interdisciplinary aspect of the project: This project aims to introduce large number of synthetic transcription factor enhancers into the Drosophila genome. While genome engineering, including CRISPR has become bread and butter for the Drosophila community, genome editing en masse is a feat that remains to be perfected. In this project we will bring together the state-of-art in Drosophila genetics, transgenesis, genome engineering and synthetic biology, the latter being a field that only starts to emerge in the Drosophila research.