Comparative single-cell transcriptomics of complete insect nervous systems

The brain is made of many types of specialized cells. Information processing in these cells is responsible for generating innate and learnt behaviour. Gene expression, neuron activity, and neuron connectivity influence information processing, but bridging the gap between genes, circuits and behaviour has been very difficult. Furthermore, behavioural state of an animal continuously changes. State changes occur across developmental stages of an organism and as a result of prior sensory experience. The principles of molecular changes of individual neurons that alter behavioural states are poorly understood. The Drosophila larva is an excellent model system to investigate genes, neurons, circuits, and behaviour. Drosophila melanogaster has one of the best annotated genomes and newly developed single cell RNA sequencing methods allow for profiling hundreds of thousands of single cells. Genetic lines exist in the larva for selective manipulation of most neurons. Electron microscopy reconstruction of the larval nervous system is close to complete. Lastly, the larva has a rich behavioural repertoire that includes associative learning. The larva therefore has all the tools necessary to study genes, neurons, and circuits involved in innate and learnt behaviours. In this thesis I used the tractable larval model system to 1) identify the comprehensive gene expression profiles of all neurons in the animal and thus generate a neuron-transcriptome map; and 2) leverage the newly generated neuron-transcriptome maps to identify experience-dependent changes in gene expression. I sequenced 202,107 single cells to obtain a gene-expression map of all larval neurons. I used RNA fluorescent in situ hybridization to detect mRNA molecules in specific anatomically defined cell types from the whole larval brain to validate my sequencing approach. I also asked how gene expression changes following specific experiences that induce alterations in behavioral states. After exposing larvae to repeated optogenetic noxious stimulation, I discovered altered behavioral state accompanied by drastically altered gene expression across the entire nervous system. Repeated activation of the memory system led to gene expression changes in specific cell populations but did not alter brain-wide gene expression. In this thesis I 1) build a first comprehensive transcriptomic atlas of the larval nervous system across multiple developmental stages; and 2) describe how repeated activation of specific cell types can alter behavioral state and gene expression across the entire nervous system. By adding a transcriptomic atlas to the existing atlases of behaviour, neuron connectivity and neuron activity, this work sets the stage for a more complete understanding of the principles that underlie the complex interplay of genes, circuits, and behaviour.

Name dc:type.qualificationname

Doctor of Philosophy (PhD)

Level dc:type.qualificationlevel

Doctoral

Grantor dc:publisher.institution

University of Cambridge

Year dc:date.issued

2020

Author dc:creator

• Cocanougher, Benjamin

Advisor dc:contributor.advisor

• Zlatic, Marta

• Neuroscience
• Single Cell Genomics
• Drosophila melanogaster

Licence

• https://apollo8-f-pro.lib.cam.ac.uk/bitstreams/dcc9d135-e998-4f6c-b6fb-c04101683364/download
• https://www.rioxx.net/licenses/all-rights-reserved/

Language dc:language

eng

Author Identifier

0000-0003-0648-554X

OAI identifier oai:identifier

oai:www.repository.cam.ac.uk:1810/324378