Annual Report FY2015: Garth Ilsley



Garth Ilsley
Science and Technology Associate


1. Introduction

The past year has led to the completion and publication of modelling work in Drosophila, as well as the completion of single-cell RNA-seq analysis in Ciona.  In addition, with the Luscombe Unit, we have established a stable culture of Oikopleura dioca at OIST.

2. Activities and Findings

1.   Modelling transcriptional enhancer function in Drosophila

In collaboration with Justin Crocker and David Stern, we have completed and published our analysis of the regulatory function of even-skipped and rhomboid enhancers in Drosophila. We validated the results of model predictions of enhancer function with experimental perturbations, particularly those using transcription activator–like effectors fused to activators or repressors (TALEAs and TALERs).


Figure 1: Comparison of experimental manipulation of the rhomboid enhancer (left and shaded areas on the right) with the modelling predictions (solid lines on the right). From Crocker, Ilsley and Stern. Nature Genetics (2016).


2.   Single-cell measurements in Ciona intestinalis

It is important to have measurements of transcription factor levels and gene outputs at single-cell resolution. Spatially averaging transcription factor measurements obscures cellular state and hence limits the effectiveness of statistical studies of the regulatory inputs and outputs in the cell. Therefore, to understand gene regulation it is crucial to develop approaches for measuring gene expression at the single cell level.

I have finished RNA-seq analysis and generated a complete dataset of single-cell expression data at a specific stage of development in Ciona, a marine chordate. Experimental validation work by my collaborators in the Luscombe Lab is continuing.


3.   Establishment of Oikopleura dioica culture

Over the past few years, the Luscombe Unit has developed expertise and knowledge working with Ciona, an invertebrate marine chordate. Future experimental work will benefit from having an organism similar to Ciona, but with a shorter lifecycle. Oikopleura dioica is such an animal. With the help of the lab of Hiroki Nishida at Osaka University we have established a reliable culture of Oikopleura dioca at OIST.


3. Collaborations

Theme: Measuring gene expression with single-cell RNA-seq

                   Type of collaboration: Joint Research

                   Researchers: Luscombe Unit (OIST)


Theme: Establishing Oikopleura dioica culture at OIST in the Luscombe Lab

                   Type of collaboration: Assistance and guidance from experts in the field

                   Researchers: Takeshi Onuma, Tatsuya Omotezako and Hiroki Nishida (Osaka University)


Theme: Modelling transcriptional enhancer function in Drosophila

Type of collaboration: Joint Research

Researchers: Justin Crocker and David Stern (Janelia Research Campus, USA)


4. Publications and other output

Crocker, J., Ilsley, G. R. & Stern, D. L. Quantitatively predictable control of Drosophila transcriptional enhancers in vivo with engineered transcription factors. Nat Genet 48, 292–298 (2016).