Rufus joined the MRC London Institute of Medical Sciences (LMS) in July 2021 to complete a summer studentship with Dr Vicky Metzis, head of the LMS Development and Transcription Control research group. In this blog, Rufus tells us about his time in the lab and what his research results showed.

Developmental biologists have long pondered how the nervous system establishes regional identity. That is, how do cells arrange themselves correctly to create specific and specialised regions along the spinal cord.

The Metzis group at the LMS uses mouse embryonic stem cells (ESCs) to try and answer this question. Their previous research has shown the generation of a healthy spinal cord requires the activity of a transcription factor called CDX2. Transcription factors are known to regulate gene expression in cells. One way they do this is through directly binding to a stretch of DNA called a promoter. By binding to a promoter, the transcription factor facilitates a gene being switched on or off. 

My research project aimed to unpick what genes CDX2 is having an impact on during development. Earlier research had demonstrated a link between CDX transcription factors and Hox genes, which are known to have a role in establishing left and right-side symmetry in the body, something necessary for a healthy spinal cord. As such, we hypothesised CDX2 could be regulating the expression of Hox genes during development of the spinal cord.

As a first step, I took DNA data from the lab’s previous experiments and looked at the level and patterns of Hox gene expression that was occurring in ESCs as they matured into different tissue types, for example, hindbrain vs. spinal cord. This analysis showed me specific Hox genes called Hoxb5os, Hoxb8 and Hoxb9 were expressed at higher levels as the mouse ESCs matured into spinal cord. This enabled me to predict which Hox genes might be directly regulated by CDX2, and therefore play a role in shaping spinal cord development. 

In order to unpick whether CDX2 is regulating the expression of these specific Hox genes I performed a series of ChIP-seq experiments. ChIP-seq shows you how and where transcription factors interact with the DNA. I wanted to see whether CDX2 binds to specific Hox gene promoter regions because if it did, this would confirm CDX2 is regulating the expression of those Hox genes during spinal cord development.  

My preliminary ChIP-seq data showed CDX2 does bind directly to specific Hox gene promoters and so is likely to be regulating their expression. However, more research is needed to understand the extent to which CDX2 regulates specific Hox gene expression, and also what effect that level of Hox expression has in cells that are developing into the nervous system. 

It was challenging completing my own independent scientific research project for the first time. It forced me outside my comfort zone and that was difficult at times. But I did enjoy my time at the LMS, and the experience I have gained is invaluable.

I’ve learnt to always approach intimidating tasks quickly, which was helped by the fact that my lab were supportive and would guide me through new techniques. I’ve also learnt to always have a plan B – it is unlikely everything will go perfectly the first time, so preparing for that is necessary to not slow down your workflow.

This project has opened my eyes to what a professional research lab is like but also the questions and challenges present in the field of developmental biology. It has encouraged me to think deeply about what we don’t already know about this field, and potentially some unanswered questions that I could look to answer in the future. I had an amazing summer at the Metzis lab, and I look forward to getting back to the bench to explore those unanswered questions!