Using sequencing technologies to study DNA break repair

Deadline for applications has passed.

Key information

Applications closed
06 February 2024, 11:59 GMT
Hours per week
36 (full time)
Application guidance
Posted 22 December 2023

Research topics

Genome Integrity & Repair
Background texture taken from the lab imagery.

This is a summer student position supervised by Nishita Parnandi in Simon Boulton's lab.

Introduction to the Science

DNA contained within our cells is the source of genetic information. If DNA gets damaged, our cells risk losing the original genetic information. DNA damage can occur from normal cellular processes or from exposure to toxic chemicals and UV radiation. One of the most harmful types of damage to the DNA is a break occurring in both its strands. DNA breaks can cause harmful mutations which lead to diseases such as cancer. Understanding 1) “where” these breaks occur and 2) “how” they will be repaired is important to prevent disease. In this project, you will use sequencing technologies to investigate the question: How are DNA breaks repaired? Sequencing technologies are an innovative tool to gain large amounts of cellular information in a single experiment. Therefore, these technologies have become indispensable in several fields including cancer diagnostics.

About the Project

In this project, you will first damage DNA in human cell lines to create DNA breaks. To understand how the breaks are repaired, you will use sequencing technologies to locate key DNA repair proteins. This will be done on a whole genome scale. Finally, you will analyse the sequencing data to identify the locations of DNA repair proteins using R programming. The specific sequencing technology you will use is called CUT&TAG (please see reference below) – this technology requires lower amounts of input DNA compared to other methods. The results from this project will then answer the following specific questions: 1) Are there breaks that are preferentially repaired by a specific repair protein 2) Are there common genomic features (for ex: exons, introns) across breaks that are biased to certain repair proteins?

About You

The project will be a great opportunity to gain exposure to sequencing technologies, including CUT&TAG and ChIP-seq, and R programming to analyse sequencing data. Therefore, the ideal student would be studying biomedical sciences/computing.

References

1.         Panier, S. and Boulton, S.J. (2014)

            Double-strand break repair: 53BP1 comes into focus.

            Nature Reviews Molecular Cell Biology 15: 7-18. PubMed abstract

2.         Kaya-Okur, H.S., Janssens, D.H., Henikoff, J.G., Ahmad, K. and Henikoff, S. (2020)

            Efficient low-cost chromatin profiling with CUT&Tag.

            Nature Protocols 15: 3264-3283. PubMed abstract