Evaluating the impact of LINE-1 retrotransposons on cancer gene expression

Abstract

Oncogenesis is accompanied by dramatic epigenetic alterations across the genome, including widespread DNA demethylation. These epigenetic changes can drive the activation of LINE-1 retrotransposons, which are normally kept in a transcriptionally inert state. LINE-1 activation can lead to genetic mutations and drive changes in gene expression. However, it remains largely unknown whether LINE-1 activity is of functional significance for cancer progression. Here we test the hypothesis that changes to LINE-1 chromatin impact on neighbouring gene expression, with potential consequences for cancer progression. 

Aims and description

LINE-1 elements are mobile elements with the capacity to self-replicate within the genome. The human genome harbours over 10,000 full-length LINE-1 copies, about 100 of which retain the capacity for genomic mobility. A number of cancers (eg breast, ovarian, colorectal) display high LINE-1 retrotransposon activity, which is thought to contribute to genomic instability. However, very few retrotransposition events have been causally linked to cancer progression. An alternative hypothesis of how LINE-1 elements may affect cancer biology is that chromatin changes at LINE-1s have a widespread impact on gene expression. Indeed, LINE-1 DNA is commonly found hypomethylated in cancer, displaying similar chromatin profiles to those seen in embryonic stem cells. Yet it remains unknown to what extent LINE-1 chromatin alterations can affect gene expression. 

The goal of this project is to test for causal links between changes to LINE-1 chromatin, gene expression and phenotypic consequence to the cancer cell. Specifically we aim to:

1. Test for transcriptional effects of LINE-1 chromatin modulation. We will use CRISPR-based epigenetic editing approaches to alter the chromatin of multiple LINE-1 copies simultaneously. This will be performed in cancer cell lines with low (eg HL-60) or high (eg MCF7) LINE-1 expression, and the impact on gene expression evaluated by RNA-seq.
2. Assign transcriptional effects to individual LINE-1 copies. We will use CRISPR to genetically excise individual copies of LINE-1 elements to confirm that specific gene expression changes are driven by a particular LINE-1 element.
3. Test for phenotypic impact of LINE-1 elements. Using models from both aims 1 and 2, we will test for potential phenotypic impact of LINE-1 elements, such as cell growth and migration. 

These experiments will lead to a new understanding of the potential impact of retrotransposons on cancer cells. The project will require the student to couple both experimental and bioinformatic approaches.

Applications are invited from candidates with at least an upper-second class honours degree or equivalent in an area relevant to the project. Proficient English language skills are essential. Please contact Dr Miguel Branco (m.branco@qmul.ac.uk) to apply.