Genetic variations in transposable elements: Germ line differences and somatic variations induced during neurogenesis

The sequencing of human and other genomes has produced an overwhelming amount of data. One challenge is to understand why 98.94% of the genome does not seem to be coding for functional proteins. Another is why over half of the sequence contains "parasitic" Transposable Elements (TE) that can produce copies of themselves anywhere else in the genome. In recent years there has been a shift in perception concerning the effects of "parasitic" and "junk" DNAs on biology. This project aims to use the data produced by next-generation sequencing technologies to determine if and how TE affect the development of the brain, whether they contribute differences between individuals and exactly how commonly they copy themselves around the genome. The occurrence and expression of TE elements have been associated with several human diseases such as cancer, diabetes and schizophrenia. A fundamental understanding of their role in normal "healthy" processes is necessary before we can hope to understand how they contribute to disease.

This proposed project aims to capitalise on the wealth of data emanating from the recent and rapid developments in next-generation DNA sequencing technologies. Transposable elements (TE) are a class of repetitive elements, which when intact, are capable of making retrocopies in the genome. Formerly considered "junk" or "parasitic" DNA these elements are suspected of being a source of non-coding regulation and phenotypic variation. TE have been associated with several human diseases such as cancer, haemophilia A, muscular dystrophy and schizophrenia.
The specific aims of this project are two-fold: (i) to identify somatic TE insertions causing alterations in expressed sequences between neuronal tissues within an individual ; (ii) to identify differences in TE insertions between mouse strains and possible association to phenotype; and, (iii) to identify TE insertion polymorphisms among 1000 individuals in the human population. The objective is to identify somatic variation arising from TE insertions occurring during neurogenesis; thereafter, I will determine if novel insertion events have preferentially occurred in neuronally active transcripts. I will achieve this by isolating RNA from cortical layers in mouse brain, by enriching sequence with TE-containing transcripts, and by performing paired-end deep sequencing with a Illumina Genome Analyzer. This will be done in collaboration with Dr. Elliott Margulies of NHGRI and Dr. Zoltan Molnar (University of Oxford).
The objective of the project focusing on TE insertion variants between mouse strain genetics is to investigate whether these variants contribute to phenotypic variation (collaboration with Dr. Jonathan Flint, Oxford University). Since the mouse strains that are currently being sequenced display a large range of phenotypes this provides a unique opportunity to determine the role of TE insertion events on trait variation. The aims of the human population genetics project are to map rare variant TE insertions in humans. A collaboration with Dr. Richard Durbin and Dr. David Adams of the Wellcome Trust Sanger Institute will allow me to gain access to, and receive advice about, efforts to sequence, assembly and analyse multiple human genomes. These world-class research groups are primary contributors to the 1000 Genome and the MRC-funded Mouse Strain Sequencing Projects, thereby providing an invaluable training opportunity.
With my background in neuroscience, repetitive elements and method development, and the many opportunities, both training and collaborative, presented in this application, there is a potential for spearheading research into the role of TE in phenotypic variation and, by extension, human disease.