Study of retrotransposons using high throughput technologies

Transposable elements (TE) account for more than half of mammalian genomes. Recent studies have identified RNA transcripts originating from TE. This thesis describes how bioinformatics analysis of current high throughput technologies can provide novel insights into transposable element biology.;To begin with, the design and application of TE-array, a novel high throughput microarray assay, is described. Traditional gene expression microarray designs target uniquely occurring exon sequences and mask out repetitive sequences, thus disallowing high throughput studies on TE. The genomic high copy numbers and RNA transcript abundance of TE made it uncertain if microarrays would reliably detect TE transcripts. But data presented in this thesis indicates that microarray technology can indeed be adapted to study TE transcript abundance reproducibly. Experiments of normal mouse tissues using TE-array have shown surprising tissue specific transcript profiles with a sense strand bias indicating that transposon transcription is not exclusively read through from gene promoters. Human prostate cancer cell line experiments have shown differential transcription profiles of LINEs, Alu and segmental portions of certain HERVs. This work is in the process of being submitted.;The next research chapter describes a Next generation sequence analysis pipeline that was developed for identifying novel translocation breakpoints in transposon rich regions. This work was published in Genome Research in October 2011.;The research chapter that follows describes a bioinformatics analysis pipeline that was developed to identify transposon insertions in the Neandertal genome that are not present in human genomes.