Toward Discovering Transcription Factor Binding Sites in and Around Human Transposable Elements

Abstract

Transposable elements compromise approximately 45% of the human genome, and a certain subset, retrotransposons, are able to copy and reinsert themselves into our DNA by using RNA intermediates. Because of their ability to somatically reinsert, transposable elements have been implicated in leading to genomic innovation over the evolutionary lifetime of the human genome, contributing transcription factor binding sites and alternative splicing cites. Transcription factors, by binding DNA sequences, are able to regulate gene expression, allowing cells to express genes at levels appropriate for their cell type. This study aims to find transcription factor binding sites in and around transposable elements on chromosome one by using the Find Individual Motif tool. There is a strong correlation between number of transposable element occurrences bound by transcription factors and the length of that transposable element. Endogenous retroviruses, a type of retro-transposon, exhibited a large number of bound transcription factors despite not being the longest types of transposable elements. The most bound transcription factors tended to be those with highly conserved binding regions. With this computational pipeline in place, further analysis of transcription factor binding sites in transposable elements is very straightforward.