title: In Silico Methods to Identify Exapted Transposable Element Families.
abstract: Transposable elements (TEs) have recently been shown to have many regulatory roles within the genome. In this chapter, we will examine two in silico methods for analyzing TEs and identifying families that may have acquired such functions. The first method will look at how the overrepresentation of a repeat family in a set of genomic features can be discovered. The example situation of OCT4 binding sites originating from LTR7 TE sequences will be used to show how this method could be applied. The second method will describe how to determine if a TE family exhibits a cell type-specific expression pattern. As an example, we will look at the expression of HERV-H, an endogenous retrovirus known to act as an lncRNA in embryonic stem cells. We will use this example to demonstrate how RNA-seq data can be used to compare cell type expression of repeats.
authors.affiliation: Department of Human Genetics, McGill University, Montréal, QC, Canada, H3A 1A4.
authors.forename: LeeAnn
authors.initials: L
authors.lastname: Ramsay
authors.affiliation: Department of Human Genetics, McGill University, Montréal, QC, Canada, H3A 1A4. guil.bourque@mcgill.ca.|McGill University and Génome Québec Innovation Center, Montréal, QC, Canada, H3A 1A4. guil.bourque@mcgill.ca.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bourque
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D004251:DNA Transposable Elements; D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D006801:Humans; D064878:Web Browser
chemical_list: D004251:DNA Transposable Elements
keywords: Bioinformatics; Endogenous retrovirus; RNA-seq; Repeats; Transcriptional regulation; Transposable elements; lncRNAs