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.
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Acknowledgements
We would like to thank Patricia Goerner-Potvin for help reviewing the manuscript. This work was supported by a grant from the Canadian Institute of Health Research (CIHR MOP-115090).
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Ramsay, L., Bourque, G. (2016). In Silico Methods to Identify Exapted Transposable Element Families. In: Garcia-Pérez, J. (eds) Transposons and Retrotransposons. Methods in Molecular Biology, vol 1400. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-3372-3_3
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DOI: https://doi.org/10.1007/978-1-4939-3372-3_3
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