Detection of LINE-1 RNAs by Northern Blot

Repetitive genetic elements have had an unprecedented success populating phylogenetically diverse species making them a common feature of most genomes. Hundreds of thousands of copies of active and non-functional transposable elements representing different classes and families can reside within and outside of host genes. In addition to creating structural variations in genomic DNA, some of these loci are expressed to contribute to the continuing amplification cycle. Transposable elements, specifically Long Interspersed Element-1 (LINE-1) produce a spectrum of RNAs, some of which are important for their mobilization, while others are processed forms of LINE-1 transcription that may or may not play relevant functions. Additionally, many LINE-1 sequences integrated into cellular genes are included into cellular transcripts creating substantial background when L1-related RNA expression is detected by some conventional methods. This chapter provides an in-depth description of the complexity of L1-generated mRNAs as well as sources of cellular transcripts containing L1 sequences. It also highlights the strengths and weaknesses of conventional methods used to detect LINE-1 expression.