Tonight, I watched Kimmo Palin from the University of Helsinki present at London Calling 2019 on “Retrotransposon variation in human genome and tumorigenesis.” They began by discussing retrotransposons and describing them as “copy-paste elements” in the genome that copy themselves with an RNA intermediate. They range in size between 300 bp and 6,000 bp. LINE1 elements are sometimes activated in tumors. The difficulty with transposable elements and short reads is that they are so common! Palin noted that there are probably hundreds or thousands in the genome. Their frequency and sequences complicate their sequencing. With long reads, some of the challenges of sequencing across retrotransposon elements can be overcome. Palin uses restriction enzymes to cut the genome. The fragments are circularized, amplified, and sequenced. This process allows the detection of insertion sites. LINE1 insertions were then sequenced from colorectal tumor samples using PromethION flow cells. With the PromethION, they are running larger projects to sequence cancer samples. Palin noted a risk of ligation artifacts in the library prep method. Nevertheless, with only a couple of reads, insertion sites of the retrotransposons can be obtained. Palin’s approach is a creative way of learning about retrotransposon insertions in the human genome.
