In principle, we could test it by looking for an age-related increase in transposon count in non-senescent cells, but that turns out to be actually-pretty-difficult in practice. (Modern DNA sequencing involves breaking the DNA into little pieces, sequencing those, then computationally reconstructing which pieces overlap with each other. That’s a lot more difficult when the pieces you’re interested in have millions of near-copies filling most of the genome. Also, the copy-events we’re interested in will vary from cell to cell.)
I wonder if something like single cell ATAC-seq could help here? There’s still the problem of aligning near-copies but it seems like there’s already some work trying to deal with this problem. (I haven’t read either of these papers in detail but the second specifically mentions transposons as a use-case.)
Yeah, I haven’t read up on the topic in depth, but there’s a few toolkits specifically intended for sequencing transposons. So it’s probably not something which would require major breakthroughs at this point, but it does require specialized tools/knowledge, rather than just the standard sequencing toolkit.
I wonder if something like single cell ATAC-seq could help here? There’s still the problem of aligning near-copies but it seems like there’s already some work trying to deal with this problem. (I haven’t read either of these papers in detail but the second specifically mentions transposons as a use-case.)
Yeah, I haven’t read up on the topic in depth, but there’s a few toolkits specifically intended for sequencing transposons. So it’s probably not something which would require major breakthroughs at this point, but it does require specialized tools/knowledge, rather than just the standard sequencing toolkit.