It was great mentoring and working with Venkat Sankar on this project. Also great working with Howard Chang, Paul Mischel, @agnanam.bsky.social, Ivy Wong, and other collaborators on this project. 11/11

Overall, we propose that ecDNA is not only selected in cancer because of oncogenes, it is also actively retained because of retention elements, allowing it to persist in a growing cancer cell population. 10/11

Finally, retention elements are unmethylated on ecDNA and when we methylate them, ecDNA becomes untethered from chromosomes. Plasmids with methylated retention elements are also no longer retained. 9/11

We found that most ecDNAs in patient tumors contain retention elements. ecDNA size is much bigger than the oncogenes themselves but is anti-correlated with abundance of retention elements in the surrounding locus, suggesting selection of these elements in the retained ecDNA. 8/11

Retention elements on ecDNA interact with previously identified mitotic bookmarks on chromosomes in chromatin conformation analysis, suggesting that retention elements may interact with chromosomes in mitosis via active DNA sites, potentially mediated by bookmarking factors. 7/11

Using live cell imaging, we found that adding a retention element to a plasmid makes it more likely to attach to chromosomes during mitosis. 6/11

We verified that these elements, when individually cloned into a plasmid, can promote retention of the plasmid in cells. Putting more copies of an element in a plasmid increases its retention additively. 5/11

We found that many of the retained DNA elements, which we call “retention elements”, are active regulatory sequences such as promoters and enhancers. This was exciting to us because these are genomic sites where many DNA-binding proteins can interact with DNA. 4/11

To identify elements within ecDNA that may act as anchors for hitchhiking, we shattered the entire human genome into short pieces of DNA, cloned them into a plasmid pool and asked which DNA pieces can be retained over many cell passages. 3/11

ecDNA does not have centromeres but is inherited along with chromosomes by tethering to them. Although this “hitchhiking” phenomenon has been observed for many years, the mechanism is unknown. 2/11

So excited for you, Rose!