Synthetic screening for essential introns and retroelements in human and animal cells

Yasunori Aizawa, Tokyo Institute of Technology

https://www.youtube.com/watch?v=Kzn1rjLwGYw&t=0s&list=PLHpV_30XFQ8RN0v_PIiPKnf8c_QHVztFM&index=7

Thank you.

My name is Yasunori Aizawa. I come from he other side of the north hemisphere. My interpretation of the project is that we're just showing our ideas here, which will be important for the future of the human genome project. Maybe we can have a small umbrella under the big umbrella of GP-write consortium to push the prospect of the GP-write consortium.

My title is "Synthetic screening for essential introns and retroelements in human and animal cells". As a first look at a project focusing on humans or other big geonme synthesis projects, my role is to remind you that the difference between genomes that have been synthesized and the ones that we are going to synthesize.

Here, I show that-- the top panel is yeast. Each one is about 300 kilobases on the top panel. You see many genes in yeast. There's probably 160 genes there, it's kind of a forest of genes. On the other hand, the genes that we have synthesized, a small portion of the total. Instead of having many genes there, we have many ... there. Deriving from virus genes, dumped in the human genome, during long evolutionary time. So it's a bunch of islands that we have synthesized, at most.

A big part of the yeast genome and human genome difference are the introns. There's a difference in the two ecosystems. We need to see and understand the ecosystem and design principle of how the genome develops. The approach I am taking right now is very simple: remove and then watch the cells. We make a mutants, we place the fragment into a wildtype cell line, and in this case we're removing some intron. Also, another ... mutant we're making is.. in the beginning, we can test .. impact of some expression .. in this case, p53 genes. And also we want to see expression at .. level, and also epigenetic status and see the effects. Also, we are making.. we have to use some.. to .. genes each.. PiggyBac terminal repeat. DNA transport-- posi/nega marker. Once we have that working in cells, by overexpressing some of the PiggyBac, you can do whole.. without any starter. Basically we can just swap the.. with the sythesis...

With the genes that we are targeting, like oncogenes and tumor suppressor genes, there are 249 genes registered in gene database. But in the beginning, we are focusing on these 5 genes, different in the lengths of the genes. ALK, MET, NOTCH1, TPS3, MYC. COSMIC database?

I think we are making some progress. We .... neurotransmitter synthesizing enzymes (Keizo Takao).

What are the benefits to GP-writers?

Sophisticate our genome ddesign by learning patterns of dispensable introns and retroelemnts. Make genes compact and simplify gene shuffling and ORF swapping with fewer introns. Reduce the risk and labor at amplico nassembly and sequence check with fewer repats. Save money, time and labor by downsizing animal genomes.

Q&A

Q: on which basis do you believe introns and retroelements are dispensable in live cells?

A: My biggest is that, some research in Drosophila showed that some introns, have the sequences for transcription. We know that, many reports on importance of regulator elements for gene expression. As you know, roughly 300 copies in the human genome are retroelements.. they are probably not important for cells, but we don't know for the ... But this is one of the key actions, is that, by removing these important factors, it could be important for development in the first phase for research. By doing mouse project, maybe we can see some that are important for development. Retroelements are different between mouse and human. That's my idea.

Q: Something that could be interesting, probably drastic for the moment, would be to segregate a range in some chromosomes very gene dense kind of configuration, and in the context of neo chromosomes, put all these introns and regulatory elements or whatever, and allow for for example by adding.. to both sides.. allow for recombination to take place and let it play out. I would say that, in evolution, if some regulatory or transposon or whatever are very important, they would be rearranged and co-opted back into the gene dense chromosomes. I think that could be quite interesting. A different way to understand which parts are very essential. It's very drastic, though.

A: By doing this, I think ... yeah, many ideas and hypothesis about the functions of retroelements. We want to stick to the function of the cells. In the cell system. By doing this, that kind of .. I don't have an idea.

Q: I think it would be a great challenge.

A: I want to start with very small gene regions and then expand to whole genome scale.