#	Pagina
attuale pagina	/open-h2020/projects/205989/results.html

Report

Teaser, summary, work performed and final results

Periodic Reporting for period 1 - GENOMIS (Illuminating GENome Organization through integrated MIcroscopy and Sequencing)

Teaser

Summary

In every cell of the human body, the genetic information encoded in two meters of genomic DNA is constantly read and interpreted inside a nucleus that has a 100,000 times smaller diameter. Understanding how this high compression is achieved in different cell types, and how biochemical reactions that involve DNA are coordinated in this dense environment, is essential to understand how normal cells work.

In this project, we aim to illuminate the general principles that govern how the human genome is folded in the cell nucleus. To do so, we develop new methods to assess how different parts of the genome are positioned with respect to the nuclear center and periphery, and then apply advanced computational approaches to model how the genome is folded in individual cells.

This project will bring us closer to understand how the genome is folded in normal cells, and how genome folding perturbations can set the basis for certain diseases, such as cancer.

Work performed

In the first year of the project, we have successfully built a platform, iFISH, that allows us to visualize specific regions of the genome directly in the cell nucleus, based on fluorescence microscopy. For this, we apply a technique known as fluorescence in situ hybridization or FISH, that uses short pieces of DNA labeled with a fluorescence dye (probes), to visualize the parts of the genome that have a complementary sequence to the one of the oligos. We have created a large repository of FISH probes targeting hundreds of different regions in the human genome, thanks to which we can now visualize every chromosome, and study how it is folded and spatially arranged in the cell nucleus.

In parallel, we have implemented a new genomic method, GPSeq, by which we can measure the distance of every part of the genome from the nuclear periphery. GPSeq works by gradually digesting genomic DNA from the nuclear periphery towards the nuclear center, by incubating fixed cells with restriction enzymes for increasing times, and sequencing the parts of the genome that have been digested at each time.

Final results

iFISH is the first example of publically available repository of DNA FISH probes, which can be freely requested by scientists all over the world. We believe that this is a valuable resource that will help not only researchers in the field of genome organization, but also researchers from other fields in life sciences and molecular diagnostics. We plan to further scale up our repository, to include many more probes targeting the human genome, and also the mouse genome.

GPSeq is the first-ever method to profile the radial organization of DNA in the nucleus, genome-wide. We expect that this method will be broadly used in the field of genome organization, as a complementary tool to existing methods, such as Hi-C.