How the Three dimensional Genome is Being Mapped by Scientists

A team of researchers discuss in this report the computational methods used to determine the three dimensional shape of the genome. They discuss the parallel development of full-genome mapping techniques and advanced computational methods and how these two things come together to create a more complete view of genome structure in the 3D form and how the 3D form relates to the function of the genome.

Article

Zhang, Y., Boninsegna, L., Yang, M. et al. Computational methods for analysing multiscale 3D genome organization. Nat Rev Genet (2023). https://doi.org/10.1038/s41576-023-00638-1

One of the more recent genome modeling platforms

Boninsegna, L., Yildirim, A., Polles, G. et al. Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations. Nat Methods 19, 938–949 (2022). https://doi.org/10.1038/s41592-022-01527-x

Designing and Programming Living Computers

 

    Graduate students and researchers from Technion and MIT collaborated to produce cells designed to perform computations similar to artificial neural circuits as explained in this article. A plasmid was inserted into a cell, acting as an artificial neural network. This was made possible by altering the plasmid’s genes, giving the plasmid the ability to activate and deactivate those genes due to stimuli. This is similar to how computer code works. Computer code consists of 0/1 switches, and the combination of those switches allows for different functions to be performed. The presence or absence of a molecule in a cell can act as a switch and perform similar functions. A cell can then be “programmed” to perform a function or set of functions such as the OR or AND functions. Artificial intelligence algorithms were also used to reduce the time and cost of genetic modifications to bacterial cells, making this technology more accessible. This technology is in a very early stage but has shown great potential to improve the dosage and effectiveness of cancer immunotherapy and diabetes drugs amongst other things.

First computer generated genome

Recently scientists have created a completely computer generated genome. The method behind this madness started by working with Proceedings of the  National Academy of Sciences (PNAS) and has even been added to the National Center of Biotechnology’s data bank of genes. PNAS is one of the second most cited scientific journals and publish quality peer reviewed articles.The genome code is based on a freshwater bacteria that can be found worldwide in different bodies of water. Within  the artificial genes there were only 580 functional genes out of the entire 680 artificial genes.

              This generated genome is Caulobacter ethensis-2.0 or C.ethensis-2.0. Being able to create synthetic microorganisms could be a new key part of pharmaceuticals and medicine. By using what is known about Caulobacter ethensis-2.0 other arificial genomes can be created making the sky the limit. Although, everything about this genome hasn't been perfected but with a few more tests it could become a model organism in genetic testing or more common in laboratories.