Genome-in-a-Box

Genome-in-a-Box: Building a Chromosome from the Bottom up

Birnie, Anthony (Kavli institute of nanoscience Delft; Student TU Delft)
Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)

2021

Chromosome structure and dynamics are essential for life, as the way that our genomes are spatially organized within cells is crucial for gene expression, differentiation, and genome transfer to daughter cells. There is a wide variety of methods available to study chromosomes, ranging from live-cell studies to single-molecule biophysics, which we briefly review. While these technologies have yielded a wealth of data, such studies still leave a significant gap between top-down experiments on live cells and bottom-up in vitro single-molecule studies of DNA-protein interactions. Here, we introduce "genome-in-a-box"(GenBox) as an alternative in vitro approach to build and study chromosomes, which bridges this gap. The concept is to assemble a chromosome from the bottom up by taking deproteinated genome-sized DNA isolated from live cells and subsequently add purified DNA-organizing elements, followed by encapsulation in cell-sized containers using microfluidics. Grounded in the rationale of synthetic cell research, the approach would enable to experimentally study emergent effects at the global genome level that arise from the collective action of local DNA-structuring elements. We review the various DNA-structuring elements present in nature, from nucleoid-associated proteins and SMC complexes to phase separation and macromolecular crowders. Finally, we discuss how GenBox can contribute to several open questions on chromosome structure and dynamics.

bottom-up biology
chromosome organization
DNA
DNA loop extrusion
DNA-binding proteins
emergent dynamics
minimal genome
phase separation
synthetic cells

http://resolver.tudelft.nl/uuid:6f0c0b7b-62d4-48f9-bcc7-fdd7ed90998d

https://doi.org/10.1021/acsnano.0c07397

1936-0851

ACS Nano (online), 15 (1), 111-124

Institutional Repository

review

© 2021 Anthony Birnie, C. Dekker