Exploring the consequences of genome radiality perturbations

NAISS 2023/6-253


NAISS Medium Storage

Principal Investigator:

Cynthia Perez Estrada


Karolinska Institutet

Start Date:


End Date:


Primary Classification:

10610: Bioinformatics and Systems Biology (methods development to be 10203)




In exciting preliminary experiments leveraging our GPSeq method we discovered that the genome of mammalian cells in interphase folds into a steep radial gradient of guanine and cytosine (GC) density, which seems to persist at the level of individual mitotic chromosomes. For the present proposal, our working hypothesis is that only karyotypes that support the formation of a radial GC-gradient in the human genome are propagated and that perturbations to the GC-gradient can significantly affect cellular fitness. Although previous studies have shown that radial repositioning of individual genes results in changes to their expression18–21, those studies were not conducted genome wide and at high resolution and did not assess the impact of radial gene repositioning or cell fitness.We build on our exciting preliminary finding that prolonged treatment of mouse Embryonic Stem cells (mESCs) with the Polycomb Repressing Complex 2 (PRC2) inhibitor EZH2i leads to a progressive drop in the correlation between GC-content and GPSeq score1 (our metric of radiality). We use this unique model system and apply GPSeq and chromatin conformation capture (Hi-C which is a statistical computational method), to help us map genome wide 3D genome re- configurations and correlate them to gene expression changes. This proposal will help us shed light onto what is the functional role of the genome’s radial architecture in cell function and survival.