MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution

TitleMiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution
Publication TypeJournal Article
Year of Publication2022
AuthorsNeguembor, Maria Victoria, Arcon Juan Pablo, Buitrago Diana, Lema Rafael, Walther Jurgen, Garate Ximena, Martin Laura, Romero Pablo, Abed Jumana AlHaj, Gut Marta, Blanc Julie, Lakadamyali Melike, Wu Chao-ting, Heath Isabelle Brun, Orozco Modesto, Dans Pablo D., and Cosma Maria Pia
JournalNat Struct Mol Biol
Volumein press
Date Published10/2022
ISBN Number1545-9985

The linear sequence of DNA provides invaluable information about genes and their regulatory elements along chromosomes. However, to fully understand gene function and regulation, we need to dissect how genes physically fold in the three-dimensional nuclear space. Here we describe immuno-OligoSTORM, an imaging strategy that reveals the distribution of nucleosomes within specific genes in super-resolution, through the simultaneous visualization of DNA and histones. We combine immuno-OligoSTORM with restraint-based and coarse-grained modeling approaches to integrate super-resolution imaging data with Hi-C contact frequencies and deconvoluted micrococcal nuclease-sequencing information. The resulting method, called Modeling immuno-OligoSTORM, allows quantitative modeling of genes with nucleosome resolution and provides information about chromatin accessibility for regulatory factors, such as RNA polymerase II. With Modeling immuno-OligoSTORM, we explore intercellular variability, transcriptional-dependent gene conformation, and folding of housekeeping and pluripotency-related genes in human pluripotent and differentiated cells, thereby obtaining the highest degree of data integration achieved so far to our knowledge.

Short TitleNature Structural & Molecular Biology