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Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

by Mccole, Ruth B , Marti-Renom, Marc A , Schreiner, John , Sheikh, Russell , C-Ting, Wu , Kishi, Jocelyn Y , Soler-Vila, Paula , Yin, Peng , Lee, Soun H , Durand, Neva C , Stuckey, Jeff , Jos N Onuchic , Jumana Alhaj Abed , Erez Lieberman Aiden , Martins, Nuno M C , Cynthia P rez Estrada , Sasaki, Hiroshi M , Callahan, Steven , Beliveau, Brian J , Michele Di Pierro , Hannan, Mohammed A , Nir, Guy , Nguyen, Son C , Erceg, Jelena , Chattoraj, Shyamtanu , Farabella, Irene , Rao, Suhas S P , Nguyen, Huy Q , Ebeling, Carl G

in Chromosome 19 / Chromosomes / DNA probes / Gene mapping / Genetics / Localization

2018

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Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

in Chromosome 19 / Chromosomes / DNA probes / Gene mapping / Genetics / Localization

2018

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Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

in Chromosome 19 / Chromosomes / DNA probes / Gene mapping / Genetics / Localization

2018

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Paper

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

Mccole, Ruth B,

Marti-Renom, Marc A,

Schreiner, John,

Sheikh, Russell,

C-Ting, Wu,

Kishi, Jocelyn Y,

Soler-Vila, Paula,

Yin, Peng,

Lee, Soun H,

Durand, Neva C,

Stuckey, Jeff,

Jos N Onuchic,

Jumana Alhaj Abed,

Erez Lieberman Aiden,

Martins, Nuno M C,

Cynthia P rez Estrada,

Sasaki, Hiroshi M,

Callahan, Steven,

Beliveau, Brian J,

Michele Di Pierro,

Hannan, Mohammed A,

Nir, Guy,

Nguyen, Son C,

Erceg, Jelena,

Chattoraj, Shyamtanu,

Farabella, Irene,

Rao, Suhas S P,

Nguyen, Huy Q,

Ebeling, Carl G

2018

Overview

Chromosome structure is thought to be crucial for proper functioning of the nucleus. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. We begin by applying Oligopaint probes and the single-molecule localization microscopy methods of OligoSTORM and OligoDNA-PAINT to image 8 megabases of human chromosome 19, discovering that chromosomal regions contributing to compartments can form distinct structures. Intriguingly, our data also suggest that homologous maternal and paternal regions may be differentially organized. Finally, we integrate imaging data with Hi-C and restraint-based modeling using a method called integrative modeling of genomic regions (IMGR) to increase the genomic resolution of our traces to 10 kb.

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Cold Spring Harbor Laboratory Press,Cold Spring Harbor Laboratory

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