Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

被引：80

作者：

Benedetti, Fabrizio ^{[1
]}

Dorier, Julien ^{[1
,2
]}

Burnier, Yannis ^{[1
,3
]}

Stasiak, Andrzej ^{[1
]}

机构：

[1] Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland

[2] SIB Swiss Inst Bioinformat, Vital IT Grp, CH-1015 Lausanne, Switzerland

[3] Ecole Polytech Fed Lausanne EPFL, Inst Theoret Phys, Lab Particle Phys & Cosmol, CH-1015 Lausanne, Switzerland

来源：

NUCLEIC ACIDS RESEARCH | 2014年 / 42卷 / 05期

基金：

瑞士国家科学基金会;

关键词：

TRANSCRIPTION; DNA; CHROMATIN; ORGANIZATION; PRINCIPLES; GENE;

D O I：

10.1093/nar/gkt1353

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

070307 [化学生物学]; 071010 [生物化学与分子生物学];

摘要：

Understanding the structure of interphase chromosomes is essential to elucidate regulatory mechanisms of gene expression. During recent years, high-throughput DNA sequencing expanded the power of chromosome conformation capture (3C) methods that provide information about reciprocal spatial proximity of chromosomal loci. Since 2012, it is known that entire chromatin in interphase chromosomes is organized into regions with strongly increased frequency of internal contacts. These regions, with the average size of similar to 1 Mb, were named topological domains. More recent studies demonstrated presence of unconstrained supercoiling in interphase chromosomes. Using Brownian dynamics simulations, we show here that by including supercoiling into models of topological domains one can reproduce and thus provide possible explanations of several experimentally observed characteristics of interphase chromosomes, such as their complex contact maps.

引用

页码：2848 / 2855

页数：8

共 37 条

[1]

DIRECT VISUALIZATION OF SUPERCOILED DNA-MOLECULES IN SOLUTION [J].