The development of new ways to probe samples for the three-dimensional (3D) structure of DNA paves the way for in depth and systematic analyses of the genome architecture. 3C-like methods coupled with high-throughput sequencing can now assess physical interactions between pairs of loci in a genome-wide fashion, thus enabling the creation of genome-by-genome contact maps. The spreading of such protocols creates many new opportunities for methodological development: how can we infer 3D models from these contact maps? Can such models help us gain insights into biological processes? Several recent studies applied such protocols to P. falciparum (the deadliest of the five human malaria parasites), assessing its genome organization at different moments of its life cycle. With its small genomic size, fairly simple (yet changing) genomic organization during its lifecyle and strong correlation between chromatin folding and gene expression, this parasite is the ideal case study for applying and developing methods to infer 3D models and use them for downstream analysis. Here, I review a set of methods used to build and analyse three-dimensional models from contact maps data with a special highlight on P. falciparum’s genome organization.

中文翻译：

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展开基因组：恶性疟原虫的案例研究

开发用于探测 DNA 三维 (3D) 结构样本的新方法为深入和系统地分析基因组结构铺平了道路。与高通量测序相结合的类 3C 方法现在可以以全基因组的方式评估基因座对之间的物理相互作用，从而能够创建基因组联系图。此类协议的传播为方法论的发展创造了许多新机会：我们如何从这些接触图中推断出 3D 模型？这些模型能否帮助我们深入了解生物过程？最近的几项研究将此类协议应用于恶性疟原虫（五种人类疟疾寄生虫中最致命的一种），在其生命周期的不同时刻评估其基因组组织。凭借其较小的基因组大小、在其生命周期中相当简单（但不断变化）的基因组组织以及染色质折叠和基因表达之间的强相关性，这种寄生虫是应用和开发方法来推断 3D 模型并将其用于下游分析的理想案例研究。在这里，我回顾了一组用于从接触地图数据构建和分析三维模型的方法，特别强调了恶性疟原虫的基因组组织。