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首页> 外文期刊>Nucleic acids research >3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome
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3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome

机译：3D-GNOME 2.0：一种三维基因组建模引擎，用于预测人类基因组中染色质空间结构的结构变化驱动改变

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摘要

Structural variants (SVs) that alter DNA sequence emerge as a driving force involved in the reorganisation of DNA spatial folding, thus affecting gene transcription. In this work, we describe an improved version of our integrated web service for structural modeling of three-dimensional genome (3D-GNOME), which now incorporates all types of SVs to model changes to the reference 3D conformation of chromatin. In 3D-GNOME 2.0, the default reference 3D genome structure is generated using ChIA-PET data from the GM12878 cell line and SVs data are sourced from the population-scale catalogue of SVs identified by the 1000 Genomes Consortium. However, users may also submit their own structural data to set a customized reference genome structure, and/or a custom input list of SVs. 3D-GNOME 2.0 provides novel tools to inspect, visualize and compare 3D models for regions that differ in terms of their linear genomic sequence. Contact diagrams are displayed to compare the reference 3D structure with the one altered by SVs. In our opinion, 3D-GNOME 2.0 is a unique online tool for modeling and analyzing conformational changes to the human genome induced by SVs across populations. It can be freely accessed at https://3dgnome.cent.uw.edu.pl/.
机译：改变DNA序列的结构变体（SVS）作为涉及DNA空间折叠重组的驱动力，从而影响基因转录。在这项工作中，我们描述了我们对三维基因组（3D-GNOME）的结构建模的集成Web服务的改进版本，其现在将所有类型的SV与染色质的参考三维构象的模型变化结合到模型变化。在3D-GNOME 2.0中，使用来自GM12878的Chia-PET数据生成默认参考3D基因组结构，并且SVS数据来自由1000个基因组联盟识别的SV的人口级目录。但是，用户还可以提交自己的结构数据以设置自定义参考基因组结构，和/或SV的自定义输入列表。 3D-Gnome 2.0提供了用于检查，可视化和比较其线性基因组序列的区域不同的新型工具。将显示联系人图以将参考3D结构与SVS更改的参考3D结构进行比较。在我们看来，3D-GNOME 2.0是一个唯一的在线工具，用于建模和分析跨越人群的SVS诱导的人类基因组的构象变化。它可以在https://3dgnome.cent.uw.edu.pl/中自由访问。

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