Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis.
Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis.
复制标题
DOI：
10.1371/journal.pone.0137526
复制
发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Sachs LM
中科院分区：
文献类型：
--
作者：
Buisine N;Ruan X;Bilesimo P;Grimaldi A;Alfama G;Ariyaratne P;Mulawadi F;Chen J;Sung WK;Liu ET;Demeneix BA;Ruan Y;Sachs LM
全基因组功能分析需要高分辨率的基因组组装和注释。我们应用ChIA-PET分析基因调控网络，包括三维染色体相互作用，潜在的甲状腺激素（TH）信号在青蛙热带爪蟾。由于热带非洲爪蟾组装和注释的可用版本缺乏ChIA-PET所需的分辨率，我们使用源自配对末端标签（PET）测序技术和方法的数据（例如，DNA-PET [gPET]、RNA-PET等）。大插入片段（~ 10 Kb，~ 17 Kb）配对末端DNA-PET与高通量NGS测序不仅显著提高了基因组组装质量，而且大大减少了基因组“片段化”，使总支架数量减少~ 60%。接下来，将设计和开发用于在全转录组研究（ENCODE consortia）中检测全长转录物和融合mRNA的RNA-PET技术应用于捕获转录物的5'和3'末端。这些组装和注释的修正是TH转录调控的ChIA-PET分析的必要先决条件。它们的应用揭示了靶基因的复杂调控结构和生理反应背后的调控网络结构。我们的工作使我们能够提高非洲爪蟾基因组资源的质量，达到ChIA-PET分析转录网络所需的标准。我们认为，提出的工作流程提供了有用的概念和方法的指导，并可以很容易地应用到其他非传统的模型，具有低分辨率的基因组数据。
Genome-wide functional analyses require high-resolution genome assembly and annotation. We applied ChIA-PET to analyze gene regulatory networks, including 3D chromosome interactions, underlying thyroid hormone (TH) signaling in the frog Xenopus tropicalis. As the available versions of Xenopus tropicalis assembly and annotation lacked the resolution required for ChIA-PET we improve the genome assembly version 4.1 and annotations using data derived from the paired end tag (PET) sequencing technologies and approaches (e.g., DNA-PET [gPET], RNA-PET etc.). The large insert (~10Kb, ~17Kb) paired end DNA-PET with high throughput NGS sequencing not only significantly improved genome assembly quality, but also strongly reduced genome “fragmentation”, reducing total scaffold numbers by ~60%. Next, RNA-PET technology, designed and developed for the detection of full-length transcripts and fusion mRNA in whole transcriptome studies (ENCODE consortia), was applied to capture the 5' and 3' ends of transcripts. These amendments in assembly and annotation were essential prerequisites for the ChIA-PET analysis of TH transcription regulation. Their application revealed complex regulatory configurations of target genes and the structures of the regulatory networks underlying physiological responses. Our work allowed us to improve the quality of Xenopus tropicalis genomic resources, reaching the standard required for ChIA-PET analysis of transcriptional networks. We consider that the workflow proposed offers useful conceptual and methodological guidance and can readily be applied to other non-conventional models that have low-resolution genome data.