A high resolution atlas of gene expression in the domestic sheep (Ovis aries).
A high resolution atlas of gene expression in the domestic sheep (Ovis aries).
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一个高分辨率的基因表达图谱在国内绵羊（绵羊）。
DOI：
10.1371/journal.pgen.1006997
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发表时间：
2017-09
期刊：
影响因子：
4.5
通讯作者：
Hume DA
中科院分区：
文献类型：
--
作者：
Clark EL;Bush SJ;McCulloch MEB;Farquhar IL;Young R;Lefevre L;Pridans C;Tsang HG;Wu C;Afrasiabi C;Watson M;Whitelaw CB;Freeman TC;Summers KM;Archibald AL;Hume DA
绵羊是全球畜牧业肉类、牛奶和纤维的主要来源，也是重要的生物医学模型。跨多个组织的基因表达的全局分析有助于基因组注释和支持哺乳动物基因的功能注释。我们提出了一个大规模的RNA-Seq数据集，代表了成年羊和几个幼羊、新生儿和产前发育时间点的所有主要器官系统。羊羊参考基因组（Oar v3.1）包括27,504个基因（20,921个蛋白质编码），其中25,350个（19,921个蛋白质编码）在绵羊基因表达图谱数据集中至少一个组织中可检测到表达。该数据集基于网络的聚类分析根据基因的表达模式分组。“联想内疚”的原则被用来从未表征基因与已知功能基因的共表达中推断其功能。我们描述了绵羊基因表达图谱中存在的总体转录特征，并在可能的情况下将这些特征分配给特定的细胞群或途径。这些发现通过关注具有免疫特征的群集与先天免疫有关，并通过检查纯种动物和杂交动物之间表现出最大表达差异的基因模式，与杂交育种的优势有关。据我们所知，绵羊的高分辨率基因表达图谱是迄今为止所有牲畜物种中最大的转录组数据集。它为改进绵羊当前参考基因组的注释提供了资源，展示了反刍动物的模型转录组，并深入了解了多个发育阶段的基因，细胞和组织功能。羊是一种反刍哺乳动物，在全球各地的农业中被当作牲畜饲养，用于生产肉、奶和羊毛。遗传和基因组信息可用于改善生产性状，如生长速度和健康和适应性状，包括抗病性。然而，绵羊的基因组缺少与基因功能相关的重要信息，而且许多可能对生产力很重要的基因没有信息性的基因名称。这可以通过rna测序来修复，通过多个器官系统和发育阶段生成所有蛋白质编码基因的全局表达谱。根据基因在组织和细胞中的表达谱进行聚类，使我们能够为这些基因分配功能。例如，如果在巨噬细胞中表达一个没有信息性基因名称的基因，并且在已知的巨噬细胞相关基因簇中发现，则可能参与巨噬细胞功能并在先天免疫中发挥作用。这些信息提高了参考基因组的质量，并提供了对影响绵羊和其他牲畜物种生产力的复杂性状的生物学过程的深入了解。
Sheep are a key source of meat, milk and fibre for the global livestock sector, and an important biomedical model. Global analysis of gene expression across multiple tissues has aided genome annotation and supported functional annotation of mammalian genes. We present a large-scale RNA-Seq dataset representing all the major organ systems from adult sheep and from several juvenile, neonatal and prenatal developmental time points. The Ovis aries reference genome (Oar v3.1) includes 27,504 genes (20,921 protein coding), of which 25,350 (19,921 protein coding) had detectable expression in at least one tissue in the sheep gene expression atlas dataset. Network-based cluster analysis of this dataset grouped genes according to their expression pattern. The principle of ‘guilt by association’ was used to infer the function of uncharacterised genes from their co-expression with genes of known function. We describe the overall transcriptional signatures present in the sheep gene expression atlas and assign those signatures, where possible, to specific cell populations or pathways. The findings are related to innate immunity by focusing on clusters with an immune signature, and to the advantages of cross-breeding by examining the patterns of genes exhibiting the greatest expression differences between purebred and crossbred animals. This high-resolution gene expression atlas for sheep is, to our knowledge, the largest transcriptomic dataset from any livestock species to date. It provides a resource to improve the annotation of the current reference genome for sheep, presenting a model transcriptome for ruminants and insight into gene, cell and tissue function at multiple developmental stages. Sheep are ruminant mammals kept as livestock for the production of meat, milk and wool in agricultural industries across the globe. Genetic and genomic information can be used to improve production traits such as growth rate and health and fitness traits including disease resilience. The sheep genome is, however, missing important information relating to gene function and many genes, which may be important for productivity, have no informative gene name. This can be remedied using RNA-Sequencing to generate a global expression profile of all protein-coding genes, across multiple organ systems and developmental stages. Clustering genes based on their expression profile across tissues and cells allows us to assign function to those genes. If, for example, a gene with no informative gene name is expressed in macrophages and is found within a cluster of known macrophage related genes it is likely to be involved in macrophage function and play a role in innate immunity. This information improves the quality of the reference genome and provides insight into biological processes underlying the complex traits that influence the productivity of sheep and other livestock species.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
12.3
作者：
Andersson L;Archibald AL;Bottema CD;Brauning R;Burgess SC;Burt DW;Casas E;Cheng HH;Clarke L;Couldrey C;Dalrymple BP;Elsik CG;Foissac S;Giuffra E;Groenen MA;Hayes BJ;Huang LS;Khatib H;Kijas JW;Kim H;Lunney JK;McCarthy FM;McEwan JC;Moore S;Nanduri B;Notredame C;Palti Y;Plastow GS;Reecy JM;Rohrer GA;Sarropoulou E;Schmidt CJ;Silverstein J;Tellam RL;Tixier-Boichard M;Tosser-Klopp G;Tuggle CK;Vilkki J;White SN;Zhao S;Zhou H;FAANG Consortium
通讯作者：
FAANG Consortium
影响因子：
4.5
作者：
Baillie JK;Arner E;Daub C;De Hoon M;Itoh M;Kawaji H;Lassmann T;Carninci P;Forrest AR;Hayashizaki Y;FANTOM Consortium;Faulkner GJ;Wells CA;Rehli M;Pavli P;Summers KM;Hume DA
通讯作者：
Hume DA
影响因子：
5.5
作者：
Allen, David L.;Loh, Amanda S.
通讯作者：
Loh, Amanda S.
影响因子：
5.4
作者：
Bain, Calum C.;Mowat, Allan McI
通讯作者：
Mowat, Allan McI