Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection.
Integrative deep sequencing of the mouse lung transcriptome reveals differential expression of diverse classes of small RNAs in response to respiratory virus infection.
复制标题
作者：
Peng X;Gralinski L;Ferris MT;Frieman MB;Thomas MJ;Proll S;Korth MJ;Tisoncik JR;Heise M;Luo S;Schroth GP;Tumpey TM;Li C;Kawaoka Y;Baric RS;Katze MG
我们以前报道了广泛的差异表达的长非蛋白编码RNA（ncRNA）在病毒感染。在这里，我们通过小RNA转录组测序分析宿主对严重急性呼吸道综合征冠状病毒（SARS-CoV）和流感病毒感染的反应，扩展了这项研究，其中包括协作杂交的四种创始小鼠品系，这是一种用于绘制复杂性状的重组近交小鼠资源。在感染过程中，我们观察到超过200种不同类型的小RNA的差异表达。大多数鉴定的microRNA（miRNAs）在SARS冠状病毒和流感病毒感染的小鼠品系中表现出不同的表达变化，并且与最低致病性季节性流感病毒分离株相比，对高致病性重建的1918年病毒的反应不同。通过对不同病毒感染中选定的miRNA进行调查，进一步阐明了对miRNA表达变化的新见解，包括与致病结果的关联以及体内和体外实验系统之间的巨大差异。鉴定的小RNA还包括许多非miRNA小RNA，例如除了未注释的小RNA之外的小核仁RNA（snoRNA）。对来自相同样品的小RNA和长转录本的整合测序分析表明，揭示感染期间miRNA差异表达的结果主要是由于转录调控，并且预测的miRNA-mRNA网络可以以组合方式调节全局宿主对病毒感染的反应。这些发现代表了宿主小RNA对病毒感染的反应的第一个综合测序分析，并表明小RNA是参与调节宿主对感染的反应的复杂网络的综合组成部分。大多数研究检查宿主对感染的转录反应只集中在蛋白质编码基因上。然而，哺乳动物基因组转录许多短和长的非蛋白质编码RNA（ncRNA）。随着深度测序技术的出现，现在可以对宿主反应进行系统的转录组分析，包括分析不同大小的ncRNA。使用这种方法，我们最近发现了响应病毒感染的宿主长（>200个核苷酸[nt]）ncRNA的广泛差异表达。在这里，再次使用了之前报告中描述的样本，但我们对转录组的另一部分进行了测序，以研究非常短（约20至30 nt）的ncRNA。我们证明，病毒感染也改变了许多不同类别的短ncRNA的表达。将这两项研究的结果放在一起，我们发现小RNA也可能在调节宿主对病毒感染的反应中发挥重要作用。
We previously reported widespread differential expression of long non-protein-coding RNAs (ncRNAs) in response to virus infection. Here, we expanded the study through small RNA transcriptome sequencing analysis of the host response to both severe acute respiratory syndrome coronavirus (SARS-CoV) and influenza virus infections across four founder mouse strains of the Collaborative Cross, a recombinant inbred mouse resource for mapping complex traits. We observed differential expression of over 200 small RNAs of diverse classes during infection. A majority of identified microRNAs (miRNAs) showed divergent changes in expression across mouse strains with respect to SARS-CoV and influenza virus infections and responded differently to a highly pathogenic reconstructed 1918 virus compared to a minimally pathogenic seasonal influenza virus isolate. Novel insights into miRNA expression changes, including the association with pathogenic outcomes and large differences between in vivo and in vitro experimental systems, were further elucidated by a survey of selected miRNAs across diverse virus infections. The small RNAs identified also included many non-miRNA small RNAs, such as small nucleolar RNAs (snoRNAs), in addition to nonannotated small RNAs. An integrative sequencing analysis of both small RNAs and long transcripts from the same samples showed that the results revealing differential expression of miRNAs during infection were largely due to transcriptional regulation and that the predicted miRNA-mRNA network could modulate global host responses to virus infection in a combinatorial fashion. These findings represent the first integrated sequencing analysis of the response of host small RNAs to virus infection and show that small RNAs are an integrated component of complex networks involved in regulating the host response to infection. Most studies examining the host transcriptional response to infection focus only on protein-coding genes. However, mammalian genomes transcribe many short and long non-protein-coding RNAs (ncRNAs). With the advent of deep-sequencing technologies, systematic transcriptome analysis of the host response, including analysis of ncRNAs of different sizes, is now possible. Using this approach, we recently discovered widespread differential expression of host long (>200 nucleotide [nt]) ncRNAs in response to virus infection. Here, the samples described in the previous report were again used, but we sequenced another fraction of the transcriptome to study very short (about 20 to 30 nt) ncRNAs. We demonstrated that virus infection also altered expression of many short ncRNAs of diverse classes. Putting the results of the two studies together, we show that small RNAs may also play an important role in regulating the host response to virus infection.