RNA-seq reveals novel transcriptome of genes and their isoforms in human pulmonary microvascular endothelial cells treated with thrombin.
RNA-seq reveals novel transcriptome of genes and their isoforms in human pulmonary microvascular endothelial cells treated with thrombin.
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DOI：
10.1371/journal.pone.0031229
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Ye SQ
中科院分区：
文献类型：
--
作者：
Zhang LQ;Cheranova D;Gibson M;Ding S;Heruth DP;Fang D;Ye SQ
凝血酶对血管内皮细胞的失调与许多病理疾病的发展有关，如炎症、癌症、糖尿病、冠心病。然而，凝血酶对血管内皮细胞的转录调控尚不完全清楚。在本研究中，利用Illumina RNA-seq分析了凝血酶处理6小时的人肺微血管内皮细胞（HMVEC-L）的转录组，以深入了解凝血酶对内皮功能的直接影响。在配对末端测序测定的1亿个总reads中，91-94%的reads与参考人类基因组中的16,000多个基因对齐。凝血酶上调150个已知基因和480个已知同种异构体，下调2190个已知基因和3574个已知同种异构体至少2倍。值得注意的是，凝血酶上调了1775种以前未知的异构体，下调了12202种以前未知的异构体至少2倍。凝血酶处理后，许多基因表现出同种异构体特异性差异表达水平和转录起始位点的不同使用。我们的RNA-seq数据与6小时凝血酶处理的HUVEC或5小时TNFα处理的HMVEC的DNA微阵列分析数据之间的交叉比较提供了差异表达基因的显著重叠列表，支持我们数据集的强大实用性。本研究报道的转录调控的进一步深入随访分析可能揭示凝血酶介导的各种疾病内皮功能障碍的分子致病机制，并为潜在的治疗靶点提供新的线索。
The dysregulation of vascular endothelial cells by thrombin has been implicated in the development of a number of pathologic disorders such as inflammatory conditions, cancer, diabetes, coronary heart disease. However, transcriptional regulation of vascular endothelial cells by thrombin is not completely understood. In the present study, Illumina RNA-seq was used to profile the transcriptome in human pulmonary microvascular endothelial cells (HMVEC-L) treated with thrombin for 6 h to gain insight into thrombin's direct effects on the endothelial function. Out of 100 million total reads from a paired end sequencing assay, 91–94% of the reads were aligned to over 16,000 genes in the reference human genome. Thrombin upregulated 150 known genes and 480 known isoforms, and downregulated 2,190 known genes and 3,574 known isoforms by at least 2 fold. Of note, thrombin upregulated 1,775 previously unknown isoforms and downregulated 12,202 previously unknown isoforms by at least 2 fold. Many genes displayed isoform specific differential expression levels and different usage of transcriptional start sites after the thrombin treatment. The cross comparisons between our RNA-seq data and those of DNA microarray analysis of either 6 h thrombin treated HUVEC or 5 h TNFα treated HMVEC have provided a significant overlapping list of differentially expressed genes, supporting the robust utility of our dataset. Further in-depth follow-up analysis of the transcriptional regulation reported in this study may shed light on molecular pathogenic mechanisms underlying thrombin mediated endothelial dysfunction in various diseases and provide new leads of potential therapeutic targets.